Brian J. Teppen

An investigation into intramolecular hydrogen bonding: impact of basis set and electron correlation on the ab initio conformational analysis of 1,2-ethanediol and 1,2,3-propanetriol

Abstract Electron correlation effects are especially important in systems with strong nonbonded interactions. Despite this, very few ab initio studies of polyfunctional alcohols have included correlation effects in their geometry optimizations. In order to better understand intramolecular hydrogen bonding and to develop more reliable energy and geometric parameters for future molecular modeling, we optimized the geometries of 10 conformers of 1,2-ethanediol (ethylene glycol) and 11 conformers of 1,2,3-propanetriol (glycerol) at the HF/4-21G, HF/6-311G∗∗ and MP2/6-311G∗∗ levels of theory. All three computational methods are able to predict differences between internal coordinates optimized in different regions of conformational space, to within typical experimental accuracies. However, the inclusion of electron correlation has a major impact on the absolute values of these internal coordinates and on the depths of the associated energy minima. Compared with our HF/6-311G∗∗ results, the MP2-optimized structures have longer Cue5f8O bonds by up to 0.020 A, Oue5f8H bonds that are up to 0.023 A longer, Oue5f8Cue5f8C angles that are often 1 ° smaller, Hue5f8Oue5f8C angles in excess of 4 ° smaller, and torsional angles that may deviate from ideal trans or gauche values by an additional 5 ° for heavy-atom torsions and 8 ° for Hue5f8Oue5f8Cue5f8C torsions. The net effect of all these conformational rearrangements is to greatly enhance intramolecular hydrogen bonding. Nonbonded O … H distances invariably decrease, by up to 0.19 A, and the alignments of hydrogens with hypothetical lone-pair orbitals on oxygen acceptors improve. Electron correlation selectively stabilizes those conformers with more intramolecular hydrogen bonds, but decreases the energy differences among conformers with the same number of hydrogen bonds. The errors associated with single-point MP2 energy calculations at HF-optimized geometries appear to increase with the size of the system, as do differences between MP2- and HF-optimized Oue5f8Cue5f8Cue5f8O torsional angles. Thus, molecular mechanics parameters derived from MP2/6-311G∗∗ optimizations of prototypical small molecules such as ethylene glycol and glycerol are expected to result in significantly different macromolecular energies and structures than those based on HF/6-311G∗∗ optimizations.

Ab initio investigations pertaining to aluminum in tetrahedral versus octahedral sites of clay minerals

Abstract The structures and atomic charges of several aluminum and silicon oxide systems—[Al(OH)4]−, Al(OH3)(H2O)3, Al(OH)2(H2O)2ue5f8(OH)2ue5f8Al(OH)2(H2O)2, [Al(OH)3ue5f8Oue5f8Si(OH)3]−, and Al(OH)2(H2O)3ue5f8Oue5f8Si(OH)3—representing compounds with tetrahedral and octahedral coordination, were investigated by ab initio RHF and MP2 geometry refinements and by density functional calculations. In addition, structures and CHELPG charges were determined for the silicic acid dimer, [Si(OH)4]2, at equilibrium and at various displacements from the equilibrium intermolecular separation, in order to determine the effects of molecular association on partial atomic charges. The calculations were performed because the investigated compounds are fragments representative of phyllosilicate soil minerals such as smectite clays, and the results can be used to augment the database available for developing force field parameters for molecular dynamics simulations of adsorption phenomena at the clay mineral/aqueous solution interface. Furthermore, the results make it possible to discuss the effects of electron correlation on structures of this kind.

Theoretical structure investigations of N-acetyl-l-proline amide

Abstract The potential energy surface of N -acetyl-l-proline amide has been investigated via RHF, AM1, and PM3 calculations. The results show significant differences between these methods: seven local minima can be found with RHF, three with AM1, 17 with PM3. The conformation of the RHF/6-31G∗ global minimum corresponds to the γ-turn structure of polypeptides. In contrast to this, the proline conformer that participates in the formation of ten-membered β-turns in peptide chains has a relatively high energy in the dipeptide.

Conformational analysis and structural study by ab initio gradient geometry optimizations of the model tripeptide N-formyl L-alanyl L-alanine amide

Abstract The geometries of 15 conformations of the model tripeptide N-formyl l -alanyl l -alanine amide (Ala-Ala) were determined by ab initio gradient geometry refinements at the HF/4-21G level. The results can be compared with previous HF/4-21G calculations on the single residue, N-formyl alanine amide (Ala), and the model hexapeptide, N-formyl pentaalanine amide (Penta-Ala). Cooperative energy effects are found in Ala-Ala that are subtle in some (φ1, ψ1 and φ2, ψ2) conformations, such as (C7eq C7ax), (β, C7eq) and (C7ax, C7ax), but more pronounced in bend forms, such as (C7eq, α), (C7eq, α l ), and (C7ax, 3 10 ). Optimization of α-helical structures leads to 3 10 -type helices, both in empirical charm m and ab initio HF/4-21G calculations, away from αR. This property of the calculated vacuum structures is in agreement with experimental investigations of short alanine based peptides in aqueous solution. The conformationally dependent structural trends found here for Ala-Ala are in agreement with the trends previously derived for Ala and Penta-Ala. They are particularly significant for the N-C(α)-C angle. This parameter shows variations of up to 8° in the selected conformers and, regardless of how the residues are combined, its extension follows the approximate sequence β 3 10 -helix.

Conformational geometry functions: additivity and cooperative effects

Abstract The conformational geometry changes associated with torsional motion about Cue5f8C single bonds are reported for some 47 basic organic molecules of the type (X,Y,Z)Cue5f8C(X′,Y′,Z′), and for the ,ψ space of the model dipeptides N-acetyl N′-methyl amides of glycine and alanine. All structures were determined by ab initio HF 4−21 G geometry optimizations. Employing natural cubic spline parameters, a program was written for use in empirical modeling parameter development, which calculates the bond lengths and angles of the reported compounds as functions of the associated torsional angles at any point in conformational space. The additivity of the conformational geometry functions is explored and illustrates how cooperative effects emerge in complex molecules. The results are instructive for procedures in which the properties of molecular fragments are used to derive force field parameters for the empirical modeling of complex molecules.

Investigation of electron correlation effects on molecular geometries

Abstract A survey is presented as part of an ongoing program in which the effects of electron correlation on molecular structures are studied for the purpose of obtaining data that can be used in developing force field parameters for empirical molecular modeling. In our approach, molecular structures devoid of dispersion forces, i.e. optimized at the Hartree-Fock (HF) level, are compared with the same structures optimized at the MP2 level, in which the dispersion forces are “switched on”. So far, the investigations have included hydrocarbons, to study aliphatic non-bonded interactions, systems with internal hydrogen bonding (ethylene glycol, glycerol, glycine and the model dipeptide N -formyl alanine amide), and silicates, which are studied in order to derive force field parameters applicable to modeling clays. In hydrocarbons, electron correlation effects lead to contractions in 1,5-non-bonded distances in all rotamers with gauche (G) torsions, particularly in GG sequences, in which small changes in torsional angles (

SOME GENERAL ASPECTS OF TORSIONAL SENSITIVITY AND THE GG-EFFECT

Abstract The geometries of 28 compounds of type X–C1–C2–C3–Y, with X,Y=CH 3 , F, Cl, OH, NH 2 , COH, and COOH, were fully optimized by ab initio HF/4-21G calculations at 30° grid points in their respective φ (X–C1–C2–C3), ψ (C1–C2–C3–Y)-torsional spaces. The results make it possible to construct parameter surfaces and their gradients in φ , ψ -space. The magnitude of the gradient, |∇ P |=[( ∂P / ∂φ ) 2 +( ∂P / ∂ψ ) 2 ] 1/2 , of a structural parameter P (a bond length, bond angle, or non-bonded distance) in φ , ψ -torsional space is a measure of torsional sensitivity (TS); i.e. a measure of the extent to which bond lengths, bond angles, and non-bonded distances change at a point in φ , ψ -space with backbone torsional angles. It is found that TS is not constant throughout the conformational space of a molecule, but varies in a characteristic way. It seems that, regardless of the nature of X or Y, extended forms are typically in regions of low TS; puckered conformations, of high TS. Conformations with two sequential gauche torsional angles (GG sequences) are characterized by high TS of 1,5-non-bonded distances concomitant with relatively low TS of other internal coordinates. This property of GG sequences is the source of a stabilizing and cooperative energy increment that is not afforded by other torsional sequences, such as trans – trans or trans – gauche . A structural data base, consisting of thousands of HF/4-21G structures of X–C–C–Y and X–C–C–C–Y systems has been assembled and is available on a CD.

Quantitation and measurement of equivalent conductance of unidentified analytes by suppressed ion chromatography using conductivity detection

Abstract Suppressed ion chromatography with conductivity detection was used to quantify organic anions in solution. A procedure is described whereby the normality and the equivalent conductance of unidentified analyte ions can be determined with an accuracy of greater than 90% using two different regenerants but only a single eluent. The proposed method is based on the fact that the conductivity detectors response is directly proportional to the concentrations of both the analyte and its counterions, which in suppressed IC are supplied by the regenerant. While results for monoprotic acids were excellent, results for polyprotic acids were less satisfactory, perhaps due to incomplete dissociation of the analyte.