Comparative study of the H-bond and FTIR spectra between 2,2-hydroxymethyl propionic acid and 2,2-hydroxymethyl butanoic acid

In the present paper, the FTIR band and H-bond differences between the two dihydroxy-based carboxyls, 2,2-hydroxymethyl butanoic acid (hereinafter abbreviated to DMBA) and 2,2-hydroxymethyl propionic acid (hereinafter abbreviated to DMPA), were analyzed based on the crystal structure as well as the relation between H-bond and FTIR band of DMPA. In addition, the energy and length of the H-bonds formed between COOH, between OH, between COOH and OH were also calculated via molecular modeling. The results showed that three H-bond types existing in DMPA while only two in DMBA. The COOH pattern and H-bond type in DMBA and DMPA can be preliminarily judged according to the band position and relative strength of the nuOH and nuCOOH in FTIR spectrum. The H atom in COOH is a stronger H-bond donor than that in primary OH, while the O atom in primary OH is a stronger H-bond acceptor than that in COOH. The H-bond formed by two COOH is, therefore, weaker than that formed by COOH (as donor) and OH (as acceptor), which makes nuC=O shift to lower frequency in DMPA than in DMBA.     

Valence state parameters of all transition metal atoms in metalloproteins—development of ABEEMσπ fluctuating charge force field

To promote accuracy of the atom‐bond electronegativity equalization method (ABEEMσπ) fluctuating charge polarizable force fields, and extend it to include all transition metal atoms, a new parameter, the reference charge is set up in the expression of the total energy potential function. We select over 700 model molecules most of which model metalloprotein molecules that come from Protein Data Bank. We set reference charges for different apparent valence states of transition metals and calibrate the parameters of reference charges, valence state electronegativities, and valence state hardnesses for ABEEMσπ through linear regression and least square method. These parameters can be used to calculate charge distributions of metalloproteins containing transition metal atoms (Sc‐Zn, Y‐Cd, and Lu‐Hg). Compared the results of ABEEMσπ charge distributions with those obtained by ab initio method, the quite good linear correlations of the two kinds of charge distributions are shown. The reason why the STO‐3G basis set in Mulliken population analysis for the parameter calibration is specially explained in detail. Furthermore, ABEEMσπ method can also quickly and quite accurately calculate dipole moments of molecules. Molecular dynamics optimizations of five metalloproteins as the examples show that their structures obtained by ABEEMσπ fluctuating charge polarizable force field are very close to the structures optimized by the ab initio MP2/6–311G method. This means that the ABEEMσπ/MM can now be applied to molecular dynamics simulations of systems that contain metalloproteins with good accuracy. © 2014 Wiley Periodicals, Inc.     

The strength with which a peptide group can form a hydrogen bond varies with the internal conformation of the polypeptide chain

The strength of the H-bond formed between a dipeptide and a proton acceptor molecule is assessed by correlated ab initio quantum calculations for a broad range of different conformations of the dipeptide. The H-bond energy is very sensitive to the internal (phi,psi) angles, even when the geometry of the H-bond does not vary significantly from one conformation to another. This result indicates that the peptide NH is a much less potent proton donor in certain conformations than in others. In particular, extended conformations of a polypeptide are capable of only weak H-bonds. Thus, the interstrand NH...O H-bonds in parallel and antiparallel beta-sheets are expected to be significantly weaker than those found in other conformations, such as helices, ribbons, and beta-bends, even if the H-bond geometries are similar.     

3D hydrogen bond thermodynamics (HYBOT) potentials in molecular modelling

A new approach is proposed to more accurately estimate the energies of H-bond interactions in three-dimensional (3D) molecular modelling. The approach is based on the use of H-bond acceptor and donor enthalpy factor values calculated by means of program HYBOT, the use of a sigmoid relationship to determine the optimum H-bond distances and established force-field methods to determine distance and angle dependencies. The base-pair interactions in a short A-form RNA double-helix are presented as an example of enthalpy calculations of hydrogen bonding for a model system.     

Self-assembled liquid crystals by hydrogen bonding between bipyridyl and alkylbenzoic acids: solvent-free synthesis by mechanochemistry

A series of thermotropic hydrogen-bonded liquid crystalline structures based on 4,4′-bipyridyl and aliphatic carboxylic acids was prepared by a mechanosynthesis technique. This series was characterised by polarising optical microscope, differential scanning calorimetry, Fourier transform infrared spectroscopy, X-ray powder diffraction and ¹H NMR relaxometry experimental techniques. In these complexes, the bipyridyl component, a non-mesogenic substance by itself, acts as a double H-bond acceptor, whereas the alkylbenzoic acid acts as a H-bond donor, in a 1:2 proportion. The so-formed complexes exhibit mesophases that are not observed by the single components. A characteristic phase (smectic A) is identified and shown to be affected by the alkyl chain length. The isotropisation temperature is increased by the supramolecular aggregation through the H-bonds.     

Charge-assisted intramolecular hydrogen bonds in disubstituted cyclohexane derivatives

In this paper, the N(+)-H···N, N(+)-H···O, and O-H···O(-) charge-assisted intramolecular hydrogen bonds (CAHBs) are investigated using different theoretical approaches. Monocharged cyclohexyldiamines (CHDA), aminocyclohexanols (ACHO), and cyclohexanediols (CHDO) are used as model compounds. Geometry optimizations at the MP2/aug-cc-pVDZ level are used to find the equilibrium structures for all possible H-bonded conformers. CAHBs are characterized geometrically and spectroscopically, and their energy is evaluated by means of homodesmic reactions. By comparison with the neutral forms, the presence of the charge is found to have a deep influence on the geometric and energetic H-bond parameters. In addition, these parameters are strongly dependent on the type of the groups involved as well as on their relative position in the cyclohexyl ring. For the systems under study, the H-bond energies vary from -23 to -113 kJ mol(-1), being classified from moderate to strong H-bonds. These H-bonds are also characterized by the application of the NBO and AIM theories. NBO analysis reveals that the energy corresponding to the charge transfer between the lone-pairs of the electron donor group and the antibonding orbitals of the acceptor group represents an important contribution in the H-bond stabilization. From the application of the AIM theory it is possible to see that these H-bonds possess some covalence which varies according to the type and relative position of the intervenient groups.     

Nature of one-dimensional short hydrogen bonding: bond distances, bond energies, and solvent effects

On the basis of recently synthesized calix[4]hydroquinone (CHQ) nanotubes which were self-assembled with infinitely long one-dimensional (1-D) short hydrogen bonds (SHB), we have investigated the nature of 1-D SHB using first-principles calculations for all the systems including the solvent water. The H-bonds relay (i.e., contiguous H-bonds) effect in CHQs shortens the H...O bond distances significantly (by more than 0.2 A) and increases the bond dissociation energy to a large extent (by more than approximately 4 kcal/mol) due to the highly enhanced polarization effect along the H-bond relay chain. The H-bonds relay effect shows a large increase in the chemical shift associated with the SHB. The average binding energies for the infinite 1-D H-bond arrays of dioles and dions increase by approximately 4 and approximately 9 kcal/mol per H-bond, respectively. The solvent effect (due to nonbridging water molecules) has been studied by explicitly adding water molecules in the CHQ tube crystals. This effect is found to be small with slight weakening of the SHB strength; the H...O bond distance increases only by 0.02 A, and the average binding energy decreases by approximately 1 kcal/mol per H-bond. All these results based on the first-principles calculations are the first detailed analysis of energy gain by SHB and energy loss by solvent effect, based on a partitioning scheme of the interaction energy components. These reliable results elucidate not only the self-assembly phenomena based on the H-bond relay but also the solvent effect on the SHB strength.     

Theoretical studies on the hydration of formic acid by ab initio and ABEEMσπ fluctuating charge model

The interaction between formic acid (FA) and water was systemically investigated by atom-bond electronegativity equalization method fused into molecular mechanics (ABEEMσπ/MM) and ab initio methods. The geometries of 20 formic acid–water complexes (FA–water) were obtained using B3LYP/aug-cc-pVTZ level optimizations, and the energies were determined at the MP2/aug-cc-pVTZ level with basis set superposition error (BSSE) and zero-point vibrational energy (ZPVE) corrections. The ABEEMσπ potential model gives reasonable properties of these clusters when compared with the present ab initio data. For interaction energies, the root mean square deviation is 0.74 kcal/mol, and the linear coefficient reaches 0.993. Next, FA in aqueous solution was also studied. The hydrogen-bonding pattern due to the interactions with water has been analyzed in detail. Furthermore, the ABEEMσπ charges changed when H₂O interacted with the FA molecule, especially at the sites where the hydrogen bonds form. These results show that the ABEEMσπ fluctuating charge model is fine giving the overall characteristic hydration properties of FA–water systems in good agreement with the high-level ab initio calculations.     

Cooperative interactions of hydrogen bonds in proton-transfer processes involving water molecules. Simulation of biochemical systems

Quantum-chemical calculations of molecular complexes simulating the proton channel of influenza A virus and the proton-transfer system of the active site of carboanhydrase enzyme were performed. These complexes comprise a proton-donor and a proton-acceptor groups bridged by a chain of water molecules. Calculations of the methylimidazole (H⁺)-H₂O-CH₃COO^? complex as a model of influenza M₂ virus revealed free translation motion of the water molecule between the donor and acceptor, as well as concerted proton transfer in both H bonds. The barrier for proton transfer is independent of the position of the bridging water molecule and varies linearly with the difference in the electrostatic potentials between the donor and acceptor. With elongation of the H-bond bridge between the donor and acceptor groups, the H-bond lengths and proton shifts in the chain links vary periodically. This process can be defined as an H-bond deformation wave (proton wave). It was shown that motion of one proton along the H bond is associated with vibrational motion of protons in other links, which results in wave propagation along the chain. The calculation results allowed the rate of the proton wave and the time of proton transfer from the donor to acceptor to be estimated.     

Comparison of various types of hydrogen bonds involving aromatic amino acids

Ab initio calculations are used to compare the abilities of the aromatic groups of the Phe, Tyr, Trp, and His amino acids (modeled respectively by benzene, phenol, indole, and imidazole) to form H-bonds of three different types. Strongest of all are the conventional H-bonds (e.g., OH..O and OH..N). His forms the strongest such H-bond, followed by Tyr, and then by Trp. Whereas OH..phi bonds formed by the approach of a proton donor to the pi electron cloud above the aromatic system are somewhat weaker, they nonetheless represent an important class of stabilizing interactions. The strengths of H-bonds in this category follow the trend Trp > His > Tyr approximately Phe. CH.O interactions are weaker still, and only those involving His and Trp are strong enough to make significant contributions to protein structure. A protonated residue such as HisH(+) makes for a very powerful proton donor, such that even its CH..O H-bonds are stronger than the conventional H-bonds formed by neutral groups.     

Effects of polar protic solvents on dual emissions of 3-hydroxychromones

3-Hydroxychromones (3HC), exhibit dual emissions highly sensitive to solvent properties due to excited state intramolecular proton transfer (ESIPT). Therefore, 3HCs find wide applications as fluorescence probes in biological systems. Here, it is particularly important to understand the fluorescence behaviour of 3HCs in polar environments. Herein, we studied 3-hydroxyflavone, 2-(2-furyl)-3-hydroxychromone and 2-(2-benzofuryl)-3-hydroxychromone in high polarity solvents characterized by different H-bond donor abilities, donor concentrations and acceptor abilities. Our results show that the dual emissions of the dyes are insensitive to solvent basicity but strongly depend on the two other parameters. Moreover, furyl-and benzofuryl-substituted dyes were significantly more sensitive than the 3-hydroxyflavone to H-bond donor ability, while all three dyes showed roughly equivalent high sensitivity to H-bond donor concentration. These results can be explained by different mechanisms. Thus, the sensitivity of all three dyes to increasing concentrations of H-bond donors probably results from increase in the population of solvated dye with disrupted intramolecular H-bonds. Meantime, the sensitivity to H-bond donor ability of the solvent, observed mainly with furyl and benzofuryl dyes, is probably related to the strength of the H-bonds between the solvent and the 4-carbonyl group of the dye with intact intramolecular H-bonds. The present results provide new insights for further applications of 3HC derivatives as environment-sensitive probes and labels of biological molecules.     

Calculating solvation energies by means of a fluctuating charge model combined with continuum solvent model

Continuum solvent models have shown to be very efficient for calculating solvation energy of biomolecules in solution. However, in order to produce accurate results, besides atomic radii or volumes, an appropriate set of partial charges of the molecule is needed. Here, a set of partial charges produced by a fluctuating charge model-the atom-bond electronegativity equalization method model (ABEEMσπ) fused into molecular mechanics is used to fit for the analytical continuum electrostatics model of generalized-Born calculations. Because the partial atomic charges provided by the ABEEMσπ model can well reflect the polarization effect of the solute induced by the continuum solvent in solution, accurate and rapid calculations of the solvation energies have been performed for series of compounds involving 105 small neutral molecules, twenty kinds of dipeptides and several protein fragments. The solvation energies of small neutral molecules computed with the combination of the GB model with the fluctuating charge protocol (ABEEMσπ∕GB) show remarkable agreement with the experimental results, with a correlation coefficient of 0.97, a slope of 0.95, and a bias of 0.34 kcal∕mol. Furthermore, for twenty kinds of dipeptides and several protein fragments, the results obtained from the analytical ABEEMσπ∕GB model calculations correlate well with those from ab initio and Poisson-Boltzmann calculations. The remarkable agreement between the solvation energies computed with the ABEEMσπ∕GB model and PB model provides strong motivation for the use of ABEEMσπ∕GB solvent model in the simulation of biochemical systems.     

Intramolecular hydrogen bonding and cooperative interactions in carbohydrates via the molecular tailoring approach

In spite of many theoretical and experimental attempts for understanding intramolecular hydrogen bonding (H-bonding) in carbohydrates, a direct quantification of individual intramolecular H-bond energies and the cooperativity among the H-bonded networks has not been reported in the literature. The present work attempts, for the first time, a direct estimation of individual intramolecular O-H...O interaction energies in sugar molecules using the recently developed molecular tailoring approach (MTA). The estimated H-bond energies are in the range of 1.2-4.1 kcal mol(-1). It is seen that the OH...O equatorial-equatorial interaction energies lie between 1.8 and 2.5 kcal mol(-1), with axial-equatorial ones being stronger (2.0-3.5 kcal mol(-1)). The strongest bonds are nonvicinal axial-axial H-bonds (3.0-4.1 kcal mol(-1)). This trend in H-bond energies is in agreement with the earlier reports based on the water-water H-bond angle, solvent-accessible surface area (SASA), and (1)H NMR analysis. The contribution to the H-bond energy from the cooperativity is also estimated using MTA. This contribution is seen to be typically between 0.1 and 0.6 kcal mol(-1) when H-bonds are a part of a relatively weak equatorial-equatorial H-bond network and is much higher (0.5-1.1 kcal mol(-1)) when H-bonds participate in an axial-axial H-bond network.     

Characterizing the strength of individual hydrogen bonds in DNA base pairs

The energies of individual hydrogen bonds (H-bonds) in A-T and G-C Watson-Crick base pairs were calculated according to the natural bond orbital (NBO) analysis of intermolecular interactions. The extent to which individual H-bonds are helpful in holding the two base pairs together was previously investigated quantitatively by a few different approaches, and the results of the present and previous estimations were compared. The method was validated by the determination of the H-bond strength changes in A-T and G-C pairs upon the substitution of the monomer (base) by two cationic substituents; the systems for which the changes were previously anticipated based on the modifications of the H-bonds' distances.     

Theoretical study on the hydration of hydrogen peroxide in terms of ab initio method and atom-bond electronegativity equalization method fused into molecular mechanics

In this paper, the interaction between hydrogen peroxide (HP) and water were systemically studied by atom-bond electronegativity equalization method fused into molecular mechanics (ABEEM/MM) and ab initio method. The results show that the optimized geometries, interaction energies and dipole moments of hydrated HP clusters HP(H₂O) _n (n = 1–6) calculated by ABEEM/MM model are fairly consistent with the MP2/aug-cc-pVTZ//MP2/aug-cc-pVDZ results. The ABEEM/MM results indicate that n = 4 is the transition state structure from 2D planar structure to 3D network structure. The variations of the average hydrogen bond length with the increasing number of water molecules given by ABEEM/MM model agree well with those of ab initio studies. Moreover, the radial distribution functions (RDFs) of water molecule around HP in HP aqueous solution have been analyzed in detail. It can be confirmed that HP is a good proton donor and poor proton acceptor in aqueous solution by analysis of the RDFs.     

精密从头算与ABEEM/MM模型对水团簇(H2O)11 9种低能结构的计算

用精密从头算方法研究了(H2O)11的9种低能异构体的性质, 包括优化的几何结构、结合能、偶极矩和氢键个数等, 并且得出了515-a是(H2O)11的全局最低能结构. 同时, 也用ABEEM/MM(atom bond electronegativity equalization method/molecular mechanics) 模型研究了这些性质, 与从头算的结果进行了比较, 得到了相符合的结果. 这显示了ABEEM/MM模型在描述中等大小的水分子团簇结构上是成功的.     

Two-way effects between hydrogen bond and intramolecular resonance effect: an ab initio study on complexes of formamide and its derivatives with water

Ab initio calculations up to MP2/aug-cc-pVTZ//MP2/cc-pVTZ level, including natural charge population and natural resonance theory analyses, have been carried out to study the two-way effects between hydrogen bond (H-bond) and the intramolecular resonance effect by using the H-bonded complexes of formamide ( FAO) and its derivatives ( FAXs, X represents the heavy atoms in the substituent groups, CH 2, NH, SiH 2, PH, and S) with water as models. Unlike NH 3 and NH 2CH 3 which prefer being H-bond acceptors ( HA) to form H-bond with water, the amino groups in the six monomers, because of the resonance effect, prefer being H-bond donors ( HD) rather HA. Six monomers can all form HD complexes with water, and only two ( FAC and FASi) with the weakest resonance effect are able to form HA complexes with water. The HD H-bond and resonance effect enhance each other (positive two-way effects) whereas the HA H-bond and resonance effect weaken each other (negative two-way effects). The H-bond energies in the six HD complexes are nearly linearly correlated with the weights of the dipolar resonance in Pauling's model and the N-C bond lengths; the correlation coefficients are 0.91 and 0.93, respectively. The positive two-way effects also happens in FAO-water complex, in which the FAO CO group serves as HA ( HA co ). Interestingly, when the HD and HA co H-bonds are present in FAO H-bond complex simultaneously, the enhancements are much more significant, and the energies of the two types of H-bonds are much larger than those when only one type of H-bond is present, reflecting the cooperative effects. By using the knowledge to the two-way effects, we computationally designed a molecule ( FAO- BH 3 ) to increase H-bond energy. Because of the oxygen lone pair donation to the empty pi orbital of BH 3, FAO- BH 3 has a much stronger resonance effect than FAO. As a result, the H-bond energy (-5.55 kcal/mol) in HD H 2O ... FAO- BH 3 complex is much greater than the -3.30 kcal/mol in the HD H 2O...FAO complex. The two-way effects can be rationalized as follows: the resonance effect leads to intramolecular charge shifts in the monomers which facilitate or prevent the charge donation or acceptation of their H-bond partners. Therefore, the H-bonds are strengthened or weakened. In reverse, the charge donations or acceptations of their H-bond partners facilitate or prevent the intramolecular charge shifts in the monomer moieties, which enhance or weaken the resonance effect. The understanding to the two-way effects may be helpful in drug design and refinement by modulating the H-bond strength and in building empirical H-bond models to study large biological molecules. The study supports Pauling's resonance model.     

Relative strengths of NH..O and CH..O hydrogen bonds between polypeptide chain segments

Correlated ab initio calculations are used to compare the energetics when the CH and NH groups of the model dipeptide CHONHCH2CONH2 are each allowed to form a H-bond with the proton acceptor O of a peptide group. When the dipeptide is in its C7 conformation, the NH..O H-bond energy is found to be 7.4 kcal/mol, as compared to only 2.8 kcal/mol for the CH..O interaction. On the other hand, the situation reverses, and the CH..O H-bond becomes stronger than NH..O, when the dipeptide adopts a C5 structure. This reversal is important as C5 is nearly equal in stability to C7 for the dipeptide, and is representative of the commonly observed beta-sheet structure in a protein. Immersing the dipeptide-peptide pair in a model solvent weakens both sorts of H-bonds, and in a fairly uniform manner. Consequently, the trends observed in the in vacuo situation retain their validity in either aqueous solution or the protein interior. Likewise, the desolvation penalty, suffered by removing a H-bonded complex from water and placing it in the less polar interior of a protein, is quite similar for the NH..O and CH..O bonds.     

Electronic properties of multifurcated bent hydrogen bonds CH3...Y and CH2...Y

H-bonding angle angleYHX has an important effect on the electronic properties of the H-bond Y...HX, such as intra- and intermolecular hyperconjugations and rehybridization, and topological properties of electron density. We studied the multifurcated bent H-bonds of the proton donors H3CZ (Z = F, Cl, Br), H2CO and H2CF2 with the proton acceptors Cl(-) and Br(-) at the four high levels of theory: MP2/6-311++G(d,p), MP2/6-311++G(2df,2p), MP2/6-311++G(3df,3pd) and QCISD/6-311++G(d,p), and found that they are all blue-shifted. These complexes have large interaction energies, 7-12 kcal mol(-1), and large blue shifts, delta r(HC) = -0.0025 --0.006 A and delta v(HC) = 30-90 cm(-1). The natural bond orbital analysis shows that the blue shifts of these H-bonds Y...HnCZ are mainly caused by three factors: rehybridization; indirect intermolecular hyperconjugation n(Y) -->sigma*(CZ), in that the electron density from n(Y) of the proton acceptor is transferred not to sigma*(CH), but to sigma*(CZ) of the donor; intramolecular hyperconjugation n(Z) -->sigma*(CH), in that the electron density in sigma*(CH) comes back to n(Z) of the donor such that the occupancy in sigma*(CH) decreases. The topological properties of the electron density of the bifurcated H-bonds Y...H2CZ are similar to those of the usual linear H-bonds, there is a bond critical point between Y and each hydrogen, and a ring critical point inside the tetragon YHCH. However, the topological properties of electron density of the trifurcated H-bonds Y...H3CZ are essentially different from those of linear H-bonds, in that the intermolecular bond critical point, which represents a closed-shell interaction, is not between Y and hydrogen, but between Y and carbon.     

Weak H-bonds. Comparisons of CH···O to NH···O in proteins and PH···N to direct P···N interactions

Whereas CH···O H-bonds are usually weaker than interpeptide NH···O H-bonds, this is not necessarily the case within proteins. The nominally weaker CH···O are surprisingly strong, comparable to, and in some cases stronger than, the NH···O H-bonds in the context of the forces that hold together the adjacent strands in protein β-sheets. The peptide NH is greatly weakened as proton donor in certain conformations of the protein backbone, particularly extended structures, and forms correspondingly weaker H-bonds. The PH group is a weak proton donor, but will form PH···N H-bonds. However, there is a stronger interaction in which P can engage, in which the P atom, not the H, directly approaches the N electron donor to establish a direct P···N interaction. This approach is stabilized by the same sort of electron transfer from the N lone pair to the P-H σ* antibond that characterizes the PH···N H-bond.