Ching-Hsing Yu

MOLECULAR DYNAMICS SIMULATIONS OF SORPTION OF ORGANIC COMPOUNDS AT THE CLAY MINERAL / AQUEOUS SOLUTION INTERFACE

The adsorption of trichloroethene, C2HCl3, on clay mineral surfaces in the presence of water has been modeled as an example describing a general program that uses molecular dynamics simulations to study the sorption of organic materials at the clay mineral/aqueous solution interface. Surfaces of the clay minerals kaolinite and pyrophyllite were hydrated at different water levels corresponding to partial and complete monolayers of water. In agreement with experimental trends, water was found to outcompete C2HCl3 for clay surface sites. The simulations suggest that at least three distinct mechanisms coexist for C2HCl3 on clay minerals in the environment. The most stable interaction of C2HCl3 with clay surfaces is by full molecular contact, coplanar with the basal surface. This kind of interaction is suppressed by increasing water loads. A second less stable and more reversible interaction involves adsorption through single‐atom contact between one Cl atom and the surface. In a third mechanism, adsorbed C2HCl3 never contacts the clay directly but sorbs onto the first water layer. To test the efficacy of existing force field parameters of organic compounds in solid state simulations, molecular dynamics simulations of several representative organic crystals were also performed and compared with the experimental crystal structures. These investigations show that, in general, in condensed‐phase studies, parameter evaluations are realistic only when thermal motion effects are included in the simulations. For chlorohydrocarbons in particular, further explorations are needed of atomic point charge assignments. © 1998 John Wiley & Sons, Inc. J Comput Chem 19: 144–153, 1998

Molecular dynamics simulations of the adsorption of proteins on clay mineral surfaces

Abstract Some initial results of molecular dynamics simulations of the adsorption of proteins on clay mineral surfaces are being reported. Specifically, the interactions of pyrophyllite surfaces with crambin, rubredoxin, and several oligopeptides were investigated. It is found that clay mineral surfaces can have a denaturing effect on adsorbed proteins for two reasons: (1) they are dehydrating agents, because they perturb the random environment of water molecules that globular proteins need to maintain their native structure; and (2) clay surfaces can establish non-bonded interactions with proteins which compete effectively with the interactions inside a peptide chain. The changes in secondary and tertiary protein structure induced by adsorption to pristine surfaces, or surfaces coated with water, lead to backbone torsions away from the most populated regions of φ,ψ-space, to regions which are not frequently populated in unperturbed proteins. β- and α R -conformations, specifically, are not stable on pyrophyllite but undergo transitions, with some preference, to an area close to C 7 eq . Because of the size of the adsorbed systems, unit cells with adsorbed peptides may be distorted, bulging at the site of adsorption, and displaying a continuously varying interlayer space between the empty parts and those that are occupied by an adsorbate. As a result, warped, or S-shaped basal planes are found.

Ab initio conformational analysis of N-formyl l-alanine amide including electron correlation

Abstract The conformational properties of N -formyl l -alanine amide (ALA) were investigated using RMP2/6-311G ∗∗ ab initio gradient geometry optimization. One hundred forty four structures of ALA were optimized at 30° grid points in its φ (N–C(α)), ψ (C(α)–C′) conformational space. Using cubic spline functions, the grid structures were then used to construct analytical representations of complete surfaces, in φ , ψ -space, of bond lengths, bond angles, torsional sensitivity and electrostatic atomic charges. Analyses show that, in agreement with previous studies, the right-handed helical conformation, α R , is not a local energy minimum of the potential energy surface of ALA. Comparisons with protein crystallographic data show that the characteristic differences between geometrical trends in dipeptides and proteins, previously found for ab initio dipeptide structures obtained without electron correlation, are also found in the electron-correlated geometries. In contrast to generally accepted features of force fields used in empirical molecular modeling, partial atomic charges obtained by the CHELPG method are found to be not constant, but to vary significantly throughout the φ , ψ -space. By comparing RHF and MP2 structures, the effects of dispersion forces on ALA were studied, revealing molecular contractions for those conformations, in which small adjustments of torsional angles entail large changes in non-bonded distances.

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)2(OH)2Al(OH)2(H2O)2, [Al(OH)3OSi(OH)3]−, and Al(OH)2(H2O)3OSi(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.

ø/ψ-Torsional dependence of peptide backbone bond-lengths and bond-angles: comparison of crystallographic and calculated parameters

Abstract The crystallographic NC(α), C(α)C′ and NC(α)C′ backbone parameters of 43 oligopeptides and the NC(α)C′ angles of 37 proteins were compared with peptide conformational geometry surfaces derived from ab initio calculations of N-acetyl N′-methyl alanine amide. The calculated values were obtained by spline-function representations of ab initio dipeptide conformational geometry maps which allow one to predict backbone bond lengths and angles in peptides and proteins as functions of the o[NC(α)]/ψ[C(α)C′]-torsions. When the parameters are ordered by regions in o/ψ-space defined by a 30° grid and region-average values calculated, the rms deviations between the crystallographic and calculated parameters in the most populated regions of the oligopeptides are 0.009A, 0.013A and 1.2°, for NC(α), C(α)C′ and NC(α)C′ respectively; and 1.2° for the NC(α)C′ angles in proteins. The flexibility in o/ψ-space is significant for the NC(α)C′ angles (observed variations of > 8°), but of lesser importance for the bond lengths (conformational variations of ∼0.02 A ). Thus, torsion dependent ideal geometry functions are recommended for the former, but not necessarily the latter, for use in various areas of protein study, such as protein crystallography and empirical molecular modeling procedures.

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.

Ab initio structural trends and torsional sensitivity in n-hexane and comparisons with crystallographic structural results

Abstract The molecular structures of n -hexane were determined by RHF/4-21G ab initio geometry optimization at 30° grid points in its three-dimensional τ 1 (C11–C8–C5–C1), τ 2 (C14–C11–C8–C5), τ 3 (C17–C14–C11–C8) conformational space. Of the resulting 12×12×12=1728 grid structures, 468 are symmetrically non-equivalent and were optimized constraining the torsions τ 1 , τ 2 , and τ 3 to the respective grid points, while all other structural parameters were relaxed without any constraints. From the results, complete parameter surfaces were constructed using natural cubic spline functions, which make it possible to calculate parameter gradients, |∇ P |=[(∂ P /∂ τ i ) 2 +(∂ P /∂ τ j ) 2 ] 1/2 , where P is a C–C bond length or C–C–C angle. The parameter gradients provide an effective measure of the torsional sensitivity of the system and indicate that dynamic activities in one part of the molecule can significantly affect the density of states, and thus the contributions to vibrational entropy, in another part. This opens the possibility of dynamic entropic conformational steering in complex molecules; i.e. the generation of free energy contributions from dynamic effects of one part of a molecule on another. When the conformational trends in the calculated C–C bond lengths and C–C–C angles are compared with average parameters taken from some 900 crystallographic structures containing n -hexyl fragments or longer C–C bond sequences, some correlation between calculated and experimental trends in angles is found, in contrast to the bond lengths for which the two sets of data are in complete disagreement. The results confirm experiences often made in crystallography. That is, effects of temperature, crystal structure and packing, and molecular volume effects are manifested more clearly in bond lengths than bond angles which depend mainly on intramolecular properties. Frequency analyses of the τ 1 , τ 2 and τ 3 torsional angles in the crystal structures show conformational steering in the sense that, if τ 1 is trans peri-planar (170°≤ τ 1 ≤180°; −180°≤ τ 1 ≤−170°), the values of τ 2 and τ 3 are clustered closely around the ideal gauche (±60°) and trans (±180°) positions. In contrast, when τ 1 is in the region (50°≤ τ 1 ≤70°), there is a definite increase in the populations of τ 2 and τ 3 at −90 and −150°.