ALBERT

Description: We propose a concurrent multiscale molecular dynamics for molecular systems in order to apply macroscale mechanical boundary conditions such as traction and average displacement for solid state materials, which is difficult to do in traditional molecular dynamics where boundary conditions are applied in terms of forces and displacements on selected particles. The multiscale model is systematically constructed in terms of multiscale structures of kinematics, force field, and dynamical equations. The idea is to extend the Anderson-Parrinello-Rahman molecular dynamics to the cases that have arbitrary finite domain and boundary, thus the model is capable of solving inhomogeneous, non-equilibrium problems. The macroscale stress loading on a representative volume element with periodic boundary condition is generalized to all kinds of macroscale mechanical boundary conditions. Unlike most multiscale techniques, our theory is aimed at understanding fundamental physics rather than achieving computing efficiency. Examples of problems with prescribed average displacements and surface tractions are presented to demonstrate the validity of the proposed multiscale molecular dynamics.

Description: We study the effect of chain rigidity on the behavior of semiflexible polymers in the vicinity of flat walls in a slit, and of surfactants at the liquid-liquid interface between immiscible liquids. Using molecular dynamics simulations, it is demonstrated that the impact of bending angle forces is particularly strong within the depletion layer at the phase boundary whereas at distance R e away from the interface, where R e is the mean distance between the ends of a semiflexible chain, the contribution of these non-local triplet interactions to pressure tensor virtually disappears. The present study also demonstrates that growing stiffness of the macromolecules leads to an increase in surface tension and total pressure.

Description: Quantum-chemical computations of nuclear quadrupole-coupling parameters for 24 open-shell states of small molecules based on non-relativistic and spin-free exact two-component (SFX2C) relativistic equation-of-motion coupled-cluster (EOM-CC) as well as spin-orbital-based restricted open-shell Hartree-Fock coupled-cluster (ROHF-CC) methods are reported. Relativistic effects, the performance of the EOM-CC and ROHF-CC methods for treating electron correlation, as well as basis-set convergence have been carefully analyzed. Consideration of relativistic effects is necessary for accurate calculations on systems containing third-row (K-Kr) and heavier elements, as expected, and the SFX2C approach is shown to be a useful cost-effective option here. Further, it is demonstrated that the EOM-CC methods constitute flexible and accurate alternatives to the ROHF-CC methods in the calculations of nuclear quadrupole-coupling parameters for open-shell states.

Description: Coherence oscillations measured in two-dimensional (2D) electronic spectra of pigment-protein complexes may have electronic, vibrational, or mixed-character vibronic origins, which depend on the degree of electronic-vibrational mixing. Oscillations from intrapigment vibrations can obscure the inter-site coherence lifetime of interest in elucidating the mechanisms of energy transfer in photosynthetic light-harvesting. Huang-Rhys factors ( S ) for low-frequency vibrations in Chlorophyll and Bacteriochlorophyll are quite small ( S ≤ 0.05), so it is often assumed that these vibrations influence neither 2D spectra nor inter-site coherence dynamics. In this work, we explore the influence of S within this range on the oscillatory signatures in simulated 2D spectra of a pigment heterodimer. To visualize the inter-site coherence dynamics underlying the 2D spectra, we introduce a formalism which we call the “site-probe response.” By comparing the calculated 2D spectra with the site-probe response, we show that an on-resonance vibration with Huang-Rhys factor as small as S = 0.005 and the most strongly coupled off-resonance vibrations ( S = 0.05) give rise to long-lived, purely vibrational coherences at 77 K. We moreover calculate the correlation between optical pump interactions and subsequent entanglement between sites, as measured by the concurrence. At 77 K, greater long-lived inter-site coherence and entanglement appear with increasing S . This dependence all but vanishes at physiological temperature, as environmentally induced fluctuations destroy the vibronic mixing.

Description: Potassium 1,1′-dinitroamino-5,5′-bistetrazolate (K 2 DNABT) is a nitrogen rich (50.3% by weight, K 2 C 2 N 12 O 4 ) green primary explosive with high performance characteristics, namely, velocity of detonation (D = 8.33 km/s), detonation pressure (P = 31.7 GPa), and fast initiating power to replace existing toxic primaries. In the present work, we report density functional theory (DFT) calculations on structural, equation of state, vibrational spectra, electronic structure, and absorption spectra of K 2 DNABT. We have discussed the influence of weak dispersive interactions on structural and vibrational properties through the DFT-D2 method. We find anisotropic compressibility behavior (b

Description: We perform direct large molecular dynamics simulations of homogeneous SPC/E water nucleation, using up to ∼ 4 ⋅ 10 6 molecules. Our large system sizes allow us to measure extremely low and accurate nucleation rates, down to ∼ 10 19  cm −3 s −1 , helping close the gap between experimentally measured rates ∼ 10 17  cm −3 s −1 . We are also able to precisely measure size distributions, sticking efficiencies, cluster temperatures, and cluster internal densities. We introduce a new functional form to implement the Yasuoka-Matsumoto nucleation rate measurement technique (threshold method). Comparison to nucleation models shows that classical nucleation theory over-estimates nucleation rates by a few orders of magnitude. The semi-phenomenological nucleation model does better, under-predicting rates by at worst a factor of 24. Unlike what has been observed in Lennard-Jones simulations, post-critical clusters have temperatures consistent with the run average temperature. Also, we observe that post-critical clusters have densities very slightly higher, ∼ 5%, than bulk liquid. We re-calibrate a Hale-type J vs. S scaling relation using both experimental and simulation data, finding remarkable consistency in over 30 orders of magnitude in the nucleation rate range and 180 K in the temperature range.

Description: Tensor factorization of the 2-electron integral matrix is a well-known technique for reducing the computational scaling of ab initio electronic structure methods toward that of Hartree-Fock and density functional theories. The simplest factorization that maintains the positive semidefinite character of the 2-electron integral matrix is the Cholesky factorization. In this paper, we introduce a family of positive semidefinite factorizations that generalize the Cholesky factorization. Using an implementation of the factorization within the parametric 2-RDM method [D. A. Mazziotti, Phys. Rev. Lett. 101 , 253002 (2008)], we study several inorganic molecules, alkane chains, and potential energy curves and find that this generalized factorization retains the accuracy and size extensivity of the Cholesky factorization, even in the presence of multi-reference correlation. The generalized family of positive semidefinite factorizations has potential applications to low-scaling ab initio electronic structure methods that treat electron correlation with a computational cost approaching that of the Hartree-Fock method or density functional theory.

Description: The reported values of bandgap of rutile GeO 2 calculated by the standard density functional theory within local-density approximation (LDA)/generalized gradient approximation (GGA) show a wide variation (∼2 eV), whose origin remains unresolved. Here, we investigate the reasons for this variation by studying the electronic structure of rutile-GeO 2 using many-body perturbation theory within the GW framework. The bandgap as well as valence bandwidth at Γ-point of rutile phase shows a strong dependence on volume change, which is independent of bandgap underestimation problem of LDA/GGA. This strong dependence originates from a change in hybridization among O- p and Ge-( s and p ) orbitals. Furthermore, the parabolic nature of first conduction band along X-Γ-M direction changes towards a linear dispersion with volume expansion.

Description: We study the pair complexation of a single, highly charged polyelectrolyte (PE) chain (of 25 or 50 monomers) with like-charged patchy protein models (CPPMs) by means of implicit-solvent, explicit-salt Langevin dynamics computer simulations. Our previously introduced set of CPPMs embraces well-defined zero-, one-, and two-patched spherical globules each of the same net charge and (nanometer) size with mono- and multipole moments comparable to those of globular proteins with similar size. We observe large binding affinities between the CPPM and the like-charged PE in the tens of the thermal energy, k B T , that are favored by decreasing salt concentration and increasing charge of the patch(es). Our systematic analysis shows a clear correlation between the distance-resolved potentials of mean force, the number of ions released from the PE, and CPPM orientation effects. In particular, we find a novel two-site binding behavior for PEs in the case of two-patched CPPMs, where intermediate metastable complex structures are formed. In order to describe the salt-dependence of the binding affinity for mainly dipolar (one-patched) CPPMs, we introduce a combined counterion-release/Debye-Hückel model that quantitatively captures the essential physics of electrostatic complexation in our systems.

Description: We introduce a set of charged patchy particle models (CPPMs) in order to systematically study the influence of electrostatic charge patchiness and multipolarity on macromolecular interactions by means of implicit-solvent, explicit-ion Langevin dynamics simulations employing the Gromacs software. We consider well-defined zero-, one-, and two-patched spherical globules each of the same net charge and (nanometer) size which are composed of discrete atoms. The studied mono- and multipole moments of the CPPMs are comparable to those of globular proteins with similar size. We first characterize ion distributions and electrostatic potentials around a single CPPM. Although angle-resolved radial distribution functions reveal the expected local accumulation and depletion of counter- and co-ions around the patches, respectively, the orientation-averaged electrostatic potential shows only a small variation among the various CPPMs due to space charge cancellations. Furthermore, we study the orientation-averaged potential of mean force (PMF), the number of accumulated ions on the patches, as well as the CPPM orientations along the center-to-center distance of a pair of CPPMs. We compare the PMFs to the classical Derjaguin-Verwey-Landau-Overbeek theory and previously introduced orientation-averaged Debye-Hückel pair potentials including dipolar interactions. Our simulations confirm the adequacy of the theories in their respective regimes of validity, while low salt concentrations and large multipolar interactions remain a challenge for tractable theoretical descriptions.

Description: In electrolyte solutions, an electric potential difference, called the Ionic Vibration Potential (IVP), related to the ionic vibration intensity, is generated by the application of an acoustic wave. Several theories based on a mechanical framework have been proposed over the years to predict the IVP for high ionic strengths, in the case where interactions between ions have to be accounted for. In this paper, it is demonstrated that most of these theories are not consistent with Onsager’s reciprocal relations. A new expression for the IVP will be presented that does fulfill the Onsager’s reciprocal relations. We obtained this expression by deriving general expressions of the corrective forces describing non-ideal effects in electrolyte solutions.

Description: In the framework of irreversible thermodynamics, we show that the sedimentation current in electrolyte solutions is mathematically equivalent to the low frequency limit of the ionic vibration current, appearing in the presence of an acoustic wave. This non-trivial result is obtained thanks to a careful choice of the reference frame used to express the mass fluxes in the context of electroacoustics. Coupled transport phenomena in electrolyte solutions can also be investigated in a mechanical framework, with a set of Newtonian equations for the dynamics of charged solutes. Both in the context of sedimentation and of electroacoustics, we show that the results obtained in the mechanical framework, in the ideal case (i.e., without interactions between ions), do satisfy the Onsager’s reciprocal relations. We also derive the general relation between corrective forces accounting for ionic interactions which must be fulfilled so that the Onsager’s reciprocal relations are verified. Finally, we show that no additional diffusion term needs to be taken into account in the flux of solutes (far from the walls), even if local concentration gradients exist, contrarily to what was done previously in the literature.

Description: Polyacenes in their armchair geometry (phenacenes) have recently been found to possess appealing electronic and optical properties with higher chemical stability and comparatively larger band gap as compared to linear polyacenes. They also behave as high-temperature superconductors upon alkali metal doping. Moreover, the optical properties of crystalline picene can be finely tuned by applying external pressure. We investigated the variation of optical gap as a function of altering the interplanar distances between parallel cofacial phenacene dimers. We employed both time-dependent density functional theory and density matrix renormalization group (DMRG) technique to investigate the lowest singlet excitations in phenacene dimer. Our study showed that the lowest singlet excitation in these systems evolved as a function of interplanar separation. The optical excitation energy gap decreases as a function of inverse interplanar separation of the phenacene dimer. The distant dependent variation of optical absorption at the dimer level may be comparable with experimental observation in picene crystal under pressure. DMRG study also demonstrates that besides picene, electronic properties of higher phenacenes can also be tunable by altering interplanar separation.

Description: A combined experimental and theoretical study is presented of fluctuations observed by field ion microscopy in the catalytic reaction of water production on a rhodium tip. A stochastic approach is developed to provide a comprehensive understanding of the different phenomena observed in the experiment, including burst noise manifesting itself in a bistability regime, noisy oscillations, and nanopatterns with a cross-like oxidized zone separating the surface into four quadrants centered on the {111} facets. The study is based on a stochastic model numerically simulating the processes of adsorption, desorption, reaction, and transport. The surface diffusion of hydrogen is described as a percolation process dominated by large clusters corresponding to the four quadrants. The model reproduces the observed phenomena in the ranges of temperature, pressures, and electric field of the experiment.

Description: A Gaussian- Sinc basis set methodology is presented for the calculation of the electronic structure of atoms and molecules at the Hartree–Fock level of theory. This methodology has several advantages over previous methods. The all-electron electronic structure in a Gaussian- Sinc mixed basis spans both the “localized” and “delocalized” regions. A basis set for each region is combined to make a new basis methodology—a lattice of orthonormal sinc functions is used to represent the “delocalized” regions and the atom-centered Gaussian functions are used to represent the “localized” regions to any desired accuracy. For this mixed basis, all the Coulomb integrals are definable and can be computed in a dimensional separated methodology. Additionally, the Sinc basis is translationally invariant, which allows for the Coulomb singularity to be placed anywhere including on lattice sites. Finally, boundary conditions are always satisfied with this basis. To demonstrate the utility of this method, we calculated the ground state Hartree–Fock energies for atoms up to neon, the diatomic systems H 2 , O 2 , and N 2 , and the multi-atom system benzene. Together, it is shown that the Gaussian- Sinc mixed basis set is a flexible and accurate method for solving the electronic structure of atomic and molecular species.

Description: The hierarchical equations of motion (HEOM) method has recently emerged as an effective approach to simulate linear and nonlinear spectroscopic signals of molecular aggregates in the intermediate coupling regime. However, its application to large systems is still limited when there are a large number of molecules in the molecular aggregate. In this work, we propose a time domain two-particle approximation (TPA) in combination with the HEOM method to calculate the absorption and circular dichroism line shapes of molecular aggregates. The new method is shown to reduce the number of auxiliary density operators (ADOs) significantly for large systems, and a further truncation of the two-bath-set excited terms based on geometric considerations can lead to a linear increase of the number of ADOs with the system size. The validity of the HEOM-TPA method is first tested on one-dimensional model systems. The new method is then applied to calculate the absorption and circular dichroism line shapes of the Photosystem I core complex, as well as the population evolution of the Fenna-Matthews-Olson complex to demonstrate its effectiveness.

Description: We consider a system consisting of two interacting qubits that are individually coupled to separate heat baths at different temperatures. The quantum effects in heat transport are investigated in a numerically rigorous manner with a hierarchial equations of motion (HEOM) approach for non-perturbative and non-Markovian system-bath coupling cases under non-equilibrium steady-state conditions. For a weak interqubit interaction, the total system is regarded as two individually thermostatted systems, whereas for a strong interqubit interaction, the two-qubit system is regarded as a single system coupled to two baths. The roles of quantum coherence (or entanglement) between the two qubits (q-q coherence) and between the qubit and bath (q-b coherence) are studied through the heat current calculated for various strengths of the system-bath coupling and interqubit coupling for high and low temperatures. The same current is also studied using the time convolutionless (TCL) Redfield equation and using an expression derived from the Fermi golden rule (FGR). We find that the HEOM results exhibit turnover behavior of the heat current as a function of the system-bath coupling strength for all values of the interqubit coupling strength, while the results obtained with the TCL and FGR approaches do not exhibit such behavior, because they do not possess the capability of treating the q-b and q-q coherences. The maximum current is obtained in the case that the q-q coherence and q-b coherence are balanced in such a manner that coherence of the entire heat transport process is realized. We also find that the heat current does not follow Fourier’s law when the temperature difference is very large, due to the non-perturbative system-bath interactions.

Description: A new high quality potential energy surface is calculated at a coupled-cluster single double triple level with an aug-cc-pV5Z basis set for the HCS + –He system. This potential energy surface is used in low energy quantum scattering calculations to provide a set of (de)-excitation cross sections and rate coefficients among the first 20 rotational levels of HCS + by He in the range of temperature from 5 K to 100 K. The paper discusses the impact of the new ab initio potential energy surface on the cross sections at low energy and provides a comparison with the HCO + –He system. The HCS + –He rate coefficients for the strongest transitions differ by factors of up to 2.5 from previous rate coefficients; thus, analysis of astrophysical spectra should be reconsidered with the new rate coefficients.

Description: A weak, paradoxically narrow resonance feature (shortly, the r -line) near the O 2 fundamental frequency in the collision-induced absorption spectrum of oxygen dissolved in liquid argon and liquid nitrogen ( T = 89 K) is resolved for the first time. An accurate band shape fitting routine to separate the r -line from the by-far more intense diffuse background and to study its behavior versus the oxygen mole fraction x which ranged from 0.03 up to 0.23 has been elaborated. At small x (≲0.07), the r -line intensity was found to scale as x 2 leaving no doubt that it is due to the solute-solute (O 2 –O 2 ) interactions. In line with our results on the p H 2 –LNe cryosystem [Herrebout, Phys. Rev. Lett. 101 , 093001 (2008)], the Lorentzian r -line shape and its extraordinary sharpness (half width at half height ≈ 1 cm −1 ) are indicative of the motional narrowing of the relative solute-solute translational spectrum. As x is further raised, ternary solute-solute interactions impede the r -line growth in the O 2 –LAr spectrum because of the cancellation effect [J. Van Kranendonk, Physica 23 , 825 (1957)]. Theoretical arguments are given that multiple interactions between the solutes should finally destroy the solute-solute induced r -line when the mixed solution approaches the limit of the pure liquid ( x = 1). Interestingly, the nonbinary effects are too weak to appreciably affect the quadratic r -line scaling in the O 2 –LN 2 cryosystem which persists up to x = 0.23. It is emphasized that studies of the resonant features in the collision-induced spectra of binary cryosolutions open up unique opportunities to spectroscopically trace the microscopic-scale diffusion.

Description: Three-body and higher intermolecular interactions can play an important role in molecular condensed phases. Recent benchmark calculations found problematic behavior for many widely used density functional approximations in treating 3-body intermolecular interactions. Here, we demonstrate that the combination of second-order Møller-Plesset (MP2) perturbation theory plus short-range damped Axilrod-Teller-Muto (ATM) dispersion accurately describes 3-body interactions with reasonable computational cost. The empirical damping function used in the ATM dispersion term compensates both for the absence of higher-order dispersion contributions beyond the triple-dipole ATM term and non-additive short-range exchange terms which arise in third-order perturbation theory and beyond. Empirical damping enables this simple model to out-perform a non-expanded coupled Kohn-Sham dispersion correction for 3-body intermolecular dispersion. The MP2 plus ATM dispersion model approaches the accuracy of O ( N 6 ) methods like MP2.5 or even spin-component-scaled coupled cluster models for 3-body intermolecular interactions with only O ( N 5 ) computational cost.

Description: A first sharp diffraction peak (FSDP) is observed in the X-ray total structure factor of a molten mixture of RbCl-AgCl, while both pure melts of RbCl and AgCl do not exhibit FSDP individually. Molecular dynamics simulations were performed to investigate the origin of the FSDP with the polarizable ion model (PIM). Coexistence of covalent Ag–Cl and ionic Rb–Cl bonds leads the system to evolve intermediate range ordering, which is simulated by introducing the induced polarization in different ways between Ag–Cl with fully polarizable treatment based on Vashishta-Raman potential and Rb–Cl with suppression over-polarization in the nearest neighbor contribution based on Born-Meyer potential. The partial structure factors for both the Ag–Ag and Rb–Rb correlations, S AgAg ( Q ) and S RbRb ( Q ), show a positive contribution to the FSDP, while S AgRb ( Q ) for the Ag–Rb correlation exhibits a negative contribution, indicating that Ag and Rb ions are distributed in an alternating manner within the intermediate-range length scale. The origin of the intermediate-range chemical ordering of cations can be ascribed to the preferred direction of the dipole moments of anions in the PIM.

Description: The recently developed density matrix quantum Monte Carlo (DMQMC) algorithm stochastically samples the N -body thermal density matrix and hence provides access to exact properties of many-particle quantum systems at arbitrary temperatures. We demonstrate that moving to the interaction picture provides substantial benefits when applying DMQMC to interacting fermions. In this first study, we focus on a system of much recent interest: the uniform electron gas in the warm dense regime. The basis set incompleteness error at finite temperature is investigated and extrapolated via a simple Monte Carlo sampling procedure. Finally, we provide benchmark calculations for a four-electron system, comparing our results to previous work where possible.

Description: Despite the fundamental importance of electron density in density functional theory, perturbations are still usually dealt with using Hartree-Fock-like orbital equations known as coupled-perturbed Kohn-Sham (CPKS). As an alternative, we develop a perturbation theory that solves for the perturbed density directly, removing the need for CPKS. This replaces CPKS with a true Hohenberg-Kohn density perturbation theory. In CPKS, the perturbed density is found in the basis of products of occupied and virtual orbitals, which becomes ever more over-complete as the size of the orbital basis set increases. In our method, the perturbation to the density is expanded in terms of a series of density basis functions and found directly. It is possible to solve for the density in such a way that it makes the total energy stationary even if the density basis is incomplete.

Description: We have developed a multi-agent quantum Monte Carlo model to describe the spatial dynamics of multiple majority charge carriers during conduction of electric current in the channel of organic field-effect transistors. The charge carriers are treated by a neglect of diatomic differential overlap Hamiltonian using a lattice of hydrogen-like basis functions. The local ionization energy and local electron affinity defined previously map the bulk structure of the transistor channel to external potentials for the simulations of electron- and hole-conduction, respectively. The model is designed without a specific charge-transport mechanism like hopping- or band-transport in mind and does not arbitrarily localize charge. An electrode model allows dynamic injection and depletion of charge carriers according to source-drain voltage. The field-effect is modeled by using the source-gate voltage in a Metropolis-like acceptance criterion. Although the current cannot be calculated because the simulations have no time axis, using the number of Monte Carlo moves as pseudo-time gives results that resemble experimental I/V curves.

Description: The characteristic properties of graphene make it useful in an assortment of applications. One particular application—the use of graphene in biosensors—requires a thorough understanding of graphene-peptide interactions. In this study, the binding of glycine (G) capped amino acid residues (termed GXG tripeptides) to trilayer graphene surfaces in aqueous solution was examined and compared to results previously obtained for peptide binding to single-layer free-standing graphene [A. N. Camden, S. A. Barr, and R. J. Berry, J. Phys. Chem. B 117 , 10691–10697 (2013)]. In order to understand the interactions between the peptides and the surface, binding enthalpy and free energy values were calculated for each GXG system, where X cycled through the typical 20 amino acids. When the GXG tripeptides were bound to the surface, distinct conformations were observed, each with a different binding enthalpy. Analysis of the binding energy showed the binding of peptides to trilayer graphene was dominated by van der Waals interactions, unlike the free-standing graphene systems, where the binding was predominantly electrostatic in nature. These results demonstrate the utility of computational materials science in the mechanistic explanation of surface-biomolecule interactions which could be applied to a wide range of systems.

Description: Transport properties for collisions of hydrogen atoms with CO and CO 2 have been computed by means of quantum scattering calculations. The carbon oxides are important species in hydrocarbon combustion. The following potential energy surfaces (PES’s) for the interaction of the molecule fixed in its equilibrium geometry were employed: for H–CO, the PES was taken from the work of Song et al. [J. Phys. Chem. A 117 , 7571 (2013)], while the PES for H–CO 2 was computed in this study by a restricted coupled cluster method that included single, double, and (perturbatively) triple excitations. The computed transport properties were found to be significantly different from those computed by the conventional approach that employs isotropic Lennard-Jones (12-6) potentials. The effect of using the presently computed accurate transport properties in 1-dimensional combustion simulations of methane-air flames was investigated.

Description: The Seebeck and Soret coefficients of ionically stabilized suspension of maghemite nanoparticles in dimethyl sulfoxide are experimentally studied as a function of nanoparticle volume fraction. In the presence of a temperature gradient, the charged colloidal nanoparticles experience both thermal drift due to their interactions with the solvent and electric forces proportional to the internal thermoelectric field. The resulting thermodiffusion of nanoparticles is observed through forced Rayleigh scattering measurements, while the thermoelectric field is accessed through voltage measurements in a thermocell. Both techniques provide independent estimates of nanoparticle’s entropy of transfer as high as 82 meV K −1 . Such a property may be used to improve the thermoelectric coefficients in liquid thermocells.

Description: The formation of aggregates in many protein systems can be significantly accelerated by secondary nucleation, a process where existing assemblies catalyse the nucleation of new species. In particular, secondary nucleation has emerged as a central process controlling the proliferation of many filamentous protein structures, including molecular species related to diseases such as sickle cell anemia and a range of neurodegenerative conditions. Increasing evidence suggests that the physical size of protein filaments plays a key role in determining their potential for deleterious interactions with living cells, with smaller aggregates of misfolded proteins, oligomers, being particularly toxic. It is thus crucial to progress towards an understanding of the factors that control the sizes of protein aggregates. However, the influence of secondary nucleation on the time evolution of aggregate size distributions has been challenging to quantify. This difficulty originates in large part from the fact that secondary nucleation couples the dynamics of species distant in size space. Here, we approach this problem by presenting an analytical treatment of the master equation describing the growth kinetics of linear protein structures proliferating through secondary nucleation and provide closed-form expressions for the temporal evolution of the resulting aggregate size distribution. We show how the availability of analytical solutions for the full filament distribution allows us to identify the key physical parameters that control the sizes of growing protein filaments. Furthermore, we use these results to probe the dynamics of the populations of small oligomeric species as they are formed through secondary nucleation and discuss the implications of our work for understanding the factors that promote or curtail the production of these species with a potentially high deleterious biological activity.

Description: The fluid-solid phase transition behavior of nano-confined Lennard-Jones fluids as a function of temperature and degree of nanoconfinement has been studied via statistical temperature molecular dynamics (STMD). The STMD method allows the direct calculation of the density of states and thus the heat capacity with high efficiency. The fluids are simulated between parallel solid surfaces with varying pore sizes, wall-fluid interaction energies, and registry of the walls. The fluid-solid phase transition behavior has been characterized through determination of the heat capacity. The results show that for pores of ideal-spacing, the order-disorder transition temperature ( T ODT ) is reduced as the pore size increases until values consistent with that seen in a bulk system. Also, as the interaction between the wall and fluid is reduced, T ODT is reduced due to weak constraints from the wall. However, for non-ideal spacing pores, quite different behavior is obtained, e.g., generally T ODT are largely reduced, and T ODT is decreased as the wall constraint becomes larger. For unaligned walls (i.e., whose lattices are not in registry), the fluid-solid transition is also detected as T is reduced, indicating non-ideality in orientation of the walls does not impact the formation of a solid, but results in a slight change in T ODT compared to the perfectly aligned systems. The STMD method is demonstrated to be a robust way for probing the phase transitions of nanoconfined fluids systematically, enabling the future examination of the phase transition behavior of more complex fluids.

Description: Liquid water is known to reorient via a combination of large angular jumps (due to exchange of hydrogen bonding (H-bond) partners) and diffusive orientations. Translation of the molecule undergoing the orientational jump and its initial and final H-bond acceptors plays a key role in the microscopic reorientation process. Here, we partition the translational dynamics into those occurring during intervals when rotating water molecules (and their initial and final H-bonding partners) undergo orientational jump and those arising when molecules wait between consecutive orientational jumps. These intervals are chosen in such a way that none of the four possible H-bonds involving the chosen water molecule undergo an exchange process within its duration. Translational dynamics is analysed in terms of the distribution of particle displacements, van Hove functions, and its moments. We observe that the translational dynamics, calculated from molecular dynamics simulations of liquid water, is fastest during the orientational jumps and slowest during periods of waiting. The translational dynamics during all temporal intervals shows an intermediate behaviour. This is the microscopic origin of temporal dynamic heterogeneity in liquid water, which is mild at 300 K and systematically increases with supercooling. Study of such partitioned dynamics in supercooled water shows increased disparity in dynamics occurring in the two different types of intervals. Nature of the distribution of particle displacements in supercooled water is investigated and it reveals signatures non-Gaussian behaviour.

Description: Cubic ice is said to have stacking disorder when the H 2 O sequences in its structure (space group F d 3 ̄ m ) are interlaced with hexagonal ice (space group P 6 3 / mmc ) sequences, known as stacking faults. Diffraction methods have shown that the extent of this disorder varies in samples made by different methods, thermal history, and the temperature T , but other physical properties of cubic and hexagonal ices barely differ. We had found that at 160 K, the thermal conductivity, κ , of cubic ice is ∼20% less than that of hexagonal ice, and this difference varies for cubic ice samples prepared by different methods and/or subjected to different thermal history. After reviewing the methods of forming cubic ice, we report an investigation of the effects of stacking disorder and other features by using new data, and by analyzing our previous data on the dependence of κ on T and on the pressure. We conclude that the lower κ of cubic ice and its weaker T -dependence is due mainly to stacking disorder and small crystal sizes. On in situ heating at 20–50 MPa pressure, κ increases and cubic ice irreversibly transforms more sharply to ice Ih, and at a higher T of ∼220 K, than it does in ex situ studies. Cooling and heating between 115 and 130 K at 0.1 K min −1 rate yield the same κ value, indicating that the state of cubic ice in these conditions does not change with time and T . The increase in κ of cubic ice observed on heat-annealing before its conversion to hexagonal ice is attributed to the loss of stacking faults and other types of disorders, and to grain growth. After discussing the consequences of our findings on other properties, we suggest that detailed studies of variation of a given property of cubic ice with the fraction of stacking faults in its structure may reveal more about the effect of this disorder. A similar disorder may occur in the mono-layers of H 2 O adsorbed on a substrate, in bulk materials comprised of two dimensional layers, in diamond and in Zirconium and in numerous other crystals.

Description: The string method is a useful numerical technique for resolving minimum energy paths in rare-event barrier-crossing problems. However, when applied to systems with relatively small energy barriers, the string method becomes inconvenient since many images trace out physically uninteresting regions where the barrier has already been crossed and recrossing is unlikely. Energy weighting alleviates this difficulty to an extent, but typical implementations still require the string’s endpoints to evolve to stable states that may be far from the barrier, and deciding upon a suitable energy weighting scheme can be an iterative process dependent on both the application and the number of images used. A second difficulty arises when treating nucleation problems: for later images along the string, the nucleus grows to fill the computational domain. These later images are unphysical due to confinement effects and must be discarded. In both cases, computational resources associated with unphysical or uninteresting images are wasted. We present a new energy weighting scheme that eliminates all of the above difficulties by actively truncating the string as it evolves and forcing all images, including the endpoints, to remain within and cover uniformly a desired barrier region. The calculation can proceed in one step without iterating on strategy, requiring only an estimate of an energy value below which images become uninteresting.

Description: The spin-vibronic energy levels of the cyanoacetylene cation have been measured using the one-photon zero-kinetic energy (ZEKE) photoelectron spectroscopic method. All three degenerate vibrational modes showing vibronic coupling, i.e., Renner-Teller (RT) effect, have been observed. All the splitting spin-vibronic energy levels of the fundamental H—C≡C bending vibration ( v 5 ) have been determined. The spin-vibronic energy levels of the degenerate vibrational modes have also been calculated using a diabatic model in which the harmonic terms as well as all the second-order vibronic coupling terms are used. The theoretical predictions are in good agreement with the experimental data and are used to assign the ZEKE spectrum. It is found that the RT effects for the H—(CC)—CN bending ( v 7 ) and the C—C≡N bending ( v 6 ) vibrations are weak, whereas they are strong for the H—C≡C bending ( v 5 ) vibration. The cross-mode RT couplings between any of the two degenerate vibrations are strong. The spin-orbit resolved fundamental vibrational energy levels of the C≡N stretching ( v 2 ) and C—H stretching ( v 1 ) vibrations have also been observed. The spin-orbit energy splitting of the ground state has been determined for the first time as 43 ± 2 cm −1 , and the ionization energy of HCCCN is found to be 93 903.5 ± 2 cm −1 .

Description: We develop a simple methodology for the computation of symmetry-adapted perturbation theory (SAPT) interaction energy contributions for intramolecular noncovalent interactions. In this approach, the local occupied orbitals of the total Hartree-Fock (HF) wavefunction are used to partition the fully interacting system into three chemically identifiable units: the noncovalent fragments A and B and a covalent linker C. Once these units are identified, the noninteracting HF wavefunctions of the fragments A and B are separately optimized while embedded in the HF wavefunction of C, providing the dressed zeroth order wavefunctions for A and B in the presence of C. Standard two-body SAPT (particularly SAPT0) is then applied between the relaxed wavefunctions for A and B. This intramolecular SAPT procedure is found to be remarkably straightforward and efficient, as evidenced by example applications ranging from diols to hexaphenyl-ethane derivatives.

Description: We address the problem of simulating biochemical reaction networks with time-dependent rates and propose a new algorithm based on our rejection-based stochastic simulation algorithm (RSSA) [Thanh et al. , J. Chem. Phys. 141 (13), 134116 (2014)]. The computation for selecting next reaction firings by our time-dependent RSSA (tRSSA) is computationally efficient. Furthermore, the generated trajectory is exact by exploiting the rejection-based mechanism. We benchmark tRSSA on different biological systems with varying forms of reaction rates to demonstrate its applicability and efficiency. We reveal that for nontrivial cases, the selection of reaction firings in existing algorithms introduces approximations because the integration of reaction rates is very computationally demanding and simplifying assumptions are introduced. The selection of the next reaction firing by our approach is easier while preserving the exactness.

Description: The nonisothermal single-component theory of droplet nucleation [N. V. Alekseechkin, Physica A 412 , 186 (2014)] is extended to binary case; the droplet volume V , composition x , and temperature T are the variables of the theory. An approach based on macroscopic kinetics (in contrast to the standard microscopic model of nucleation operating with the probabilities of monomer attachment and detachment) is developed for the droplet evolution and results in the derived droplet motion equations in the space ( V , x , T )—equations for V ̇ ≡ d V / d t , x ̇ , and T ̇ . The work W ( V , x , T ) of the droplet formation is obtained in the vicinity of the saddle point as a quadratic form with diagonal matrix. Also, the problem of generalizing the single-component Kelvin equation for the equilibrium vapor pressure to binary case is solved; it is presented here as a problem of integrability of a Pfaffian equation. The equation for T ̇ is shown to be the first law of thermodynamics for the droplet, which is a consequence of Onsager’s reciprocal relations and the linked-fluxes concept. As an example of ideal solution for demonstrative numerical calculations, the o -xylene- m -xylene system is employed. Both nonisothermal and enrichment effects are shown to exist; the mean steady-state overheat of droplets and their mean steady-state enrichment are calculated with the help of the 3 D distribution function. Some qualitative peculiarities of the nucleation thermodynamics and kinetics in the water-sulfuric acid system are considered in the model of regular solution. It is shown that there is a small kinetic parameter in the theory due to the small amount of the acid in the vapor and, as a consequence, the nucleation process is isothermal.

Description: Recently, an approximate theoretical framework was introduced, called local reduced density matrix functional theory (local-RDMFT), where functionals of the one-body reduced density matrix (1-RDM) are minimized under the additional condition that the optimal orbitals satisfy a single electron Schrödinger equation with a local potential. In the present work, we focus on the character of these optimal orbitals. In particular, we compare orbitals obtained by local-RDMFT with those obtained with the full minimization (without the extra condition) by contrasting them against the exact NOs and orbitals from a density functional calculation using the local density approximation (LDA). We find that the orbitals from local-RMDFT are very close to LDA orbitals, contrary to those of the full minimization that resemble the exact NOs. Since local RDMFT preserves the good quality of the description of strong static correlation, this finding opens the way to a mixed density/density matrix scheme, where Kohn-Sham orbitals obtain fractional occupations from a minimization of the occupation numbers using 1-RDM functionals. This will allow for a description of strong correlation at a cost only minimally higher than a density functional calculation.

Description: A density functional theory (DFT) based composite electronic structure approach is proposed to efficiently compute structures and interaction energies in large chemical systems. It is based on the well-known and numerically robust Perdew-Burke-Ernzerhoff (PBE) generalized-gradient-approximation in a modified global hybrid functional with a relatively large amount of non-local Fock-exchange. The orbitals are expanded in Ahlrichs-type valence-double zeta atomic orbital (AO) Gaussian basis sets, which are available for many elements. In order to correct for the basis set superposition error (BSSE) and to account for the important long-range London dispersion effects, our well-established atom-pairwise potentials are used. In the design of the new method, particular attention has been paid to an accurate description of structural parameters in various covalent and non-covalent bonding situations as well as in periodic systems. Together with the recently proposed three-fold corrected (3c) Hartree-Fock method, the new composite scheme (termed PBEh-3c) represents the next member in a hierarchy of “low-cost” electronic structure approaches. They are mainly free of BSSE and account for most interactions in a physically sound and asymptotically correct manner. PBEh-3c yields good results for thermochemical properties in the huge GMTKN30 energy database. Furthermore, the method shows excellent performance for non-covalent interaction energies in small and large complexes. For evaluating its performance on equilibrium structures, a new compilation of standard test sets is suggested. These consist of small (light) molecules, partially flexible, medium-sized organic molecules, molecules comprising heavy main group elements, larger systems with long bonds, 3d-transition metal systems, non-covalently bound complexes (S22 and S66×8 sets), and peptide conformations. For these sets, overall deviations from accurate reference data are smaller than for various other tested DFT methods and reach that of triple-zeta AO basis set second-order perturbation theory (MP2/TZ) level at a tiny fraction of computational effort. Periodic calculations conducted for molecular crystals to test structures (including cell volumes) and sublimation enthalpies indicate very good accuracy competitive to computationally more involved plane-wave based calculations. PBEh-3c can be applied routinely to several hundreds of atoms on a single processor and it is suggested as a robust “high-speed” computational tool in theoretical chemistry and physics.

Description: The response of strong polyelectrolyte (PE) brushes grafted on an electrode to electric fields generated by opposite surface charges on the PE-grafted electrode and a second parallel electrode has been numerically investigated by self-consistent field theory. The influences of grafting density, average charge fraction, salt concentration, and mobile ion size on the variation of the brush height against an applied voltage bias were investigated. In agreement with molecular dynamics simulation results, a higher grafting density requires a larger magnitude of voltage bias to achieve the same amount of relative change in the brush height. In the experimentally relevant parameter regime of the applied voltage, the brush height becomes insensitive to the voltage bias when the grafting density is high. Including the contribution of surface charges on the grafting electrode, overall charge neutrality inside the PE brushes is generally maintained, especially for PE brushes with high grafting density and high average charge fraction. Our numerical study further reveals that the electric field across the two electrodes is highly non-uniform because of the complex interplay between the surface charges on the electrodes, the charges on the grafted PE chains, and counterions.

Description: Unbiased stochastic sampling of the one- and two-body reduced density matrices is achieved in full configuration interaction quantum Monte Carlo with the introduction of a second, “replica” ensemble of walkers, whose population evolves in imaginary time independently from the first and which entails only modest additional computational overheads. The matrices obtained from this approach are shown to be representative of full configuration-interaction quality and hence provide a realistic opportunity to achieve high-quality results for a range of properties whose operators do not necessarily commute with the Hamiltonian. A density-matrix formulated quasi-variational energy estimator having been already proposed and investigated, the present work extends the scope of the theory to take in studies of analytic nuclear forces, molecular dipole moments, and polarisabilities, with extensive comparison to exact results where possible. These new results confirm the suitability of the sampling technique and, where sufficiently large basis sets are available, achieve close agreement with experimental values, expanding the scope of the method to new areas of investigation.

Description: Evolution of proteins in bacteria and archaea living in different conditions leads to significant correlations between amino acid usage and environmental temperature. The origins of these correlations are poorly understood, and an important question of protein theory, physics-based prediction of types of amino acids overrepresented in highly thermostable proteins, remains largely unsolved. Here, we extend the random energy model of protein folding by weighting the interaction energies of amino acids by their frequencies in protein sequences and predict the energy gap of proteins designed to fold well at elevated temperatures. To test the model, we present a novel scalable algorithm for simultaneous energy calculation for many sequences in many structures, targeting massively parallel computing architectures such as graphics processing unit. The energy calculation is performed by multiplying two matrices, one representing the complete set of sequences, and the other describing the contact maps of all structural templates. An implementation of the algorithm for the CUDA platform is available at http://www.github.com/kzeldovich/galeprot and calculates protein folding energies over 250 times faster than a single central processing unit. Analysis of amino acid usage in 64-mer cubic lattice proteins designed to fold well at different temperatures demonstrates an excellent agreement between theoretical and simulated values of energy gap. The theoretical predictions of temperature trends of amino acid frequencies are significantly correlated with bioinformatics data on 191 bacteria and archaea, and highlight protein folding constraints as a fundamental selection pressure during thermal adaptation in biological evolution.

Description: We present coupled cluster calculations of NMR shielding constants of aluminum, gallium, and indium in water-ion clusters. In addition, relativistic and dynamical corrections and the influence of the second solvation shell are evaluated. The final NMR shielding constants define new absolute shielding scales, 600.0 ± 4.1 ppm, 2044.4 ± 31.4 ppm, and 4507.7 ± 63.7 ppm for aluminum, gallium, and indium, respectively. The nuclear magnetic dipole moments for 27 Al, 69 Ga, 71 Ga, 113 In, and 115 In isotopes are corrected by combining the computed shielding constants with experimental NMR frequencies. The absolute magnitude of the correction increases along the series and for indium isotopes it reaches approximately −8.0 × 10 −3 of the nuclear magneton.

Description: This work describes the implementation and applications of non-Hermitian self-consistent field (NH-SCF) theory with complex basis functions for the ab initio computation of positions and widths of shape resonances in molecules. We utilize both the restricted open-shell and the previously unexplored spin-unrestricted variants to compute Siegert energies of several anionic shape resonances in small diatomic and polyatomic molecules including carbon tetrafluoride which has been the subject of several recent experimental studies. The computation of general molecular properties from a non-Hermitian wavefunction is discussed, and a density-based analysis is applied to the 2 B 1 shape resonance in formaldehyde. Spin-unrestricted NH-SCF is used to compute a complex potential energy surface for the carbon monoxide anion which correctly describes dissociation.

Description: We report the observation of eigenstates that embody large-amplitude, local-bending vibrational motion in acetylene by stimulated emission pumping spectroscopy via vibrational levels of the S 1 state involving excitation in the non-totally symmetric bending modes. The N b = 14 level, lying at 8971.69 cm −1 ( J = 0), is assigned on the basis of degeneracy due to dynamical symmetry breaking in the local-mode limit. The level pattern for the N b = 16 level, lying at 10 218.9 cm −1 , is consistent with expectations for increased separation of ℓ = 0 and 2 vibrational angular momentum components. Increasingly poor agreement between our observations and the predicted positions of these levels highlights the failure of currently available normal mode effective Hamiltonian models to extrapolate to regions of the potential energy surface involving large-amplitude displacement along the acetylene ⇌ vinylidene isomerization coordinate.

Description: The electronic spectra of neutral NpO and NpO 2 as well as of their mono- (NpO + , NpO 2 + ) and dications (NpO 2+ , NpO 2 2+ ) were studied using multiconfigurational relativistic quantum chemical calculations at the complete active space self-consistent field/CASPT2 level of theory taking into account spin-orbit coupling. The active space included 16 orbitals: all the 7s, 6d, and 5f orbitals of neptunium together with selected orbitals of oxygen. The vertical excitation energies on the ground state geometries have been computed up to ca. 35 000 cm −1 . The gas-phase electronic spectra were evaluated on the basis of the computed Einstein coefficients at 298 K and 3000 K. The computed vertical transition energies show good agreement with previous condensed-phase results on NpO 2 + and NpO 2 2+ .

Description: An implementation of coupled-cluster (CC) theory to treat atoms and molecules in finite magnetic fields is presented. The main challenges for the implementation stem from the magnetic-field dependence in the Hamiltonian, or, more precisely, the appearance of the angular momentum operator, due to which the wave function becomes complex and which introduces a gauge-origin dependence. For this reason, an implementation of a complex CC code is required together with the use of gauge-including atomic orbitals to ensure gauge-origin independence. Results of coupled-cluster singles–doubles–perturbative-triples (CCSD(T)) calculations are presented for atoms and molecules with a focus on the dependence of correlation and binding energies on the magnetic field.

Description: In Titan’s atmosphere, photochemical pathways that lead to nitrogen heteroaromatics may incorporate photoisomerization of their structural isomers as a final step. (E)- and (Z)-phenylvinylnitrile ((E)- and (Z)-PVN, C 6 H 5 —CH=CHCN) are structural isomers of quinoline that themselves possess extensive absorptions in the ultraviolet, and thus may engage in such photoisomerization pathways. The present study explores the vibronic spectroscopy and photo-induced isomerization of gas-phase (E)- and (Z)-PVN in the 33,600-35,850 cm −1 region under jet-cooled conditions. The S 0 -S 1 origins for (E)- and (Z)-PVN have been identified at 33 827 cm −1 and 33 707 cm −1 , respectively. Isomer-specific UV-UV hole-burning and UV depletion spectra reveal sharp vibronic structure that extends over almost 2000 cm −1 , with thresholds for fast non-radiative decay identified by a comparison between hole-burning and UV depletion spectra. Dispersed fluorescence spectra of the two isomers enable the assignment of many low frequency transitions in both molecules, aided by harmonic frequency calculations (B3LYP/6-311++G(d,p)) and a comparison with the established spectroscopy of phenylvinylacetylene, the ethynyl counterpart to PVN. Both isomers are proven to be planar in both the S 0 ground and S 1 electronic excited states. (E)-PVN exhibits extensive Duschinsky mixing involving out-of-plane modes whose frequencies and character change significantly in the ππ ∗ transition, which modulates the degree of single- and double-bond character along the vinylnitrile substituent. This same mixing is much less evident in (Z)-PVN. The spectroscopic characterization of (E)- and (Z)-PVN served as the basis for photoisomerization experiments using ultraviolet hole-filling spectroscopy carried out in a reaction tube affixed to the pulsed valve. Successful interconversion between (E) and (Z)-PVN was demonstrated via ultraviolet hole-filling experiments. Photoexcitation of (E)- and (Z)-PVN at their respective S 0 -S 1 origins failed to produce quinoline, a simple polycyclic aromatic nitrogen heterocylcle, within the detection sensitivity of our experiments. Stationary points along the potential energy surface associated with (Z)-PVN → quinoline isomerization showed a barrier of 93 kcal/mol associated with the first step in the isomerization process, slowing the interconversion process at the excitation energies used (96 kcal/mol) to timescales beyond those probed in the present experiment.

Description: At the molecular level, biochemical processes are governed by random interactions between reactant molecules, and the dynamics of such systems are inherently stochastic. When the copy numbers of reactants are large, a deterministic description is adequate, but when they are small, such systems are often modeled as continuous-time Markov jump processes that can be described by the chemical master equation. Gillespie’s Stochastic Simulation Algorithm (SSA) generates exact trajectories of these systems, but the amount of computational work required for each step of the original SSA is proportional to the number of reaction channels, leading to computational complexity that scales linearly with the problem size. The original SSA is therefore inefficient for large problems, which has prompted the development of several alternative formulations with improved scaling properties. We describe an exact SSA that uses a table data structure with event time binning to achieve constant computational complexity with respect to the number of reaction channels for weakly coupled reaction networks. We present a novel adaptive binning strategy and discuss optimal algorithm parameters. We compare the computational efficiency of the algorithm to existing methods and demonstrate excellent scaling for large problems. This method is well suited for generating exact trajectories of large weakly coupled models, including those that can be described by the reaction-diffusion master equation that arises from spatially discretized reaction-diffusion processes.

Description: First principles studies on the geometric structure, stability, and electronic structure of WSi n clusters, n = 6-16, have been carried out to show that the observed differing “magic sizes” for WSi n clusters are associated with the nature of the growth processes. The WSi 12 cluster, observed as a magic species in experiments reacting transition metal ions with silane, is not stable due to a filled shell of 18 electrons, as previously proposed, but due to its atomic structure that arrests further growth because of an endohedral transition metal site. In fact, it is found that all of these clusters, n = 6-16, have filled 5d shells except for WSi 12 , which has a 5d 8 configuration that is caused by crystal field splitting. The stability of WSi 15 + , observed as highly stable in clusters generated by vaporizing silicon and metal carbonyls, is shown to be associated with a combination of geometric and electronic features. The findings are compared with previous results on CrSi n clusters.

Description: Most existing treatments of induced dipoles in polarizable molecular mechanics force field calculations use either the self-consistent variational method, which is solved iteratively, or the “direct” approximation that is non-iterative as a result of neglecting coupling between induced dipoles. The variational method is usually implemented using assumptions that are only strictly valid under tight convergence of the induced dipoles, which can be computationally demanding to enforce. In this work, we discuss the nature of the errors that result from insufficient convergence and suggest a strategy that avoids such problems. Using perturbation theory to reintroduce the mutual coupling into the direct algorithm, we present a computationally efficient method that combines the precision of the direct approach with the accuracy of the variational approach. By analyzing the convergence of this perturbation series, we derive a simple extrapolation formula that delivers a very accurate approximation to the infinite order solution at the cost of only a few iterations. We refer to the new method as extrapolated perturbation theory. Finally, we draw connections to our previously published permanent multipole algorithm to develop an efficient implementation of the electric field and Thole terms and also derive some necessary, but not sufficient, criteria that force field parameters must obey.

Description: The intermetallic compound InPd (CsCl type of crystal structure with a broad compositional range) is considered as a candidate catalyst for the steam reforming of methanol. Single crystals of this phase have been grown to study the structure of its three low-index surfaces under ultra-high vacuum conditions, using low energy electron diffraction (LEED), X-ray photoemission spectroscopy (XPS), and scanning tunneling microscopy (STM). During surface preparation, preferential sputtering leads to a depletion of In within the top few layers for all three surfaces. The near-surface regions remain slightly Pd-rich until annealing to ∼580 K. A transition occurs between 580 and 660 K where In segregates towards the surface and the near-surface regions become slightly In-rich above ∼660 K. This transition is accompanied by a sharpening of LEED patterns and formation of flat step-terrace morphology, as observed by STM. Several superstructures have been identified for the different surfaces associated with this process. Annealing to higher temperatures (≥750 K) leads to faceting via thermal etching as shown for the (110) surface, with a bulk In composition close to the In-rich limit of the existence domain of the cubic phase. The Pd-rich InPd(111) is found to be consistent with a Pd-terminated bulk truncation model as shown by dynamical LEED analysis while, after annealing at higher temperature, the In-rich InPd(111) is consistent with an In-terminated bulk truncation, in agreement with density functional theory (DFT) calculations of the relative surface energies. More complex surface structures are observed for the (100) surface. Additionally, individual grains of a polycrystalline sample are characterized by micro-spot XPS and LEED as well as low-energy electron microscopy. Results from both individual grains and “global” measurements are interpreted based on comparison to our single crystals findings, DFT calculations and previous literature.

Description: A number of important cellular functions rely on the formation of intracellular protein concentration gradients. Experimental studies discovered a number of mechanisms for the formation of such gradients. One of the mechanisms relies on the intracellular shuttling of a protein that interconverts between the two states with different diffusivities, under the action of two enzymes, one of which is localized to the plasma membrane, whereas the second is uniformly distributed in the cytoplasm. Recent work reported an analytical solution for the steady state gradient in this mechanism, obtained in the framework of a one-dimensional reaction-diffusion model. Here, we study the dynamics in this model and derive analytical expressions for the Laplace transforms of the time-dependent concentration profiles in terms of elementary transcendental functions. Inverting these transforms numerically, one can obtain time-dependent concentration profiles of the two forms of the protein.

Description: Brownian aggregation rates are determined for concentrated dispersions of interacting particles with Brownian dynamics (BD) simulations and various theoretical models. Using simulation results as benchmarks, the predictions of the classical Fuchs-Smoluchowski (FS) model are shown to be quite inaccurate for concentrated dispersions. A new aggregation model is presented which provides significantly improved predictions. This model is developed on the basis of the fundamental measure theory (FMT) which is a rigorous “liquid-state” dynamic density-functional theory (DDFT) approach. It provides a major improvement of the FS model by considering short-range ordering, non-ideal diffusion, and unsteady-state effects. These were recently shown by the authors to play important roles in Brownian aggregation of hard spheres at high concentrations. Two types of interparticle interaction potentials are examined, the purely attractive van der Waals potential and the DLVO potential which includes van der Waals attraction and electrostatic double layer repulsion. For dispersions of particles with purely attractive interactions, the FS model underpredicts the aggregation rates by up to 1000 fold. In the presence of strong interparticle repulsive forces, its predictions are in fair agreement with the BD simulation results for dilute systems with particle volume fractions ϕ 〈 〈 0.1. In contrast, the predictions of the new FM-DDFT based model compare favorably with the BD simulation results, in both cases, up to ϕ = 0.3. A new quantitative measure for colloidal dispersion stability, different from the classical FS stability ratio, is proposed on the basis of aggregation half-times. Hence, a better mechanistic understanding of Brownian aggregation is obtained for concentrated dispersions of particles with either attractive or repulsive interactions, or both.

Description: We report a facile method of doping cations from an electrospray ionization (ESI) source into superfluid helium droplets. By decelerating and stopping the ion pulse of reserpine and substance P from an ESI source in the path of the droplet beam, about 10 4 ion-doped droplets (one ion per droplet) can be recorded, corresponding to a pickup efficiency of nearly 1 out of 1000 ions. We attribute the success of this simple approach to the long residence time of the cations in the droplet beam. The resulting size of the doped droplets, on the order of 10 5 /droplet, is measured using deflection and retardation methods. Our method does not require an ion trap in the doping region, which significantly simplifies the experimental setup and procedure for future spectroscopic and diffraction studies.

Description: Hyperdynamics is a powerful method to significantly extend the time scales amenable to molecular dynamics simulation of infrequent events. One outstanding challenge, however, is the development of the so-called bias potential required by the method. In this work, we design a bias potential using information about all minimum energy pathways (MEPs) out of the current state. While this approach is not suitable for use in an actual hyperdynamics simulation, because the pathways are generally not known in advance, it allows us to show that it is possible to come very close to the theoretical boost limit of hyperdynamics while maintaining high accuracy. We demonstrate this by applying this MEP-based hyperdynamics (MEP-HD) to metallic surface diffusion systems. In most cases, MEP-HD gives boost factors that are orders of magnitude larger than the best existing bias potential, indicating that further development of hyperdynamics bias potentials could have a significant payoff. Finally, we discuss potential practical uses of MEP-HD, including the possibility of developing MEP-HD into a true hyperdynamics.

Description: Nitrate and nitrite ions are of considerable interest, both for their widespread use in commercial and research contexts and because of their central role in the global nitrogen cycle. The chemistry of atmospheric aerosols, wherein nitrate is abundant, has been found to depend on the interfacial behavior of ionic species. The interfacial behavior of ions is determined largely by their hydration properties; consequently, the study of the hydration and interfacial behavior of nitrate and nitrite comprises a significant field of study. In this work, we describe the study of aqueous solutions of sodium nitrate and nitrite via X-ray absorption spectroscopy (XAS), interpreted in light of first-principles density functional theory electronic structure calculations. Experimental and calculated spectra of the nitrogen K-edge XA spectra of bulk solutions exhibit a large 3.7 eV shift between the XA spectra of nitrate and nitrite resulting from greater stabilization of the nitrogen 1s energy level in nitrate. A similar shift is not observed in the oxygen K-edge XA spectra of NO 3 − and NO 2 − . The hydration properties of nitrate and nitrite are found to be similar, with both anions exhibiting a similar propensity towards ion pairing.

Description: In this work, we study diffusion of gases in porous amorphous carbon at high temperatures using equilibrium molecular dynamics simulations. Microporous and mesoporous carbon structures are computationally generated using liquid quench method and reactive force fields. Motivated by the need to understand high temperature diffusivity of light weight gases like H 2 , O 2 , H 2 O, and CO in amorphous carbon, we investigate the diffusion behavior as function of two important parameters: (a) the pore size and (b) the concentration of diffusing gases. The effect of pore size on diffusion is studied by employing multiple realizations of the amorphous carbon structures in microporous and mesoporous regimes, corresponding to densities of 1 g/cm 3 and 0.5 g/cm 3 , respectively. A detailed analysis of the effect of gas concentration on diffusion in the context of these two porosity regimes is presented. For the microporous structure, we observe that predominantly, a high diffusivity results when the structure is highly anisotropic and contains wide channels between the pores. On the other hand, when the structure is highly homogeneous, significant molecule-wall scattering leads to a nearly concentration-independent behavior of diffusion (reminiscent of Knudsen diffusion). The mesoporous regime is similar in behavior to the highly diffusive microporous carbon case in that diffusion at high concentration is governed by gas-gas collisions (reminiscent of Fickian diffusion), which transitions to a Knudsen-like diffusion at lower concentration.

Description: We propose a multireference linearized coupled cluster theory using matrix product states (MPSs-LCC) which provides remarkably accurate ground-state energies, at a computational cost that has the same scaling as multireference configuration interaction singles and doubles, for a wide variety of electronic Hamiltonians. These range from first-row dimers at equilibrium and stretched geometries to highly multireference systems such as the chromium dimer and lattice models such as periodic two-dimensional 1-band and 3-band Hubbard models. The MPS-LCC theory shows a speed up of several orders of magnitude over the usual Density Matrix Renormalization Group (DMRG) algorithm while delivering energies in excellent agreement with converged DMRG calculations. Also, in all the benchmark calculations presented here, MPS-LCC outperformed the commonly used multi-reference quantum chemistry methods in some cases giving energies in excess of an order of magnitude more accurate. As a size-extensive method that can treat large active spaces, MPS-LCC opens up the use of multireference quantum chemical techniques in strongly correlated ab initio Hamiltonians, including two- and three-dimensional solids.

Description: Using the probabilistic language of conditional expectations, we reformulate the force matching method for coarse-graining of molecular systems as a projection onto spaces of coarse observables. A practical outcome of this probabilistic description is the link of the force matching method with thermodynamic integration. This connection provides a way to systematically construct a local mean force and to optimally approximate the potential of mean force through force matching. We introduce a generalized force matching condition for the local mean force in the sense that allows the approximation of the potential of mean force under both linear and non-linear coarse graining mappings (e.g., reaction coordinates, end-to-end length of chains). Furthermore, we study the equivalence of force matching with relative entropy minimization which we derive for general non-linear coarse graining maps. We present in detail the generalized force matching condition through applications to specific examples in molecular systems.

Description: We developed a simple method to calculate exchange repulsion between a quantum mechanical (QM) solute and a molecular mechanical (MM) molecule in the QM/MM approach. In our method, the size parameter in the Buckingham type potential for the QM solute is directly determined in terms of the one-electron wave functions of the solute. The point of the method lies in the introduction of the exchange core function (ECF) defined as a Slater function which mimics the behavior of the exterior electron density at the QM/MM boundary region. In the present paper, the ECF was constructed in terms of the Becke-Roussel (BR) exchange hole function. It was demonstrated that the ECF yielded by the BR procedure can faithfully reproduce the radial behavior of the electron density of a QM solute. The size parameter of the solute as well as the exchange repulsion are, then, obtained using the overlap model without any fitting procedure. To examine the efficiency of the method, it was applied to calculation of the exchange repulsions for minimal QM/MM systems, hydrogen-bonded water dimer, and H 3 O + –H 2 O. We found that our approach is able to reproduce the potential energy curves for these systems showing reasonable agreements with those given by accurate full quantum chemical calculations.

Description: The results of application of the quantum-mechanical adiabatic theory to vibrational predissociation (VPD) of water dimers, (H 2 O) 2 and (D 2 O) 2 , are presented. We consider the VPD processes including the totally symmetric OH mode of the dimer and the bending mode of the fragment. The VPD in the adiabatic representation is induced by breakdown of the vibrational adiabatic approximation, and two types of nonadiabatic coupling matrix elements are involved: one provides the VPD induced by the low-frequency dissociation mode and the other provides the VPD through channel interactions induced by the low-frequency modes. The VPD rate constants were calculated using the Fermi golden rule expression. A closed form for the nonadiabatic transition matrix element between the discrete and continuum states was derived in the Morse potential model. All of the parameters used were obtained from the potential surfaces of the water dimers, which were calculated by the density functional theory procedures. The VPD rate constants for the two processes were calculated in the non-Condon scheme beyond the so-called Condon approximation. The channel interactions in and between the initial and final states were taken into account, and those are found to increase the VPD rates by 3(1) orders of magnitude for the VPD processes in (H 2 O) 2 ((D 2 O) 2 ). The fraction of the bending-excited donor fragments is larger than that of the bending-excited acceptor fragments. The results obtained by quantum-mechanical approach are compared with both experimental and quasi-classical trajectory calculation results.

Description: Molecular dynamics simulations and integral equation calculations of a simple equimolar mixture of diatomic molecules and monomers interacting via attractive and repulsive short-range potentials show the existence of pattern formation (microheterogeneity), mostly due to depletion forces away from the demixing region. Effective site-site potentials extracted from the pair correlation functions using an inverse Monte Carlo approach and an integral equation inversion procedure exhibit the features characteristic of a short-range attractive and a long-range repulsive potential. When charges are incorporated into the model, this becomes a coarse grained representation of a room temperature ionic liquid, and as expected, intermediate range order becomes more pronounced and stable.

Description: In this article, we present a new microscopic theoretical approach to the description of spin crossover in molecular crystals. The spin crossover crystals under consideration are composed of molecular fragments formed by the spin-crossover metal ion and its nearest ligand surrounding and exhibiting well defined localized (molecular) vibrations. As distinguished from the previous models of this phenomenon, the developed approach takes into account the interaction of spin-crossover ions not only with the phonons but also a strong coupling of the electronic shells with molecular modes. This leads to an effective coupling of the local modes with phonons which is shown to be responsible for the cooperative spin transition accompanied by the structural reorganization. The transition is characterized by the two order parameters representing the mean values of the products of electronic diagonal matrices and the coordinates of the local modes for the high- and low-spin states of the spin crossover complex. Finally, we demonstrate that the approach provides a reasonable explanation of the observed spin transition in the [Fe(ptz) 6 ](BF 4 ) 2 crystal. The theory well reproduces the observed abrupt low-spin → high-spin transition and the temperature dependence of the high-spin fraction in a wide temperature range as well as the pronounced hysteresis loop. At the same time within the limiting approximations adopted in the developed model, the evaluated high-spin fraction vs. T shows that the cooperative spin-lattice transition proves to be incomplete in the sense that the high-spin fraction does not reach its maximum value at high temperature.

Description: The so-called “raspberry” model refers to the hybrid lattice-Boltzmann (LB) and Langevin molecular dynamics schemes for simulating the dynamics of suspensions of colloidal particles, originally developed by Lobaskin and Dünweg [New J. Phys. 6 , 54 (2004)], wherein discrete surface points are used to achieve fluid-particle coupling. In this paper, we present a follow up to our study of the effectiveness of the raspberry model in reproducing hydrodynamic interactions in the Stokes regime for spheres arranged in a simple-cubic crystal [Fischer et al. , J. Chem. Phys. 143 , 084107 (2015)]. Here, we consider the accuracy with which the raspberry model is able to reproduce such interactions for particles confined between two parallel plates. To this end, we compare our LB simulation results to established theoretical expressions and finite-element calculations. We show that there is a discrepancy between the translational and rotational mobilities when only surface coupling points are used, as also found in Part I of our joint publication. We demonstrate that adding internal coupling points to the raspberry can be used to correct said discrepancy in confining geometries as well. Finally, we show that the raspberry model accurately reproduces hydrodynamic interactions between a spherical colloid and planar walls up to roughly one LB lattice spacing.

Description: Semiclassical approximations to response functions can allow the calculation of linear and nonlinear spectroscopic observables from classical dynamics. Evaluating a canonical response function requires the related tasks of determining thermal weights for initial states and computing the dynamics of these states. A class of approximations for vibrational response functions employs classical trajectories at quantized values of action variables and represents the effects of the radiation-matter interaction by discontinuous transitions. Here, we evaluate choices for a thermal weight function which are consistent with this dynamical approximation. Weight functions associated with different semiclassical approximations are compared, and two forms are constructed which yield the correct linear response function for a harmonic potential at any temperature and are also correct for anharmonic potentials in the classical mechanical limit of high temperature. Approximations to the vibrational linear response function with quantized classical trajectories and proposed thermal weight functions are assessed for ensembles of one-dimensional anharmonic oscillators. This approach is shown to perform well for an anharmonic potential that is not locally harmonic over a temperature range encompassing the quantum limit of a two-level system and the limit of classical dynamics.

Description: The stability limits of the isotropic state of melt of rod-rod AB polydisperse diblock copolymer have been studied within weak segregation theory. The number of units in A block is assumed to be a random variable distributed by the Schulz-Zimm distribution. Inspection of the spinodal curves shows that the copolymer melt with polydisperse rigid blocks is less stable with respect to formation of the nematic and microphase separated states than the monodisperse melt. The values of ratios between strengths of isotropic and anisotropic interactions in the system strongly influences the forms of isotropic-nematic boundary curves.

Description: Rotational spectra of the weakly bound H 2 O—N 2 O complex and its HOD—N 2 O isotopologue in a supersonic jet are reported. Rotational constants of the singly substituted deuterium in water and each singly substituted nitrogen-15 are presented. Combinations of isotopic data and high level ab initio calculations place the water in a similar position to those of the isoelectronic H 2 O—CO 2 complex, with a slight tilt of the OH towards the NNO axis. The deuterium nuclear quadrupole coupling constant places the deuterium on the O—H axis quasi-parallel to the NNO axis.

Description: The anisotropy of thermal diffusivity in four homologues of ( p -alkoxybenzylidene)- p ′-octylaniline ( n O.8, n = 4 − 7) was measured using a temperature wave method. The results show that the thermal diffusivity component along the director ( α ∥ ) is considerably larger than that perpendicular to the director ( α ⊥ ) in all mesophases, i.e., nematic (N), smectic A (SmA), smectic B (SmB), and smectic G (SmG) phases. Both components of the thermal diffusivity show a dip at the second- or weakly first-order N-SmA phase transition due to the heat capacity anomaly. In contrast, at the first-order SmA-SmB phase transition, thermal diffusivity exhibits a stepwise increase. The x-ray and calorimetric measurements enable a calculation of the thermal conductivity and the study of the effect of the molecular length on the thermal conductivity and diffusivity in the SmA and SmB phases. For the homologues n = 4, 5, and 6, which exhibit the same phase sequence upon cooling, the parallel component of the thermal conductivity k ∥ in the SmA and SmB phases systematically increases with increasing length of the molecular tails, while no such increase is observed in the thermal diffusivity α ∥ . We thus conclude that the molecular model [Urbach et al. , J. Chem. Phys. 78 , 5113 (1983)] is valid for the qualitative prediction of the effect of the molecular length on the magnitude of the thermal conductivity.

Description: Large-scale domain motions in alcohol dehydrogenase (ADH) have been observed previously by neutron spin-echo spectroscopy (NSE). We have extended the investigation on the dynamics of ADH in solution by using high-resolution neutron time-of-flight (TOF) and neutron backscattering (BS) spectroscopy in the incoherent scattering range. The observed hydrogen dynamics were interpreted in terms of three mobility classes, which allowed a simultaneous description of the measured TOF and BS spectra. In addition to the slow global protein diffusion and domain motions observed by NSE, a fast internal process could be identified. Around one third of the protons in ADH participate in the fast localized diffusive motion. The diffusion coefficient of the fast internal motions is around two third of the value of the surrounding D 2 O solvent. It is tempting to associate the fast internal process with solvent exposed amino acid residues with dangling side chains.

Description: We apply Thermostatted Ring Polymer Molecular Dynamics (TRPMD), a recently proposed approximate quantum dynamics method, to the computation of thermal reaction rates. Its short-time transition-state theory limit is identical to rigorous quantum transition-state theory, and we find that its long-time limit is independent of the location of the dividing surface. TRPMD rate theory is then applied to one-dimensional model systems, the atom-diatom bimolecular reactions H + H 2 , D + MuH, and F + H 2 , and the prototypical polyatomic reaction H + CH 4 . Above the crossover temperature, the TRPMD rate is virtually invariant to the strength of the friction applied to the internal ring-polymer normal modes, and beneath the crossover temperature the TRPMD rate generally decreases with increasing friction, in agreement with the predictions of Kramers theory. We therefore find that TRPMD is approximately equal to, or less accurate than, ring polymer molecular dynamics for symmetric reactions, and for certain asymmetric systems and friction parameters closer to the quantum result, providing a basis for further assessment of the accuracy of this method.

Description: We report on three new noble-gas molecules, FKrCN, FXeCN, and FXeNC, prepared in low-temperature Kr and Xe matrices. These molecules are made by UV photolysis of FCN in the matrices and subsequent thermal annealing. The FCN precursor is produced by deposition of the matrix gas containing (FCN) 3 through a microwave discharge. The new noble-gas molecules are assigned with the help of quantum chemical calculations at the MP2(full) and CCSD(T) levels of theory. Similar Ar compounds (FArCN and FArNC) as well as FKrNC are not found in these experiments, which is in agreement with the calculated energetics.

Description: We investigate experimentally and theoretically thin layers of colloid particles held adjacent to a solid substrate by gravity. Epifluorescence, confocal, and holographic microscopy, combined with Monte Carlo and hydrodynamic simulations, are applied to infer the height distribution function of particles above the surface, and their diffusion coefficient parallel to it. As the particle area fraction is increased, the height distribution becomes bimodal, indicating the formation of a distinct second layer. In our theory, we treat the suspension as a series of weakly coupled quasi-two-dimensional layers in equilibrium with respect to particle exchange. We experimentally, numerically, and theoretically study the changing occupancies of the layers as the area fraction is increased. The decrease of the particle diffusion coefficient with concentration is found to be weakened by the layering. We demonstrate that particle polydispersity strongly affects the properties of the sedimented layer, because of particle size segregation due to gravity.

Description: We present results from molecular-dynamics simulations of a generic bead-spring model of copolymer chains confined between solid walls and report on the glass-transition temperature and segmental dynamics as a function of film thickness and mesh size (the end-to-end distance of the subchains in the crosslinked polymer networks). Apparently, the glass-transition temperature displayed a steep increase for mesh-size values much smaller than the radius of gyration of the bulk chains, otherwise it remained invariant to mesh-size variations. The rise in the glass-transition temperature with decreasing mesh size and film thickness was accompanied by a monotonic slowing-down of segmental dynamics on all studied length scales. This observation is attributed to the correspondingly decreased width of the bulk density layer that was obtained in films whose thickness was larger than the end-to-end distance of the bulk polymer chains. To test this hypothesis, additional simulations were performed in which the crystalline walls were replaced with amorphous or rough walls. In the amorphous case, the high polymer density close to the walls vanished, but the dynamic response of the film was not affected. The rough walls, on the other hand, only slightly decreased the density close to the walls and led to a minor slowing-down in the dynamics at large length-scales.

Description: In this work, we show that the standard method to obtain nucleation rate-predictions with the aid of atomistic Monte Carlo simulations leads to nucleation rate predictions that deviate 3 − 5 orders of magnitude from the recent brute-force molecular dynamics simulations [Diemand et al. , J. Chem. Phys. 139 , 074309 (2013)] conducted in the experimental accessible supersaturation regime for Lennard-Jones argon. We argue that this is due to the truncated state space the literature mostly relies on, where the number of atoms in a nucleus is considered the only relevant order parameter. We here formulate the nonequilibrium statistical mechanics of nucleation in an extended state space, where the internal energy and momentum of the nuclei are additionally incorporated. We show that the extended model explains the lack in agreement between the molecular dynamics simulations by Diemand et al. and the truncated state space. We demonstrate additional benefits of using the extended state space; in particular, the definition of a nucleus temperature arises very naturally and can be shown without further approximation to obey the fluctuation law of McGraw and LaViolette. In addition, we illustrate that our theory conveniently allows to extend existing theories to richer sets of order parameters.

Description: Manifestations of the “cage effect” at the encounters of reactants are theoretically treated by the example of multistage reactions in liquid solutions including bimolecular exchange reactions as elementary stages. It is shown that consistent consideration of quasi-stationary kinetics of multistage reactions (possible only in the framework of the encounter theory) for reactions proceeding near reactants contact can be made on the basis of the concepts of a “cage complex.” Though mathematically such a consideration is more complicated, it is more clear from the standpoint of chemical notions. It is established that the presence of the “cage effect” leads to some important effects not inherent in reactions in gases or those in solutions proceeding in the kinetic regime, such as the appearance of new transition channels of reactant transformation that cannot be caused by elementary event of chemical conversion for the given mechanism of reaction. This results in that, for example, rate constant values of multistage reaction defined by standard kinetic equations of formal chemical kinetics from experimentally measured kinetics can differ essentially from real values of these constants.

Description: The geometric structure of ultra-thin cerium oxide films on Rh(111), prepared by annealing the metallic cerium films at a very low coverage between 0.3 and 1.5 monolayers in an oxygen atmosphere, is investigated using scanning tunneling microscopy (STM), low-energy electron diffraction (LEED), X-ray photoelectron spectroscopy, and density functional theory (DFT) calculations. The STM image and LEED pattern indicate that cerium oxide films epitaxially grown as ordered CeO 2 (111) layers aligned to the 110 azimuthal direction of Rh(111). The in-plane lattice parameter measured from the LEED pattern appears to be contracted with respect to the bulk ceria lattice. The measured ratio Ce:O for two-trilayer cerium oxide film is 1.96:1, which is close to the stoichiometric ratio. The simulated STM image on the basis of DFT+U calculations is in good agreement with the experimental STM images.

Description: Force analyses are crucial for a comprehensive understanding of mechanochemical processes. The choice of coordinate system in these kinds of analyses is a nontrivial task that determines the quality and validity of the obtained results. Here, we study the suitability of different sets of coordinates for mechanical force analyses, i.e., normal modes, delocalized internal, redundant internal, and Z-matrix coordinates. After discussing the theoretical foundations of force analyses using different coordinate systems, we investigate a number of test molecules. We show that normal modes and Z-matrix coordinates deliver useful results only if certain requirements are fulfilled and that only redundant internal coordinates yield meaningful results in all cases.

Description: Compact and extended dendrimers are two important classes of dendritic polymers. The impact of the underlying structure of compact dendrimers on dynamical processes has been much studied, yet the relation between the dynamical and structural properties of extended dendrimers remains not well understood. In this paper, we study the trapping problem in extended dendrimers with generation-dependent segment lengths, which is different from that of compact dendrimers where the length of the linear segments is fixed. We first consider a particular case that the deep trap is located at the central node, and derive an exact formula for the average trapping time (ATT) defined as the average of the source-to-trap mean first passage time over all starting points. Then, using the obtained result we deduce a closed-form expression for the ATT to an arbitrary trap node, based on which we further obtain an explicit solution to the ATT corresponding to the trapping issue with the trap uniformly distributed in the polymer systems. We show that the trap location has a substantial influence on the trapping efficiency measured by the ATT, which increases with the shortest distance from the trap to the central node, a phenomenon similar to that for compact dendrimers. In contrast to this resemblance, the leading terms of ATTs for the three trapping problems differ drastically between extended and compact dendrimers, with the trapping processes in the extended dendrimers being less efficient than in compact dendrimers.

Description: We report on a combined experimental and molecular modelling study on Zn 4 O ion clusters stabilized by acetate molecules (OAc). In particular, ab initio calculations of acetate substitution by hydroxide ions are compared with mass spectrometry data. Though quantum calculations in the gas phase indicate strong energetic preference, no experimental evidence of stable Zn 4 O(OAc) 6−x (OH) x clusters in ethanolic solutions could be observed. This apparent contradiction is rationalized by identifying the supportive role of hydroxide ions for the association of (OAc − → OH − substituted) Zn 4 O(OAc) 6 and Zn 4 O(OAc) 5 + clusters. Mass spectrometry and quantum calculations hint at the stability of (Zn 4 O) 2 (OAc) 12−x (OH) x dimers with x = 1, 2. Therein, the hydroxide ions establish salt-bridges that allow for the formation of additional Zn 3 motifs with the OH above the triangle center—a structural motif close to that of the ZnO-crystal. The association of Zn 4 O(OAc) 6 clusters is thus suggested to involve OAc − → OH − substitution as an activation step, quickly followed by dimerization and the subsequent agglomeration of oligomers.

Description: The thermodynamic, dynamic, structural, and rigidity properties of densified liquid germania (GeO 2 ) have been investigated using classical molecular dynamics simulation. We construct from a thermodynamic framework an analytical equation of state for the liquid allowing the possible detection of thermodynamic precursors (extrema of the derivatives of the free energy), which usually indicate the possibility of a liquid-liquid transition. It is found that for the present germania system, such precursors and the possible underlying liquid-liquid transition are hidden by the slowing down of the dynamics with decreasing temperature. In this respect, germania behaves quite differently when compared to parent tetrahedral systems such as silica or water. We then detect a diffusivity anomaly (a maximum of diffusion with changing density/volume) that is strongly correlated with changes in coordinated species, and the softening of bond-bending (BB) topological constraints that decrease the liquid rigidity and enhance transport. The diffusivity anomaly is finally substantiated from a Rosenfeld-type scaling law linked to the pair correlation entropy, and to structural relaxation.

Description: We report experimental results on the diffusivity of water in two ionic liquids obtained using the pulsed-gradient spin-echo NMR method. Both ionic liquids have the same cation, 1-butyl-1-methylpyrrolidinium, but different trifluoromethyl-containing anions. One has a strongly hydrophobic anion, bis(trifluoromethylsulfonyl)amide, while the second has a hydrophilic anion, trifluoromethylsulfonate. Transport of water in these ionic liquids is much faster than would be predicted from hydrodynamic laws, indicating that the neutral water molecules experience a very different friction than the anions and cations at the molecular level. Temperature-dependent viscosities, conductivities, and densities are reported as a function of water concentration to further analyze the properties of the ionic liquid-water mixtures. These results on the properties of water in ionic liquids should be of interest to researchers in diverse areas ranging from separations, solubilizing biomass and energy technologies.

Description: We present a formalism and an implementation for calculating spin-orbit couplings (SOCs) within the EOM-CCSD (equation-of-motion coupled-cluster with single and double substitutions) approach. The following variants of EOM-CCSD are considered: EOM-CCSD for excitation energies (EOM-EE-CCSD), EOM-CCSD with spin-flip (EOM-SF-CCSD), EOM-CCSD for ionization potentials (EOM-IP-CCSD) and electron attachment (EOM-EA-CCSD). We employ a perturbative approach in which the SOCs are computed as matrix elements of the respective part of the Breit-Pauli Hamiltonian using zeroth-order non-relativistic wave functions. We follow the expectation-value approach rather than the response-theory formulation for property calculations. Both the full two-electron treatment and the mean-field approximation (a partial account of the two-electron contributions) have been implemented and benchmarked using several small molecules containing elements up to the fourth row of the periodic table. The benchmark results show the excellent performance of the perturbative treatment and the mean-field approximation. When used with an appropriate basis set, the errors with respect to experiment are below 5% for the considered examples. The findings regarding basis-set requirements are in agreement with previous studies. The impact of different correlation treatment in zeroth-order wave functions is analyzed. Overall, the EOM-IP-CCSD, EOM-EA-CCSD, EOM-EE-CCSD, and EOM-SF-CCSD wave functions yield SOCs that agree well with each other (and with the experimental values when available). Using an EOM-CCSD approach that provides a more balanced description of the target states yields more accurate results.

Description: A second order classical perturbation theory is developed to calculate the sticking probability of a particle scattered from an uncorrugated thermal surface. An analytic expression for the temperature dependent energy loss of the particle to the surface is derived by employing a one-dimensional generalized Langevin equation. The surface temperature reduces the energy loss, since the thermal surface transfers energy to the particle. Using a Gaussian energy loss kernel and the multiple collision theory of Fan and Manson [J. Chem. Phys. 130 , 064703 (2009)], enables the determination of the fraction of particles trapped on the surface after subsequent momentum reversals of the colliding particle. This then leads to an estimate of the trapping probability. The theory is tested for the model scattering of Ar on a LiF(100) surface. Comparison with numerical simulations shows excellent agreement of the analytical theory with simulations, provided that the energy loss is determined by the second order perturbation theory.

Description: A subspace formulation of time-dependent density functional theory (TDDFT) is proposed for large-scale calculations based on density functional perturbation theory. The formulation is implemented in conjunction with projector augmented-wave method and plane-wave basis set. A key bottleneck of conventional TDDFT method is circumvented by projecting the time-dependent Kohn-Sham eigenvalue equations from a full Hilbert space to a substantially reduced sub-Hilbert space. As a result, both excitation energies and ionic forces can be calculated accurately within the reduced subspace. The method is validated for several model systems and exhibits the similar accuracy as the conventional TDDFT method but at a computational cost of the ground state calculation. The Born-Oppenheimer molecular dynamics can be successfully performed for excited states in C 60 and T 12 molecules, opening doors for many applications involving excited state dynamics.

Description: In this work, we investigate the correlations among structure, topology, and properties in a series of sodium phosphosilicate glasses with [SiO 2 ]/[SiO 2 + P 2 O 5 ] ranging from 0 to 1. The network structure is characterized by 29 Si and 31 P magic-angle spinning nuclear magnetic resonance and Raman spectroscopy. The results show the formation of six-fold coordinated silicon species in phosphorous-rich glasses. Based on the structural data, we propose a formation mechanism of the six-fold coordinated silicon, which is used to develop a quantitative structural model for predicting the speciation of the network forming units as a function of chemical composition. The structural model is then used to establish a temperature-dependent constraint description of phosphosilicate glass topology that enables prediction of glass transition temperature, liquid fragility, and indentation hardness. The topological constraint model provides insight into structural origin of the mixed network former effect in phosphosilicate glasses.

Description: The localized Hartree-Fock potential has proven to be a computationally efficient alternative to the optimized effective potential, preserving the numerical accuracy of the latter and respecting the exact properties of being self-interaction free and having the correct −1/ r asymptotics. In this paper we extend the localized Hartree-Fock potential to fractional particle numbers and observe that it yields derivative discontinuities in the energy as required by the exact theory. The discontinuities are numerically close to those of the computationally more demanding Hartree-Fock method. Our potential enjoys a “direct-energy” property, whereby the energy of the system is given by the sum of the single-particle eigenvalues multiplied by the corresponding occupation numbers. The discontinuities c ↑ and c ↓ of the spin-components of the potential at integer particle numbers N ↑ and N ↓ satisfy the condition c ↑ N ↑ + c ↓ N ↓ = 0. Thus, joining the family of effective potentials which support a derivative discontinuity, but being considerably easier to implement, the localized Hartree-Fock potential becomes a powerful tool in the broad area of applications in which the fundamental gap is an issue.

Description: The relaxation dynamics in unfreezing process of metallic glasses is investigated by the activation-relaxation technique. A non-monotonic dynamical microstructural heterogeneities evolution with temperature is discovered, which confirms and supplies more features to flow units concept of glasses. A flow unit perspective is proposed to microscopically describe this non-monotonic evolution of the dynamical heterogeneities as well as its relationship with the deformation mode development of metallic glasses.

Description: When a classical master equation (CME) is used to describe the nonadiabatic dynamics of a molecule at metal surfaces, we show that in the regime of reasonably strong molecule-metal couplings, the CME can be reduced to a Fokker-Planck equation with an explicit form of electronic friction. For a single metal substrate at thermal equilibrium, the electronic friction and random force satisfy the fluctuation-dissipation theorem. When we investigate the time scale for an electron transfer (ET) event between the molecule and metal surface, we find that the ET rates show a turnover effect (just as in Kramer’s theory) as a function of frictional damping.

Description: In a three-site representation, we study a spin polarization transfer from radical pair spins to a nearby electron or nuclear spin. The quantum dynamics of the radical pair spins is governed by a constant exchange interaction between the radical pair spins which have different Zeeman frequencies. Radical pair spins can recombine to the singlet ground state or to lower energy triplet states. It is then shown that the coherent dynamics of the radical pair induces spin polarization on the nearby third spin in the presence of a magnetic field. The spin polarization transfer depends on the difference between Zeeman frequencies, the singlet and triplet recombination rates, and on the exchange and dipole-dipole interactions between the different spins. In particular, the sign of the polarization depends on the exchange coupling between radical pair spins and also on the difference between singlet and triplet recombination rate constants.

Description: The likelihood that an undercooled liquid vitrifies or crystallizes depends on the cooling rate . The critical cooling rate , below which the liquid crystallizes upon cooling, characterizes the glass-forming ability (GFA) of the system. While pure metals are typically poor glass formers with , specific multi-component alloys can form bulk metallic glasses (BMGs) even at cooling rates below . Conventional wisdom asserts that metal alloys with three or more components are better glass formers (with smaller ) than binary alloys. However, there is currently no theoretical framework that provides quantitative predictions for for multi-component alloys. In this manuscript, we perform simulations of ternary hard-sphere systems, which have been shown to be accurate models for the glass-forming ability of BMGs, to understand the roles of geometric frustration and demixing in determining . Specifically, we compress ternary hard sphere mixtures into jammed packings and measure the critical compression rate, below which the system crystallizes, as a function of the diameter ratios σ B / σ A and σ C / σ A and number fractions x A , x B , and x C . We find two distinct regimes for the GFA in parameter space for ternary hard spheres. When the diameter ratios are close to 1, such that the largest ( A ) and smallest ( C ) species are well-mixed, the GFA of ternary systems is no better than that of the optimal binary glass former. However, when σ C / σ A ≲ 0.8 is below the demixing threshold for binary systems, adding a third component B with σ C 〈 σ B 〈 σ A increases the GFA of the system by preventing demixing of A and C . Analysis of the available data from experimental studies indicates that most ternary BMGs are below the binary demixing threshold with σ C / σ A 〈 0.8. R R c R c 〉 1 0 12 K/s R ∼ 1 K / s R c R c R c

Description: While a wide range of non-trivial predictions of the generalized entropy theory (GET) of glass-formation in polymer melts agree with a large number of observed universal and non-universal properties of these glass-formers and even for the dependence of these properties on monomer molecular structure, the huge mathematical complexity of the theory precludes its extension to describe, for instance, the perplexing, complex behavior observed for technologically important polymer films with thickness below ∼100 nm and for which a fundamental molecular theory is lacking for the structural relaxation. The present communication describes a hugely simplified version of the theory, called the simplified generalized entropy theory (SGET) that provides one component necessary for devising a theory for the structural relaxation of thin polymer films and thereby supplements the first required ingredient, the recently developed Flory-Huggins level theory for the thermodynamic properties of thin polymer films, before the concluding third step of combining all the components into the SGET for thin polymer films. Comparisons between the predictions of the SGET and the full GET for the four characteristic temperatures of glass-formation provide good agreement for a highly non-trivial model system of polymer melts with chains of the structure of poly(n- α olefins) systems where the GET has produced good agreement with experiment. The comparisons consider values of the relative backbone and side group stiffnesses such that the glass transition temperature decreases as the amount of excess free volume diminishes, contrary to general expectations but in accord with observations for poly(n-alkyl methacrylates). Moreover, the SGET is sufficiently concise to enable its discussion in a standard course on statistical mechanics or polymer physics.

Description: We propose a way of obtaining effective low energy Hubbard-like model Hamiltonians from ab initio quantum Monte Carlo calculations for molecular and extended systems. The Hamiltonian parameters are fit to best match the ab initio two-body density matrices and energies of the ground and excited states, and thus we refer to the method as ab initio density matrix based downfolding. For benzene (a finite system), we find good agreement with experimentally available energy gaps without using any experimental inputs. For graphene, a two dimensional solid (extended system) with periodic boundary conditions, we find the effective on-site Hubbard U ∗ / t to be 1.3 ± 0.2, comparable to a recent estimate based on the constrained random phase approximation. For molecules, such parameterizations enable calculation of excited states that are usually not accessible within ground state approaches. For solids, the effective Hamiltonian enables large-scale calculations using techniques designed for lattice models.

Description: To understand the microsolvation of sodium acetate (CH 3 COONa, NaOAc) in water, we studied NaOAc(H 2 O) n − (n = 0–3) clusters by photoelectron spectroscopy. We also investigated the structures of NaOAc(H 2 O) n − (n = 0–5) anions and NaOAc(H 2 O) n (n = 0–7) neutrals by quantum chemistry calculations. By comparing the theoretical results with the photoelectron experiment, the most probable structures of NaOAc(H 2 O) n −/0 (n = 0–3) were determined. The study also shows that, with increasing n, the solvent-separated ion pair (SSIP) structures of NaOAc(H 2 O) n − anions become nearly energetically degenerate with the contact ion pair (CIP) structures at n = 5, while the SSIP structures of the neutral NaOAc(H 2 O) n clusters appear at n = 6 and become dominant at n = 7.

Description: Water is a ubiquitous liquid that displays a wide range of anomalous properties and has a delicate structure that challenges experiment and simulation alike. The various intermolecular interactions that play an important role, such as repulsion, polarization, hydrogen bonding, and van der Waals interactions, are often difficult to reproduce faithfully in atomistic models. Here, electronic structure theories including all these interactions at equal footing, which requires the inclusion of non-local electron correlation, are used to describe structure and dynamics of bulk liquid water. Isobaric-isothermal (NpT) ensemble simulations based on the Random Phase Approximation (RPA) yield excellent density (0.994 g/ml) and fair radial distribution functions, while various other density functional approximations produce scattered results (0.8-1.2 g/ml). Molecular dynamics simulation in the microcanonical (NVE) ensemble based on Møller-Plesset perturbation theory (MP2) yields dynamical properties in the condensed phase, namely, the infrared spectrum and diffusion constant. At the MP2 and RPA levels of theory, ice is correctly predicted to float on water, resolving one of the anomalies as resulting from a delicate balance between van der Waals and hydrogen bonding interactions. For several properties, obtaining quantitative agreement with experiment requires correction for nuclear quantum effects (NQEs), highlighting their importance, for structure, dynamics, and electronic properties. A computed NQE shift of 0.6 eV for the band gap and absorption spectrum illustrates the latter. Giving access to both structure and dynamics of condensed phase systems, non-local electron correlation will increasingly be used to study systems where weak interactions are of paramount importance.

Description: The dynamics of the O( 1 D ) + Xe electronic quenching reaction was investigated in a crossed beam experiment at four collision energies. Marked large-scale oscillations in the differential cross sections were observed for the inelastic scattering products, O( 3 P ) and Xe. The shape and relative phases of the oscillatory structure depend strongly on collision energy. Comparison of the experimental results with time-independent scattering calculations shows qualitatively that this behavior is caused by Stueckelberg interferences, for which the quantum phases of the multiple reaction pathways accessible during electronic quenching constructively and destructively interfere.

Description: The first-order liquid-liquid phase transition in supercooled Si is revisited by long-time first-principle molecular dynamics simulations. As the focus of the present paper, its nature is revealed by analyzing the inherent structures of low-density liquid (LDL) and high-density liquid (HDL). Our results show that it is a transition between a sp 3 -hybridization LDL and a white-tin-like HDL. This uncovers the origin of the semimetal-metal transition accompanying it and also proves that HDL is the metastable extension of high temperature equilibrium liquid into the supercooled regime. The pressure-temperature diagram of supercooled Si thus can be regarded in some respects as shifted reflection of its crystalline phase diagram.

Description: We have determined the initial sticking probability of O 2 on Pd(100) using the King and Wells method for various kinetic energies, surface temperatures, and incident angles. The data suggest two different mechanisms to sticking and dissociation. Dissociation proceeds mostly through a direct process with indirect dissociation contributing only at low kinetic energies. We suggest a dynamical precursor state to account for the indirect dissociation channel, while steering causes the high absolute reactivity. A comparison of our results to those previously obtained for Pd(111) and Pd(110) highlights how similar results for different surfaces are interpreted to suggest widely varying dynamics.

Description: The nuclear electronic orbital (NEO) reduced explicitly correlated Hartree-Fock (RXCHF) approach couples select electronic orbitals to the nuclear orbital via Gaussian-type geminal functions. This approach is extended to enable the use of a restricted basis set for the explicitly correlated electronic orbitals and an open-shell treatment for the other electronic orbitals. The working equations are derived and the implementation is discussed for both extensions. The RXCHF method with a restricted basis set is applied to HCN and FHF − and is shown to agree quantitatively with results from RXCHF calculations with a full basis set. The number of many-particle integrals that must be calculated for these two molecules is reduced by over an order of magnitude with essentially no loss in accuracy, and the reduction factor will increase substantially for larger systems. Typically, the computational cost of RXCHF calculations with restricted basis sets will scale in terms of the number of basis functions centered on the quantum nucleus and the covalently bonded neighbor(s). In addition, the RXCHF method with an odd number of electrons that are not explicitly correlated to the nuclear orbital is implemented using a restricted open-shell formalism for these electrons. This method is applied to HCN + , and the nuclear densities are in qualitative agreement with grid-based calculations. Future work will focus on the significance of nonadiabatic effects in molecular systems and the further enhancement of the NEO-RXCHF approach to accurately describe such effects.