Preferential formation of the different hydrogen bonds and their effects in tetrahydrofuran and tetrahydropyran microhydrated complexes

The role of cycloether-water (c-w) and water-water (w-w) hydrogen bonds (H-bonds) on the stability of the tetrahydrofuran THF/(H(2)O)(n) and the tetrahydropyran THP/(H(2)O)(n) complexes with n = 1-4 was investigated herein using the density functional and ab initio methods and the atoms in molecules theory. Geometry optimizations for these complexes were carried out with various possible initial guess structures. It was revealed that the major contributions of the mono and dihydrated complexes came from c-w H-bonds. A competition between c-w and w-w H-bonds contribution was observed for trihydrated complexes. For most of tetrahydrated complexes, the inter-water H-bonds provided the greatest contribution, whereas the c-w contributions were small but not negligible. It was confirmed that to produce a hydrophobic hydration of cycloethers, the C-H···O(w) H-bond should be associated with a network of H-bonds that connects both portions of the solute, through the formation of a bifunctional H-bond. A linear correlation is obtained for the sum of electron density at the bond critical points (ρ(b)) with the interaction energy (ΔE) and with the solute-solvent interaction energy (ΔE(s-w)) of the microhydrated complexes. In addition, a new way to estimate the energetic contribution as well as the preferential formation of the different H-bonds based completely on ρ(b) was found. Even more, it allows to differentiate the contribution from c-w interactions in both hydrophilic and hydrophobic contributions, it is therefore a useful tool for studying the hydration of large biomolecules. The analysis of the modifications in the atomic and group properties brought about by successive addition of H(2)O molecules allowed to pinpoint the atoms or molecular groups that undergo the greatest changes in electron population and energetic stabilization. It was identified that the remarkable stabilization of the water oxygen atoms is crucial for the stabilization of the complexes.     

The possible covalent nature of N-H...O hydrogen bonds in formamide dimer and related systems: an ab initio study

The N-H...O hydrogen bonds are analyzed for formamide dimer and its simple fluorine derivatives representing a wide spectrum of more or less covalent interactions. The calculations were performed at the MP2/6-311++G(d,p) level of approximation. To explain the nature of such interactions, the Bader theory was also applied, and the characteristics of the bond critical points (BCPs) were analyzed: the electron density at BCP and its Laplacian, the electron energy density at BCP and its components, the potential electron energy density, and the kinetic electron energy density. These parameters are used to justify the statement that some of the interactions analyzed are partly covalent in nature. An analysis of the interaction energy components for the systems considered indicates that the covalent character of the hydrogen bond is manifested by a markedly increased contribution of the delocalization term relative to the electrostatic interaction energy. Moreover, the ratio of stabilizing the delocalization/electrostatic contributions grows linearly with the decreasing lengths of the hydrogen bond.     

Density functional theory and topological analysis on the hydrogen bonds in cysteine–propanoic acid complexes

The complexes formed via hydrogen bonding interactions between cysteine and propanoic acid have been studied at the density three-parameter hybrid functional DFT-B3LYP/6-311++G(d,p) level regarding their geometries, energies, vibrational frequencies, and topological features of the electron density. The quantum theory of atoms in molecules (QTAIM) and natural bond orbital (NBO) analysis was employed to elucidate the interaction characteristics in cysteine–propanoic acid (Cys–Prop) complexes. More than 10 kinds of hydrogen bonds (H-bonds) including intra- and inter-molecular H-bonds have been found in Cys–Prop complexes. The results show that both the strength of H-bonds and the deformation are important factors for the stability of Cys–Prop complexes. The strongest H-bonds (O2H^A···O1^B and O2H^A···O1^B) exist in the most stable Cys–Prop complex. The stronger H-bonds formed between hydroxyl and O (or N) atom usually stronger than those involve C (or S) atom. Relationships between the electron density (ρ) of BCP and H-bond length as well as the Fock matrix element (F _ij) has also been investigated and used to study the nature of H-bonds. Moreover, the results show that the change of the bond length linearly correlates with the corresponding frequency shift.     

Density functional theory and topological analysis on the hydrogen bonding interactions in N-protonated adrenaline–DMSO complexes

In this study, complexes formed via hydrogen bond interactions between N-protonated adrenaline (AdH⁺) and DMSO have been studied by density functional theory (DFT). The relevant geometries, energies, and IR characteristics of the hydrogen bonds (H-bonds) have been systematically investigated. The natural bond orbital (NBO) and the quantum theory of atoms in molecule (QTAIM) analysis have also been applied to understand the nature of the hydrogen bonding interactions in complexes. The H-bonds involving amino or hydroxyls as H-donor are dominant H-bonds in complexes and are attributed to strong H-bonds. The weak H-bonds, such as π H-bonds and H-bonds involving methyl (DMSO) or methenyls (C2H6 and C5H7 of AdH⁺) as H-acceptors, were found in complexes as well. The complexes in which the dominant H-bond involves amino of AdH⁺ as H-donor are more stable than those with the dominant H-bond involving hydroxyls as H-donor. Some relationships between various properties of QTAIM, NBO, geometry as well as frequency were also investigated.     

Cooperativity in hydrogen-bonded interactions: ab initio and "atoms in molecules" analyses

The H(2)CO...(HF)(n) (n = 1, ..., 9) complexes were investigated using the MP2 method and the following basis sets: 6-311++G(d,p), aug-cc-pVDZ and aug-cc-pVTZ. It was found that the cooperativity effect enhances significantly the F-H...O hydrogen bond; in some of cases one can detect the covalent nature of hydrogen bonding. To deepen the nature of the interactions investigated, the scheme of decomposition of the interaction energy was applied; for stronger H-bonds where the cooperativity is more important, the delocalization energy term increases. The ratio of delocalization energy to electrostatic energy increases for stronger hydrogen bonds where the proton...acceptor distance is shorter. The Bader theory was also applied, and it was found that for stronger H-bonds the electronic energy density at the proton...acceptor bond critical point is negative and may be attributed to the partly covalent interaction.     

Theoretical investigation on the structural and electronic properties of complexes formed by thymine and 2′-deoxythymidine with different anions

Hydrogen bonding interactions between thymine nucleobase and 2′-deoxythymidine nucleoside (dT) with some biological anions such as F⁻ (fluoride), Cl⁻ (chloride), OH⁻ (hydroxide), and NO₃ ⁻ (nitrate) have been explored theoretically. In this study, complexes have been studied by density functional theory (B3LYP method and 6-311++G (d,p) basis set). The relevant geometries, energies, and characteristics of hydrogen bonds (H-bonds) have been systematically investigated. There is a correlation between interaction energy and proton affinity for complexes of thymine nucleobase. The nature of all the interactions has been analyzed by means of the natural bonding orbital (NBO) and quantum theory atoms in molecules (QTAIM) approaches. Donors, acceptors, and orbital interaction energies were also calculated for the hydrogen bonds. Excellent correlations between structural parameter (δR) and electron density topological parameter (ρ _b) as well as between E(2) and ρ _b have been found. It is interesting that hydrogen bonds with anions can affect the geometry of thymine and 2′-deoxythymidine molecules. For example, these interactions can change the bond lengths in thymine nucleobase, the orientation of base unit with respect to sugar ring, the furanose ring puckering, and the C1′–N1 glycosidic linkage in dT nucleoside. Thus, it is necessary to obtain a fundamental understanding of chemical behavior of nucleobases and nucleosides in presence of anions.     

Single‐electron halogen bond: Ab initio study

Ab initio calculations have been performed on single‐electron halogen bonds between methyl radical and bromine‐containing molecules to gain a deeper insight into the nature of such noncovalent interactions. Bader's atoms in molecules (AIM) theory have also been applied to the analysis of the linking of the single‐electron halogen bond. Various characteristics of the R? Br…CH₃ interaction, i.e., binding energies, geometrical parameters and topological properties of the electron density have been determined. The presence of the bond critical points (BCPs) between the bromine atom and methyl radical and the values of electron density and Laplacian of electron density at these BCPs indicate the closed‐shell interactions in the complexes. The single‐electron halogen bonds, which are significantly weaker than the normal halogen bonds, exhibit equally bond strength as compared to the single‐electron hydrogen bond. It has been also found that plotting of the binding energies versus topological properties of the electron density at the BCPs gives two straight lines. © 2006 Wiley Periodicals, Inc. Int J Quantum Chem, 2007     

Arrangement and nature of intermolecular hydrogen bonding in complex biomolecular systems: modeling the vitamin C---L-alanine interaction

Vitamin C is known as an essential dietary supplement and implicated in diverse biological processes. We present here a theoretical study on the nature of hydrogen bonding of vitamin C in biological systems. For this reason, the complexes of vitamin C (VC) with neutral and zwitterionic L-alanine (as the simplest chiral amino acid) were studied at the MP2/6-311++G(d,p) level of theory. In the gas phase, neutral L-alanine leads to more stable complexes than the zwitterionic forms while the reverse is true in the aqueous phase. The complexes are formed via two hydrogen bond interactions, which result in a ring-like hydrogen-bonded networks. The nature of H-bonds was characterized in terms of natural bond orbital and quantum theory of atoms in molecule analyses (QTAIM). The H-bonds in the studied complexes were electrostatic in nature; however, in the case of shorter and directional H-bonds and ionic interactions, contributions of covalent character were also non-negligible. Natural energy decomposition analysis of hydrogen-bonded complexes reveals that the charge transfer and electrical components are the largest contributors for the interaction energies of complexes. Natural resonance theory analysis suggests higher resonance weight for charge-assisted interactions of vitamin C---alanine (zwitterionic) complexes, where the total interaction energy is considerably higher than that of neutral alanine.     

How resonance assists hydrogen bonding interactions: an energy decomposition analysis

Block-localized wave function (BLW) method, which is a variant of the ab initio valence bond (VB) theory, was employed to explore the nature of resonance-assisted hydrogen bonds (RAHBs) and to investigate the mechanism of synergistic interplay between pi delocalization and hydrogen-bonding interactions. We examined the dimers of formic acid, formamide, 4-pyrimidinone, 2-pyridinone, 2-hydroxpyridine, and 2-hydroxycyclopenta-2,4-dien-1-one. In addition, we studied the interactions in beta-diketone enols with a simplified model, namely the hydrogen bonds of 3-hydroxypropenal with both ethenol and formaldehyde. The intermolecular interaction energies, either with or without the involvement of pi resonance, were decomposed into the Hitler-London energy (DeltaEHL), polarization energy (DeltaEpol), charge transfer energy (DeltaECT), and electron correlation energy (DeltaEcor) terms. This allows for the examination of the character of hydrogen bonds and the impact of pi conjugation on hydrogen bonding interactions. Although it has been proposed that resonance-assisted hydrogen bonds are accompanied with an increasing of covalency character, our analyses showed that the enhanced interactions mostly originate from the classical dipole-dipole (i.e., electrostatic) attraction, as resonance redistributes the electron density and increases the dipole moments in monomers. The covalency of hydrogen bonds, however, changes very little. This disputes the belief that RAHB is primarily covalent in nature. Accordingly, we recommend the term "resonance-assisted binding (RAB)" instead of "resonance-assisted hydrogen bonding (RHAB)" to highlight the electrostatic, which is a long-range effect, rather than the electron transfer nature of the enhanced stabilization in RAHBs.     

The influence of universal and specific interactions on structural properties of liquid formamide

Monte Carlo simulation of the structure of liquid formamide at 298 K was carried out. Intermolecular interactions were calculated using five different potentials. No essential changes in the spatial structure and topological properties of the network of hydrogen bonds of liquid formamide occur upon varying the electrostatic intermolecular interactions, strength of H-bonds, and temperature. Fragments of crystal structure are partly retained in liquid formamide. It was found that the network of H-bonds is structurally inhomogeneous and contains long-lived associates of closed cycles of H-bonds as well as tree-like and chain-like structures. The energy, topological, and statistical characteristics of closed cycles of H-bonds were determined. Translated fromIzvestiya Akademii Nauk. Seriya Khimicheskaya, No. 12, pp. 2227–2236, December, 1999.     

The nature of bond critical points in dinuclear copper(I) complexes

Closed-shell contacts between two copper(I) ions are expected to be repulsive. However, such contacts are quite frequent and are well documented. Crystallographic characterization of such contacts in unsupported and bridged multinuclear copper(I) complexes has repeatedly invited debates on the existence of cuprophilicity. Recent developments in the application of Bader's theory of atoms-in-molecules (AIM) to systems in which weak hydrogen bonds are involved suggests that the copper(I)-copper(I) contacts would benefit from a similar analysis. Thus the nature of electron-density distributions in copper(I) dimers that are unsupported, and those that are bridged, have been examined. A comparison of complexes that are dimers of symmetrical monomers and those that are dimers of two copper(I) monomers with different coordination spheres has also been made. AIM analysis shows that a bond critical point (BCP) between two Cu atoms is present in most cases. The nature of the BCP in terms of the electron density, ρ, and its Laplacian is quite similar to the nature of critical points observed in hydrogen bonds in the same systems. The ρ is inversely correlated to Cu-Cu distance. It is higher in asymmetrical systems than what is observed in corresponding symmetrical systems. By examining the ratio of the local electron potential-energy density (V(c)) to the kinetic energy density (G(c)), |V(c)|/G(c) at the critical point suggests that these interactions are not perfectly ionic but have some shared nature. Thus an analysis of critical points by using AIM theory points to the presence of an attractive metallophilic interaction similar to other well-documented weak interactions like hydrogen bonding.     

Hydrogen bonding interactions between <Emphasis Type="Italic">N</Emphasis>,<Emphasis Type="Italic">N</Emphasis>-dimethylformamide and cysteine: DFT studies of structures,properties, and topologies

The hydrogen bonding interactions between cysteine and N,N-dimethylformamide (DMF) were studied at the extended hybrid functional DFT-X3LYP/6-311++G(d,p) level regarding their geometries, energies, vibrational frequencies, and topological features of the electron density. The quantum theory of atoms in molecules (QTAIM) and natural bond orbital (NBO) analyses were employed to elucidate the interaction characteristics in the complexes. The results show that two intermolecular hydrogen bonds (H-bonds) are formed in one complex except few complexes with one intermolecular H-bond. The H-bonds involving O atom of DMF as H-bond acceptor usually are red-shifting H-bonds, while the blue-shifting H-bond usually involve methyl of DMF or methenyl of cysteine moiety as H-bond donors. Both hydrogen bonding interaction and structural deformation play important roles in the relative stabilities of the complexes. Due to the π-bond cooperativity, the strongest H-bond is formed between hydroxyl of cysteine moiety and O atom of DMF, however, the serious deformation counteract the hydrogen bonding interaction to a great extent. The complex involves a stronger hydrogen bonding interaction as well as the smaller deformation is the most stable one. The electron density (ρ_b) as well as its Laplacian (∇²ρ_b) at the H-bond critical point predicted by QTAIM is strongly correlated with the H-bond structural parameter (δR _H···Y) and the second-perturbation energies E(2) in the NBO scheme.     

Dimers of formic acid, acetic acid, formamide and pyrrole-2-carboxylic acid: an ab initio study

The intermolecular hydrogen bonds in dimers of formic acid, acetic acid, and formamide were investigated. Additionally, three configurations of the pyrrole-2-carboxylic acid (PCA) dimer were studied to analyze how the pyrrole pi-electron system influences the carboxylic groups connected by double O-H...O hydrogen bonds. The ab initio calculations for the systems investigated were performed at MP2/6-311++G(d,p), MP2/aug-cc-pVDZ, and MP2/aug-cc-pVTZ//MP2/aug-cc-pVDZ levels of theory. The "atoms in molecules" theory of Bader was used and the analysis of the critical points was performed to study the nature of hydrogen bonds. The decomposition of the total interaction energy applied here reveals that the delocalization energy term is a particularly important attractive contribution in these systems, more important in the case of systems forming homonuclear O-H...O double hydrogen bonds than in the case of those connected through heteronuclear N-H...O bonds. Because the systems analyzed may be formally classified as the resonance-assisted hydrogen bonds (RAHBs), it seems that the dominant contribution from the delocalization interaction energy term is a distinguished feature of such interactions.     

Structures,vibrational frequencies,topologies, and energies of hydrogen bonds in cysteine‐formaldehyde complexes

The hydrogen bonding interactions between cysteine (Cys) and formaldehyde (FA) were studied with density functional theory regarding their geometries, energies, vibrational frequencies, and topological features of the electron density. The quantum theory of atoms in molecules and natural bond orbital analyses were employed to elucidate the interaction characteristics in the Cys‐FA complexes. The intramolecular hydrogen bonds (H‐bonds) formed between the hydroxyl and the N atom of cysteine moiety in some Cys‐FA complexes were strengthened because of the cooperativity. Most of intermolecular H‐bonds involve the O atom of cysteine/FA moiety as proton acceptors, while the strongest H‐bond involves the O atom of FA moiety as proton acceptor, which indicates that FA would rather accept proton than providing one. The H‐bonds formed between the CH group of FA and the S atom of cysteine in some complexes are so weak that no hydrogen bonding interactions exist among them. In most of complexes, the orbital interaction of H‐bond is predominant during the formation of complex. The electron density (ρ_b) and its Laplace (?²ρ_b) at the bond critical point significantly correlate with the H‐bond parameter δR, while a linearly relationship between the second‐perturbation energy E(2) and ρ_b has been found as well. © 2011 Wiley Periodicals, Inc. Int J Quantum Chem, 2012     

Explorations of the nature of the coupling interactions between vitamin C and methylglyoxal: a DFT study

As the first step toward understanding the augment role of vitamin C (Vc) for the anticancer effect of methylglyoxal (MG), the nature of the coupling interactions between Vc and MG has been systematically investigated at the B3LYP/6-311++G** level of theory in combination with the atoms in molecules (AIM) theory, natural bond orbital (NBO) method, and energy decomposition analysis (EDA). The possible stable complexes have been located on their potential energy surface (PES). Most of them are characterized by one or two intermolecular H-bonds with the binding energies varying from −11.1 to −2.0 kcal/mol. AIM analyses suggest that all the intermolecular H-bonds have been predominated by the electrostatic interaction. A good linear correlation between the intermolecular H-bond distance and the electron density as well as its Laplacian at the bond critical point of the intermolecular H-bond has been observed. Depending on the selected coupling modes between Vc and MG, the origin of the blue-shifts of the stretching vibrational frequencies of different C–H bonds has been elucidated. Additionally, the inherent reason for the positive role of Vc in the anticancer process for MG has been verified through the investigation of the one-electron oxidation behaviors of the most stable complex.     

Microsolvation of formamide: a rotational study

Microsolvated formamide clusters have been generated in a supersonic jet expansion and characterized using Fourier transform microwave spectroscopy. Three conformers of the monohydrated cluster and one of the dihydrated complex have been observed. Seven monosubstituted isotopic species have been measured for the most stable conformer of formamide...H(2)O, which adopts a closed planar ring structure stabilized by two intermolecular hydrogen bonds (N-H...O(H)-H...O=C). The two higher energy forms of formamide...H(2)O have been observed for the first time. The second most stable conformer is stabilized by a O-H...O=C and a weak C-H...O hydrogen bond, while, in the less stable form, water accepts a hydrogen bond from the anti hydrogen of the amino group. For formamide...(H(2)O)(2), the parent and nine monosubstituted isotopic species have been observed. In this cluster the two water molecules close a cycle with the amide group through three intermolecular hydrogen bonds (N-H...O(H)-H...O(H)-H...O=C), the nonbonded hydrogen atoms of water adopting an up-down configuration. Substitution (r(s)) and effective (r(0)) structures have been determined for formamide, the most stable form of formamide...H(2)O and formamide...(H(2)O)(2). The results on monohydrated formamide clusters can help to explain the observed preferences of bound water in proteins. Clear evidence of sigma-bond cooperativity effects emerges when comparing the structures of the mono- and dihydrated formamide clusters. No detectable structural changes due to pi-bond cooperativity are observed on formamide upon hydration.     

Quantitative classification of covalent and noncovalent H-bonds

The covalent nature of interactions within various hydrogen bonded molecular aggregates has been characterized by the two entirely different computational methods: Bader analysis of the electron density and variation-perturbation partitioning of the intermolecular interaction energy. Analysis of 34 complexes representing different types of hydrogen bonds indicates that the proton-acceptor distance approximately 1.8 A and the ratio of delocalization and electrostatic terms approximately 0.45 constitutes approximately a borderline between covalent and noncovalent hydrogen bonds. The latter ratio could be used to characterize quantitatively the degree of the covalent nature of transition state interactions with active site residues, a quantity essential for an enzyme catalytic activity.     

Ab initio EOM-CCSD spin-spin coupling constants for hydrogen-bonded formamide complexes: bridging complexes with NH3, (NH3)2, H2O, (H2O)2, FH, and (FH)2

EOM-CCSD spin-spin coupling constants across hydrogen bonds have been computed for complexes in which NH3, H2O, and FH molecules and their hydrogen-bonded dimers form bridging complexes in the amide region of formamide. The formamide one-bond N-H coupling constant [(1)J(N-H)] across N-H...X hydrogen bonds increases in absolute value upon complexation. The signs of the one-bond coupling constants (1h)J(H-X) indicate that these complexes are stabilized by traditional hydrogen bonds. The two-bond coupling constants for hydrogen bonds with N-H as the donor [(2h)J(N-X)] and the carbonyl oxygen as the acceptor [(2h)J(X-O)] increase in absolute value in the formamide/dimer relative to the corresponding formamide/monomer complex as the hydrogen bonds acquire increased proton-shared character. The largest changes in coupling constants are found for complexes of formamide with FH and (FH)2, suggesting that bridging FH monomers and dimers in particular could be useful NMR spectroscopic probes of amide hydrogen bonding.     

Effects of microsolvation on the adenine-uracil base pair and its radical anion: adenine-uracil mono- and dihydrates

Microhydration effects upon the adenine-uracil (AU) base pair and its radical anion have been investigated by explicitly considering various structures of their mono- and dihydrates at the B3LYP/DZP++ level of theory. For the neutral AU base pair, 5 structures were found for the monohydrate and 14 structures for the dihydrate. In the lowest-energy structures of the neutral mono- and dihydrates, one and two water molecules bind to the AU base pair through a cyclic hydrogen bond via the N(9)-H and N(3) atoms of the adenine moiety, while the lowest-lying anionic mono- and dihydrates have a water molecule which is involved in noncyclic hydrogen bonding via the O4 atom of the uracil unit. Both the vertical detachment energy (VDE) and adiabatic electron affinity (AEA) of the AU base pair are predicted to increase upon hydration. While the VDE and AEA of the unhydrated AU pair are 0.96 and 0.40 eV, respectively, the corresponding predictions for the lowest-lying anionic dihydrates are 1.36 and 0.75 eV, respectively. Because uracil has a greater electron affinity than adenine, an excess electron attached to the AU base pair occupies the pi* orbital of the uracil moiety. When the uracil moiety participates in hydrogen bonding as a hydrogen bond acceptor (e.g., the N(6)-H(6a)...O(4) hydrogen bond between the adenine and uracil bases and the O(w)-H(w)...N and O(w)-H(w)...O hydrogen bonds between the AU pair and the water molecules), the transfer of the negative charge density from the uracil moiety to either the adenine or water molecules efficiently stabilizes the system. In addition, anionic structures which have C-H...O(w) contacts are energetically more favorable than those with N-H...O(w) hydrogen bonds, because the C-H...O(w) contacts do not allow the unfavorable electron density donation from the water to the uracil moiety. This delocalization effect makes the energetic ordering for the anionic hydrates very different from that for the corresponding neutrals.     

Density functional theory and topological analysis on the hydrogen bonding interactions in cysteine‐thymine complexes

Hydrogen bonding interactions between amino acids and nucleic acid bases constitute the most important interactions responsible for the specificity of protein binding. In this study, complexes formed by hydrogen bonding interactions between cysteine and thymine have been studied by density functional theory. The relevant geometries, energies, and IR characteristics of hydrogen bonds (H‐bonds) have been systematically investigated. The quantum theory of atoms in molecule and natural bond orbital analysis have also been applied to understand the nature of the hydrogen bonding interactions in complexes. More than 10 kinds of H‐bonds including intra‐ and intermolecular H‐bonds have been found in complexes. Most of intermolecular H‐bonds involve O (or N) atom as H‐acceptor, whereas the H‐bonds involving C or S atom usually are weaker than other ones. Both the strength of H‐bonds and the structural deformation are responsible for the stability of complexes. Because of the serious deformation, the complex involving the strongest H‐bond is not the most stable structures. Relationships between H‐bond length (ΔR_X‐H), frequency shifts (Δv), and the electron density (ρ_b) and its Laplace (?²ρ_b) at bond critical points have also been investigated. © 2010 Wiley Periodicals, Inc. Int J Quantum Chem, 2011