Antisymmetry and stability of water systems. II. Polyhedral clusters

The generalized symmetry of proton configurations of water polyhedral clusters is studied. A change in the directions of all hydrogen bonds is used as the additional approximate operation of antisymmetry. The dependence of the energy of antisymmetric configurations on the cluster stabilization energy is found. It is concluded that the internal molecular asymmetry of water that is caused by the approximate character of antisymmetry of hydrogen bonding can be of fundamental scientific importance.     

Antisymmetry and stability of aqueous systems. IV. Small clusters of arbitrary form

The antisymmetry of small water clusters of various configurations with three to five molecules, which are stable according to the ab initio calculated data, was analyzed. The antisymmetry operation was alteration of the direction of all hydrogen bonds including the direction of the external unrealized H-bonds. It was found that most configurations of small clusters were antisymmetric. Other configurations form pairs of antipode configurations with very close energies.     

Antisymmetry and stability of aqueous systems. III. Conformations of the hexagonal rings

The antisymmetry of proton configurations was studied for the hexagonal water rings with different conformations. The change in the direction of all hydrogen bonds was used as an additional symmetry operation. The ring configuration energies were calculated using the intermolecular interaction potentials. For different ring conformations, the relationships between antisymmetry and energy were analyzed and compared.     

Atlas of Optimal Proton Configurations of Water Clusters in the Form of Gas Hydrate Cavities

All nonisomorphic proton configurations of water clusters in the form of gas hydrate cavities that are most stable in the number of strong hydrogen bonds corresponding to trans conformations have been found. The symmetry of these configurations is analyzed with allowance for the antisymmetry peration changing the directions of all Hbonds. The proton configurations of a cluster shaped like a pentagonal dodecahedron are considered in more detail.     

Single electron densities: a new tool to analyze molecular wavefunctions

A new partitioning scheme for the electron density of a many-electron wavefunction into single electron densities is proposed. These densities are based on the most probable arrangement of the electrons in an atom or molecule. Therefore, they contain information about the electron-electron interaction and, most notably, the Fermi hole due to the antisymmetry of the many-electron wavefunction. The single electron densities overlap and can be combined to electron pair distributions close to the qualitative electron pairs that represent, for instance, the basis of the valence shell electron pair repulsion model. Single electron analyses are presented for the water, ethane, and ethene molecules. The effect of electron correlation on the single electron and pair densities is investigated for the water molecule.     

Configuration interaction matrix elements. III. Spin functions relating the unitary and symmetric group approaches

Spin functions that are compatible with orbital ordering and geminal antisymmetry conditions are investigated. It is shown that two widely used classes of spin functions, namely, the spin-bonded functions and Yamanouchi–Kotani (or, equivalently, Gelfand–Tsetlin) functions possess these properties. The relationship of the latter with Young–Yamanouchi spin functions is also outlined using graphical techniques of spin algebras. These techniques are also used to rederive the Hamiltonian matrix elements between spin-bonded functions and to show the relationship among the various schemes used in this case.     

The forces of symmetry and the physical meaning of the Pauli exclusion principle

Russian Chemical Bulletin - A mathematically strict analysis of the consequences of the requirement of wave function antisymmetry is presented. It is shown that the probability density for...     

Energy optimization of water polyhedra. II. Classification of optimal configurations in clusters from a cube up to fullerene

Using a combinatory optimization method based on discrete models of intermolecular interaction, the classes of optimal configurations in polyhedral water clusters have been calculated. By means of calculations with various pair potentials an essential advantage in energy of discretely optimized configurations is ascertained. The effect of the dipole moment of clusters on their energy is studied.     

Molecular dynamics simulations of pressure effects on hydrophobic interactions.

We report results on the pressure effects on hydrophobic interactions obtained from molecular dynamics simulations of aqueous solutions of methanes in water. A wide range of pressures that is relevant to pressure denaturation of proteins is investigated. The characteristic features of water-mediated interactions between hydrophobic solutes are found to be pressure-dependent. In particular, with increasing pressure we find that (1) the solvent-separated configurations in the solute-solute potential of mean force (PMF) are stabilized with respect to the contact configurations; (2) the desolvation barrier increases monotonically with respect to both contact and solvent-separated configurations; (3) the locations of the minima and the barrier move toward shorter separations; and (4) pressure effects are considerably amplified for larger hydrophobic solutes. Together, these observations lend strong support to the picture of the pressure denaturation process proposed previously by Hummer et al. (Proc. Natl. Acad. Sci. U.S.A. 1998, 95, 1552): with increasing pressure, the transfer of water into protein interior becomes key to the pressure denaturation process, leading to the dissociation of close hydrophobic contacts and subsequent swelling of the hydrophobic protein interior through insertions of water molecules. The pressure dependence of the PMF between larger hydrophobic solutes shows that pressure effects on the interaction between hydrophobic amino acids may be considerably amplified compared to those on the methane-methane PMF.     

Two-photon absorption cross sections: an investigation of solvent effects. Theoretical studies on formaldehyde and water

The effects of a solvent on the two-photon absorption of microsolvated formaldehyde and liquid water have been studied using hybrid coupled-cluster/molecular mechanics (CC/MM) response theory. Both water and formaldehyde were considered solvated in water, where the solvent water molecules were described within the framework of molecular mechanics. Prior to the CC/MM calculations, molecular dynamics simulations were performed on the water/formaldehyde and water/water aggregates and many configurations were generated. By carrying out CC/MM response calculations on the individual configurations, it was possible to obtain statistically averaged results for both the excitation energies and two-photon absorption cross sections. For liquid water, the comparison between one- and two-photon absorption spectra is in good agreement with the experimental data available in the literature. In particular, the lowest energy transition occurring in the one-photon absorption spectrum of water only occurs with a relatively small strength in the two-photon absorption spectrum. This result is important for the interpretation of two-photon absorption data as these results show that in the absence of selection rules that determine which transitions are forbidden, the spectral profile of the two-photon absorption spectrum can be significantly different from the spectral profile of the one-photon absorption spectrum.     

THEORETICAL STUDY OF COLOR CONTROL MECHANISM IN RETINAL PROTEINS. I. ROLE OF THE TRYPTOPHAN RESIDUE, TYROSINE RESIDUE and WATER MOLECULE

Abstract –We calculated the opsin shift due to the electrostatic interaction between tryptophan or tyrosine residues and the chromophore by the perturbation method for various mutual configurations. The obtained opsin shift maps for these configurations demonstrated that when the above residues reside around the ionone ring side, the positive opsin shift (bathochromic shift) is obtained, and when they reside around the Schiff-base side, the negative opsin shift (hypsochromic shift) is obtained. These properties hold true, irrespective of the orientation of those residues, indicating that higher order multipoles of the group play a central role. The maximum value of the opsin shift by these groups amounts to several hundred wavenumbers. These results indicate that the location of some of those amino acid residues at proper positions around the chromophore can cause a considerable opsin shift. We also calculated opsin shift maps for the various mutual configurations between a water molecule and the chromophore for comparison.     

THEORETICAL STUDY OF COLOR CONTROL MECHANISM IN RETINAL PROTEINS.: I. ROLE OF THE TRYPTOPHAN RESIDUE, TYROSINE RESIDUE AND WATER MOLECULE

Abstract: We calculated the opsin shift due to the electrostatic interaction between tryptophan or tyrosine residues and the chromophore by the perturbation method for various mutual configurations. The obtained opsin shift maps for these configurations demonstrated that when the above residues reside around the ionone ring side, the positive opsin shift (bathochromic shift) is obtained, and when they reside around the Schiff-base side, the negative opsin shift (hypsochromic shift) is obtained. These properties hold true, irrespective of the orientation of those residues, indicating that higher order multipoles of the group play a central role. The maximum value of the opsin shift by these groups amounts to several hundred wavenumbers. These results indicate that the location of some of those amino acid residues at proper positions around the chromophore can cause a considerable opsin shift. We also calculated opsin shift maps for the various mutual configurations between a water molecule and the chromophore for comparison.     

Structure and dynamics of water confined in dimethyl sulfoxide.

We study the structure and dynamics of hydrogen-bonded complexes of H2O/D2O and dimethyl sulfoxide (DMSO) by infrared spectroscopy, NMR spectroscopy and ab initio calculations. We find that single water molecules occur in two configurations. For one half of the water monomers both OH/OD groups form strong hydrogen bonds to DMSO molecules, whereas for the other half only one of the two OH/OD groups is hydrogen-bonded to a solvent molecule. The H-bond strength between water and DMSO is in the order of that in bulk water. NMR deuteron relaxation rates and calculated deuteron quadrupole coupling constants yield rotational correlation times of water. The molecular reorientation of water monomers in DMSO is two-and-a-half times slower than in bulk water. This result can be explained by local structure behavior.     

Efficient sampling of ice structures by electrostatic switching

An electrostatic switching procedure is introduced that enables the systematic generation of high-quality ice configurations at various temperatures. Proton disordered ice Ih configurations were generated for the TIP4P water model at temperatures from 50 to 240 K, for the SPC/Fw water model from 100 to 240 K, and for the DC97 water model at 240 K. The resulting configurations were found to properly sample the canonical ensemble. The dielectric constant of ice Ih was determined from the net dipole fluctuation of the ice configurations. The calculated dielectric constant compares favorably with the study by Rick and Haymet [J. Chem. Phys. 2003, 118, 9291]. However, our method gives smaller error bars, especially at lower temperatures. At temperatures above 200 K, a type of hydrogen-bond defect is identified that cannot be categorized as a D or L type defect.     

The analysis of electron pair distribution functions in molecules

Electron pair distribution functions are analyzed for a variety of SCF+CI wavefunctions, for a range of simple molecules. The statistical correlation between electrons of like spin introduced by the antisymmetry requirement on the many-electron wavefunction is contrasted with the manner in which unlike-spin electron correlation is introduced through the inclusion of configuration interaction.     

Hydrophobicity within the three-dimensional Mercedes-Benz model: potential of mean force

We use the three-dimensional Mercedes-Benz model for water and Monte Carlo simulations to study the structure and thermodynamics of the hydrophobic interaction. Radial distribution functions are used to classify different cases of the interaction, namely, contact configurations, solvent separated configurations, and desolvation configurations. The temperature dependence of these cases is shown to be in qualitative agreement with atomistic models of water. In particular, while the energy for the formation of contact configurations is favored by entropy, its strengthening with increasing temperature is accounted for by enthalpy. This is consistent with our simulated heat capacity. An important feature of the model is that it can be used to account for well-converged thermodynamics quantities, e.g., the heat capacity of transfer. Microscopic mechanisms for the temperature dependence of the hydrophobic interaction are discussed at the molecular level based on the conceptual simplicity of the model.     

Molecular dynamics simulations of the mononuclear zinc-beta-lactamase from Bacillus cereus.

Herein, we report molecular dynamics simulations of the mononuclear form of the Bacillus cereuszinc-beta-lactamase. We studied two different configurations which differ in the presence of a zinc-bound hydroxide or a zinc-bound water and in the protonation state of the essential His210 residue. Contacts of the catalytically important residues (Asp90, His210, Cys168, etc.) with the zinc center are characterized by the MD analyses. The nature of the Zn-OH(2) --> His210 proton transfer pathway connecting the two configurations was studied by means of QM calculations on cluster models while the relative stability of the two configurations was estimated from QM/MM calculations in the enzyme. From these results, a theoretical model for the kinetically active form of the B. cereus metalloenzyme is proposed. Some mechanistic implications and the influence of mutating the Cys168 residue are also discussed.     

The use of explicitly correlated,partially antisymmetric wave functions in atomic and molecular calculations

Trial wave functions, written as the sum of a configuration interaction expansion and an explicitly correlated term which is not antisymmetric, are proposed for use in calculating the electronic properties of atoms and molecules. A variational principle, modified to allow the use for such partially antisymmetric wave functions, is developed. It is shown that the consequences of partial antisymmetry on calculated expectation values can be estimated. The method avoids difficult three-electron integrals which arise in other theories.     

Kinetic Investigations of Reactions with Maleic Anhydride Copolymers and Model Compounds

Alternating copolymers that contain maleic anhydride (MAn) as a component occur in two different stereochemical configurations which are differentiated by their reactivity. Model compounds, 2, 3-dialkylsuccinic acids and their anhydrides, were investigated and it was demonstrated that there is a distinct difference between threo and erythro configurations in their chemical and physical behavior. Both configurations also occur in the alternating copolymers. Beside the model compounds, the alternating copolymers ethylene-MAn, propylene-MAn, and styrene-MAn were investigated in their reactions with amines, alcohols, and water (hydrolysis). The cis configurations showed the higher reaction rates. Reactions of the anhydride moieties with equimolar amounts of aniline, ethanol, and water demonstrated that reactions follow second-order rate laws. With excess reactant, the reaction follows a pseudo-first-order rate law. The rate constants depend on the degree of polymerization and on the comonomer. Increasing steric hindrance and molecular weight lead to a decrease of the reaction rate. Catalysis of the hydrolysis reaction by tertiary amines results in similar rate constants for the configurations of the substituted succinic acid anhydrides. The reasons are discussed.     

Molecular dynamics simulations of LiCl association and NaCl association in water by means of ABEEM/MM

Constrained molecular dynamics simulations have been used to investigate the LiCl and NaCl ionic association in water in terms of atom-bond electronegativity equalization method fused into molecular mechanics (ABEEM/MM). The simulations make use of the seven-site fluctuating charge and flexible ABEEM-7P water model, based on which an ion-water interaction potential has been constructed. The mean force and the potential of mean force for LiCl and NaCl in water, the charge distributions, as well as the structural and dynamical properties of contact ion pair dissociation have been investigated. The results are reasonable and informative. For LiCl ion pair in water, the solvent-separated ion pair configurations are more stable than contact ion pair configurations. The calculated PMF for NaCl in water indicates that contact ion pair and solvent-separated ion pair configurations are of comparable stability.