Quantum chemical investigation of hydrogen-bond strengths and partition into donor and acceptor contributions

We present a simple increment model for use in the rapid scoring of hydrogen bond strengths employing 15 chemically diverse donor and 28 acceptor terms. The increments cover a large variety of hydrogen bond donor and acceptor groups and are more specific than SYBYL atom types. The increments have been fitted to quantum chemical ab initio interaction energies of 81 small hydrogen‐bonded complexes determined at the level of second‐order Møller‐Plesset perturbation theory (MP2). The complexes have been chosen such as to represent the most important types of donor‐acceptor pairs found in biological systems. Sulphur is found to be a strong hydrogen bond acceptor while its donor capacities are weak. By taking CH acidic H donors into account, a linear correlation between MP2 energies and the increment model with a coefficient of correlation of r² = 0.994 has been accomplished. The transferability of the fitted parameters has been assessed on a second set of complexes including larger molecules of biological relevance. Very good agreement has been achieved for noncyclic hydrogen bonds. Cooperative effects are not accounted for by the current increment model. For this reason, binding energies of strong cyclic hydrogen bonds, as e.g. present in DNA base pairs, are underestimated by about 30–40%. © 2007 Wiley Periodicals, Inc. J Comput Chem, 2007     

Interplay between hydrogen bond formation and multicenter pi-electron delocalization: intermolecular hydrogen bonds

The interplay between aromatic electron delocalization and intermolecular hydrogen bonding is thoroughly investigated using multicenter delocalization analysis. The effect on the hydrogen bond strength of aromatic electron delocalization within the acceptor and donor molecules is determined by means of the interaction energies between monomers, calculated at the B3LYP/6-311++G(d,p) level of theory. This magnitude is compared to variations of multicenter electron delocalization indices and covalent hydrogen bond indices, which are shown to correlate perfectly with the relative values of the interaction energies for the different complexes studied. The multicenter electron delocalization indices and covalent bond indices have been computed using the quantum theory of atoms in molecules approach. All the hydrogen bonds are formed with oxygen as the acceptor atom; however, the atom bonded to the donor hydrogen has been either oxygen or nitrogen. The water-water complex is taken as reference, where the donor and acceptor molecular environments are modified by substituting the hydrogens and the hydroxyl group by phenol, furan, and pyrrole aromatic rings. The results here shown match perfectly with the qualitative expectations derived from the resonance model.     

Toward assessing the position-dependent contributions of backbone hydrogen bonding to beta-sheet folding thermodynamics employing amide-to-ester perturbations

An amide-to-ester backbone substitution in a protein is accomplished by replacing an alpha-amino acid residue with the corresponding alpha-hydroxy acid, preserving stereochemistry, and conformation of the backbone and the structure of the side chain. This substitution replaces the amide NH (a hydrogen bond donor) with an ester O (which is not a hydrogen bond donor) and the amide carbonyl (a strong hydrogen bond acceptor) with an ester carbonyl (a weaker hydrogen bond acceptor), thus perturbing folding energetics. Amide-to-ester perturbations were used to evaluate the thermodynamic contribution of each hydrogen bond in the PIN WW domain, a three-stranded beta-sheet protein. Our results reveal that removing a hydrogen bond donor destabilizes the native state more than weakening a hydrogen bond acceptor and that the degree of destabilization is strongly dependent on the location of the amide bond replaced. Hydrogen bonds near turns or at the ends of beta-strands are less influential than hydrogen bonds that are protected within a hydrophobic core. Beta-sheet destabilization caused by an amide-to-ester substitution cannot be directly related to hydrogen bond strength because of differences in the solvation and electrostatic interactions of amides and esters. We propose corrections for these differences to obtain approximate hydrogen bond strengths from destabilization energies. These corrections, however, do not alter the trends noted above, indicating that the destabilization energy of an amide-to-ester mutation is a good first-order approximation of the free energy of formation of a backbone amide hydrogen bond.     

Substituent effects in halogen bonding complexes between aromatic donors and acceptors: a comprehensive ab initio study

Substituent effects in halogen bonding complexes involving aromatic rings are investigated. We have analyzed how the interaction energy (the RI-MP2/aug-cc-pVDZ level of theory) is affected by the substitution in both halogen bond donor and acceptor aromatic moieties. In addition, we have used two different aromatic electron donor molecules pyridine and cyanobenzene, which allow us to study the effect of having the electron donor nitrogen atom forming part of the ring or outside the ring (-CN). Interestingly, the effect of the substituents on the interaction energies is similar in both cases. We have obtained the Hammett's plots for four combinations of aromatic donors and acceptors and in all cases we have obtained good regression plots (interaction energies vs. Hammett's σ parameter). We have also studied and compared bifurcated halogen bonds using both possible combinations, that is two donors and one acceptor and vice versa. In addition, we have analyzed the effect of the solvent on the interaction energies using COSMO. Finally, we have used Bader's theory of "atoms-in-molecules" to demonstrate that the electron density computed at the bond critical point that emerges upon complexation can be used as a measure of bond order in this noncovalent interaction.     

C-H⋯O, O-H⋯C, and C-H⋯C interactions in complexes of carbocations and carboanions

Molecular complexes formed by different forms of carbocations (carbenium ions) and carboanions with water, acetylene, and methane molecules have been calculated by the MP2/6-311++G(2df,2pd) method. In complexes with water where the carbon atom of the carbocation (carboanion) acts as the proton donor (acceptor), the energies of the C-H?O and O-H?C hydrogen bonds turn out to be approximately the same being 13–20 kcal/mol for carbocation (carboanion) species differing in the valence state of the carbon atom. Two types of C-H?C interactions have been revealed depending on the charge at the bridging hydrogen atom, which is determined by the hybridization of the donor carbon atom. The C-H?C interaction energy in molecular complexes with the positively charged hydrogen atom (carboanion complexes with acetylene) is an order of magnitude higher than in the complexes where the bridging hydrogen atom has an excess of electron density (carbocation complexes with methane). In all the complexes under consideration, the covalent C-H bond involved in interaction is elongated, and the negative charge is transferred from the acceptor to the donor.     

Interplay between hydrogen-bond formation and multicenter pi-electron delocalization: intramolecular hydrogen bonds

The specific case of intramolecular hydrogen bonds assisted by pi-electron delocalization is thoroughly investigated using multicenter delocalization analysis. The effect of the pi-electron delocalization on the intramolecular hydrogen-bond strength is determined by means of the relative molecular energies of "open" and "closed" structures, calculated at the B3LYP/6-311++G(d,p) level of theory. These relative energies are compared to variations in the multicenter electron delocalization indices and covalent hydrogen-bond indices, which are shown to correlate very well with the relative strength of the intramolecular hydrogen bonds studied. The multicenter electron delocalization indices and covalent bond indices have been computed using the quantum theory of atoms in molecules approach. The hydrogen bonds are formed with oxygen, nitrogen, or sulfur as acceptor atom, which are also the atoms considered to be bonded to the donor hydrogen. Malonaldehyde is taken as reference; the substitution of oxygen by other atoms at the acceptor and donor positions and the effect of the aromaticity have been studied. The results shown here match perfectly with the qualitative expectations derived from the resonance models. In addition, they provide a quantitative picture of the role played by the pi-electron delocalization on the relative strength of intramolecular hydrogen bonds.     

Time‐dependent Density Functional Theory Study on the Hydrogen‐bonded Dimers Formed by Gauche‐1PA and Trans‐1PA

Three hydrogen bonding complexes of the gauche‐1PA dimer (GG), trans‐1PA dimer (TT) and mixed dimer (GT) have been calculated for the geometry conformations and excited‐state energies. The electron distribution at the site of C‐O of H‐donor moiety in HOMO transfers to the direction of O‐H of H‐acceptor moiety in LUMO. The hydrogen bond between two 1PAs is the bridge of the intermolecular charge transfer. By the Zhao and Han's excited‐state hydrogen bonding dynamics rule, the first excited‐state hydrogen bonding change has been discussed without optimizing the excited‐state geometry conformations. According to the distinct difference between GT and GG (TT), we concluded that two gauche‐1PA monomers of one dimer are transformed at the same time to two trans‐1PA monomers.     

Frequency analysis of amide-linked rotaxane mimetics

A vibrational analysis of 2-fold hydrogen bonds between an isophthalic amide donor and different acceptors is presented. These systems can be considered as mimetics for the hydrogen-binding situation of numerous supramolecular compounds such as rotaxanes, catenanes, knotanes, and anion receptors. We calculated pronounced red-shifts up to 65 cm(-1) for the stretching modes of the acceptor carbonyl as well as for the donor NH2 groups, whereas we observe a blue shift for the NH2 bending modes and an additional weak hydrogen bond between the acceptor and the middle C-H group of the donor. The red and blue shifts observed for different modes in various complexes have been correlated with the binding energy of the complexes, independently. In comparison with comparable single hydrogen bonds, we find for the 2-fold hydrogen bonds smaller red shifts for the N-H stretch modes of the donor but larger red shifts for the C=O stretch mode of the acceptor. Furthermore, our results indicate that the pronounced blue shift of the C-H stretch mode is basically caused by the fact that the acceptor is fixed directly above this group due to the 2-fold hydrogen bond.     

Influence of substitution, hybridization, and solvent on the properties of C-HO single-electron hydrogen bond in CH3-H2O complex

The effect of substitution, hybridization, and solvent on the properties of the C...HO single-electron hydrogen bond has been investigated with quantum chemical calculations. Methyl radical, ethyl radical, and vinyl radical are used as the proton acceptors and are paired with water, methanol, HOCl, and vinyl alcohol. Halogenation (Cl) of the proton donor strengthens this type of hydrogen bond. The methyl group in the proton donor and proton acceptor plays a different role in the formation of the C...HO single-electron hydrogen bond. The former is electron-withdrawing, and the latter is electron-donating, both making a constructive contribution to the enhancement of the interaction. The contribution of the methyl group in the proton acceptor is larger than that in the proton donor. The increase of acidity of the proton is helpful to form a single-electron hydrogen bond. As the proton acceptor varies from the methyl radical to the vinyl radical, the interaction strength also increases. The solvent has an enhancing influence on the strength of the C...HO single-electron hydrogen bond. These factors affect the C...HO single-electron hydrogen bond in a similar way that they do other types of hydrogen bonds.     

Weak Intermolecular Hydrogen Bonds with Fluorine: Detection and Implications for Enzymatic/Chemical Reactions,Chemical Properties,and Ligand/Protein Fluorine NMR Screening

It is known that strong hydrogen‐bonding interactions play an important role in many chemical and biological systems. However, weak or very weak hydrogen bonds, which are often difficult to detect and characterize, may also be relevant in many recognition and reaction processes. Fluorine serving as a hydrogen‐bond acceptor has been the subject of many controversial discussions and there are different opinions about it. It now appears that there is compelling experimental evidence for the involvement of fluorine in weak intramolecular or intermolecular hydrogen bonds. Using established NMR methods, we have previously characterized and measured the strengths of intermolecular hydrogen‐bond complexes involving the fluorine moieties CH₂F, CHF₂, and CF₃, and have compared them with the well‐known hydrogen‐bond complex formed between acetophenone and the strong hydrogen‐bond donor p‐fluorophenol. We now report evidence for the formation of hydrogen bonds involving fluorine with significantly weaker donors, namely 5‐fluoroindole and water. A simple NMR method is proposed for the simultaneous measurement of the strengths of hydrogen bonds between an acceptor and a donor or water. Important implications of these results for enzymatic/chemical reactions involving fluorine, for chemical and physical properties, and for ligand/protein ¹⁹F NMR screening are analyzed through experiments and theoretical simulations.     

四氰基乙烯—四甲基乙烯体系光诱导电子转移的溶剂效应及电荷分离激发态研究

用从头算方法,在HF/6-31 G^**和CASSCF（8,8）/6-31G^*基组水平上对四氰基乙烯与四甲基乙烯间电子转移的溶剂效应及电荷分离激发态进行了理论计算与研究。通过对给、受体各种几何构型的优化,计算了孤立给、受体之间的电荷分离反应热。在假定碰撞络合物形成过程中给、受体内部结构不发生变化的前提下,通过优化给、受体中心间距的方法,找出了络合物的稳定构型。计算了水溶剂及二氯甲烷溶剂中两种稳定构型络合物的电荷分离激发态,计算结果表明光激发可以直接导致体系的电荷分离。     

Estimates of the energy of intramolecular hydrogen bonds

A method for the estimation of the energy of intramolecular hydrogen bonds in conjugated systems existing in a variety of conformations is presented. The method is applied to determine the intramolecular hydrogen bond energy in 3-aminopropenal and 3-aminopropenthial. According to the proposed estimation scheme, the intramolecular H-bond energies are found to be of the order of 5-7 kcal/mol. These results are compared with those obtained by using other estimation schemes as well as with the recent results by other authors. Also, the H-bond energies in dimers and trimers of the two molecules are calculated and compared with the corresponding data for internally hydrogen-bonded monomers. This comparison shows that the bond equalization effect is primarily due to proton donor-proton acceptor proximity. In comparison with intermolecular hydrogen bonds, the rigidity of the chelate skeleton enhances this proximity effect. The same effect can be seen in systems with intermolecular hydrogen bonds, although its magnitude is diminished because of the absence of additional forces which pull the proton donor and proton acceptor groups toward each other. No specific resonance-assisted origin of the intramolecular hydrogen bond energy seems to be needed to elucidate the energetics of these bonds.     

Fluorescence solvatochromism in lumichrome and excited-state tautomerization: a combined experimental and DFT study

Fluorescence solvatochromism of lumichrome (LC) was studied by steady-state and time-resolved fluorescence spectroscopy. The excited-state properties of LC do not show any correlation with solvent polarity, however, reasonably good correlation with solvent E(T)(30) parameter was observed. A quantitative estimation of contribution from different solvatochromic parameters, like solvent polarizability (π*), hydrogen bond donor (α), and hydrogen bond acceptor (β) ability of the solvent, was made using linear free energy relationship on the basis of Kamlet-Taft equation. The analysis reveals that hydrogen bond donating ability (acidity) of the solvent is the most important parameter that characterizes the excited-state behavior of lumichrome. Quantum mechanical calculations using density functional theory (DFT) were done to study the most stable structure and excited-state tautomerization process of LC toward the formation of isoalloxazines. Charge localization in the excited state and formation of hydrogen-bonded cluster through solvent hydrogen bond donation on the N10 atom of alloxazine moiety were predicted to be the key step toward this water-catalyzed tautomerization process.     

Multilinear regression and comparative molecular field analysis (CoMFA) of azo dye-fiber affinities. 2. Inclusion of solution-phase molecular orbital descriptors

For a data set with 30 direct azo dyes taken from literature, quantitative structure-activity relationship (QSAR) analyses have been performed to model the affinity of the dye molecules for the cellulose fiber. The electronic structure of the compounds was characterized using quantum chemical gas-phase (AM1) and continuum-solvation molecular orbital parameters. As regards the solution phase, COSMO appears to be better suited than SM2 in quantifying relative trends of the aqueous solvation energy. For the dye-fiber affinity, the leave-one-out prediction capability of multilinear regression equations is superior to CoMFA, with predictive squared correlation coefficients ranging from 0.63 (pure CoMFA) to 0.89. At the same time, solution-phase CoMFA is superior to previously derived AM1-based CoMFA models. As a general trend, the dye-fiber affinity increases with increasing electron donor capacity that corresponds to an increasing hydrogen bond acceptor strength of the azo dyes. The discussion includes the consideration of structural features that are likely to be involved in dye-fiber and dye-dye hydrogen bonding interactions, and possible links between CoMFA electrostatic results and the atomic charge distribution of the compounds.     

Redox‐Controlled Hydrogen Bonding: Turning a Superbase into a Strong Hydrogen‐Bond Donor

Herein the synthesis, structures and properties of hydrogen‐bonded aggregates involving redox‐active guanidine superbases are reported. Reversible hydrogen bonding is switched on by oxidation of the hydrogen‐donor unit, and leads to formation of aggregates in which the hydrogen‐bond donor unit is sandwiched by two hydrogen‐bond acceptor units. Further oxidation (of the acceptor units) leads again to deaggregation. Aggregate formation is associated with a distinct color change, and the electronic situation could be described as a frozen stage on the way to hydrogen transfer. A further increase in the basicity of the hydrogen‐bond acceptor leads to deprotonation reactions.     

Synthesis of a soluble ureido-naphthyridine oligomer that self-associates via eight contiguous hydrogen bonds

[structure; see text] An iterative synthetic route to organic-soluble ureido-naphthyridine oligomers has been developed. Use of this protocol allowed synthesis of a short ureido-naphthyridine oligomer, which presents a self-complementary DDAADDAA hydrogen bonding array (D = hydrogen bond donor, A = hydrogen bond acceptor). Strong self-association via eight hydrogen bonds was observed in organic solution.     

Nature of the Hydrogen Bond Enhanced Halogen Bond

The factors responsible for the enhancement of the halogen bond by an adjacent hydrogen bond have been quantitatively explored by means of state-of-the-art computational methods. It is found that the strength of a halogen bond is enhanced by ca. 3 kcal/mol when the halogen donor simultaneously operates as a halogen bond donor and a hydrogen bond acceptor. This enhancement is the result of both stronger electrostatic and orbital interactions between the XB donor and the XB acceptor, which indicates a significant degree of covalency in these halogen bonds. In addition, the halogen bond strength can be easily tuned by modifying the electron density of the aryl group of the XB donor as well as the acidity of the hydrogen atoms responsible for the hydrogen bond.     

Hydrogen bonds not only provide a structural scaffold to assemble donor and acceptor moieties of zinc porphyrin-quinone dyads but also control the photoinduced electron transfer to afford the long-lived charge-separated states

A series of zinc porphyrin-quinone linked dyads [ZnP-CONH-Q, ZnP-NHCO-Q, and ZnP-n-Q (n = 3, 6, 10)] were designed and synthesized to investigate the effects of hydrogen bonds which can not only provide a structural scaffold to assemble donor and acceptor moieties but also control the photoinduced electron-transfer process. In the case of ZnP-CONH-Q and ZnP-NHCO-Q, the hydrogen bond between the N-H proton and the carbonyl oxygen of Q results in the change in the reduction potential of Q. The strong hydrogen bond between the N-H proton and the carbonyl oxygen of Q*- in ZnP-CONH-Q*-,ZnP-NHCO-Q*-, and ZnP-n-Q*- (n = 3, 6, 10) generated by the chemical reduction has been confirmed by the ESR spectra, which exhibit hyperfine coupling constants in agreement those predicted by the density functional calculations. In the case of ZnP-n-Q (n = 3, 6, 10), on the other hand, the hydrogen bond between two amide groups provides a structural scaffold to assemble the donor (ZnP) and the acceptor (Q) moiety together with the hydrogen bond between the N-H proton and the carbonyl oxygen of Q, leading to attainment of the charge-separated state with a long lifetime up to a microsecond.     

Regulating function of methyl group in strength of CH...O hydrogen bond: a high-level ab initio study

An ab initio computational study of the regulating function of the methyl group in the strength of the CH...O hydrogen bond (HB) with XCC-H (X = H, CH3, F) as a HB donor and HOY (Y = H, CH3, Cl) as a HB acceptor has been carried out at the MP2/aug-cc-pVDZ and MP2/aug-cc-pVTZ levels. The bond lengths, interaction energies, and stretching frequencies are compared in the gas phase. The results indicate that the methyl substitution of the proton acceptor strengthens the CH...O HB, whereas that of the proton donor weakens the CH...O HB. NBO analysis demonstrates that the methyl group of the proton acceptor is electron-withdrawing and that of the proton donor is electron-donating in the formation of the CH...O HB. The electron-donation of the methyl group in the proton acceptor plays a positive contribution to the formation of the CH...O HB, whereas the electron-withdrawing action of the methyl group in the proton donor plays a negative contribution to the formation of the CH...O HB. The positive contribution of methyl group in the proton acceptor is larger than the negative contribution of methyl group in the proton donor.     

New supramolecular architectures based on hydrogen bonding

Heterocyclic compounds containing two and three adjacent hydrogen bond donor and acceptor sites in all possible arrangements were synthesized (see generalized structures shown below) to study and use their “base-pairing” capabilities. With two adjacent donor and acceptor groups there are three possible arrangements and these form two types of complexes (DA·AD and AA·DD). Three adjacent hydrogen bond donor and acceptor sites can be arranged in six different ways and these form three different complexes (ADA·DAD, AAD·DDA, and AAA·DDD).