Encoding and decoding hydrogen-bond patterns of organic compounds

A new derivation of the GLYCAM06 force field, which removes its previous specificity for carbohydrates, and its dependency on the AMBER force field and parameters, is presented. All pertinent force field terms have been explicitly specified and so no default or generic parameters are employed. The new GLYCAM is no longer limited to any particular class of biomolecules, but is extendible to all molecular classes in the spirit of a small-molecule force field. The torsion terms in the present work were all derived from quantum mechanical data from a collection of minimal molecular fragments and related small molecules. For carbohydrates, there is now a single parameter set applicable to both alpha- and beta-anomers and to all monosaccharide ring sizes and conformations. We demonstrate that deriving dihedral parameters by fitting to QM data for internal rotational energy curves for representative small molecules generally leads to correct rotamer populations in molecular dynamics simulations, and that this approach removes the need for phase corrections in the dihedral terms. However, we note that there are cases where this approach is inadequate. Reported here are the basic components of the new force field as well as an illustration of its extension to carbohydrates. In addition to reproducing the gas-phase properties of an array of small test molecules, condensed-phase simulations employing GLYCAM06 are shown to reproduce rotamer populations for key small molecules and representative biopolymer building blocks in explicit water, as well as crystalline lattice properties, such as unit cell dimensions, and vibrational frequencies.

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GLYCAM06: a generalizable biomolecular force field. Carbohydrates.

Starting from known properties of non-specific salt effects on the surface tension at an air–water interface, we propose the first general, detailed qualitative molecular mechanism for the origins of ion-specific (Hofmeister) effects on the surface potential difference at an air–water interface; this mechanism suggests a simple model for the behaviour of water at all interfaces (including water–solute interfaces), regardless of whether the non-aqueous component is neutral or charged, polar or non-polar Specifically, water near an isolated interface is conceptually divided into three layers, each layer being 1 water-molecule thick We propose that the solute determines the behaviour of the adjacent first interfacial water layer ( I 1 ); that the bulk solution determines the behaviour of the third interfacial water layer ( I 3 ), and that both I 1 and I 3 compete for hydrogen-bonding interactions with the intervening water layer ( I 2 ), which can be thought of as a transition layer The model requires that a polar kosmotrope (polar water-structure maker) interact with I 1 more strongly than would bulk water in its place; that a chaotrope (water-structure breaker) interact with I 1 somewhat less strongly than would bulk water in its place; and that a non-polar kosmotrope (non-polar water-structure maker) interact with I 1 much less strongly than would bulk water in its place We introduce two simple new postulates to describe the behaviour of I 1 water molecules in aqueous solution The first, the ‘relative competition’ postulate, states that an I 1 water molecule, in maximizing its free energy (—δG), will favour those of its highly directional polar (hydrogen-bonding) interactions with its immediate neighbours for which the maximum pairwise enthalpy of interaction (—δ H ) is greatest; that is, it will favour the strongest interactions We describe such behaviour as ‘compliant’, since an I 1 water molecule will continually adjust its position to maximize these strong interactions Its behaviour towards its remaining immediate neighbours, with whom it interacts relatively weakly (but still favourably), we describe as ‘recalcitrant’, since it will be unable to adjust its position to maximize simultaneously these interactions The second, the ‘charge transfer’ postulate, states that the strong polar kosmotrope–water interaction has at least a small amount of covalent character, resulting in significant transfer of charge from polar kosmotropes to water–especially of negative charge from Lewis bases (both neutral and anionic); and that the water-structuring effect of polar kosmotropes is caused not only by the tight binding (partial immobilization) of the immediately adjacent ( I 1 ) water molecules, but also by an attempt to distribute among several water molecules the charge transferred from the solute When extensive, cumulative charge transfer to solvent occurs, as with macromolecular polyphosphates, the solvation layer (the layer of solvent whose behaviour is determined by the solute) can become up to 5- or 6-water-molecules thick We then use the ‘relative competition’ postulate, which lends itself to simple diagramming, in conjunction with the ‘charge transfer’ postulate to provide a new, startlingly simple and direct qualitative explanation for the heat of dilution of neutral polar solutes and the temperature dependence of relative viscosity of neutral polar solutes in aqueous solution This explanation also requires the new and intriguing general conclusion that as the temperature of aqueous solutions is lowered towards o °C, solutes tend to acquire a non-uniform distribution in the solution, becoming increasingly likely to cluster 2 water molecules away from other solutes and surfaces (the driving force for this process being the conversion of transition layer water to bulk water) The implications of these conclusions for understanding the mechanism of action of general (gaseous) anaesthetics and other important interfacial phenomena are then addressed

https://www.cambridge.org/core/services/aop-cambridge-core/content/view/S0033583500005369

The Hofmeister effect and the behaviour of water at interfaces.

Protein Radicals in Enzyme Catalysis.

Systematic analysis of structural data as a research technique in organic chemistry

A detailed single‐crystal structure analysis is reported for ethylene oxide hydrate. This confirms the polyhedral host lattice formed by 46 hydrogen‐bonded water molecules in a cubic unit cell of 12.03 A with space‐group symmetry Pm3n. Disordered ethylene oxide molecules occupy the six equivalent tetrakaidecahedral cavities, and their electron‐density distribution suggests that they are hindered axial rotors. Additional guest molecules, either ethylene oxide, oxygen, or nitrogen molecules occupy the two dodecahedral cavities with high disorder and low statistical weight. The compound is therefore nonstoichiometric having the limiting formula 2M·6C2H4O·46H2O, in which the percentage of M is variable. If M is assumed to be entirely ethylene oxide, as is likely from the method of preparation, the composition of the crystals obtained from an equilibrated aqueous solution of 8 mole % ethylene oxide at 9°C is 6.4C2H4O·46H2O.

Polyhedral Clathrate Hydrates. IX. Structure of Ethylene Oxide Hydrate

The compounds [(n−C4H9)4N+]nXn−·nyH2O have been prepared where X is F‐, Cl‐, Br‐, CH3CO2‐, CrO42‐, WO42‐, C2O42‐, HCO3‐, HPO42‐, and y is approximately 32. They form an isomorphous crystal series which is tetragonal with a=23.65±0.15 A, c=12.40±0.15 A.A similar series of the type [(i−C5H11)4N+]nXn−⋅ny′H2O has been prepared where X is F‐, Cl‐, CrO42‐, WO42‐, and y′ is approximately 40. They also form an isomorphous group which is orthorhombic with a=12.10±0.10 A, b=21.50±0.15 A, c=12.65±0.15 A.These compounds are believed to be of the clathrate type, similar in general character to the gas hydrates.

Hydrates of the Tetra n‐butyl and Tetra i‐amyl Quaternary Ammonium Salts

So that possible relationships between hydrogen-bond lengths and hydrogen-bond types could be investigated, it was decided to study by neutron diffraction the crystal structures of several molecules having nearly the same size and shape. Feasibility of crystallization of a homogeneous species was a prime criterion. The three methyl pyranosides selected for the studies had been previously investigated by X-ray diffraction. These were the crystals of methyl ..cap alpha..-glucopyranoside, methyl ..cap alpha..-mannopyranoside, and methyl ..cap alpha..-altopyranoside. Hydrogen bonding in these three structures is especially significant because they contain examples of five of the ten possible types of O-H-O interactions shown in Table I. The results of these neutron diffraction studies provided a systematic relationship between hydrogen-bond length and hydrogen-bond type in the three structures. Not all crystalline carbohydrates fall into their classifications as ''neatly'' as did those from the first three pyranosides. Complicating factors include the competitive effects of hydrogen bonds, polar and dipolar interactions, and van der Waals forces. Most noticeable feature of Table I is the predominance of the bonds of the donor-acceptor type which correspond to the shorter, stronger bonds and are part of the infinite chains or are the inner bonds of finite chains, a consequence ofmore » the ''cooperative effect'' which is also discussed. The anomeric effect of hydrogen bonding is also evaluated and the results are tabulated. Table II illustrates comparative X-ray data and neutron diffraction data on H--O bond lengths. Authors believe that the systematics of the hydrogen-bond data presented will form a useful framework with which to compare future experimental measurements and theoretical calculations.« less

G. A. Jeffrey

Papers

Polyhedral Clathrate Hydrates. IX. Structure of Ethylene Oxide Hydrate

Hydrates of the Tetra n‐butyl and Tetra i‐amyl Quaternary Ammonium Salts

Hydrogen-bond structure in carbohydrate crystals

Water structure in organic hydrates

A neutron diffraction study of the hydrogen bonding in the crystal structures of methyl α-d-mannopyranoside and methyl α-d-glucopyranoside