Description Of Hydrogen Bonds Research Articles

Crystal Structure and Physicochemical Properties of a New 4,4′-Diammoniumdiphenylether Triphosphate [C12H14N2O]2HP3O10 ·2H2O

Crystals of 4,4′-diammoniumdiphenylether triphosphate, [C12H14N2O]2HP3O10·2H2O (1), were prepared and grown at room temperature. Species 1 crystallizes in the triclinic system with centric space group $$ P\overline{1} $$ . Its unit cell dimensions are a = 10.487(2), b = 10.766(2), c = 15.553(2) A, α = 98.53(1)°, β = 107.55(1)°, γ = 103.31(2), with V = 1588.8(5) A3 and Z = 2. The structure was determined by X-ray data collection on a single-crystal and gives a clear description of hydrogen bonds interconnecting the triphosphoric groups so as to build [(HP3O10)2(H2O)]8− infinite inorganic chains that extend along the [110] direction. Organic cations, spreading along the [101] direction establish hydrogen bonding connections between the inorganic chains. The IR spectrum for the crystal confirms that most of the vibrational modes are comparable to similar triphosphates. The thermal properties reveal that the compound is stable to 90 °C.

Model of cooperative character of hydrogen bonds in water

A quantitative description of hydrogen bonds in liquid water is developed using a simple model. The proposed approach is based on the notion of a hydrogen bond as mediated by proton exchange between neighboring hydroxyl groups under adiabatic conditions with respect to the electron subsystem. Application of the model is illustrated by means of the example of analysis of the IR absorption spectrum of a thin water layer. It is shown that the structure of water in layers with thicknesses on the order of 1 μm differs from the structure of bulk water.

Proton transfer and polarity changes in ionic liquid–water mixtures: a perspective on hydrogen bonds from ab initio molecular dynamics at the example of 1-ethyl-3-methylimidazolium acetate–water mixtures—Part 1

The ionic liquid 1-ethyl-3-methylimidazolium acetate [C(2)C(1)Im][OAc] shows a great potential to dissolve strongly hydrogen bonded materials, related with the presence of a strong hydrogen bond network in the pure liquid. A first step towards understanding the solvation process is characterising the hydrogen bonding ability of the ionic liquid. The description of hydrogen bonds in ionic liquids is a question under debate, given the complex nature of this media. The purpose of the present article is to rationalise not only the existence of hydrogen bonds in ionic liquids, but also to analyse their influence on the structure of the pure liquid and how the presence of water, an impurity inherent to ionic liquids, affects this type of interaction. We perform an extensive study using ab initio molecular dynamics on the structure of mixtures of the ionic liquid 1-ethyl-3-methylimidazolium acetate with water, at different water contents. Hydrogen bonds are present in the pure liquid, and the presence of water modifies and largely disturbs the hydrogen bond network of the ionic liquid, and also affects the formation of other impurities (carbenes) and the dipole moment of the ions. The use of ab initio molecular dynamics is the recommended tool to explore hydrogen bonding in ionic liquids, as an explicit electronic structure calculation is combined with the study of the condensed phase.

Redetermination of despujolsite, Ca3Mn4+(SO4)2(OH)6·3H2O

The crystal structure of despujolsite [tricalcium manganese bis­(sulfate) hexahydroxide tri­hydrate], the Ca/Mn member of the fleischerite group, ideally Ca3Mn4+(SO4)2(OH)6·3H2O, was previously determined based on X-ray diffraction intensity data from photographs, without H-atom positions located [Gaudefroy et al. (1968 ▶). Bull. Soc. Fr. Minéral. Crystallogr. 91, 43–50]. The current study redetermines the structure of despujolsite from a natural specimen, with all H atoms located and with higher precision. The structure of despujolsite is characterized by layers of CaO8 polyhedra (m.. symmetry) inter­connected by Mn(OH)6 octa­hedra (32. symmetry) and SO4 tetra­hedra (3.. symmetry) along [001]. The average Ca—O, Mn—O and S—O bond lengths are 2.489, 1.915, and 1.472 Å, respectively. There are two distinct hydrogen bonds that stabilize the structural set-up. This work represents the first description of hydrogen bonds in the fleischerite group of minerals.

An improved semiempirical method for hydrated systems

Hydrogen bonding is a key feature in many chemical and biochemical processes as well as in hydration phenomena. In previous works, it has been shown that description of hydrogen bonds by standard semiempirical methods is rather inaccurate and contains serious nonphysical artifacts. We have recently suggested a scheme to overcome this important limitation. Basically, we have proposed to replace the Gaussian correction function in the core-core interaction term of standard Austin model 1 (AM1) or parameterized model 3 (PM3) methods by a suitable function that is parameterized to correctly reproduce the long-range behavior of the interaction potential. A set of parameters for describing water-water interactions was derived using a highly refined ab initio potential energy surface for the water dimer. The present work extends that approach to the case of solute-solvent interactions of organic molecules in aqueous solution. Specifically, parameters for HH, HC, HN, HO, OC, ON and OO core-core terms are reported for use with the PM3 method. A series of tests for prototypical 1:1 complexes have been carried out and comparison with high-level ab initio results made. Errors in computed interaction energies are substantially smaller than those obtained in standard PM3 calculations, the root mean square decreasing from 3.41 to 1.74 kcal/mol. Artifacts in the potential energy surfaces (shoulders, spurious minima) present in PM3 are corrected with the new parameterization.

Study on the Correlation and Prediction of Octanol/Water Partition Coefficients by Quantum Chemical Calculations

The influence and applicability of several quantum chemically obtained descriptors on the correlation/prediction of octanol/water partition coefficients (log Pow) at 298 K is thoroughly studied. The log Pow values are expressed as a linear equation in terms of several contributions to the chemical potential. The chosen parameters reflect the molecular interactions between the solute and the solvent molecules and account for cavity effects, polarity and polarizability, and the distribution of the electrostatic potential. The description of hydrogen-bonding by the sums of minima and maxima of the electrostatic potential is studied in detail for a wide variety of molecules. All descriptors can be easily computed by standard ab initio methods and result in good correlations with experimental log Pow values. The prediction power of the method is tested for a set of solutes, possessing multiple functional groups, intramolecular hydrogen-bonding, and zwitterionic structures.

MODELLING OF BETA -CYCLODEXTRIN WITH L-ALPHA -AMINOACIDS RESIDUES

A computational study of host-guest inclusion complexes between β-cyclodextrin (β-CD) and the 20 natural L-α-aminoacids and some selected pentapeptides was carried out and aimed at understanding the nature of the driving forces and mechanism leading to their formation. Relative complexation energies for the complexes with β-CD were calculated in both cases and the solvation Gibbs free energies were also evaluated for the single L-α-aminoacids. The computed results indicate strong possibilities of formation of inclusion complexes between β-CD and single L-α-aminoacids as well as pentapeptides which have hydrophobic side chains. In addition, noteworthy interactions of the side chain of the pentapeptides with the β-CD were also elucidated. A detailed molecular dynamics calculation of one of the representative pentapeptide/β-CD inclusion complex (β-CD/CH3-Ala-Ala- TYR-Ala-Ala-CH3) in aqueous solution has also been carried out. Molecular dynamics calculations support aspects connected with the formation and description of hydrogen bonds and with the role of dispersion forces in the inclusion complex in water.

Highly Accurate Estimates of Hydrogen-Bond Energies Relying on Basis Set Convergence Patterns

We introduce a method for the determination of highly accurate estimates of the electronic interaction energies in uncharged hydrogen-bonded clusters, using basis set convergence patterns (=BSCP) of the aug-cc-pVxZ series of basis sets at MP2(FC) level of theory. The method is characterized by its robustness toward systematic deficiencies of MP2(FC)/aug-cc-pVxZ description of hydrogen bonds. The achieved reliability is due to a one parameter scaling ansatz that transforms the disadvantages of the basis set superposition error into precious information. The method is applied to the trimer of hydrogen fluoride and the trimer of water which were both fully geometry optimized up to MP2(FC)/aug-cc-pVQZ level of theory. The electronic interaction energy is predicted to be −15.05 kcal/mol for the trimer of hydrogen fluoride and −15.91 kcal/mol for the trimer of water.