An ab initio molecular dynamics study on hydrogen bonds between water molecules

The quantitative estimation of the total interaction energy of a molecular system containing hydrogen bonds (H bonds) depends largely on how to identify H bonding. The conventional geometric criteria of H bonding are simple and convenient in application, but a certain amount of non-H bonding cases are also identified as H bonding. In order to investigate the wrong identification, we carry out a systematic calculation on the interaction energy of two water molecules at various orientation angles and distances using ab initio molecular dynamics method with the dispersion correction for the Becke-Lee-Yang-Parr (BLYP) functionals. It is shown that, at many orientation angles and distances, the interaction energies of the two water molecules exceed the energy criterion of the H bond, but they are still identified as H-bonded by the conventional "distance-angle" criteria. It is found that in these non-H bonding cases the wrong identification is mainly caused by short-range interaction between the two neighbouring water molecules. We thus propose that, in addition to the conventional distance and angle criteria of H bonding, the distance d(H···H) between the two neighbouring hydrogen atoms of the two water molecules should also be taken as a criterion, and the distance r(O···H) between the hydrogen atom of the H-bond donor molecule and the oxygen atom of the acceptor molecule should be restricted by a lower limit. When d(H···H) and r(O···H) are small (e.g., d(H···H) < 2.0 ? and r(O···H) < 1.62 ?), the repulsion between the two neighbouring atoms increases the total energy of the two water molecules dramatically and apparently weakens the binding of the water dimer. A statistical analysis and comparison of the numbers of the H bonds identified by using different criteria have been conducted on a Car-Parrinello ab initio molecular dynamics simulation with dispersion correction for a system of 64 water molecules at near-ambient temperature. They show that the majority of the H-bonds counted by using the conventional criteria combined with the d(H···H) criterion and the restriction of r(O···H) match what is identified by the binding energy criteria (e.g., E ≤ -10 kJ/mol), while some of them still have a binding energy that exceeds the energy criterion, indicating that the complicated quantum effects in H bonding can only be described by the three geometric parameters to a certain extent.     

Matrix isolation infrared and ab initio study of the hydrogen bonding between formic acid and water

The infrared spectra of the formic acid-water complexes isolated in argon matrices are reported. Both supersonic jet expansion and a conventional effusive source followed by trapping in solid argon at 10K are used to obtain the matrices. The experimental IR spectra are compared to the data obtained from high level ab initio (MP2) and DFT (B3LYP) calculations with 6-311++G(d,p) and aug-cc-pVTZ basis sets. The complex formation results in red shifts in the C=O and O-H stretching vibrations and a blue shift in the C-O stretching vibration of formic acid. The O-H stretching modes of water also exhibit pronounced red shifts. Both the MP2 and B3LYP calculations located three minima corresponding to cyclic HCOOH...H2O complexes with two hydrogen bond interactions. The binding energies are -10.3, -5.1, and -3.5 kcal mol(-1), respectively, for the three complexes at the MP2/ aug-cc-pVTZ level, corrected for the basis set superposition error (BSSE) using the Boys-Bernardi counterpoise scheme. Comparison of the calculated frequencies of the three complexes with the matrix IR spectrum reveals that the lowest energy complex is formed. In addition, a complex of formic acid with two water molecules is observed.     

An ab initio benchmark study of hydrogen bonded formamide dimers

The five singly and doubly hydrogen bonded dimers of formamide are calculated at the correlated level by using resolution of identity M?ller-Plesset second-order perturbation theory (RIMP2) and the coupled cluster with singles, doubles, and perturbative triples [CCSD(T)] method. All structures are optimized with the Dunning aug-cc-pVTZ and aug-cc-pVQZ basis sets. The binding energies are extrapolated to the complete basis set (CBS) limit by using the aug-cc-pVXZ (X = D, T, Q) basis set series. The effect of extending the basis set to aug-cc-pV5Z on the geometries and binding energies is studied for the centrosymmetric doubly N-H...O bonded dimer FA1 and the doubly C-H...O bonded dimer FA5. The MP2 CBS limits range from -5.19 kcal/mol for FA5 to -14.80 kcal/mol for the FA1 dimer. The DeltaCCSD(T) corrections to the MP2 CBS limit binding energies calculated with the 6-31+G(d,p), aug-cc-pVDZ, and aug-cc-pVTZ basis sets are mutually consistent to within < or =0.03 kcal/mol. The DeltaCCSD(T) correction increases the binding energy of the C-H...O bonded FA5 dimer by 0.4 kcal/mol or approximately 9% over the distance range +/-0.5 Angstrom relative to the potential minimum. This implies that the ubiquitous long-range C-H...O interactions in proteins are stronger than hitherto calculated.     

An ab initio study of the guanidinium fragments in tetrodotoxin and saxitoxin

SCF Hartree–Fock calculations are used to predict properties of the guanidinium fragment present in tetrodotoxin and saxitoxin, toxins known to block the sodium channels of the nerve cell membrane. The results, in terms of net atomic charges and geometries, are compared to similar calculation results obtained for the Na⁺–H₂O complex.     

Effect of intermolecular hydrogen bonding on the molecular structures of imidazole and 1,2,4-triazole: A study by ab initio molecular orbital calculations

The effect of intermolecular hydrogen bonding in the solid state on the molecular structures of imidazole and 1,2,4-triazole has been studied by SCF ab initio molecular orbital calculations at the HF/6-31G^* level. The crystals of these species contain endless chains of molecules, connected by unusually strong N-H N hydrogen bonds. Our simulation of the crystal field, based on two simple models, unequivocally shows that hydrogen bond formation not only lengthens the N-H bond but also causes a concerted change in the length of two N-C bonds. The change indicates that the contribution of a polar canonical form to the structure of the molecule increases in going from the gaseous phase to the crystal. This provides a rationale for the strong intermolecular hydrogen bond occurring in the solid state. We have also optimized the geometry of the free molecules at the MP2/6-31G^* level, to investigate the effect that correcting for electron correlation has on the equilibrium structure of these systems.     

Cooperative effects at water-crystalline silica interfaces strengthen surface silanol hydrogen bonding. An ab initio molecular dynamics study

Silica and silica based materials are widely used in chemistry and materials science due to their importance in many technological fields. The properties of these materials, which are crucial for their applications, are mainly determined by the presence of hydrogen bonding between surface silanols. Here, we present ab initio molecular dynamics simulations (AIMD) on different surfaces derived from the crystallographic α-quartz (100) and the α-cristobalite (001) and (101) faces, both free and at the interface with liquid water. The focus was on studying whether water adsorption can disrupt the H-bond pattern at the pristine free silica surface and how deep the perturbation due to the contact with the surface affects the structure of the water multilayer. Results highlight that the water phase is over structured at the interface with silica, as compared to water bulk. Furthermore, an apparent counterintuitive behavior has been observed for quartz (100) and cristobalite (001) surfaces: the interaction with water does not cleave the pre-existent H-bonds between the surface silanol groups. On the contrary, in several cases, it is observed that SiOH···OHSi H-bonds are even strengthened, as the result of a mutual cooperative H-donor/H-acceptor enhancement between silanols and water molecules, which may alter the adsorption capability of these silica surfaces.     

Hydrogen bonding and dimeric self-association of 2-pyrrolidinone: An ab initio study

Ab initio calculations on the different associated structures of 2-pyrrolidinone with water and with itself were carried out using 3-21G and 6-31G^* basis sets at the Hartree–Fock level, including electron correlation using second-order Møller–Plesset perturbation theory. The calculated free energy changes for the intermolecular hydrogen bonded dimer and hydrated species indicated that the molecular systems with cyclic dimerization and association with two water molecules are dominant. The results are compared to the available experimental data in the literature.     

An ab initio study of formamide

Calculated energy and molecular properties of the ground and low-energy excited states of formamide are presented at the ground state geometry. Satisfactory results are obtained except for the ¹* energy which remains too high by 1 eV (which is nevertheless a large improvement over previous calculations). The predicted triplet energies lie at 5.4 eV (³ n*) and 5.8 eV (³*).     

The effect of hydrogen bonding on structural parameters : IV. An ab initio study of formamide—ammonia complexes

Four hydrogen-bonded formamide—ammonia complexes have been studied by ab initio calculations, two where the amino group acts as a donor and two where the carbonyl oxygen is acceptor. In all cases the formation of a hydrogen bond leads to increased conjugation, expressed as a shortening of the CN bond and a corresponding lengthening of the CO bond. In two of the complexes the effect of varying the hydrogen bond length has been studied in some detail. It is found that the effect on the conjugated system depends on the length of the hydrogen bond. Potential functions for the N—HN and N—HO hydrogen bonds have been derived.     

An ab initio study of ascorbic acid

The conformations of ascorbic acid and its singly ionized analog are found to agree with the X-ray structures. The calculations are discussed in terms of the known chemistry of ascorbic acid and its metabolites.     

An ab initio study of pyruvic acid

The geometries and vibrational frequencies of two conformers of pyruvic acid have been obtained at the ab initio second order Möller-Plesset level of theory using the 6-311++G^** basis set. While the calculated geometries have been compared to the experimental microwave data, the vibrational frequencies have been assigned, using the experimental gas phase IR spectra of 13 isotopes of pyruvic acid by a recently developed scaling procedure (IRPROG). An attempt has been made to explain the stability of the eclipsed conformation over the staggered conformation of pyruvic acid by taking account of the molecular orbitals.     

An ab initio and density functional theory study of the structure and bonding of sulfur ylides

Sulfur ylides are useful synthetic intermediates that are formed from the interaction between singlet carbenes and sulfur-containing molecules. Partial double-bond character frequently has been proposed as a key contributor to the stability of sulfur ylides. Calculations at the B3LYP, MP2, and CCSD(T) levels of theory employing various basis sets have been performed on the sulfur ylides H(2)S-CH(2) and (CH(3))(2)S-CH(2) in order to investigate the structure and bonding of these systems. The following general properties of sulfur ylides were observed from the computational studies: C-S bond distances that are close in length to that of a typical C-S double bond, high charge transfer from the sulfide to the carbene, and large torsional rotation barriers. Analysis of the sulfur ylide charge distribution indicates that the unusually short C-S bond distance can be attributed in part to the electrostatic attraction between highly oppositely charged carbon and sulfur atoms. Furthermore, n --> sigma* stabilization arising from donation of electron density from the carbon lone pair orbital into S-H or S-C antibonding orbitals leads to larger than expected torsional barriers. Finally, natural resonance theory analysis indicates that the bond order of the sulfur ylides H(2)S-CH(2) and (CH(3))(2)S-CH(2) is 1.4-1.5, intermediate between a single and double bond.     

Combined electrostatics and hydrogen bonding determine intermolecular interactions between polyphosphoinositides

Membrane lipids are active contributors to cell function as key mediators in signaling pathways controlling cell functions including inflammation, apoptosis, migration, and proliferation. Recent work on multimolecular lipid structures suggests a critical role for lipid organization in regulating the function of both lipids and proteins. Of particular interest in this context are the polyphosphoinositides (PPI's), especially phosphatidylinositol (4,5) bisphosphate (PIP 2). The cellular functions of PIP 2 are numerous but the organization of PIP 2 in the inner leaflet of the plasma membrane, as well as the factors controlling targeting of PIP 2 to specific proteins, remains poorly understood. To analyze the organization of PIP 2 in a simplified planar system, we used Langmuir monolayers to study the effects of subphase conditions on monolayers of purified naturally derived PIP 2 and other anionic or zwitterionic phospholipids. We report a significant molecular area expanding effect of subphase monovalent salts on PIP 2 at biologically relevant surface densities. This effect is shown to be specific to PIP 2 and independent of subphase pH. Chaotropic agents (e.g., salts, trehalose, urea, temperature) that disrupt water structure and the ability of water to mediate intermolecular hydrogen bonding also specifically expanded PIP 2 monolayers. These results suggest a combination of water-mediated hydrogen bonding and headgroup repulsion in determining the organization of PIP 2, and may contribute to an explanation for the unique functionality of PIP 2 compared to other anionic phospholipids.     

An ab initio study of electrophilic aromatic substitution

Proton affinities are calculated at all reactive positions for the normal benzenoid hydrocarbons, benzene, naphthalene, phenanthrene and anthracene, a strained benzenoid hydrocarbon, biphenylene, and a nonalternant hydrocarbon, fluoranthene, and the results are compared to experimental protodetritiation rates. Methods used include PM3 and Hartree-Fock calculations at the STO-3G, 3-21G*, 6-31G* and MP2//6-31G* levels. Generally good agreement is found between theory and experiment with 6-31G* giving the best correlations. Received: 11 June 1998 / Accepted: 3 September 1998 / Published online: 23 February 1999     

An ab initio study of the hydrated positron

Ab initio calculations are presented for the hydration energy of the positron. Tetrahedral molecular-dipole-oriented clusters e⁺(H₂O)₄ are considered. In performing these calculations, the Hartree—Fock MO LCAO SCF approximation with the 4-31G split-valence basis set is used. The method was modified to treat the positron problem. It is shown that e⁺ in liquid water, like an electron, can be strongly solvated, with the hydration energy 0.2–0.3 eV greater than that of e⁺.     

Incommensurability induced by intermolecular hydrogen bonding

Non-symmetric dimesogens are composed of two different mesogenic units linked via a flexible spacer. In this study, a new type of non-symmetric dimesogen has been built through the self-assembly via intermolecular hydrogen bonding between appropriately designed H-bond donor (3-cholesteryloxycarbonylpentanoic acid) and acceptor (aromatic mesogen with a pyridyl group) moieties. As for covalently linked dimesogens, several types of smectic periodicities are observed for these H-bonded cholesteryl compounds depending on the length of the terminal chain of the acceptor moiety: a smectic periodicity resulting from associated dimesogens is observed for long terminal chains, while short chain homologues display an intercalated structure corresponding to half the molecular length. The competition between these two incommensurate lengths can induce an incommensurate smectic phase where the two smectic periodicities coexist at long range.     

An ab initio study of the keto-enol tautomerism

The keto-enol tautomerism is studied using an approximative HF method outlined in the appendix. The following results are obtained: (1) The experimentally observed alternance of G in acyclic monoketones could not be reproduced. (2) The stabilization of C=C double bonds, especially of conjugated double bonds, by CH₃- or -CH₂- groups is responsible for the observed difference between acyclic and cyclic 1.2-diketones, e.g. for the different enol content of diacetyl and cyclopentane-1.2-dione. (3) The enols of 1.2-diketones contain a hydrogen bond which differs from the hydrogen bond in enols of 1.3-diketones. (4) A system of two conjugated C=O double bonds is not favoured compared to a system of two C=O bonds which are separated by one (or more) -CH₂- group. (5) 5-ring enols with a C=C double bond in the ring are more stable than one would expect by an energy estimation from acyclic compounds.     

Potential energy function for cation–peptide interactions: An ab initio study

A potential energy function is developed to represent the interaction of small monovalent cations, Li⁺, Na⁺, and K⁺, with the backbone of polypeptides. The results are based on ab initio calculations up to the 6-31G* level of the interactions of the ions with acetamide and N-methylacetamide. Basis set superposition errors are corrected with the counterpoise method. A systematic overestimate of the bond polarities is taken into account by an empirical scaling procedure that uses the ratio of the experimental to ab initio dipole moment. The calculated binding energies obtained with this procedure show consistent convergence with different basis sets and are in good agreement with experimental data on cation–water and cation–dimethylformamide systems. Investigations of the calculated ab initio potential energy surface indicate that the cation–peptide interaction is dominated by electrostatics and includes a nonnegligible contribution from polarization of the peptide group by the ion. The induced polarization results in a steeper-than-Coulombic interaction and cannot be described by fixed ion–peptide partial charges electrostatics. Atomic polarizabilities located on the atoms of the ligand molecule are introduced to account for the induced polarization in the empirical energy function. A ～1/r⁴ attractive interaction appears in the potential function. The resulting radial and angular dependence of the potential energy surface is well reproduced. © 1995 by John Wiley & Sons, Inc.     

An ab initio study of solvent polarity and hydrogen bonding effects on the nitrogen NMR shieldings of N,N‐dimethylacetamidine

Density functional theory combined with the polarizable continuum model (PCM) and continuous set of gauge transformations method is applied to investigate the effects of solvent polarity on the nitrogen NMR shieldings of N, N‐dimethylacetamidine. Hydrogen bonding effects on shielding are likewise calculated using a supermolecule approach, where the imino group of the solute is hydrogen bonded with solvent. Theoretical results are compared with published experimental data. The PCM shielding calculations utilizing PCM‐optimized solute geometries yield results comparable to those obtained with the supermolecule approach. Geometry optimization of the solute appears to be more important in PCM shielding calculations than in the supermolecule approach. The large solvent shifts observed in water can only be reproduced when the N·H distance used in the calculation indicates full proton transfer from water to the imino nitrogen of the solute. Copyright © 2002 John Wiley & Sons, Ltd.     

The effect of hydrogen bonding on structural parameters ii. an ab initio study of the monohydrated formamide molecule

Four hydrogen-bonded formamide-water complexes have been studied by ab initio calculations, two where the amino group acts as a donor and two where the carbonyl oxygen is an acceptor. The results indicate that the effect on the conjugated NCO fragment depends on both the type and the energy of the hydrogen bond formed. Although, in all cases the formation of a hydrogen bond leads to increased conjugation, expressed as a shortening of the CN bond and a corresponding lengthening of the CO bond, there is a significant difference in the effect of the two types of hydrogen bonds. This difference may be explained by changes in the electron populations. In two of the complexes the effect of varying the hydrogen bond length has been studied in some detail. It is found that the effect on the conjugated system depends on the length of the hydrogen bond, and analytical expressions have been found for the variations of the CO and CN bond lengths with changes in the hydrogen bond length. Potential functions for the N-H β O and O-H β O hydrogen bonds have also been derived.