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  • 1
    ISSN: 1432-2234
    Keywords: Mutually consistent field calculations ; solvation energies ; glycine-water-system
    Source: Springer Online Journal Archives 1860-2000
    Topics: Chemistry and Pharmacology
    Notes: Abstract We have performed calculations of the glycine zwitterion surrounded by water molecules with the help of the mutually consistent field (MCF) method and perturbation theoretical expressions. Two different models for the hydration shell have been chosen, the glycine·6H2O and glycine·12H2O complexes, representing the most probable first and second solvation shell, respectively. To calculate the exchange and charge transfer energy contributions we have applied approximative expressions derived from perturbation theory for weakly overlapping subunits. For the sake of comparison we also calculated the interaction energy in the supermolecule approach for the smaller of the two solvation complexes. Furthermore, we have investigated the part of the potential energy surface which is determined by varying the lengths of the hydrogen bonds between glycine and water in the complex glycine·12H2O using the electrostatic approach. The exchange energy contribution to the interaction energy for different points on the surface was approximated with the help of an analytical expression fitted to three directly calculated points. For the charge transfer energy a polynomial expansion of second order was established on the basis of five values, computed with the aid of the perturbation theoretical expression. To get a more detailed insight in the relatively strong hydrogen bonds between the water molecules and the ionic hydrophilic parts of glycineab initio model studies on NH 4 + ·3H2O and HCOO−·3H2O systems are reported.
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  • 2
    ISSN: 1432-2234
    Keywords: Mutually consistent field calculations ; solvation energies ; glycine-water-system
    Source: Springer Online Journal Archives 1860-2000
    Topics: Chemistry and Pharmacology
    Notes: Abstract We have performed calculations of the glycine zwitterion surrounded by water molecules with the help of the mutually consistent field (MCF) method and perturbation theoretical expressions. Two different models for the hydration shell have been chosen, the glycine·6H2O and glycine·12H2O complexes, representing the most probable first and second solvation shell, respectively. To calculate the exchange and charge transfer energy contributions we have applied approximative expressions derived from perturbation theory for weakly overlapping subunits. For the sake of comparison we also calculated the interaction energy in the supermolecule approach for the smaller of the two solvation complexes. Furthermore, we have investigated the part of the potential energy surface which is determined by varying the lengths of the hydrogen bonds between glycine and water in the complex glycine·12H2O using the electrostatic approach. The exchange energy contribution to the interaction energy for different points on the surface was approximated with the help of an analytical expression fitted to three directly calculated points. For the charge transfer energy a polynomial expansion of second order was established on the basis of five values, computed with the aid of the perturbation theoretical expression. To get a more detailed insight in the relatively strong hydrogen bonds between the water molecules and the ionic hydrophilic parts of glycineab initio model studies on NH 4 + ·3H2O and HCOO−·3H2O systems are reported.
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  • 3
    ISSN: 0948-5023
    Keywords: Proteins ; Davydov Model ; Special Cases ; Expansion of Exact Solutions
    Source: Springer Online Journal Archives 1860-2000
    Topics: Chemistry and Pharmacology
    Notes: Abstract For the Davydov Hamiltonian several special cases are known which can be solved analytically. Starting from these cases we show that the initial state for a simulation using Davydov′s |D1〉 approximation has to be constructed from a given set of initial lattice displacements and momenta in form of a coherent state with its amplitudes independent of the lattices site, corresponding to Davydov′s |D2〉 approximation. In the |D1〉 ansatz the coherent state amplitudes are site dependent. The site dependences evolve from this initial state exclusively via the equations of motion. Starting the |D1〉 simulation from an ansatz with site dependent coherent state amplitudes leads to an evolution which is different from the analytical solutions for the special cases. Further we show that simple construction of such initial states from the expressions for displacements and momenta as functions of the amplitudes leads to results which are inconsistent with the expressions for the lattice energy. The site-dependence of coherent state amplitudes can only evolve through the exciton-phonon interactions and cannot be introduced already in the initial state. Thus also in applications of the |D1〉 ansatz to polyacetylene always |D2〉 type initial states have to be used in contrast to our previous suggestion [W. Förner, J. Phys.: Condens. Matter 1994, 6, 9089-9151, on p. 9105]. Further we expand the known exact solutions in Taylor serieses in time and compare expectation values in different orders with the exact results. We find that for an approximation up to third order in time (for the wave function) norm and total energy, as well as displacements and momenta are reasonably correct for a time up to 0.12-0.14 ps, depending somewhat on the coupling strengh for the transportless case. For the oscillator system in the decoupled case the norm is correct up to 0.6-0.8 ps, while the expectation values of the number operators for different sites are reasonably correct up to roughly 0.6 ps, when calculated from the third order wave function. The most important result for the purpose to use such expansions for controlling the validity of ansatz states is, however, that the accuracy of S(t) and H(t) (constant in time, exact values known in all cases) is obviously a general indicator for the time region in which a given expansion yields reliable values also for the other, physically more interesting expectation values.
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  • 4
    Electronic Resource
    Electronic Resource
    Springer
    Journal of molecular modeling 2 (1996), S. 103-135 
    ISSN: 0948-5023
    Keywords: Proteins ; Davydov Model ; Nonlinear Dynamics ; Expansion of Exact Solutions ; Ansätze
    Source: Springer Online Journal Archives 1860-2000
    Topics: Chemistry and Pharmacology
    Notes: Abstract We performed long time simulations using the |D1〉 approximation for the solution of the Davydov Hamiltonian. In addition we computed expectation values of the relevant operators with the state (Ĥ D /J)|D 1〉 and the deviation |δ〉 from the exact solution over long times, namely 10 ns. We found that in the very long time scale the |D1〉 ansatz is very close to an exact solution, showing expectation values of the relevant physical observables in the state (Ĥ D /J)|D 1〉 being about 5-6 orders of magnitudes larger than in the deviation state |δ〉. In the intermediate time scale of the ps range such errors, as known from our previous work, are somewhat larger, but still more or less negligibly. Thus we also report results from an investigation of the very short time (in the range 0-0.4 ps) behaviour of the |D1〉 state compared with that of an expansion of the exact solution in powers of time t. This expansion is reliable for about 0.12 ps for special cases as shown in the previous paper. However, the accuracy of the exactly known value of the norm and the expectation value of the Hamiltonian finally indicates up to what time a given expansion is valid, as also shown in the preceding paper. The comparison of the expectation values of the operators representing the relevant physical observables, formed with the third order wave function and with the corresponding results of |D1〉 simulations has shown, that our expansion is valid up to a time of roughly 0.10-0.15 ps. Within this time the second and third order corrections turned out to be not very important. This is due to the fact that our first order state contains already some terms of the expansion, summed up to inifinite order. Further we found good agreement of the results obtained with our expansion and those from the corresponding |D1〉 simulations within the time of about 0.10 ps. At later times, the factors with explicit powers of t in second and third order become dominant, making the expansion meaningless. Possibilities for the use of such expansions for larger times are described. Alltogether we have shown (together with previous work on medium times), that the |D1〉 state, although of approximative nature, is very close to an exact solution of the Davydov model on time scales from some femtoseconds up to nanoseconds. Especially the very small time region is of importance, because in this time a possible soliton formation from the initial excitation would start.
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  • 5
    ISSN: 0948-5023
    Keywords: Proteins ; Davydov model ; Dynamics ; Vibrational spectra
    Source: Springer Online Journal Archives 1860-2000
    Topics: Chemistry and Pharmacology
    Notes: Abstract The mechanism for energy and signal transport in proteins as suggested by Davydov is discussed. The idea is based on a coupling of amide-I oscillators to acoustic phonons in a hydrogen bonded chain. Results as obtained with the usually used ansätze are discussed. The quality of these states for an approximate solution of the time-dependent Schrödinger equation is investigated. It is found that the semiclassical ansatz is a poor approximation, while the more sophisticated |D1〉 state seems to represent the exact dynamics quite well. This was shown by extensive calculations, both analytically and numerically in the two preceding papers. Calculations at a temperature of 300K for one chain, as well as for three coupled ones (as they are present in an α-helix) are presented and discussed. From the calculations it is evident, that Davydov solitons are stable for reasonable parameter values at 300K for special initial excitations close to the terminal sites of the chain. Further vibrational spectra are presented and discussed. Our results suggest, that due to their strong dependence on the initial state, the Davydov |D1〉 model system might be a (quantum) chaotic one.
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  • 6
    Electronic Resource
    Electronic Resource
    Springer
    Journal of molecular modeling 4 (1998), S. 12-32 
    ISSN: 0948-5023
    Keywords: Keywords Conducting polymers ; Nonlinear dynamics ; Solitons ; Polarons ; Electronic spectra
    Source: Springer Online Journal Archives 1860-2000
    Topics: Chemistry and Pharmacology
    Notes: Abstract  Conjugated organic polymers are intrinsically semiconductors but become conducting upon doping and photoconducting after optical excitation. In the low doping regime they show usually conduction without an associated spin transport. Thus as charge carriers in this regime nonlinear quasiparticles are assumed, such as charged solitons in materials with a degenerate ground state like e.g. trans-polyacetylene or pernigraniline. In the case of materials with a non-degenerate ground state the situation is often less clear but it is assumed that charged polarons or bipolarons are the charge carriers in them. We present a theoretical model for the description of the dynamics of such quasiparticles which yields also information on their mobility, their nature and stability, as well as their spectral properties. The model is based on a π-electron Hamiltonian including electron-electron interactions. On the basis of the prototype material polyacetylene it is demonstrated how such a model can be parametrized with the help of correlated ab initio or density functional calculations and applied. We discuss in some detail the dynamics of the pristine material, as well as of doped and of electronically excited polyene chains. With the help of these dynamics a scenario for the conduction mechanism assumed for polyacetylene is given. Further we calculate optical spectra from the dynamics for charged solitons and for excited chains which are in fair agreement with experiments. The thermal mobility of neutral solitons is also studied. Further we show how the model can be extended for applications to polymers different from polyacetylene. Such modifications could yield informations about the nature of nonlinear quasiparticles involved in the process of charge transport in cases where the question is not completely solved. This is the case in cis-polyacetylene where recent literature suggests that bipolarons should be instable. However, we could show that both charged polarons and bipolarons are stable in the material with bipolarons favored over charged polarons. Due to the fact that the model can be extended to other polymers, also to chemical stuctures not yet synthesized, it could gain also predictive power after further development.
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  • 7
    ISSN: 0948-5023
    Keywords: Ab initio ; Structural stability ; Rotational barrier ; 3-Cyclopropenecarboxaldehyde ; 3-Cyclo-propenecarboxylic acid fluoride
    Source: Springer Online Journal Archives 1860-2000
    Topics: Chemistry and Pharmacology
    Notes: Abstract The structural stability and internal rotation in 3-cyclopropenecarboxaldehyde and 3-cyclo-propenecarboxylic acid fluoride were investigated by ab initio calculations with a 6-31G* atomic basis in the latter and a 6-311G* atomic basis set in the former case. For the sake of comparison also results obtained with a 3-21G basis are given in the paper. As expected, it turned out that this basis set is not large enough for three-membered rings. The calculations were carried out both at the Restricted Hartree-Fock (HF) and the second order Moller-Plesset (MP2) levels. The trans-form is predicted to be the lower energy conformer for both molecules. However, in case of the fluoride the two conformers have nearly the same energy. Full optimization was performed at the transition states and the asymmetric potential function for the CXO internal rotations was predicted for both molecules.
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  • 8
    ISSN: 0948-5023
    Keywords: Keywords Vibrational spectra and assignments, Rotational barriers, 3,3,3-trifluoropropanal
    Source: Springer Online Journal Archives 1860-2000
    Topics: Chemistry and Pharmacology
    Notes: Abstract The conformational behavior and structure of 3,3,3,-trifluoropropal have been investigated by utilizing ab initio calculations with the 6-31G** basis set (valence double zeta basis with polarization functions on all atoms) at the restricted Hartree Fock (RHF), second-order Møller-Plesset perturbation (MP2), and Density Functional (B3LYP) levels. The molecule is predicted to have a cisÛgauche conformational equilibrium. Full optimization of the transition states was performed and the rotational barriers of both the CHO and CF3 rotors were calculated. Vibrational frequencies were computed at the three levels and the zero-point corrections were included into the calculated asymmetric CHO rotational barrier. Complete vibrational assignments were made on the basis of normal coordinate calculations for both stable conformers of the molecule.
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  • 9
    ISSN: 1520-5126
    Source: ACS Legacy Archives
    Topics: Chemistry and Pharmacology
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  • 10
    Electronic Resource
    Electronic Resource
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 13 (1992), S. 275-313 
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: The performance of a Runge-Kutta method of fourth order in dynamic simulations within Davydov's so-called |D2〉 state ansatz is studied by comparison with analytical solutions available for two special cases. Further, the Runge-Kutta method is compared with the one-step procedure used by Su and Schrieffer. A detailed analysis of the structure and energetics of Davydov solitons is given. The differences in the dynamics between open chain ends and periodic boundary conditions are also discussed. The properties of the soliton detector plot introduced by Lomdahl and Kerr are studied. Finally, three widely used initial states for Davydov soliton dynamics are compared.
    Additional Material: 14 Ill.
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