Structure and hydrogen bonding in neat N-methylacetamide: classical molecular dynamics and Raman spectroscopy studies of a liquid of peptidic fragments

The results of classical molecular dynamics (MD) simulations and Raman spectroscopy studies of neat liquid N-methylacetamide (NMA), the simplest model system relevant to the peptides, are reported as a function of temperature and pressure. The MD simulations predict that near ambient conditions, the molecules form a hydrogen bond network consisting primarily of linear chains. Both the links between molecules within the hydrogen-bonded chains and the associations between chains are stabilized by weak methyl-donated "improper" hydrogen bonds. The three-dimensional structural motifs observed in the liquid show some similarity to protein beta-sheets. The temperature and pressure dependence of the hydrogen bond network, as probed by the mode frequency of the experimentally determined amide-I Raman band, blue shifts on heating and red shifts under compression, respectively, suggesting weakened and enhanced hydrogen bonding in response to temperature and pressure increases. Disruption of the hydrogen-bonding network is clearly observed in the simulation data as temperature is increased, whereas the improper hydrogen bonding is enhanced under compression to reduce the energetic cost of increasing the packing fraction. Because of the neglect of polarizability in the molecular model, the computed dielectric constant is underestimated compared to the experimental value, indicating that the simulation may underestimate dipolar coupling in the liquid.     

The effect of pressure and temperature on the vibrational spectra of different hydrogen bonded systems

The effect of pressure and temperature on the vibrational spectra of hydrogen bonded systems has been studied on amides, thioamides, carboxylic acids and urea. The compounds under investigation are indicative for the kind of hydrogen bonding changing from pure intermolecular to intramolecular and dimeric forms. The discussion of the temperature dependence on the fundamentals involved in the hydrogen bonding is straightforward but the pressure data are much more complicated and only if the changes in the crystalline state at different pressures are known, we will have a better understanding of the dependence of some fundamentals in the hydrogen bonded systems. A clear example of this approach is given for urea.     

Hydrogen Bonding in Liquid Water and in the Hydration Shell of Salts

A near‐IR spectral study on pure water and aqueous salt solutions is used to investigate stoichiometric concentrations of different types of hydrogen‐bonded water species in liquid water and in water comprising the hydration shell of salts. Analysis of the thermodynamics of hydrogen‐bond formation signifies that hydrogen‐bond making and breaking processes are dominated by enthalpy with non‐negligible heat capacity effects, as revealed by the temperature dependence of standard molar enthalpies of hydrogen‐bond formation and from analysis of the linear enthalpy–entropy compensation effects. A generalized method is proposed for the simultaneous calculation of the spectrum of water in the hydration shell and hydration number of solutes. Resolved spectra of water in the hydration shell of different salts clearly differentiate hydrogen bonding of water in the hydration shell around cations and anions. A comparison of resolved liquid water spectra and resolved hydration‐shell spectra of ions highlights that the ordering of absorption frequencies of different kinds of hydrogen‐bonded water species is also preserved in the bound state with significant changes in band position, band width, and band intensity because of the polarization of water molecules in the vicinity of ions.     

Intermolecular force constants of hcn in the condensed phase

A simple theory of linear lattice is applied to the hydrogen bonded linear chain system of HCN to calculate the intermolecular force constants at different temperatures in the condensed phase. The strong CN bond is assumed to remain unperturbed in the hydrogen bond formation. The sharp change in intermolecular force constant while passing from the crystalline to the liquid phase is interpreted as a characteristic of this phase transition (fusion).     

Dielectric studies of water clusters in cyclodextrins: Relevance to the transition between slow and fast forms of thrombin

Cyclodextrins are useful models in the study of hydrogen bonded water clusters. In alpha-cyclodextrin hexahydrate (alpha-CD.6H2O), water molecules are ordered and occupy well-defined positions whereas in the larger beta-cyclodextrin dodecahydrate (beta-CD.12H2O), there is considerable disorder with water molecules freely arranged over several possible sites. Here it is shown that beta-CD exhibits substantial structural flexibility and proton mobility compared with alpha-CD which is relatively very rigid and exhibits negligible short-range protonic conduction. These properties are directly controlled by the effective dielectric constant of the molecule, which is determined by the rotational freedom of water molecules in the hydrogen bond network. This model may be relevant to proteins where water clusters of this kind are found on the protein surface and occasionally in the protein interior. The case of thrombin, an allosteric enzyme incorporating a network of 20 internal hydrogen bonded water molecules, is discussed.     

Cooperative enhancement of water binding to crownophane by multiple hydrogen bonds: analysis by high level ab initio calculations.

The intermolecular interaction energy of the model system of the water-crownophane complex was analyzed. The water molecule has four hydrogen bonds, with the two hydrogen-donating phenolic hydroxy groups and two hydrogen-accepting oxygen atoms of the poly-oxyethylene chain of the crownophane in the complex. The MP2/6-311G(2d,2p) level calculations of the model system of the complex (hydrogen donating unit + hydrogen accepting unit + water) indicate that the binding energy of the water is 21.85 kcal/mol and that the hydrogen bond cooperativity increases the binding energy as much as 3.67 kcal/mol. The calculated interaction energies depend on the basis set, while the basis set dependence of the cooperative increment is negligible. Most of the cooperative increment is covered by the HF level calculation, which suggests that the major source of the hydrogen bond cooperativity in this system has its origin in induction. The BLYP/6-311G** and PW91/6-311G** level interaction energies of the model system are close to the MP2/6-311G** interaction energies, which suggests that the DFT calculations with these functionals are useful methods to evaluated the interactions of hydrogen bonded systems.     

A tight binding model for water

We demonstrate for the first time a tight binding model for water incorporating polarizable oxygen atoms. A novel aspect is that we adopt a "ground up" approach in that properties of the monomer and dimer only are fitted. Subsequently we make predictions of the structure and properties of hexamer clusters, ice-XI and liquid water. A particular feature, missing in current tight binding and semiempirical hamiltonians, is that we reproduce the almost two-fold increase in molecular dipole moment as clusters are built up toward the limit of bulk liquid. We concentrate on properties of liquid water, particularly dielectric constant and self diffusion coefficient, which are very well rendered in comparison with experiment. Finally we comment on the question of the contrasting densities of water and ice which is central to an understanding of the subtleties of the hydrogen bond.     

Spectroscopic characterization of microscopic hydrogen-bonding disparities in supercritical water

The local hydrogen-bonding environment in supercritical water (380 degrees C, 300 bars, density 0.54 gcm3) was studied by x-ray Raman scattering at the oxygen K edge. The spectra are compared to those of the gas phase, liquid surface, bulk liquid, and bulk ice, as well as to calculated spectra. The experimental model systems are used to assign spectral features and to quantify specific local hydrogen-bonding situations in supercritical water. The first coordination shell of the molecules is characterized in more detail with the aid of the calculations. Our analysis suggests that approximately 65% of the molecules in supercritical water are hydrogen bonded in configurations that are distinctly different from those in liquid water and ice. In contrast to liquid water the bonded molecules in supercritical water have four intact hydrogen bonds and in contrast to ice large variations of bond angles and distances are observed. The remaining approximately 35% of the molecules exhibit two free O-H bonds and are thus either not involved in hydrogen bonding at all or have one or two hydrogen bonds on the oxygen side. We determine an average O-O distance of 3.1+/-0.1 A in supercritical water for the H bonded molecules at the conditions studied here. This and the corresponding hydrogen bond lengths are shown to agree with neutron- and x-ray-diffraction data at similar conditions. Our results on the local hydrogen-bonding environment with mainly two disparate hydrogen-bonding configurations are consistent with an extended structural model of supercritical water as a heterogeneous system with small patches of bonded molecules in various tetrahedral configurations and surrounding nonbonded gas-phase-like molecules.     

Segmental‐ and normal‐mode dielectric relaxation of poly(propylene glycol) under pressure

Dielectric measurements were obtained on poly(propylene glycol) (molecular weight: 4000 Da) at pressures in excess of 1.2 GPa. The segmental (α process) and normal‐mode (α′ process) relaxations exhibited different pressure sensitivities of their relaxation strengths, as well as their relaxation times. Such results are contrary to previous reports, and (at least for the dielectric strength) can be ascribed to the capacity for intermolecular hydrogen‐bond formation in this material. With equation‐of‐state measurements, the relative contributions of volume and thermal energy to the α‐relaxation times were quantified. Similar to other H‐bonded liquids, temperature is the more dominant control variable, although the effect of volume is not negligible. © 2003 Wiley Periodicals, Inc. J Polym Sci Part B: Polym Phys 41: 3047–3052, 2003     

Solvent effect on hydrogen bonded Tyr⋯Asp⋯Arg triads: Enzymatic catalyzed model system

The hydrogen bond plays a vital role in structural arrangement, intermediate state stabilization, materials function, and biological activity of certain enzymatic reactions. The solvent and electronic effects on hydrogen bonds are illustrated employing the polarizable contimuum model at B3LYP/6–311++G(d,p) level. Geometry optimizations reflect the significant solvent and electronic effect. The proton departs spontaneously upon oxidation from the hydroxyl group of tyrosyl in hydrogen bonded Tyr⋯Asp⋯Arg triads in both gas phase and solvents. The electron transfer isomers are observed for anionic triads, no matter what the solvent is. The difference of distance between two hydrogen bonds is enlarged in solvent as compared to that in gas phase. The electronic effect on IR spectra is distinctive. The tyrosyl fragment tends to be oxidized and the arginine moiety is easier to bind an excess electron. The variations of chemical shift and spin-spin coupling constant are more significant upon electron transfer than upon solvent dielectric constant. The augmentation of solvent dielectric constant stabilizes the system, enhances the difference of isomers, and increases the vertical ionization potential and vertical electron affinity values.     

Thermodynamic and dynamic anomalies in a one-dimensional lattice model of liquid water

We investigate the occurrence of waterlike thermodynamic and dynamic anomalous behavior in a one dimensional lattice gas model. The system thermodynamics is obtained using the transfer matrix technique and anomalies on density and thermodynamic response functions are found. When the hydrogen bond (molecules separated by holes) is more attractive than the van der Waals interaction (molecules in contact) a transition between two fluid structures is found at null temperature and high pressure. This transition is analogous to a 'critical point' and intimately connects the anomalies in density and in thermodynamic response functions. Monte Carlo simulations were performed in the neighborhood of this transition and used to calculate the self diffusion constant, which increases with density as in liquid water.     

Hydrogen network fluctuations of associating liquids: dielectric relaxation of ethylene glycol oligomers and their mixtures with water

Complex dielectric spectra of ethylene glycol and of various derivatives as well as of mixtures of water with an ethylene glycol oligomer and with a poly(ethylene glycol) dimethyl ether oligomer have been measured. The spectra can be well represented by a Cole-Cole [Cole and Cole, J. Chem. Phys. 9, 341 (1941)] spectral function. The extrapolated low frequency (static) permittivity of this function has been evaluated to yield the effective dipole orientation correlation factor of the liquids. The relaxation time of the ethylene glycols displays a characteristic dependence upon the ratio of concentrations of hydrogen bond donating and accepting groups, indicating two opposing effects. With increasing availability of hydrogen bonding sites effects of association and also of dynamical destabilization increase. Both effects exist also in the mixture of water with the oligomers. They are discussed in terms of a wait-and-switch model of dipole reorientation in associating liquids. Another feature in the dependence of the dielectric relaxation time of poly(ethylene glycol)/water mixtures upon mixture composition has been tentatively assigned to precritical demixing behavior of the binary liquids in some temperature range.     

Intermolecular proton transport along the hydrogen bond and the dielectric properties of ice crystals

Conclusion We have attempted here to explain some of the dielectric properties of ice crystals by a concept involving the activated transport of a proton along the hydrogen bond. The choice of the almost symmetrical curve with two minima for a proton in the hydrogen bridge and the rejection of tunnel transport of a proton makes it possible to suggest a theory which explains adequately the dependence of the low frequency dielectric constant on temperature and the phenomenon of the dielectric relaxation of ice. The electrical polarization of an ice crystal according to our model is produced by the defect structure of the ice, the ion pairs, which arises when the proton moves between two neutral water molecules.This particular model does not involve orientation or Bjerrum defects in the ice structure and raises a doubt as to the necessity of introducing them into explanations of the dielectric properties of ice.Moscow Physicotechnical Institute. Translated from Zhurnal Strukturnoi Khimii, Vol. 11, No. 3, pp. 415–420, May–June, 1970.     

The effect of pressure on the hydration structure around hydrophobic solute: a molecular dynamics simulation study

Molecular dynamics simulations are performed to study the effects of pressure on the hydrophobic interactions between neopentane molecules immersed in water. Simulations are carried out for five different pressure values ranging from 1 atm to 8000 atm. From potential of mean force calculations, we find that with enhancement of pressure, there is decrease in the well depth of contact minimum (CM) and the relative stability of solvent separated minimum over CM increases. Lower clustering of neopentane at high pressure is also observed in association constant and cluster-structure analysis. Selected site-site radial distribution functions suggest efficient packing of water molecules around neopentane molecules at elevated pressure. The orientational profile calculations of water molecules show that the orientation of water molecules in the vicinity of solute molecule is anisotropic and this distribution becomes flatter as we move away from the solute. Increasing pressure slightly changes the water distribution. Our hydrogen bond properties and dynamics calculations reveal pressure-induced formation of more and more number of water molecules with five and four hydrogen bond at the expense of breaking of two and three hydrogen bonded water molecules. We also find lowering of water-water continuous hydrogen bond lifetime on application of pressure. Implication of these results for relative dispersion of hydrophobic molecules at high pressure are discussed.     

Excited‐State Hydrogen Bonding Strengthening and Weakening with Intramolecular Charge Transfer in Resorufin‐Water Complexes: A TD‐DFT Study

The geometric structures, infrared spectra and hydrogen bond binding energies of the various hydrogen‐bonded Res^?‐water complexes in states S0 and S1 have been calculated using the density functional theory (DFT) and time‐dependent density functional theory (TD‐DFT) methods, respectively. Based on the changes of the hydrogen bond lengths and binding energies as well as the spectral shifts of the vibrational mode of the hydroxyl groups, it is demonstrated that hydrogen bonds HB‐II, HB‐III and HB‐IV are strengthened while hydrogen bond HB‐I is weakened in the four singly hydrogen‐bonded Res^?‐Water complexes upon photoexcitation. When the four hydrogen bonds are formed simultaneously between one resorufin anion and four water molecules in the Res^?‐4Water complex, all the hydrogen bonds are weakened in both the ground and excited states compared with those in the corresponding singly hydrogen‐bonded Res^?‐Water complexes. Furthermore, in complex Res^?‐4Water, hydrogen bonds HB‐II and HB‐IV are strengthened while hydrogen bonds HB‐I and HB‐III are weakened after the electronic excitation. The hydrogen bond strengthening and weakening in the various hydrogen‐bonded Res^?‐water complexes should be due to the redistribution of the charges among the four heteroatoms (O_1‐3 and N₁) within the resorufin molecule upon the optical excitation.     

Self‐Assembly and Gelation of Poly(aryl ether) Dendrons Containing Hydrazide Units: Factors Controlling the Formation of Helical Structures

Self‐assembly of AB₂ and AB₃ type low molecular weight poly(aryl ether) dendrons that contain hydrazide units were used to investigate mechanistic aspects of helical structure formation during self‐assembly. The results suggest that there are three important aspects that control helical structure formation in such systems with acyl hydrazide/hydrazone linkage: i) J‐type aggregation, ii) the hydrogen‐bond donor/acceptor ability of the solvent, and iii) the dielectric constant of the solvent. The monomer units self‐assemble to form dimer structures through hydrogen‐bonding and further assembly of the hydrogen‐bonded dimers leads to macroscopic chirality in the present case. Dimer formation was confirmed by NMR spectroscopy and by mass spectrometry. The self‐assembly in the system was driven by hydrogen‐bonding and π–π stacking interactions. The morphology of the aggregates formed was examined by scanning electron microscopy, and the analysis suggests that aprotic solvent systems facilitate helical fibre formation, whereas introduction of protic solvents results in the formation of flat ribbons. This detailed mechanistic study suggests that the self‐assembly follows a nucleation–elongation model to form helical structures, rather than the isodesmic model.     

Hydrogen bonding to divalent sulfur

A combination of vapor phase infrared spectroscopy and ab initio calculations has been used to show that sulfur is weaker than, but nearly equivalent to, oxygen as a hydrogen bond acceptor. Enthalpies of hydrogen bond formation were obtained for the hydrogen bonded complexes formed between methanol and either dimethyl sulfide or dimethyl ether by temperature dependence studies of the infrared spectra.     

Effect of temperature and pressure on the structure, dynamics, and hydrogen bond properties of liquid N-methylacetamide: a molecular dynamics study

The structure and dynamical properties of liquid N-methylacetamides (NMA) are calculated at five different temperatures and at four different pressures using classical molecular dynamics simulations. Our results are analyzed in terms of pressure-induced changes in structural properties by investigating the radial distribution functions of different atoms in NMA molecule. It is found that the first peak and also the second peak of C-O and N-H are well defined even at higher temperature and pressure. It is also observed that the number of hydrogen bonds increase with application of pressure at a given temperature. On the other hand, the calculated hydrogen bond energy (E(HB)) shows that the stability of hydrogen bond decreases with increasing of pressure and temperature. Various dynamical properties associated with translational and rotational motion of neat NMA are calculated and the self-diffusion coefficient of NMA is found to be in excellent agreement with the experiment and the behavior is non-Arrhenius at low temperatures with application of pressures. The single particle orientational relaxation time for dipole vector and N-C vector are also calculated and it is found that the orientational relaxation time follows Arrhenius behavior with a variation of temperature and pressure.     

Synergistic effect between metal coordination and hydrogen bonding in phosphate and halide recognition

The equilibrium constant for binding of dimethyl phosphate to a Co(III) complex in water increases from 6.2 to 210 M-1 upon addition of a single hydrogen bond between the bound phosphate and the metal complex. Crystal structure reveals that the hydrogen bond distance is 1.96 A. The synergistic effect between metal coordination and hydrogen bonding can also be observed for fluoride binding but not for bromide binding.     

A non-polarizable model of water that yields the dielectric constant and the density anomalies of the liquid: TIP4Q

A four-site rigid water model is presented, whose parameters are fitted to reproduce the experimental static dielectric constant at 298 K, the maximum density of liquid water and the equation of state at low pressures. The model has a positive charge on each of the three atomic nuclei and a negative charge located at the bisector of the HOH bending angle. This charge distribution allows increasing the molecular dipole moment relative to four-site models with only three charges and improves the liquid dielectric constant at different temperatures. Several other properties of the liquid and of ice Ih resulting from numerical simulations with the model are in good agreement with experimental values over a wide range of temperatures and pressures. Moreover, the model yields the minimum density of supercooled water at 190 K and the minimum thermal compressibility at 310 K, close to the experimental values. A discussion is presented on the structural changes of liquid water in the supercooled region where the derivative of density with respect to temperature is a maximum.