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.     

Antisymmetry and stability of water systems. I. Planar cyclic clusters

All topologically distinct configurations of planar cyclic water clusters consisting of three to six molecules are calculated. The symmetry of configurations is analyzed using an additional operation of antisymmetry that changes the directions of all hydrogen bonds. It is concluded that the concept of antisymmetry and the presence of similar in properties but inequivalent “configurations-antipodes” reflects a new fundamental feature of water systems, namely, the internal molecular asymmetry.     

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.     

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.     

Structure of an accurate ab initio model of the aqueous Cl- ion at high temperatures

The structure of an accurate ab initio model of aqueous chloride ion was calculated at two high-temperature state points (573 K, 0.725 g/cm(3) and 723 K, 0.0098 g/cm(3)) by a two-step procedure. First, the structure of an approximate model was calculated from a molecular dynamics simulation of the model. Then the difference between the structure of the ab initio model and the approximate model was calculated by non-Boltzmann weighting of a sample of configurations taken from the approximate model simulation. Radial distribution functions, average coordination numbers, the distribution of coordination numbers, an analysis of orientations of water in the first coordination shell, and the free energy of hydration of the chloride ion are reported for both state points. The most common water structure has one hydrogen close to the chloride ion and one pointing away (46% at 573 K and 57% at 723 K). Waters in the first coordination shell that are not strongly bound to the chloride ions are common. Several variations of the method were tested. Models in which the water-water interaction is calculated with ab initio methods predict only a slightly different structure than models in which water-water interactions are determined from the approximate models. Similarly, using the approximate model for solute-water interactions when the water is far from the chloride ion did not affect the results. Uncertainties due to the limited sample of configurations are estimated and found to be small. The results are in qualitative agreement with X-ray and neutron diffraction experiments and with simulations of approximate models.     

Multidimensional infrared spectroscopy of water. II. Hydrogen bond switching dynamics

We use multidimensional infrared spectroscopy of the OH stretch of HOD in D2O to measure the interconversion of different hydrogen bonding environments. The OH stretching frequency distinguishes hydrogen bonded (HB) and non-hydrogen-bonded (NHB) configurations by their absorption on the low (red) and high (blue) sides of the line shape. Measured asymmetries in the two dimensional infrared OH line shapes are manifestations of the fundamentally different spectral relaxations of HB and NHB. HB oscillators exhibit coherent oscillations within the hydrogen-bonded free energy well before undergoing activated barrier crossing, resulting in the exchange of hydrogen bonded partners. Conversely, NHB oscillators rapidly return to HB frequencies within 150 fs. These results support a picture where NHB configurations are only visited transiently during large fluctuations about a hydrogen bond or during the switching of hydrogen bonding partners. The results are not consistent with the presence of entropically stabilized dangling hydrogen bonds or a conceptual picture of water as a mixture of environments with varying hydrogen bond strength separated by barriers >kT.     

Thermodynamic functions of liquid water calculated from the temperature evolution of the vibration spectrum contour

Configurational contributions of hydrogen bonds to thermodynamic properties of water (internal energy, entropy, and heat capacity) are calculated on the basis of statistical distributions of frequencies of the OH vibrations of liquid water, calculated earlier from the experimental Raman spectra in frameworks of the fluctuation theory of hydrogen bonding. Distributions of the energy of hydrogen bonds are determined. It is shown by comparison with computer experiments that previously established dependence of energy on frequency, E(nu), must be considered in this formalism as the effective energy of hydrogen bonding averaged over those configurations of hydrogen bridge O-H...O which lead to the given frequency nu in the vibrational spectrum. Contribution of van der Waals interactions not affecting the frequency shift to heat capacity is evaluated.     

An analysis of the electrostatic interaction between nucleic acid bases

Results from several commonly used approximate methods of evaluating electrostatic interactions have been compared to the rigorous, nonexpanded electrostatic energies at both uncorrelated and correlated levels of theory. We examined a number of energy profiles for both hydrogen bonded and stacked configurations of the nucleic acid base pairs. We found that the penetration effects play an extremely important role and the expanded electrostatic energies are significantly underestimated with respect to the ab initio values. Apart from the inability to reproduce the magnitudes of the ab initio electrostatic energy, there are other problems with the available approximate electrostatic models. For example, the distributed multipole analysis, one of the most advanced methods, is extremely sensitive to the basis set and level of theory used to evaluate the multipole moments. Detailed ab initio results are provided that other researchers could use to test their approximate models.     

Analysis of the structures,energetics, and vibrational frequencies for the hydrogen-bonded interaction of nucleic acid bases with Carmustine pharmaceutical agent: a detailed computational approach

In the present study, it is attempted to scrutinize the hydrogen bonding interaction between Carmustine drug and DNA pyrimidine bases by means of density functional theory calculations regarding their geometries, binding energies, vibrational frequencies, and topological features of the electron density in the gas phase and the water solution. Based on the density functional theory results, it is found that the process of intermolecular interaction between Carmustine drug and nucleobases is exothermic and all of the optimized configurations are stable. Furthermore, the negative stability energy represented by a polarizable continuum model shows the significant increase in the solubility of the nucleobase after hydrogen bonding intermolecular interaction in the presence of water solvent. It is also found that the intermolecular hydrogen bonds between drug and the nucleobases play the significant role in the stability of the physisorption configurations. Hydrogen bond energies for hydrogen-bonded complexes are obtained from Espinosa method and the atoms-in-molecules theory are also applied to get a more precise insight into the nature of the intermolecular hydrogen bond interactions.     

PCILO calculation of intermolecular energies: The water dimer

The PCILO (perturbative configuration interaction using localized orbitals) method for approximating the electronic structure of molecules has been used with some success for calculating intramolecular interactions in large molecules where intramolecular hydrogen bonding is involved. In this note we show that the PCILO method may be used to calculate the energy of interaction between two water molecules in selected configurations.     

团簇Ni4P催化析氢性能研究

为探究团簇Ni₄P催化析氢最强的结构,基于密度泛函理论,在B3LYP/Lan12dz水平下,对团簇Ni₄P的初始构型进行计算和优化,得到5种优化构型。从热力学稳定性、前线轨道图和前线轨道能级差对团簇Ni₄P的析氢性能分析发现,构型1^（4）和1^（2）的热力学稳定性较强;团簇Ni₄P各优化构型均易吸附水中的氢原子,Ni原子为团簇Ni₄P催化活性位点,且构型1^（4）、1^（2）和2^（4）催化析氢的活性更强。(1^（2）)-H、(2^（2）)-H在电化学脱附法和化学重组法中均具有较强的催化活性。以上说明构型1^（2）是团簇Ni₄P催化析氢最强的结构。     

Perturbative ab initio calculations of intermolecular energies. III. The water dimer

The interaction energy between two water molecules A and B is calculated by the method described in Paper I [1], previously applied for the interaction between two helium atoms (Paper II) [2]. This interaction energy is obtained as the difference between the energies of the complex (A + B) and the monomers (A) and (B), obtained by a perturbation method. The results obtained with the perturbation developed up to the second order in a minimal atomic basis set are decomposed into classical contributions and contributions linked to the exchange possibility. Charge transfer contributions are important and the localized character of the hydrogen bond is examined. It is pointed out that the definition of the set of excited configurations for the calculation of the energies of the isolated monomers is important, especially when one tries to use a small atomic basis set. A similar effect in SCF -type calculations is evaluated. The contribution of higher orders is evaluated by the CIPSI method.     

Electron correlation described by extended geminal models: The EXGEM4 and EXGEM5 models

Within the framework of the general extended geminal model, two new approximate models EXGEM 4 and EXGEM 5 are introduced. The models are tested against full CI calculations on the water molecule for three different nuclear configurations and a full CI potential energy curve for the LiH molecule in the ground state. On the basis of these calculations, it is suggested that the models will yield electronic correlation energies with an accuracy of 1–2% of the corresponding full CI result.     

X-ray absorption spectra of hexagonal ice and liquid water by all-electron Gaussian and augmented plane wave calculations

Full potential x-ray spectroscopy simulations of hexagonal ice and liquid water are performed by means of the newly implemented methodology based on the Gaussian augmented plane waves formalism. The computed spectra obtained within the supercell approach are compared to experimental data. The variations of the spectral distribution determined by the quality of the basis set, the size of the sample, and the choice of the core-hole potential are extensively discussed. The second part of this work is focused on the understanding of the connections between specific configurations of the hydrogen bond network and the corresponding contributions to the x-ray absorption spectrum in liquid water. Our results confirm that asymmetrically coordinated molecules, in particular, those donating only one or no hydrogen bond, are associated with well identified spectral signatures that differ significantly from the ice spectral profile. However, transient local structures, with half formed hydrogen bonds, may still give rise to spectra with dominant postedge contributions and relatively weaker oscillator strengths at lower energy. This explains why by averaging the spectra over all the O atoms of liquid instantaneous configurations extracted from ab initio molecular dynamics trajectories, the spectral features indicating the presence of weak or broken hydrogen bonds turn out to be attenuated and sometimes not clearly distinguishable.     

Analysis of catalytic mechanism of serine proteases. Viability of the ring-flip hypothesis

Quantum calculations are applied to the active site of serine proteases, including four specific residues and a water molecule, as well as a substrate and proton donors in the oxyanion hole. Residues are tethered to the protein backbone of an X-ray structure but otherwise allowed to move freely to their lowest energy positions. The viability of the ring-flip hypothesis, which proposes that a 180 degrees rotation of the His-57 imidazole ring facilitates the catalysis, is assessed by comparison of energies of configurations both before and after such a flip. Specifically considered is the contribution to catalysis of the Ser-214 residue and a water molecule that is observed in the active site. The calculations provide detailed information concerning the nature, geometry, and strength of hydrogen bonds that are formed within the active site at each stage of the enzymatic mechanism.     

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.     

Excess electron localization sites in neutral water clusters

We present approximate pseudopotential quantum-mechanical calculations of the excess electron states of equilibrated neutral water clusters sampled by classical molecular dynamics simulations. The internal energy of the clusters are representative of those present at temperatures of 200 and 300 K. Correlated electronic structure calculations are used to validate the pseudopotential for this purpose. We find that the neutral clusters support localized, bound excess electron ground states in about 50% of the configurations for the smallest cluster size studied (n = 20), and in almost all configurations for larger clusters (n > 66). The state is always exterior to the molecular frame, forming typically a diffuse surface state. Both cluster size and temperature dependence of energetic and structural properties of the clusters and the electron distribution are explored. We show that the stabilization of the electron is strongly correlated with the preexisting instantaneous dipole moment of the neutral clusters, and its ground state energy is reflected in the electronic radius. The findings are consistent with electron attachment via an initial surface state. The hypothetical spectral dynamics following such attachment is also discussed.     

Assessing the accuracy of quantum Monte Carlo and density functional theory for energetics of small water clusters

We present a detailed study of the energetics of water clusters (H(2)O)(n) with n ≤ 6, comparing diffusion Monte Carlo (DMC) and approximate density functional theory (DFT) with well converged coupled-cluster benchmarks. We use the many-body decomposition of the total energy to classify the errors of DMC and DFT into 1-body, 2-body and beyond-2-body components. Using both equilibrium cluster configurations and thermal ensembles of configurations, we find DMC to be uniformly much more accurate than DFT, partly because some of the approximate functionals give poor 1-body distortion energies. Even when these are corrected, DFT remains considerably less accurate than DMC. When both 1- and 2-body errors of DFT are corrected, some functionals compete in accuracy with DMC; however, other functionals remain worse, showing that they suffer from significant beyond-2-body errors. Combining the evidence presented here with the recently demonstrated high accuracy of DMC for ice structures, we suggest how DMC can now be used to provide benchmarks for larger clusters and for bulk liquid water.     

Dynamic Properties of Local Structures in Aqueous Model Systems

A method for describing structural and dynamic inhomogeneity in aqueous model systems is proposed. The method is based on the construction of ranked distributions of measured quantities (lifetime of hydrogen bonds and local configurations of water molecules). Asymptotic estimates were obtained for the lifetimes of hydrogen bonds and local configurations of hydrogenbonded water molecules selected by a dynamic criterion for hydrogen bonds.     

Interaction energy of a water molecule with a single-layer graphitic surface modeled by hydrogen- and fluorine-terminated clusters

In ab initio calculations a finite graphitic cluster model is often used to approximate the interaction energy of a water molecule with an infinite single-layer graphitic surface (graphene). In previous studies, the graphitic cluster model is a collection of fused benzene rings terminated by hydrogen atoms. In this study, the effect of using fluorine instead of hydrogen atoms for terminating the cluster model is examined to clarify the role of the boundary. The interaction energy of a water molecule with the graphitic cluster was computed using ab initio methods at the MP2 level of theory and with the 6-31G(d = 0.25) basis set. The interaction energy of a water molecule with graphene is estimated by extrapolation of two series of increasing size graphitic cluster models (C(6n2)H(6n) and C(6n2)F(6n), n = 1-3). Two fixed orientations of water molecule are considered: (a) both hydrogen atoms of water pointing toward the cluster (mode A) and (b) both hydrogen atoms of water pointing away from the cluster (mode B). The interaction energies for water mode A are found to be -2.39 and -2.49 kcal/mol for C(6n2)H(6n) and C(6n2)F(6n) cluster models, respectively. For water mode B, the interaction energies are -2.32 and -2.44 kcal/mol for C(6n2)H(6n) and C(6n2)F(6n) cluster models, respectively.