Defining the hydrogen bond: An account (IUPAC Technical Report)

The term “hydrogen bond” has been used in the literature for nearly a century now. While its importance has been realized by physicists, chemists, biologists, and material scientists, there has been a continual debate about what this term means. This debate has intensified following some important experimental results, especially in the last decade, which questioned the basis of the traditional view on hydrogen bonding. Most important among them are the direct experimental evidence for a partial covalent nature and the observation of a blue-shift in stretching frequency following X–H···Y hydrogen bond formation (XH being the hydrogen bond donor and Y being the hydrogen bond acceptor). Considering the recent experimental and theoretical advances, we have proposed a new definition of the hydrogen bond, which emphasizes the need for evidence. A list of criteria has been provided, and these can be used as evidence for the hydrogen bond formation. This list is followed by some characteristics that are observed in typical hydrogen-bonding environments.

The term 'Hydrogen Bond' has been used in the literature for nearly a century now. While its importance has been realized by physicists, chemists, biologists and material scientists, there has been a continual debate about what this term means. This debate has intensified following some important experimental results, especially in the last decade, which questioned the basis of the traditional view on hydrogen bonding. Most important among them are the direct experimental evidence for a partial covalent nature and the observation of a blue-shift in stretching frequency following X-H···Y hydrogen bond formation (XH being the hydrogen bond donor and Y being the hydrogen bond acceptor). Considering the recent experimental and theoretical advances, we have proposed a new definition of the hydrogen bond, which emphasizes the need for evidence. A list of criteria has been provided and these can be used as evidence for the hydrogen bond formation. This list is followed by some characteristics that are observed in typical hydrogen bonding environments.

With a view toward a better understanding of changes in the peak position and shape of the first absorption band of water with condensation or temperature, results from electronic structure calculations using high level wavefunction based and time-dependent density functional methods are reported for water pentamers. Excitation energies, oscillator strengths, and redistributions of electron density are determined for the quasitetrahedral water pentamer in its C(2v) equilibrium geometry and for many pentamer configurations sampled from molecular simulation of liquid water. Excitations associated with surface molecules are removed in order to focus on those states associated with the central molecule, which are the most representative of the liquid environment. The effect of hydrogen bonding on the lowest excited state associated with the central molecule is studied by adding acceptor or donor hydrogen bonds to tetramer and trimer substructures of the C(2v) pentamer, and by sampling liquid-like configurations having increasing number of acceptor or donor hydrogen bonds of the central molecule. Our results provide clear evidence that the blueshift of excitation energies upon condensation is essentially determined by acceptor hydrogen bonds, and the magnitudes of these shifts are determined by the number of such, whereas donor hydrogen bonds do not induce significant shifts in excitation energies. This qualitatively different role of donor and acceptor hydrogen bonds is understood in terms of the different roles of the 1b(1) monomer molecular orbitals, which establishes an intimate connection between the valence hole and excitation energy shifts. Since the valence hole of the lowest excitation associated with the central molecule is found to be well localized in all liquid-like hydrogen bonding environments, with an average radius of gyration of ~1.6 Å that is much lower than the nearest neighbor O-O distance, a clear and unambiguous connection between hydrogen bonding environments and excitation energy shifts can be established. Based on these results, it is concluded that peak position of the first absorption band is mainly determined by the relative distribution of single and double acceptor hydrogen bonding environments, whereas the shape of the first absorption band is mainly determined by the relative distribution of acceptor and broken acceptor hydrogen bonding environments. The temperature dependence of the peak position and shape of the first absorption band can be readily understood in terms of changes to these relative populations.

The structure, relative energies, and bonding in morpholine(water) n ( n = 1–4) clusters have been investigated at the Becke, three‐parameter, Lee–Yang–Parr/6–311 + G(3df,2p)//Becke, three‐parameter, Lee–Yang–Parr/6–311 + G(d,p) level of theory. Cooperative effects have been analyzed through the use of structural, energetic, and electron density indexes. Our analysis shows that these effects are crucial to trace the relative stability of the complexes formed. In all cases water molecules prefer to self‐associate forming chains in which each individual molecule behaves as a hydrogen bond (HB) donor and HB acceptor. The chain so formed behaves in turn as HB donor and HB acceptor with respect to morpholine, being the most stable arrangements those in which the NH group of morpholine behaves simultaneously as HB donor and HB acceptor. Higher in energy lie complexes in which the HB acceptor continues to be the NH group, but the HB donor is a CH group, or alternative structures in which the HB acceptor is the ether‐like oxygen of morpholine and the HB donor its NH group. Cooperativity increases with the number of solvent molecules, but there is a clear attenuation effect. Thus, whereas the additive interaction energy on going from dihydrated to trihydrated species increases by a factor of 3, this increase is about half on going from trihydrated to tetrahydrated complexes. Copyright © 2012 John Wiley & Sons, Ltd.

Bolaamphiphiles are well-known naturally occurring structures that can increase the thermal and mechanical stability of the phospholipid membrane by incorporation in a transmembrane manner. Modifications of bolaamphiphiles to introduce particular structural elements such as a conjugated aromatic backbone and lateral side chains in the hydrophobic region lead to bolapolyphiles (BPs). We investigated the ability of BPs to form lyotropic phases in water. The BPs had an identical backbone and side chains, but different headgroup structures, leading to different abilities to act as hydrogen bond donors and acceptors. BPs with hydrophilic headgroups capable of acting as hydrogen bond donors as well as acceptors did not form lyotropic phases and were insoluble in water, independent of whether the polar groups were small or large. The extended lipophilic core structure and the multiple intermolecular hydrogen bonds between the headgroups prevented the formation of well-hydrated lyotropic aggregates. A BP with two large hydrophilic headgroups of several ethylene oxide moieties terminated by methyl groups formed sheet- and vesicle-like aggregates in water. These headgroups act only as hydrogen bond acceptors and cannot form hydrogen bonds in the absence of water. The miscibility of BPs with vesicles of 1,2-dipalmitoyl- sn-glycero-3-phosphocholine (DPPC) in water and the resulting aggregate structures were also investigated. For BPs with headgroups acting as donors and acceptors of hydrogen bonds, macroscopic phase separation occurred in the mixed membranes, and two different membrane domains, a DPPC-rich one containing only little polyphile and a BP-rich one containing varying amounts of lipid, were formed. For headgroups without the ability to act as hydrogen bond donors, small BP aggregates were formed that were homogeneously distributed over the membrane. The lateral organization of BPs in lipid membranes can thus be controlled by the nature of the BP headgroup.

The effects of a hydrogen bond acceptor and hydrogen bond donor on carbon dioxide absorption via natural deep eutectic solvents were studied in this work. Naturally occurring non-toxic deep eutectic solvent constituents were considered; choline chloride, b-alanine, and betaine were selected as hydrogen bond acceptors; lactic acid, malic acid, and fructose were selected as hydrogen bond donors. Experimental gas absorption data were collected via experimental methods that uses gravimetric principles. Carbon dioxide capture data for an isolated hydrogen bond donor and hydrogen bond acceptor, as well as natural deep eutectic solvents, were collected. In addition to experimental data, a theoretical study using Density Functional Theory was carried out to analyze the properties of these fluids from the nanoscopic viewpoint and their relationship with the macroscopic behavior of the system, and its ability for carbon dioxide absorption. The combined experimental and theoretical reported approach work leads to valuable discussions on what is the effect of each hydrogen bond donor or acceptor, as well as how they influence the strength and stability of the carbon dioxide absorption in deep eutectic solvents. Theoretical calculations explained the experimental findings, and combined results showed the superiority of the hydrogen bond acceptor role in the gas absorption process, with deep eutectic solvents. Specifically, the cases in which choline chloride was used as hydrogen bond acceptor showed the highest absorption performance. Furthermore, it was observed that when malic acid was used as a hydrogen bond donor, it led to low carbon dioxide solubility performance in comparison to other studied deep eutectic solvents. The cases in which lactic acid was used as a hydrogen bond donor showed great absorption performance. In light of this work, more targeted, specific, deep eutectic solvents can be designed for effective and alternative carbon dioxide capture and management.

Three neurokinin (NK) antagonist pharmacophore models (Models 1-3) accounting for hydrogen bonding groups in the 'head' and 'tail' of NK receptor ligands have been developed by use of a new procedure for treatment of hydrogen bonds during superimposition. Instead of modelling the hydrogen bond acceptor vector in the strict direction of the lone pair, an angle is allowed between the hydrogen bond acceptor direction and the ideal lone pair direction. This approach adds flexibility to hydrogen bond directions and produces more realistic RMS values. By using this approach, two novel pharmacophore models were derived (Models 2 and 3) and a hydrogen bond acceptor was added to a previously published NK2 pharmacophore model [Poulsen et al., J. Comput.-Aided Mol. Design, 16 (2002) 273] (Model 1). Model 2 as well as Model 3 are described by seven pharmacophore elements: three hydrophobic groups, three hydrogen bond acceptors and a hydrogen bond donor. Model 1 contains the same hydrophobic groups and hydrogen bond donor as Models 2 and 3, but only one hydrogen bond acceptor. The hydrogen bond acceptors and donor are represented as vectors. Two of the hydrophobic groups are always aromatic rings whereas the other hydrophobic group can be either aromatic or aliphatic. In Model 1 the antagonists bind in an extended conformation with two aromatic rings in a parallel displaced and tilted conformation. Model 2 has the same two aromatic rings in a parallel displaced conformation whereas Model 3 has the rings in an edge to face conformation. The pharmacophore models were evaluated using both a structure (NK receptor homology models) and a ligand based approach. By use of exhaustive conformational analysis (MMFFs force field and the GB/SA hydration model) and least-squares molecular superimposition studies, 21 non-peptide antagonists from several structurally diverse classes were fitted to the pharmacophore models. More antagonists could be fitted to Model 2 with a low RMS and a low conformational energy penalty than to Models 1 and 3. Pharmacophore Model 2 was also able to explain the NK1, NK2 and NK3 subtype selectivity of the compounds fitted to the model. Three NK 7TM receptor models were constructed, one for each receptor subtype. The location of the antagonist binding site in the three NK receptor models is identical. Compounds fitted to pharmacophore Model 2 could be docked into the NK1, NK2 and NK3 receptor models after adjustment of the conformation of the flexible linker connecting the head and tail. Models I and 3 are not compatible with the receptor models.

The aim of this work was to synthesize zeolitic imidazolate framework-8 (ZIF-8) by an alternative method and then modify the surface properties for enhancing the CO2 adsorption performance. The ZIF-8 was synthesized by a water based synthesis method using 2-methyl imidazole (2-MeIM) as a hydrogen bond donor and quaternary ammonium salts (QAS) as a hydrogen bond acceptor. The optimal synthesis conditions were investigated by varying (i) the order of precursor mixing during the synthesis process (ii) different QAS (tetrabutyl ammonium bromide (TBAB), tetraethyl ammonium bromide (TEAB) and trimethyl phenyl ammonium bromide (TMPAB)) and (iii) the ratio between 2-MeIM and QAS. The results show that the optimal synthesis condition was using TMPAB as the hydrogen bond acceptor with the ratio between 2-MeIM and TMPAB of 8:2 and in the order of first mixing both hydrogen bond donor and acceptor before adding Zn(NO3)2⋅6H2O solution. TMPAB can provide uniform size distribution with the smallest particle sizes of ZIF-8. This can be explained by the higher hydrogen bond strength between hydrogen bond donor (2-MeIM) and hydrogen bond acceptor (TMPAB) when compared with that of the rest of two QAS. The synthesized ZIF-8 was modified by solvent-assisted ligand exchange methods. The organic linker of ZIF-8 (2-MeIM) was exchanged by 2-aminobenzimidazole (2-NH2bZIM) and 2-phenylimidazole (2-PhIM). The CO2 uptake of modified ZIF-8 was enhanced upon exchanging with 2-NH2bZIM. The increase in CO2 uptake was due to an additional interaction between CO2 and exchanged imidazole linker and an increase in surface properties (higher surface area, pore size and pore volume).

The distinction of enantiomers based on residual anisotropic parameters obtained by alignment in chiral poly-γ-benzyl-L-glutamate (PBLG) is among the strongest in high-resolution NMR spectroscopy. However, large variations in enantiodifferentiation among different solutes are frequently observed. One hypothesis is that the formation of hydrogen bonds between solute and PBLG is important for the distinction of enantiomers. With a small set of three almost spherical enantiomeric pairs, for which 1DCH residual dipolar couplings are measured, we address this issue in a systematic way: borneol contains a single functional group that can act as a hydrogen bond donor, camphor has a single group that may act as a hydrogen bond acceptor, and quinuclidinol can act as both hydrogen bond donor and acceptor. The results are unambiguous: although camphor shows low enantiodifferentiation with PBLG and alignment that can be predicted well by the purely steric TRAMITE approach, the distinction of enantiomers for the other enantiomeric pairs is significantly higher with alignment properties that must involve a specific interaction in addition to steric alignment.

We present machine learning (ML) models for hydrogen bond acceptor (HBA) and hydrogen bond donor (HBD) strengths. Quantum chemical (QC) free energies in solution for 1:1 hydrogen-bonded complex formation to the reference molecules 4-fluorophenol and acetone serve as our target values. Our acceptor and donor databases are the largest on record with 4426 and 1036 data points, respectively. After scanning over radial atomic descriptors and ML methods, our final trained HBA and HBD ML models achieve RMSEs of 3.8 kJ mol−1 (acceptors), and 2.3 kJ mol−1 (donors) on experimental test sets, respectively. This performance is comparable with previous models that are trained on experimental hydrogen bonding free energies, indicating that molecular QC data can serve as substitute for experiment. The potential ramifications thereof could lead to a full replacement of wetlab chemistry for HBA/HBD strength determination by QC. As a possible chemical application of our ML models, we highlight our predicted HBA and HBD strengths as possible descriptors in two case studies on trends in intramolecular hydrogen bonding.

Hydrogen bond is an important type of interaction between drug molecules and their receptors. We present here a computational method for accurately predicting the hydrogen-bonding strength for different acceptors with respect to a given donor or vice versa. The method is based on quantum chemistry DFT calculation of the interaction energy between hydrogen bond donors and acceptors. An excellent linear correlation is observed between the calculated hydrogen-bonding energies and the experimentally measured hydrogen-bonding constants log Kβ on a variety of known hydrogen bond acceptors and donors. These results not only indicate the predictive power of this method but also shed light on factors that determine the magnitude of experimentally measured hydrogen-bonding constants for different acceptors with respect to a given donor, suggesting a primarily enthalpic contribution from hydrogen-bonding energy. The method can be used for evaluating the effects of steric interference and inhibitor binding geometry on hydrogen-bonding strength in drug design.

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.

High-level quantum chemical techniques were used to study the hydrogen bonding interactions in dimers of simple hydrogen bond donors and acceptors. The dimers studied were formed from combinations of CH(4), NH(3), OH(2) with each other and with the *CH(3), *NH(2), and *OH radicals. It was found that complexes in which a radical serves as a hydrogen bond donor, i.e. *AH(x)-BH(y), are more strongly bound than dimers in which the hydrogen bond donor is the analogous parent molecule, i.e. AH(x+1)-BH(y). Complexes in which a radical serves as a hydrogen bond acceptor, i.e. BH(y) (-) *AH(x), are more weakly bound than dimers in which the hydrogen bond acceptor is the analogous parent molecule, i.e. BH(y)-AH(x+1). The differences in these binding properties are attributable to the facts that, in radicals, the A-H bonds are more polar and the A atoms have less negative partial charges than in molecules. Detailed analyses of spin densities revealed that spin delocalization from a radical to a molecule is negligible. Therefore, spin delocalization plays no role in the binding within the complexes studied in this work. Density functional theory methods were also used to calculate the binding energies of the complexes. It was found that the PBE0 and B971 functionals predict binding energies that are in good agreement with the high-level wavefunction data, whereas the performance of the common B3LYP method is not as good. Correcting the functionals for their ability to treat dispersion interactions in carbon-containing compounds improves the binding energies computed with the B3LYP and PBE0 functionals but results in over-binding with B971.

The interactions between two hydrogen bond donors and two hydrogen bond acceptors (DD∶AA) have been used to form extended linear polymers based on bis(thiosemicarbazide)nickel(II) cations and terephthalate anions. In order to investigate the influence of the other hydrogen bond donors and acceptors present on these structures, the bis(thiosemicarbazide)nickel(II) complexes trans-[NiL2]2+, where L is the methyl substituted thiosemicarbazides L2 [NHMeC(S)NHNH2], L3 [NHMeC(S)NHNMe2] and L4 [NH2C(S)NHNMe2], have been prepared as terephthalate (tere) salts and their crystal structures investigated. The supramolecular structures of trans-[Ni(L2)2][tere]·4H2O 2 and trans-[Ni(L3)2(OH2)2][tere] 3 show the expected R22(8) motif linking the cations and anions into chains which are, in turn, cross-linked into sheets via amino N–H· · ·O hydrogen bonds in 2 and aqua O–H· · ·O hydrogen bonds in 3. The supramolecular structure of trans-[Ni(L4)2(OH2)2][tere]·2H2O 4, in contrast, shows the absence of the expected cation· · ·anion· · ·cation chains. In this case, the cations and anions are linked by only one hydrogen bond, though interactions with the water molecules lead to an efficient hydrogen bonded structure with all potential hydrogen bond donors and acceptors involved in hydrogen bonding interactions. These structures demonstrate that the presence or absence of NH groups that are not involved in cation· · ·anion· · ·cation chain formation has a marked effect on both the nickel co-ordination geometry and the presence or absence of the anticipated linear hydrogen bonded chains.

The potential energy surface of l-homoselenocysteine (HSEC) has been explored through the use of B3LYP/6-311+G(d,p) calculations. In this survey, seventy-seven different conformers have been located. These local minima can be classified in four groups, A–D. Structures A, B, and D are stabilized by intramolecular hydrogen bonds (IMHBs) with the amino group acting as the hydrogen bond (HB) donor and the carbonyl group (structures A and D) or the hydroxyl group (structure B) as HB acceptors. The structures in set C present an IMHB with the amino group acting as the HB acceptor and the hydroxyl group as the HB donor. The stability order decreases in the following order: A > B > C > D. From their relative stabilities it can be concluded that only three of these conformers, namely A1, A4, and A5, would exist in the gas phase at room temperature. The most stable deprotonated form corresponds to a Se-deprotated species stabilized by a strong IMHB between the hydroxyl group and the Se atom. However, a direct deprotonation of the most stable neutrals lead to O-deprotonated species, which eventually isomerize to yield the global minimum. Hence, we can conclude that, quite unexpectedly, HSEC behaves as a Se acid in the gas phase, its intrinsic acidity being 1374 kJ mol–1at the B3LYP/6-311++G(3df,2p) level of theory. The most stable protonated forms are systematically the N-protonated ones, the global minimum being a structure stabilized through an IMHB involving the protonated amino group as the HB donor and the SeH group as the HB acceptor. The calculated gas-phase proton affinity (PA) at the B3LYP/6-311++G(3df,2p) level of theory is 930 kJ mol–1.