Dynamics of the intermolecular hydrogen bonds in the polymorphs of paracetamol in relation to crystal packing and conformational transitions: a variable-temperature polarized Raman spectroscopy study

The properties of the intermolecular hydrogen bonds in the monoclinic (Form I) and the orthorhombic (Form II) polymorphs of paracetamol, C(8)H(9)NO(2), have been studied by single crystal polarized Raman spectroscopy (40 to 3700 cm(-1)) in a wide temperature range (5 K < T < 300 K) in relation to the dynamics of methyl-groups of the two forms. A detailed analysis of the temperature dependence of the wavenumbers, bandwidths and integral intensities of the spectral bands has revealed an essential difference between the two polymorphs in the strength and ordering of OH···O and NH···O hydrogen bonds. The compression of intermolecular hydrogen bonds is interrelated with crystal packing and the dynamics of methyl-groups. On structural compression of the orthorhombic polymorph on cooling, a compromise is to be sought between the shortening of OH···O and NH···O bonds, attractive CH···O and repulsive CH···H contacts in the crystal structure. As a result of a steric conflict at temperatures below 100 K, N-H···O hydrogen bonds become significantly disordered, and an extended intramolecular transition from the conformation "staggered" with respect to the C=O bond to the one "staggered" with respect to the NH bond is observed. In most of the studied crystals this transition was only about 60% complete even at 5 K, but in some of the crystals the orientation of all the methyl-groups became staggered with respect to the NH bond at low temperatures. This complete transition was coupled to a sharp shortening of the OH···O and NH···O hydrogen bonds at <100 K, the appearance of new additional positions of the protons in these H-bonds, and a slight strengthening of the C-HO bonds formed by methyl-groups. The same conformational transition has been observed also in the monoclinic polymorph at T < 80 K. The crystal packing in Form I prevents the O-H···O hydrogen bonds from adopting the optimum geometry, and they are significantly disordered at all the temperatures, especially at ≤200 K. The packing of molecules in Form I is also not favourable to form C-H···O hydrogen bonds involving methyl-groups. One can conclude from the comparison of diffraction and spectroscopic data that the higher stability of Form I results not from a larger strength of individual OH···O and NH···O hydrogen bonds, but is a cumulative effect: all the hydrogen bonds together stabilize the structure of the monoclinic polymorph more than that of the orthorhombic polymorph.     

Infrared-optical double resonance spectroscopic investigation of trifluoromethylphenols and their water complexes

The hydrogen bonding behavior of trifluoromethylphenols and their water complexes were investigated using IR-UV double resonance spectroscopy. Both ortho- and meta-trifluoromethylphenols exist in the syn conformer, which is the global minimum in both the cases. The IR spectrum in the O-H stretching region reveals the absence of an intramolecular O-H···F hydrogen bond in the syn-o-trifluoromethylphenol, which is in contrast to the results reported in the literature. The water complexes of both o-trifluoromethylphenol and m-trifluoromethylphenol are characterized by formation of O-H···O hydrogen bonds between the donor phenolic OH group and the acceptor water molecule. In addition, the o-trifluoromethylphenol-(water)(2) complex was also observed.     

Hydrogen bonding in 1,1'-Bi-2-naphthol within the polarizable continuum model

Intra- and intermolecular hydrogen bonding of 1,1'-bi-2-naphthol in a series of solvents and in solid phase has been investigated by means of mid-IR spectroscopy and DFT reaction field calculations. The polarizable continuum model has been used to estimate the relative stability of isomers differing in the positions of the hydroxyl groups. The height of the potential barriers between them was also calculated and the corresponding transition states characterized. In hydrogen bond nonaccepting solvents, the isomer preference does not change relative to the gas phase, although the less stable isomers are more probable in solvents of higher relative permittivity. In hydrogen bond forming solvents, the least stable isomer is most probably prevalent due to the additional stabilization through intermolecular hydrogen bonds with solvent molecules. A detailed vibrational analysis revealed the spectral regions specific to the OH vibrations with the observed solvent effects concerning the redistribution of vibrational intensities rather than wavenumber shifts.     

Conformation-changing aggregation in hydroxyacetone: a combined low-temperature FTIR, jet, and crystallographic study

Aggregation in hydroxyacetone (HA) is studied using low-temperature FTIR, supersonic jet expansion, and X-ray crystallographic (in situ cryocrystallization) techniques. Along with quantum chemical methods (MP2 and DFT), the experiments unravel the conformational preferences of HA upon aggregation to dimers and oligomers. The O-H···O═C intramolecular hydrogen bond present in the gas-phase monomer partially opens upon aggregation in supersonic expansions, giving rise to intermolecular cooperatively enhanced O-H···O-H hydrogen bonds in competition with isolated O-H···O═C hydrogen bonds. On the other hand, low-temperature IR studies on the neat solid and X-ray crystallographic data reveal that HA undergoes profound conformational changes upon crystallization, with the HOCC dihedral angle changing from ~0° in the gas phase to ~180° in the crystalline phase, hence giving rise to a completely new conformation. These conclusions are supported by theoretical calculations performed on the geometry derived from the crystalline phase.     

Neutral and ionic hydrogen bonding in Schiff bases

Low-temperature, high-resolution X-ray studies of charge distributions in the three Schiff bases, the dianil of 2-hydroxy-5-methylisophthaldehyde, 3,5-dinitro-N-salicylidenoethylamine and 3-nitro-N-salicylidenocyclohexylamine, have been carried out. These structures exhibit interesting weak interactions, including two extreme cases of intramolecular hydrogen bonds that are ionic N(+)-H...O- and neutral O-H...N in nature. These two types of hydrogen bond reflect differences in geometrical parameters and electron density distribution. At the level of geometry, the neutral O-H...N hydrogen bond is accompanied by an increase in the length of the C(1)-O(1) bond, opening of the ipso-C(1) angle, elongation of the aromatic C-C bonds, shortening of the C(7)-N(2) bond and increased length of the C(1)-C(7) bond, relative to the ionic hydrogen bond type. According to the geometrical and critical point parameters, the neutral O-H...N hydrogen bond seems to be stronger than the ionic ones. There are also differences between charge density parameters of the aromatic rings consistent with the neutral hydrogen bond being stronger than the ionic ones, with a concomitant reduction in the aromaticity of the ring. Compounds with the ionic hydrogen bonds show a larger double-bond character in the C-O bond than appears in the compound containing a neutral hydrogen bond; this suggests that the electronic structure of the former pair of compounds includes a contribution from a zwitterionic canonical form. Furthermore, in the case of ionic hydrogen bonds, the corresponding interaction lines appear to be curved in the vicinity of the hydrogen atoms. In the 3-nitro-N-salicylidenocyclohexylamine crystal there exists, in addition to the intramolecular hydrogen bond, a pair of intermolecular O...H interactions in a centrosymmetric dimer unit.     

Solvent effects on glycine II. Water-assisted tautomerization

The water-assisted tautomerization of glycine has been investigated at the B3LYP/6-31+G** level using supermolecules containing up to six water molecules as well as considering a 1:1 glycine-water complex embedded in a continuum. The conformations of the tautomers in this mechanism do not display an intramolecular H bond, instead the functional groups are bridged by a water molecule. The replacement of the intramolecular H bond by the bridging water reduces the polarity of the N-H bond in the zwitterion and increases that of the O-H bond in the neutral, stabilizing the zwitterion. Both the charge transfer effects and electrostatic interactions stabilize the nonintramolecularly H-bonded zwitterion conformer over the intramolecularly hydrogen bonded one. The nonintramolecularly H-bonded neutral is favored only by charge transfer effects. Although there is no strong evidence whether the intramolecularly hydrogen bonded or non hydrogen bonded structures are favored in the bulk solution represented as a dielectric continuum, it is likely that the latter species are more stable. The free energy of activation of the water-assisted mechanism is higher than the intramolecular proton transfer channel. However, when the presumably higher conformational energy of the zwitterion reacting in the intramolecular mechanism is taken into account, both mechanisms are observed to compete. The various conformers of the neutral glycine may form via multiple proton transfer reactions through several water molecules instead of a conformational rearrangement.     

An atomic charge-charge flux-dipole flux atom-in-molecule decomposition for molecular dipole-moment derivatives and infrared fundamental intensities

The molecular dipole moment and its derivatives are determined from atomic charges, atomic dipoles, and their fluxes obtained from AIM formalism and calculated at the MP2(FC)/6-311++G(3d,3p) level for 16 molecules: 6 diatomic hydrides, CO, HCN, OCS, CO2, CS2, C2H2, C2N2, H2O, H2CO, and CH4. Root-mean-square (rms) errors of 0.052 D and 0.019 e are found for the dipole moments and their derivatives calculated using AIM parameters when compared with those obtained directly from the MP2(FC)/6-311++G(3d,3p) calculations and 0.097 D and 0.049 e when compared to the experimental values. The major deviations occur for the NaH, HF, and H2O molecules. Parallel polar tensor elements for the diatomic and linear polyatomic molecules, except H2, HF, LiH, and NaH, have values resulting from cancellations of substantial contributions from atomic charge fluxes and atomic dipole fluxes. These fluxes have a large negative correlation coefficient, -0.97. IR fundamental intensity sums for CO, HCN, OCS, CO2, CS2, C2H2, C2N2, H2CO, and CH4 calculated using AIM charges, charge fluxes, and atomic dipole fluxes have rms errors of 14.9 km mol(-1) when compared with sums calculated directly from the molecular wave function and 36.2 km mol(-1) relative to experimental values. The classical model proposed here to calculate dipole-moment derivatives is compared with the charge-charge flux-overlap model long used by spectroscopists for interpreting IR vibrational intensities. The utility of the AIM atomic charges and dipoles was illustrated by calculating the forces exerted on molecules by a charged particle. AIM quantities were able to reproduce forces due to a +0.1 e particle over a 3-8-A separation range for the CO and HF molecules in collinear and perpendicular arrangements. These results show that IR intensities do contain information relevant to the study of intermolecular interactions.     

低阶煤中氢键作用的色散校正密度泛函理论研究

本研究以苯酚…苯酚、苯酚…苯、苯酚…二苯醚、苯酚…喹啉和苯甲酸…苯甲酸为对象，采用色散校正的密度泛函理论分别研究褐煤中自缔合OH、OH-π、OH-醚O、OH-N和COOH-COOH之间形成的氢键。此外，还研究了氢键供体中取代基(CH₃-、CH₃O-、OH-、NH₂-、COOH-和NO₂-)对氢键的影响。对上述复合物进行了几何优化，并计算了能量、Mulliken电荷分布及振动频率。从优化的结构中可以看出上述复合物之间都存在氢键，所有复合物中O-H键键长都比苯酚中自由羟基的长，这表明这些复合物之间存在相互作用。其中，羧酸…羧酸复合物中O-H键的键长最长。此外，通过Mulliken电荷分布可看出上述复合物之间存在电荷转移。基于振动频率分析，所有的O-H键伸缩振动都发生了红移，尤其是羧酸…羧酸和苯酚…喹啉复合物，这可为煤中羟基振动的红外光谱分析提供依据。根据键能不同氢键强度按以下顺序依次递减：COOH-COOH>OH-N > 自缔合OH≈OH-醚O > OH-π，这与振动频率的分析结果一致。此外，不同取代基对氢键作用的影响不同。     

Strength from weakness: opportunistic CH···O hydrogen bonds differentially dictate the conformational fate in solid and solution states

We show that the CH···O hydrogen bond can be opportunistic to differentially dictate the conformation of cyclitols in solution and solid states. While several intermolecular CH···O stabilize the chair-conformation in the solid, single intramolecular CH···O stabilizes an otherwise unfavorable boat-conformation in solutions analogous to the boat-conformation of cis-1,4-cyclohexanediols by OH···O bonds.     

Continuum treatment of electronic polarization effect

A continuum treatment of electronic polarization has been explored for in molecular mechanics simulations in implicit solvents. The dielectric constant for molecule interior is the only parameter in the continuum polarizable model. A value of 4 is found to yield optimal agreement with high-level ab initio quantum mechanical calculations for the tested molecular systems. Interestingly, its performance is not sensitive to the definition of molecular volume, in which the continuum electronic polarization is defined. In this model, quantum mechanical electrostatic field in different dielectric environments from vacuum, low-dielectric organic solvent, and water can be used simultaneously in atomic charge fitting to achieve consistent treatment of electrostatic interactions. The tests show that a single set of atomic charges can be used consistently in different dielectric environments and different molecular conformations, and the atomic charges transfer well from training monomers to tested dimers. The preliminary study gives us the hope of developing a continuum polarizable force field for more consistent simulations of proteins and nucleic acids in implicit solvents.     

Cation-anion hydrogen bonds: a new class of hydrogen bonds that extends their strength beyond the covalent limit. A theoretical characterization

The existence of O-H···O hydrogen bonds having a strength within the -80 to -210 kcal/mol range, that is, in the range of strength of covalent bonds and well beyond the so-called covalent limit (-50 kcal/mol), is reported on complexes where the O-H proton donor and O acceptor groups are located in ions of opposite sign. A complete analysis of short distance O-H···O hydrogen bonds between charged fragments was performed for cases where the OH and O groups are both located on charged molecules. It shows that these interactions (a) are nonsymmetrical for the O-H and H···O distances, (b) have a noncovalent H···O bond critical point, and (c) have a strong and energetically stable electrostatic component when the OH and O groups are located in oppositely charged molecules. These cation-anion O-H···O interactions are energetically stable, satisfy the usual topology for hydrogen bonds, HBs, and also have the same directionality found in other HBs. Therefore, they should be considered as a new class of HBs, the cation-anion hydrogen bonds.     

Solvation properties of N-acetyl-β-glucosamine: molecular dynamics study incorporating electrostatic polarization

N-Acetyl-β-glucosamine (NAG) is an important moiety of glycoproteins and is involved in many biological functions. However, conformational and dynamical properties of NAG molecules in aqueous solution, the most common biological environment, remain ambiguous due to limitations of experimental methods. Increasing efforts are made to probe structural properties of NAG and NAG-containing macromolecules, like peptidoglycans and polymeric chitin, at the atomic level using molecular dynamics simulations. In this work, we develop a polarizable carbohydrate force field for NAG and contrast simulation results of various properties using this novel force field and an analogous nonpolarizable (fixed charge) model. Aqueous solutions of NAG and its oligomers are investigated; we explore conformational properties (rotatable bond geometry), electrostatic properties (dipole moment distribution), dynamical properties (self-diffusion coefficient), hydrogen bonding (water bridge structure and dynamics), and free energy of hydration. The fixed-charge carbohydrate force field exhibits deviations from the gas phase relative rotation energy of exocyclic hydroxymethyl side chain and of chair/boat ring distortion. The polarizable force field predicts conformational properties in agreement with corresponding first-principles results. NAG-water hydrogen bonding pattern is studied through radial distribution functions (RDFs) and correlation functions. Intermolecular hydrogen bonding between solute and solvent is found to stabilize NAG solution structures while intramolecular hydrogen bonds define glycosidic linkage geometry of NAG oligomers. The electrostatic component of hydration free energy is highly dependent on force field atomic partial charges, influencing a more favorable free energy of hydration in the fixed-charge model compared to the polarizable model.     

Theoretical study of formic acid-sulfur dioxide dimers

We report the first theoretical study of noncovalent and covalent interactions in formic acid (FA)-SO(2) complexes. Using ab initio and DFT model chemistries, five stable noncovalent complexes were identified, as well as a covalent adduct, formic sulfurous anhydride HOSO(2)CHO. syn-FA is predicted to form two nonplanar bidentate complexes with SO(2): the more stable one contains a normal hydrogen bond donated by OH, and the less stable one contains a blue-shifted hydrogen bond donated by CH. Both are stabilized by charge transfer from FA to SO(2). anti-FA forms three planar complexes of nearly equal energy containing OH-to-SO(2) hydrogen bonds. Formic sulfurous anhydride forms via an endothermic concerted cycloaddition. Natural bond orbital analysis showed that the bidentate SO(2)-FA complexes are stabilized by n → π* donation from FA to SO(2), and back-donation from SO(2) n and π* orbitals into FA σ(OH)* or σ(CH)* orbitals. The bidentate formic acid-SO(2) complex that contains an O-H···O hydrogen bond is more stable than the similar nitric acid-SO(2) complex. The latter contains a stronger hydrogen bond but shows no O→S charge transfer interaction.     

A scheme estimating the energy of intramolecular hydrogen bonds in diols

The relative energies of conformers of 1,2-ethanediol, 1,3-propanediol, and 1,4-butanediol are split into a sum of five different terms including the intramolecular OH?O interaction. This scheme allows to estimate the energy of the O-H?O intramolecular hydrogen bond of the tGG′g and gGG′g conformers of 1,3-propanediol, the g′GG′Gt and g′GG′Gg conformers of 1,4-butanediol, and the energy of the non-bonded O-H?O interaction in the g′Gt, g′Gg and g′Gg′ conformers of 1,2-ethanediol. This scheme provides pure hydrogen bond energies without assuming the geometry and/or electronic features to be constant between the conformation having a IHB and a reference conformation. The fitted energies show a perfect linear correlation with the corresponding r(H?O)⁻¹ values. QTAIM atomic electron population and energies of the donor hydrogen calculated along the H-O-C-C internal rotation are found to be linearly correlated. These linear correlations display small changes at the BCP formation in 1,3-propanediol.     

New approach to the semiempirical calculation of atomic charges for polypeptides and large molecular systems

Starting from the bond polarization theory (BPT), a new semiempirical method for the calculation of net atomic charges is developed. The bond polarization theory establishes a linear dependence of atomic charges from the bond polarization energy. This energy is calculated from the hybrid orbitals forming a bond and the point charges within the neighborhood. Empirical parameters are introduced for the polarity of an unpolarized bond and for the change of the atomic charge with σ- and π-bond polarization. Because these parameters are linear, they can be calibrated directly using net atomic charges from ab initio calculations. This procedure was performed using the charges from STO3G calculations on a set of 18 amino acids. Using the two parameters for CH, OH, σ-CO, and NH bonds and the three parameters for CC, CO, and CN bonds, the 350 ab initio charges can be reproduced with high accuracy by solving sets of linear equations for the charges. The calculation of charges for large molecular systems including all inter- and intramolecular mutual polarizations requires only a few seconds (up to 100 atoms) or minutes (700 atoms) on a PC. This procedure is well suited for the application in molecular mechanics or molecular dynamics programs to overcome the limitations of most force fields used up to now. One of the weakest points in these programs is the use of fixed or topological charges to define the electrostatic potential. As an application of the new method, we calculated the interaction energy of an ion with valinomycin. This ring molecule forms octahedral oxygen cages around ions like potassium and acts thereby as selective ion carrier. To accomplish this function, valinomycin has to strip off the hydratization spheres of the ions, and therefore its preference for certain types of ions could be deduced from the interaction energies. © 1994 by John Wiley & Sons, Inc.     

TDDFT Study on Excited-State Hydrogen Bonding of 2'-Deoxyguano-sine in H2O Solution

The mono and dihydrated complexes of 2'-deoxyguanosine have been used to elucidate the importance of the 2'-hydroxy group in the hydration. Density functional theory and time-dependent density functional theory methods were performed to investigate the ground-and excited-state hydrogen bonding properties of 2'-deoxyguanosine-water (2'-dG-W) and 2'-deoxyguanosine-2water (2'-dG-2W). Infrared spectra, geometric optimizations, frontier molecular orbitals and Mulliken charges have also been studied. The results demonstrated that the excited-state intramolecular hydrogen bonding dynamics of complexes 2'-dG-W and 2'-dG-2W behaves differently upon photoexcitation, while their intermolecular hydro-gen bonding dynamics behaves similarly. Moreover, the significant weakening of the inter-molecular hydrogen bond O4···H1?N1 and the formation of the new strong hydrogen bond O4···H3?N2 in the 2'-dG-2W upon photoexcitation were due to the geometric structure bending of guanine and the rigidity of related molecules. In addition, the charge transfer properties were theoretically investigated by analysis of molecular orbital.     

An ab initio SCF calculation of the dipole-moment derivatives and infrared-absorption intensities of the water-dimer molecule

The dipole-moment derivatives and infrared-absorption intensities of the water dimer including several deuterated species have been calculated using ab initio SCF techniques. The results are compared with the analogous, quantities for monomeric water. In addition to the highly enhanced intensity of the intramolecular OH stretch most intermolecular modes that occur in the 90–600 cm^?1 region are also found to be very intense. An electrostatic model for the water dimer has been explored with a view to developing a possible scheme for the calculation of infrared intensities of larger clusters. As a result of the significant exchange and charge-transfer effects such a model is found to be unreliable in describing the dipole-moment derivatives that directly involve the hydrogen bond.     

Variation of atomic charges during proton transfer in hydrogen bonds

The point atomic charges in a number of ionic H-bonded systems are studied by ab initio calculations as functions of the proton transfer coordinate. In the proton-bound complexes of water–water, ammonia–ammonia, formamide–water, formamide–ammonia, and dimethylether–ammonia, the net atomic charges were obtained using Mulliken population analysis and from the diagonal elements of the atomic polar tensors calculated at the HF/4–31G and MP2/6–31 + G** levels. The dependence of the atomic charges upon the coordinate of the transferring proton was found to be close (within an error of 0.02 e) to a linear function for intermolecular distances in the 2.5–2.8 Å range. The obtained charge and charge flux dependencies highlight the electron redistribution during the proton transfer process and provide insights into the source of the high infrared (IR) intensities of stretching modes of N? H and O? H bonds undergoing hydrogen bonding. © 1994 by John Wiley & Sons, Inc.     

Nuclear magnetic resonance parameters for methane molecule trapped in clathrate hydrates

The calculations of the nuclear shielding and spin-spin coupling constants were carried out for two models of clathrate hydrates, 5(12) and 5(12)6(8), using the density functional theory three-parameter Becke-Lee-Yang-Parr method with the basis set aug-cc-pVDZ (optimization) and HuzIII-su3 (NMR parameters). Particular attention has been devoted to evaluate the influence of a geometrical arrangement, the effect of long-range interactions on the NMR shielding of methane molecule, and to predict whether (13)C and (1)H chemical shifts can distinguish between guests in two clathrate hydrates cages. The correlation of the changes in the (17)O shielding constants depend strongly on the hydrogen-bonding topology. The intermolecular hydrogen-bond transmitted (1h)J(OH) spin-spin coupling constants are substantial. The increase of their values is connected with the elongation of the intramolecular O-H bond and the shortening of the intermolecular O···H distance. These data suggests that hydrogen bonds between double donor-single acceptor (DDA)-type water molecules acting as a proton acceptor from single donor-double acceptor (DAA)-type water molecules are stronger than ones formed by DAA-type water molecules acting as an acceptor for a DDA water proton. These state-of-the-art calculations confirmed the earlier experimental findings of the cage-dependency of (13)C chemical shift of methane.