ALBERT

Notes: ---The cooperative nature of non-covalent interactions which give rise to inclusion complexes involving cyclobis(paraquat-p-phenylene), 14+, and related cyclophane derivatives, 24+-44+, with substituted 1,4-phenyl and 4,4′-biphenyl guests has been studied by spectroscopic techniques and ab initio and semiempirical molecular orbital methods. Inclusion complex formation and stability are primarily determined by the combination of two main interaction modes involving aromatic stacking of the guest within the cyclophane cavity and external interactions between guest side arms and the exterior of the cyclophane. A balance between cavity and external forces results in supramolecular association and is shown to change depending upon the functionality and substitution of the guest. Cavity binding was probed using 1,4-phenyl and 4,4′-biphenyl guests, where for the 1,4-phenyl guests the primary basis for energy stabilization with 14+ is found to be short-range stabilizing electrostatic forces complemented by small amounts of polarizability and charge-transfer. In contrast, the cavity binding between substituted 4,4′-biphenyl guests and 14+ is determined by almost equal contributions of polarizability and electrostatics. The effect of solvent is shown to have only a small effect on the computed geometry of 14+ complexes, but its impact upon binding energies is substantial. The first solvation shell of the cyclophanes is computationally approximated by 12 acetonitriles and satisfies the requirements of the 16 relatively acidic protons on the bipyridinium groups. Good correlations between the computed (with solv ation) and experimental 14+ binding energies are found. The degree of linear correlation improves substantially when the comparison between computed and experimentally observed binding energies is restricted to structurally similar (number of aromatic rings, number of substituents and position of substitution) molecular guests. Furthermore, computed molecular properties, such as polarizability, maximum hardness, softness and electronegativity of the isolated guests, correlate well with 14+ binding energies based upon the same requirement of guest similarity. The non-covalent forces associated with the external cyclophane interactions were studied with guest molecules built from symmetrical 1,4-extensions of hydroquinone composed of aliphatic or ethyleneoxy side arms. In particular, side arm length and functionality, and the position and type of heteroatoms along the chain, were systematically varied to define the external interactions between the guest side arms and different host cyclophanes. Specifically, the ethyleneoxy linkages are shown to provide a large chelate and cooperative effect which direct the binding with 14+. In order to probe further the special geometric and electronic character of 14+, we have synthesized and tested a new supramolecular host, 24+, similar to 14+ but where a pentacycloundecane unit replaces one of the xylyl groups. Both experimental and computed data on the new host emphasize the ideal geometry and electronic nature of the 14+ molecular receptor for aromatic guests. The inclusion complexes discussed in this paper are important not only because they, or similar entities, are the main components of many rotaxanes, catenanes and other switchable molecules, but because the intermolecular interactions involved, such as electrostatics, polarizability and charge-transfer, are ubiquitous in supramolecular chemistry. The information reported on the specific interactions involving the 14+-44+ molecular receptors with substituted aromatic guests can also be extended by analogy to many systems of broad interest. © 1997 John Wiley & Sons, Ltd.

Notes: We describe the direct photodesorption of CO from the Ni(001) metal surface during the absorption of a short pulse of UV light by the adsorbate and account for the dynamics of the desorbing species coupled to electronic excitations of the substrate, which lead to energy dissipation. The interaction potentials and couplings for the ground and excited states are obtained from electronic structure calculations and from experimental information. The time evolution of CO vibrational populations is studied for propagating wavepackets for the adsorbate-substrate complex with a split-operator algorithm, followed by a perturbative treatment of dissipation and response to the light pulse. Direct photodesorption is found to occur predominantly in the excited electronic state and is compatible with dissipation. Results are presented for CO photodesorption by Gaussian pulses with several durations to show the effect of light pulse shapes on the time evolution of populations. Shorter pulses in the femtosecond range are shown to give relatively larger populations of excited vibrational states during the desorption of CO.   © 1997 John Wiley & Sons, Inc. Int J Quant Chem 64: 71-83, 1997

Notes: To obtain new insight into the nature of the correlations in distributions of nucleotides in DNA sequences, an efficient algorithm is presented by means of which one can generate nucleotide sequences with prescribed correlational properties. It is demonstrated in the case of human T-cell receptor beta chain gene segment that by extracting a finite number of parameters from the natural sequence one can generate artificial sequences which reproduce the correct correlational properties. It is shown how the apparent long-range correlations, or - what is equivalent - the 1/f form of the spectral density result due to the arrangement of DNA segments with different functional roles which also differ in composition in terms of nucleotide classes. This approach enables one to get under control the impact of statistical fluctuations which represent a major obstacle in the analyses of finite natural sequences.   © 1997 John Wiley & Sons, Inc. Int J Quant Chem 64: 387-392, 1997

Notes: ---The photochemical reactions of N-(methylphenylamino)-2,4,6-trimethylpyridinium tetrafluoroborate were studied to find evidence of photodecomposition to a nitrenium ion reactive intermediate. Stable products were formed that were consistent with a singlet-state methylphenylnitrenium ion precursor. The methoxy and chloro adducts. N-methyl-p-anisidine and 4- (and 2-)chloro-N-methylaniline, were identified and quantified by high-performance liquid chromatographic analysis. A hydride shift from the N-methyl group of the nitrenium ion is also proposed based on the detection of aniline which would result from hydrolysis of the iminium ion rearrangement product. The rate constant for this rearrangement is estimated to be 108 s-1. The reduction product, N-methylaniline, is produced, and is believed to form, at least in part, from the hydrogen atom abstractions of the triplet nitrenium ion. This is supported by the results of triplet sensitized irradiations. Laser flash photolysis studies yielded the transient spectrum of a long-lived intermediate absorbing at 470 nm. This transient species is believed to be the cation radical of N-methylaniline. © 1997 John Wiley & Sons, Ltd.

Notes: Geometry optimizations were performed for singlet, triplet, and quintet states on the planar structures (in C2h and C2v symmetries) of the diacetylene dimer, using restricted open-shell Hartree-Fock (ROHF), unrestricted Hartree-Fock (UHF), and unrestricted hybrid density functional theory (UB3LYP) methods, with 6-31G(d) and 6-311G(d, p) basis sets. The 1Ag state of the planar van der Waals dimer is lower in energy than are any covalently bonded dimers. At our best B3LYP/6-311G(d, p) level, the most stable covalently bonded diacetylene dimer is the 3Bu state in C2h symmetry, 11 kcal mol-1 above the van der Waals dimer, followed by the 3B2 state in C2v symmetry with 13 kcal mol-1 above the van der Waals dimer. Both structures were confirmed to be local minima. The two diacetylene monomers of these structures are bridged through a single bond and they exhibit a small bend at the neighboring carbons to the bridge, trans to the hydrogens. The 1Bu and 5Ag states in C2h and the 1B2 and 5A1 states in C2v are between 39 and 43 kcal mol-1 above the van der Waals dimer.   © 1998 John Wiley & Sons, Inc. Int J Quant Chem 66: 189-202, 1998

Notes: Variational calculations utilizing the analytic gradient of explicitly correlated Gaussian molecular integrals are presented for the ground state of the hydrogen molecule. Preliminary results serve to motivate the need for general formulas for analytic first derivatives of molecular integrals involving multicenter, explicitly correlated Gaussian geminals with respect to Gaussian exponents and coordinates of the orbital centers. Explicit formulas for analytic first derivatives of Gaussian functions containing correlation factors of the form exp(-βrij2) are derived and discussed. © 1997 John Wiley & Sons, Inc. Int J Quant Chem 63: 991-999, 1997

Notes: An approach to the calculation of molecular electronic structures, solvation energies, and pKa values in condensed phases is described. The electronic structure of the solute is described by density functional quantum mechanics, and electrostatic features of environmental effects are modeled through external charge distributions and continuum dielectrics. The reaction potential produced by a mode of the molecular charge distribution is computed via finite-difference solutions to the Poisson-Boltzmann equation and incorporated into the self-consistent field procedure. Here we report results on three sets of organic acids, whose pKa values range over 16 pH units. The first set provides models for ionizable side chains in proteins; the second set considers the effects of substituting one to three chlorine atoms for hydrogens in acetic acid; and the final set consists of 4-substituted-bicyclo-[2.2.2]-octanecarboxylic acids. Successful prediction of “absolute” pKa values places stringent requirements on the computation of gas-phase proton affinities and on the response to solvation. In some cases the current model shows substantial errors, but overall the results and trends are in good agreement with experiment. Prospects for extending this approach to more complex systems such as proteins are briefly discussed. © 1997 John Wiley & Sons, Inc.

Notes: The sensitivity of aqueous solvation free energies (SFEs), estimated using the GB/SA continuum solvent model, on charge sets, protocols, and force fields, was studied. Simple energy calculations using the GB/SA solvent model were performed on 11 monofunctional organic compounds. Results indicate that calculated SFEs are strongly dependent on the charge sets. Charges derived from electrostatic potential fitting to high level ab initio wave functions using the CHELPG procedure and “class IV” charges from AM1/CM1a or PM3/CM1p calculations yielded better results than the corresponding Mulliken charges. Calculated SFEs were similar to MC/FEP energies obtained in the presence of explicit TIP4P water. Further improvements were obtained by using GVB/6-31G** and MP2/6-31+G** (CHELPG) charge sets that included correlation effects. SFEs calculated using charge sets assigned by the OPLSA* force field gave the best results of all standard force fields (MM2*, MM3*, MMFF, AMBER*, and OPLSA*) implemented in MacroModel. Comparison of relative and absolute SFEs computed using either the GB/SA continuum model or MC/FEP calculations in the presence of explicit TIP4P water showed that, in general, relative SFEs can be estimated with greater accuracy. A second set of 20 mono- and difunctional molecules was also studied and relative SFEs estimated using energy minimization and thermodynamic cycle perturbation (TCP) protocols. SFEs calculated from TCP calculations using the GB/SA model were sensitive to bond lengths of dummy bonds (i.e., bonds involving dummy atoms). In such cases, keeping the bond lengths of dummy bonds close to the corresponding bond lengths of the starting structures improved the agreement of TCP-calculated SFEs with energy minimization results. Overall, these results indicate that GB/SA solvation free energy estimates from simple energy minimization calculations are of similar accuracy and value to those obtained using more elaborate TCP protocols.   © 1998 John Wiley & Sons, Inc.   J Comput Chem 19: 769-780, 1998

Notes: The potential energy surface of un-ionized glycine has been explored with density functional theory. The performance of several nonlocal functionals has been evaluated and the results are presented in the context of available experimental information and post-Hartree-Fock quantum chemical results. The zero-point and thermal vibrational energies along with vibrational entropies play a very important role in determining the relative stability of glycine conformers; the realization of this has led to some revision and reinterpretation of the experimental results. Uncertainties in the vibrational contributions to the energy differences of several tenths of a kilocalorie/mole remain. The uncertainty in the vibrational free energy is even larger, about 1 kcal/mol. In the final analysis, we suggest that the best estimate of the electronic energy difference between the two lowest glycine conformers should be revised downward from 1.4 to 1.0 kcal/mol. Thirteen stationary points on the potential energy surface have been localized. For the majority of these, there is close agreement among various nonlocal density functionals and the post-Hartree-Fock methods. However, the second conformer (IIn), which has a strong hydrogen bond between the hydroxyl hydrogen and the nitrogen of the amine group, presents a distinct challenge. The relative energy of this conformer is extremely sensitive to the basis set, the level of correlation, or the functional used. The widely used BP86, PP86, and BP91 nonlocal functionals overestimate the strength of the hydrogen bond and predict that this conformer is the lowest energy structure. This contradicts both experiment and high-level post-Hartree-Fock studies. The adiabatic connection method (ACM) and the BLYP functional yield the correct order. The ACM method, in particular, gives energies which are in reasonable agreement with MP2, although these are somewhat low as compared with experiment. Based on this study, ACM should perform well for this type of bioorganic application, with typical errors of a few tenths of a kilocalorie/mole and only rarely exceeding 0.5 kcal/mol.   © 1997 John Wiley & Sons, Inc.   J Comput Chem 18: 1609-1631, 1997

Notes: Photo-induced electron donor-acceptor reactions between 1-cyanonaphthalene (CNN) and norbornadiene (N) generate products of several structure types. Methanol adducts (1-3) formed in polar solvents are rationalized via the radical cation, N+·, and stereospecific (exo-) nucleophilic attack by methanol. In less polar solvents, CNN and N form [2 + 2]-cycloadducts, exclusively on the exo-face of N. In non-polar solvents containing methanol, CNN, N and methanol combine to form 1:1:1 adducts, containing the sensitizer on the endo- and the methoxy groups on the exo-face. The formation of these products is rationalized via the trapping of encounter complexes of different geometries. Any rearrangement of the norbornenyl system can be eliminated, since neither tricyclyl nor 7-methoxynorbornenyl structures are formed. Apparently, the alcohol captures an endo-encounter complex of CNN and N by attack from the exo-face, similar to the attack of methanol on N+·. © 1998 John Wiley & Sons, Ltd.