A scheme for rapid prediction of cooperativity in hydrogen bond chains of formamides,acetamides, and N‐methylformamides

A scheme is proposed in this article to predict the cooperativity in hydrogen bond chains of formamides, acetamides, and N‐methylformamides. The parameters needed in the scheme are derived from fitting to the hydrogen bonding energies of MP2/6‐31+G** with basis set superposition error (BSSE) correction of the hydrogen bond chains of formamides containing from two to eight monomeric units. The scheme is then used to calculate the individual hydrogen bonding energies in the chains of formamides containing 9 and 12 monomeric units, in the chains of acetamides containing from two to seven monomeric units, in the chains of N‐methylformamides containing from two to seven monomeric units. The calculation results show that the cooperativity predicted by the scheme proposed in this paper is in good agreement with those obtained from MP2/6‐31+G** calculations by including the BSSE correction, demonstrating that the scheme proposed in this article is reasonable. Based on our scheme, a cooperativity effect of almost 240% of the dimer hydrogen bonding energy in long hydrogen bond formamide chains, a cooperativity effect of almost 190% of the dimer hydrogen bonding energy in long hydrogen bond acetamide chains, and a cooperativity effect of almost 210% of the dimer hydrogen bonding energy in long hydrogen bond N‐methylformamide chains are predicted. The scheme is further applied to some heterogeneous chains containing formamide, acetamide, and N‐methylformamide. The individual hydrogen bonding energies in these heterogeneous chains predicted by our scheme are also in good agreement with those obtained from Møller‐Plesset calculations including BSSE correction. © 2009 Wiley Periodicals, Inc. J Comput Chem, 2010     

An analytic potential energy function for the amide–amide and amide–water intermolecular hydrogen bonds in peptides

An analytic potential energy function is proposed and applied to evaluate the amide–amide and amide–water hydrogen‐bonding interaction energies in peptides. The parameters in the analytic function are derived from fitting to the potential energy curves of 10 hydrogen‐bonded training dimers. The analytic potential energy function is then employed to calculate the N? H…O?C, C? H…O?C, N? H…OH₂, and C?O…HOH hydrogen‐bonding interaction energies in amide–amide and amide–water dimers containing N‐methylacetamide, acetamide, glycine dipeptide, alanine dipeptide, N‐methylformamide, N‐methylpropanamide, N‐ethylacetamide and/or water molecules. The potential energy curves of these systems are therefore obtained, including the equilibrium hydrogen bond distances R(O…H) and the hydrogen‐bonding energies. The function is also applied to calculate the binding energies in models of β‐sheets. The calculation results show that the potential energy curves obtained from the analytic function are in good agreement with those obtained from MP2/6‐31+G** calculations by including the BSSE correction, which demonstrate that the analytic function proposed in this work can be used to predict the hydrogen‐bonding interaction energies in peptides quickly and accurately. © 2009 Wiley Periodicals, Inc. J Comput Chem, 2009     

Evaluation of the individual hydrogen bonding energies in N-methylacetamide chains

The individual hydrogen bonding energies in N-methylacetamide chains were evaluated at the MP2/6-31+G** level including BSSE correction and at the B3LYP/6-311++G(3df,2pd) level including BSSE and van der Waals correction. The calculation results indicate that compared with MP2 results, B3LYP calculations without van der Waals correction underestimate the individual hydrogen bonding energies about 5.4 kJ mol^?1 for both the terminal and central hydrogen bonds, whereas B3LYP calculations with van der Waals correction produce almost the same individual hydrogen bonding energies as MP2 does for those terminal hydrogen bonds, but still underestimate the individual hydrogen bonding energies about 2.5 kJ mol^?1 for the hydrogen bonds near the center. Our calculation results show that the individual hydrogen bonding energy becomes more negative (more attractive) as the chain becomes longer and that the hydrogen bonds close to the interior of the chain are stronger than those near the ends. The weakest individual hydrogen bonding energy is about ?29.0 kJ mol^?1 found in the dimer, whereas with the growth of the N-methylacetamide chain the individual hydrogen bonding energy was estimated to be as large as ?62.5 kJ mol^?1 found in the N-methylacetamide decamer, showing that there is a significant hydrogen bond cooperative effect in N-methylacetamide chains. The natural bond orbital analysis indicates that a stronger hydrogen bond corresponds to a larger positive charge for the H atom and a larger negative charge for the O atom in the N-H?O=C bond, corresponds to a stronger second-order stabilization energy between the oxygen lone pair and the N-H antibonding orbital, and corresponds to more charge transfer between the hydrogen bonded donor and acceptor molecules.     

Theoretical Study of the Interplay between Lithium Bond and Hydrogen Bond in Complexes Involved with HLi and HCN

The lithium‐ and hydrogen‐bonded complex of HLi? NCH? NCH is studied with ab initio calculations. The optimized structure, vibrational frequencies, and binding energy are calculated at the MP2 level with 6‐311++G(2d,2p) basis set. The interplay between lithium bonding and hydrogen bonding in the complex is investigated with these properties. The effect of lithium bonding on the properties of hydrogen bonding is larger than that of hydrogen bonding on the properties of lithium bonding. In the trimer, the binding energies are increased by about 19 % and 61 % for the lithium and hydrogen bonds, respectively. A big cooperative energy (?5.50 kcal mol^?1) is observed in the complex. Both the charge transfer and induction effect due to the electrostatic interaction are responsible for the cooperativity in the trimer. The effect of HCN chain length on the lithium bonding has been considered. The natural bond orbital and atoms in molecules analyses indicate that the electrostatic force plays a main role in the lithium bonding. A many‐body interaction analysis has also been performed for HLi? (NCH)_N (N=2–5) systems.     

BSSE‐corrected geometry and harmonic and anharmonic vibrational frequencies of formamide–water and formamide–formamide dimers

The basis set superposition error (BSSE) influence in the geometry structure, interaction energies, and intermolecular harmonic and anharmonic vibrational frequencies of cyclic formamide–formamide and formamide–water dimers have been studied using different basis sets (6‐31G, 6‐31G**, 6‐31++G**, D95V, D95V**, and D95V++**). The a posteriori “counterpoise” (CP) correction scheme has been compared with the a priori “chemical Hamiltonian approach” (CHA) both at the Hartree–Fock (HF) and second‐order Møller–Plesset many‐body perturbation (MP2) levels of theory. The effect of BSSE on geometrical parameters, interaction energies, and intermolecular harmonic vibrational frequencies are discussed and compared with the existing experimental data. As expected, the BSSE‐free CP and CHA interaction energies usually show less deep minima than those obtained from the uncorrected methods at both the HF and MP2 levels. Focusing on the correlated level, the amount of BSSE in the intermolecular interaction energies is much larger than that at the HF level, and this effect is also conserved in the values of the force constants and harmonic vibrational frequencies. All these results clearly indicate the importance of the proper BSSE‐free correlation treatment with the well‐defined basis functions. At the same time, the results show a good agreement between the a priori CHA and a posteriori CP correction scheme; this agreement is remarkable in the case of large and well‐balanced basis sets. The anharmonic frequency correction values also show an important BSSE dependence, especially for hydrogen bond stretching and for low frequencies belonging to the intermolecular normal modes. © 2005 Wiley Periodicals, Inc. Int J Quantum Chem, 2005     

Cooperative influence of water binding to peptides by N?H···OH2 and CO···HOH hydrogen bonds: Study by Ab Initio calculations

In this article, the geometry structures of hydrogen bond chains of formamide and N‐methylacetamide and their hydrogen‐bonded complexes with water were optimized at the MP2/6‐31G* level. Then, we performed Møller–Plesset perturbation method with 6‐311++g**, aug‐cc‐pvtz basis sets to study the cooperative influence to the total hydrogen bond energy by the N? H ··· OH₂ and C?O ··· HOH hydrogen bonds. On the basis of our results, we found that the cooperativity of the hydrogen‐bonded complexes become weaker as N? H ··· OH₂ and C?O ··· HOH hydrogen bonds replacing N? H ··· O?C hydrogen bonds in protein and peptide. It means that the N? H and C?O bonds in peptide prefer to form N? H ··· O?C hydrogen bond rather than to form C?O ··· HOH and N? H ··· OH₂. It is significant for understanding the structures and properties of the helical or sheet structures of protein and peptide in biological systems. © 2011 Wiley Periodicals, Inc. Int J Quantum Chem, 2011     

Rapid Evaluation of Individual Hydrogen Bonding Energies in Linear Water Chains

A model is proposed to rapidly evaluate the individual hydrogen bonding energies in linear water chains. We regarded the two O--H bonds of a water molecule as two dipoles. The magnitude of the O--H bond dipole mo- ment can be varied due to the other water molecules＇ presence. An analytic potential energy function, which explicitly contains the permanent dipole-dipole interactions, the polarization interactions, the van der Waals interactions and the covalent interactions, was therefore established. The individual hydrogen bonding energies in a series of linear water chains were evaluated via the analytic potential energy function and compared with those obtained from the CP-corrected MP2/aug-cc-pVTZ calculations. The results show that the analytic potential energy function not only can produce the individual hydrogen bonding energies as accurately as the CP-corrected MP2/aug-cc-pVTZ method, but is very efficient as well, demonstrating the model proposed is reasonable and useful. Based on the individual hy- drogen bonding energies obtained, the hydrogen bonding cooperativity in the linear water chains was explored and the natures of the hydrogen bonding in these water chains were discussed.     

Complete basis set limit of Ab initio binding energies and geometrical parameters for various typical types of complexes

Using basis‐set extrapolation schemes for a given data set, we evaluated the binding energies and geometries at the complete basis set (CBS) limit at the levels of the second order Møller–Plesset perturbation theory (MP2) and the coupled cluster theory with singles, doubles, and perturbative triples excitations [CCSD(T)]. The systems include the hydrogen bonding (water dimer), aromatic interaction (benzene dimer), π–H interaction (benzene–water), cation–water, anion–water, π–cation interaction (cation–benzene), and π–anion interaction (anion–triazine). One extrapolation method is to exploit both BSSE‐corrected and BSSE‐uncorrected binding energies for the aug‐cc‐pVNZ (N = 2, 3, 4, …) basis set in consideration that both binding energies give the same CBS limit (CBS^B). Another CBS limit (CBS^C) is to use the commonly known extrapolation approach to exploit that the electron correlation energy is proportional to N^?3. Since both methods are complementary, they are useful for estimating the errors and trend of the asymptotic values. There is no significant difference between both methods. Overall, the values of CBS^C are found to be robust because of their consistency. However, for small N (in particular, for N = 2, 3), CBS is found to be slightly better for water–water interactions and cation–water and cation–benzene interactions, whereas CBS is found to be more reliable for bezene–water and anion–water interactions. We also note that the MP2 CBS limit value based on N = 2 and 3 combined with the difference between CCSD(T) and MP2 at N = 2 would be exploited to obtain a CCSD(T)/CBS value for aromatic–aromatic interactions and anion–π interactions, but not for cationic complexes. © 2007 Wiley Periodicals, Inc. J Comput Chem, 2008     

Cooperativity between the Dihydrogen Bond and the N⋅⋅⋅HC Hydrogen Bond in LiH–(HCN)n Complexes

The cooperativity between the dihydrogen bond and the N???HC hydrogen bond in LiH–(HCN)_n (n=2 and 3) complexes is investigated at the MP2 level of theory. The bond lengths, dipole moments, and energies are analyzed. It is demonstrated that synergetic effects are present in the complexes. The cooperativity contribution of the dihydrogen bond is smaller than that of the N???HC hydrogen bond. The three‐body energy in systems involving different types of hydrogen bonds is larger than that in the same hydrogen‐bonded systems. NBO analyses indicate that orbital interaction, charge transfer, and bond polarization are mainly responsible for the cooperativity between the two types of hydrogen bonds.     

Density functional theory study on hydrogen‐bonded complexes of adenine with polyformamide molecules

The structures of hydrogen‐bonded complexes A–F_n (n = 2–7) of adenine with polyformamide molecules have been fully optimized at B3LYP/6‐31G(d) basis set level. All the formamide molecules prefer to be N? H proton donor rather than C? H proton donor and are favorably bound to the five‐numbered moiety of adenine. A displacement of formamide molecules to one side of adenine mean plane has happened with an increasing number of formamide molecules. An obvious effect of hydrogen‐bonding cooperativity can be seen during the complex process. The most interesting geometrical change of adenine upon the complex is the shortening of the bond C4? N6 resulting from the strengthening of the conjugation between the π system of the adenine ring and the lone pair of the nitrogen atom. An existence of weak N? H···π bonding interaction between the π system of adenine and N? H bond of F7 is found and further conformed by an natural bond orbital analysis specially carried out on A–F₇. © 2008 Wiley Periodicals, Inc. Int J Quantum Chem, 2008     

Cooperativity between the Halogen Bond and the Hydrogen Bond in H3N⋅⋅⋅XY⋅⋅⋅HF Complexes (X,Y=F,Cl, Br)

Ab initio calculations are used to provide information on H₃N???XY???HF triads (X, Y=F, Cl, Br) each having a halogen bond and a hydrogen bond. The investigated triads include H₃N???Br₂‐HF, H₃N???Cl₂???HF, H₃N???BrCI???HF, H₃N???BrF???HF, and H₃N???ClF???HF. To understand the properties of the systems better, the corresponding dyads are also investigated. Molecular geometries, binding energies, and infrared spectra of monomers, dyads, and triads are studied at the MP2 level of theory with the 6‐311++G(d,p) basis set. Because the primary aim of this study is to examine cooperative effects, particular attention is given to parameters such as cooperative energies, many‐body interaction energies, and cooperativity factors. The cooperative energy ranges from ?1.45 to ?4.64 kcal mol^?1, the three‐body interaction energy from ?2.17 to ?6.71 kcal mol^?1, and the cooperativity factor from 1.27 to 4.35. These results indicate significant cooperativity between the halogen and hydrogen bonds in these complexes. This cooperativity is much greater than that between hydrogen bonds. The effect of a halogen bond on a hydrogen bond is more pronounced than that of a hydrogen bond on a halogen bond.     

Rapid evaluation of the binding energies in hydrogen-bonded amide-thymine and amide-uracil dimers in gas phase

The binding energies and the equilibrium hydrogen bond distances as well as the potential energy curves of 48 hydrogen‐bonded amide–thymine and amide–uracil dimers are evaluated from the analytic potential energy function established in our lab recently. The calculation results show that the potential energy curves obtained from the analytic potential energy function are in good agreement with those obtained from MP2/6‐311+G** calculations by including the BSSE correction. For all the 48 dimers, the analytic potential energy function yields the binding energies of the MP2/6‐311+G** with BSSE correction within the error limits of 0.50 kcal/mol for 46 dimers, only two differences are larger than 0.50 kcal/mol and the largest one is only 0.60 kcal/mol. The analytic potential energy function produces the equilibrium hydrogen bond distances of the MP2/6‐311+G** with BSSE correction within the error limits of 0.050 Å for all the 48 dimers. The analytic potential energy function is further applied to four more complicated hydrogen‐bonded amide–base systems involving amino acid side chain and β‐sheet. The values of the binding energies and equilibrium hydrogen bond distances obtained from the analytic potential energy function are also in good agreement with those obtained from MP2 calculations with the BSSE correction. These results demonstrate that the analytic potential energy function can be used to evaluate the binding energies in hydrogen‐bonded amide–base dimers quickly and accurately. © 2010 Wiley Periodicals, Inc. J Comput Chem, 2011     

Theoretical Study on the Hydrogen Bonding Interactions in Complexes of 5‐Hydroxytryptamine with Water

The energies, geometries and harmonic vibrational frequencies of 1:1 5‐hydroxytryptamine‐water (5‐HT‐H₂O) complexes are studied at the MP2/6‐311++G(d,p) level. Natural bond orbital (NBO), quantum theory of atoms in molecules (QTAIM) analyses and the localized molecular orbital energy decomposition analysis (LMO‐EDA) were performed to explore the nature of the hydrogen‐bonding interactions in these complexes. Various types of hydrogen bonds (H‐bonds) are formed in these 5‐HT‐H₂O complexes. The intermolecular C4H5^5‐HT···O^w H‐bond in HTW3 is strengthened due to the cooperativity, whereas no such cooperativity is found in the other 5‐HT‐H₂O complexes. H‐bond in which nitrogen atom of amino in 5‐HT acted as proton donors was stronger than other H‐bonds. Our researches show that the hydrogen bonding interaction plays a vital role on the relative stabilities of 5‐HT‐H₂O complexes.     

Directional hydrogen bonding in the MM3 force field: II

Extensive calculations on hydrogen bonded systems were carried out using the improved MM3 directional hydrogen bond potential. The resulting total function was reoptimized. Comparisons of the hydrogen bonding potential function from ab initio calculations (MP2/6-31G**); the original MM3(89); and the reoptimized MM3 force field MM3(96), for a variety of C, N, O, and Cl systems including the formamide dimer and formamide–water complex, are described herein. Hydrogen bonding is shown to be a far more complicated and ubiquitous phenomenon than is generally recognized. © 1998 John Wiley & Sons, Inc. J Comput Chem 19: 1001–1016, 1998     

Hydrogen bonding interaction in sarcosine–water complex using ab initio and DFT method

The hydrogen bonding interaction in the Sarcosine (N‐methylglycine)–water complex is studied using ab initio, MP2, and density functional theory (DFT/B3LYP). For this complex, binding energies, dipole–dipole interactions, chemical hardness, and chemical potential have been calculated. Three different basis sets, viz. 6‐311+G, 6‐311++G, and 6‐311++G*, have been used to optimize the geometries by all three methods. The basis set superposition errors are also calculated, and the corrected binding energies are reported for this complex. © 2004 Wiley Periodicals, Inc. Int J Quantum Chem, 2005     

Preparing Gold(I) for Interactions with Proton Donors: The Elusive [Au]⋅⋅⋅HO Hydrogen Bond

MP2 and DFT calculations with correlation consistent basis sets indicate that isolated linear anionic dialkylgold(I) complexes form moderately strong (ca. 10 kcal mol^?1) Au???H hydrogen bonds with single H₂O molecules as donors in the absence of sterically demanding substituents. Relativistic effects are critically important in the attraction. Such bonds are significantly weaker in neutral, strong σ‐donor N‐heterocyclic carbene (NHC) complexes (ca. 5 kcal mol^?1). The overall association (>11 kcal mol^?1), however, is strengthened by co‐operative, synergistic classical hydrogen bonding when the NHC ligands bear NH units. Further manipulation of the interaction by ligands positioned trans to the carbene, is possible.     

Conformational Stability of Bovine Serum Albumin in Aqueous Amides: A Further Insight into the Mechanism of Urea Acting on the Protein

The binding distances of fluorescein to bovine serum albumin (BSA) in formamide‐water and N,N‐dimethyl‐ formamide‐water mixtures were determined by fluorescence quenching method and compared with the values in urea‐water mixtures in our previous work. The results, together with the analysis of fluorescence spectra, were utilized to probe the conformational stability of protein in aqueous amides, providing a further insight into the mechanism of urea acting on protein. The spectral properties of BSA showed significant difference in the aqueous solutions of the three kinds of amide and indicated that both NH₂ group and C=O group could form hydrogen bond with the protein, serving as donor and acceptor, respectively. However, the results revealed that the multiple hydrogen bonds of NH₂ group with back bond and hydrophilic side chains of the protein played a key role in the nonspecific urea‐mediated network of intramolecular interaction due to its higher hydrogen bonding capability compared to C=O group.     

Comparative study on formamide–water complex

The hydrogen bonding of 1:1 complexes formed between formamide and water molecule have been investigated systematically using Hartree–Fock (HF), hybrid density functional theory (B3LYP), and post‐Hartree–Fock (MP2 and CCSD(T)) methods with range of basis sets 6‐31G(d), cc‐pVXZ (X = D, T, Q) and aug‐cc‐pVYZ (Y = D, T). Three stable structures are considered on the potential energy surface of formamide and water system. The optimized geometric parameters and interaction energies for various isomers at different levels are estimated. The IR frequencies, intensities, and frequency shifts are reported. This study shows that B3LYP/aug‐cc‐pVDZ method gives better performance for formamide‐water complexes. © 2009 Wiley Periodicals, Inc. Int J Quantum Chem, 2010.     

A polymeric zinc thio­sulfate complex containing anionic and cationic chains based on tetra­hedral and octa­hedral zinc sites

catena‐Poly[[[tetra­aqua­zinc(II)]‐μ‐4,4′‐bipyridine‐κ²N:N′] [[μ‐thio­sulfato‐κ²O:S‐bis­[(thio­sulfato‐κS)zinc(II)]]‐di‐μ‐4,4′‐pyridine‐κ⁴N:N′] dihydrate], {[Zn(C₁₀H₈N₂)(H₂O)₄][Zn₂(S₂O₃)₃(C₁₀H₈N₂)₂]·2H₂O}_n, is a polymeric zinc complex built up from thio­sulfate‐containing anionic chains, where the Zn atom is tetra­hedrally coordinated, and aqua‐containing cationic chains incorporating octa­hedrally coordinated Zn. In each type of chain, the 4,4′‐bipyridine units act as spacers, and the chains run along three non‐inter­secting almost orthogonal directions in space. The profusion of hydrogen‐bond donors (all the H atoms of the water mol­ecules) and acceptors (the thio­sulfate O and S atoms) generates a very complex hydrogen‐bonding scheme.