A theoretical study of substituent effects on the structure of isolated and condensed three-membered rings. A comparison between radicals and parent hydrocarbons

Substituent effects on the structure of radicals and parent hydrocarbons formed by isolated or condensed three-membered rings have been investigated by Hartree-Fock, post-Hartree-Fock and density functional methods. The trends of structural parameters computed for the hydrocarbon systems are in agreement with available experimental data. Substituent effects can be rationalized in terms of interactions between localized orbitals obtained by natural bond analysis. The effects are even larger in free radicals and can be analyzed using the same model. Received: 13 March 1998 / Accepted: 13 July 1998 / Published online: 9 October 1998     

Analyzing patterns between regular secondary structures using short structural building blocks defined by a hidden Markov model

Hidden Markov models were used to identify recurrent short 3D structural building blocks (SSBBs) describing protein backbones. Polypeptide chains were broken down into successive short segments defined by their inter-alpha-carbon distances. Fitting the model to a database of nonredundant proteins identified 12 distinct SSBBs and described the preferred pathways by which SSBBs were assembled to form the 3D structure of the proteins. Protein backbones were labelled in terms of these SSBBs. The observed SSBB preferences for fragments located between regular secondary structures suggested that they depended more on the following regular structure than on the preceding one. Extraction of repeated series of SSBBs between regular secondary structures showed some structural specificity within different connection types. These results confirm that SSBBs can be used as building blocks for analyzing protein structures, and can yield new information on the structures of the coils flanking secondary structures. Received: 14 May 1998 / Accepted: 4 August 1998 / Published online: 16 November 1998     

Visual valence bond rules for chemical reactions

A symmetry-adaptation rule of the valence bond structure for concerted reactions was developed within the bonded tableau valence bond formalism. According to a symmetry analysis of the valence bond structure segments accounting for the reaction, one can predict whether a chemical process is favored or unfavored. This method is based on conceptual resonance theory and the visual valence bond approach, without carrying out any explicitly theoretical calculations to know orbital details. Furthermore, by imposing a phase factor on each bonding pair, namely, the phase alternation postulate, the mechanisms of the concerted reactions can be easily outlined. These rules have been applied to organic and inorganic reactions including the participation of biradicals and species with multi-reference character. Received: 7 September 1998 / Accepted: 9 November 1998 / Published online: 1 February 1999     

New approaches to chiral discrimination in coupling between molecules

Results in the coupling of chiral molecules are reviewed from elementary points of view and some new results are given. We show that interactions between chiral molecules can be treated by using molecular quantum electrodynamics in electric and magnetic dipole approximation in ways different from standard diagrammatic perturbation theory. The interactions are the dispersive coupling of ground-state chiral molecules and excitation transfer, with emphasis on chiral discrimination. For ground-state molecules the coupling is dealt with first by calculating the coupling, at all separation distances, of electric and magnetic dipoles induced in the two molecules by fluctuations in the vacuum radiation field. The second method is the response by one chiral molecule to the field generated by the other. Excitation transfer is treated as the response by the accepting ground-state molecule to the dipole field of the donor. A novel variant in finding the rate of excitation transfer is by using Poynting's theorem. Received: 17 June 1998 / Accepted: 6 October 1998 / Published online: 16 March 1999     

Modification of Guest and Saunders open shell SCF equations to exclude BSSE from molecular interaction calculations

The self-consistent field (SCF) for molecularinteractions algorithm, particularly devised to compute intermolecular interactions, is extended to the case in which one of the two interacting fragments is an open shell system. The method excludes the basis set superposition error in an a priori fashion. To preserve the simplicity of the standard SCF procedure, Guest and Saunders equations concerning the open shell fragment are modified at the cost of a negligible complication with respect to the usual algorithm. Received: 27 May 1997 / Accepted: 29 May 1998 / Published online: 18 September 1998     

Global geometry optimization of small silicon clusters at the level of density functional theory

By an application to small silicon clusters Si _N (with N = 4,5,7,10) it is shown that truly global geometry optimization on an ab initio or density functional theory level can be achieved, at a computational cost of approximately 1–5 traditional local optimization runs (depending on cluster size). This extends global optimization from the limited area of empirical potentials into the realm of ab initio quantum chemistry. Received: 24 February 1998 / Accepted: 6 March 1998 / Published online: 17 June 1998     

High level ab initio and density functional theory study of bond selective dissociation of CH3SH and CH3CH2SH radical cations

Selective bond dissociation energies for CH₃SH and CH₃CH₂SH radical cations were evaluated with G1, G2, G2MP2, B3LYP, BLYP, and SVWN computational methods. It was determined that both G2 and CBSQ evaluate very accurate bond dissociation energies for thiol radical cations, while gradient-corrected BLYP computes the best energies of three employed DFT methods. For the CH₃CH₂SH radical cation, new, higher than previously estimated selective bond dissociation energies were suggested. Received: 10 September 1997 / Accepted: 9 September 1998 / Published online: 11 November 1998     

Convergence of the density functional one-centre expansion for the molecular continuum: N2 and (CH3)3N

A large-scale one-centre expansion with a radial B-spline basis set is implemented for bound and continuum states. A Kohn-Sham hamiltonian is employed with Hartree and exchange-correlation potentials calculated from the SCF electron density taken from a previous LCAO calculation. An inverse iteration method is used to obtain the continuum wavefunction, from which the cross section and asymmetry parameter are calculated. The convergence with respect to angular momentum and cut-off radius is analysed for N₂. The relevance of multipolar contributions even at large distances is shown and suggestions for further improvements are given. In order to show that the present method is suitable to treat systems of moderate size, the (CH₃)₃N molecule has also been calculated and the results are compared with experiment. Received: 19 May 1998 / Accepted: 20 August 1998 / Published online: 7 December 1998     

Dissociative recombination of HeH+. I. Rovibrational spectrum of HeH Rydberg states

The repulsive ground electronic state X²Σ⁺ of HeH is strongly coupled to the Rydberg states at small interatomic distances. Such large couplings also occur between some of the Rydberg states. HeH⁺ ions that capture an electron in a Rydberg state end up in separated He and H atoms by indirect predissociation. This paper presents a study of potential functions and pertinent matrix elements involving the lowest electronic states: the ²Σ⁺ states, X, A, C, and D, and the ²Π states B and E. Individual transition rates as well as total radiative and non-radiative lifetimes have been computed for the lowest vibrational and rotational levels. Received: 22 June 1998 / Accepted: 21 August 1998 / Published online: 12 October 1998     

Calculation of ground- and excited-state potential energy curves for barium-rare gas complexes in a pseudopotential approach

Adiabatic potential curves for the ground state and several low-lying excited states of the barium atom interacting with Ne, Ar, Kr and Xe have been obtained from valence ab initio configuration-interaction calculations. Atomic cores are replaced by scalar-relativistic l-dependent pseudopotentials, while core-polarization potentials are used for describing correlation contributions of the rare-gas atoms and the Ba²⁺ cores. Implications of the resulting potential curves for the interpretation of experimental data are discussed, together with first applications of the curves for calculating absorption profiles of the (6s ²)¹S→(6p)¹P Ba transition. Received: 7 April 1998 / Accepted: 27 July 1998 / Published online: 12 October 1998     

Prediction of stability changes upon single-site mutations using database-derived potentials

One of the purposes of studying protein stability changes upon mutations is to get information about the dominating interactions that drive folding and stabilise the native structure. With this in mind, we present a method that predicts folding free-energy variations caused by point mutations using combinations of two types of database-derived potentials, i.e. backbone torsion-angle potentials and distance potentials, describing local and non-local interactions along the chain, respectively. The method is applied to evaluate the folding free-energy changes of 344 single-site mutations introduced in six different proteins and a synthetic peptide. We found that the relative importance of local versus non-local interactions along the chain is essentially a function of the solvent accessibility of the mutated residues. For the subset of totally buried residues, the optimal potential is the sum of a distance potential and a torsion potential weighted by a factor of 0.4. This combination yields a correlation coefficient between measured and computed changes in folding free energy of 0.80. For mutations of partially buried residues, the best potential is the sum of a torsion potential and a distance potential weighted by 0.7. For fully accessible residues, the torsion potentials taken alone perform best, reaching correlation coefficients of 0.87 on all but 10 mutations; the excluded mutations seem to modify the backbone structure or to involve interactions that are atypical for the surface. These results show that the relative weight of non-local interactions along the sequence decreases as the solvent accessibility of the mutated residue increases, and vanishes at the protein surface. On the contrary, the weight of local interactions increases with solvent accessibility. The latter interactions are nevertheless never negligible, even for the most buried residues. Received: 20 May 1998 / Accepted: 3 September 1998 / Published online: 7 December 1998     

Density functional study of ethylene oxidation on an Ag(111) surface

The mechanism of ethylene epoxidation on Ag surfaces has been investigated using the density functional method and Ag _n clusters (n = 3 to 10) modeling the Ag(111) surface. The adsorption energy of O₂ to the Ag clusters was strongly dependent on the HOMO level of the cluster, and the clusters with higher HOMO levels afforded larger O₂ adsorption energies. The energetics was investigated for both the molecular and atomic oxygen epoxidation mechanisms. For the atomic oxygen mechanism, epoxidation was found to proceed without an activation energy, whereas a small amount of activation energy (about 5 kcal/mol) was calculated for the molecular oxygen mechanism. Received: 2 July 1998 / Accepted: 9 September 1998 / Published online: 8 February 1999     

Identifying key electrostatic interactions in Rhizomucor miehei lipase: the influence of solvent dielectric

The conformational change associated with the interfacial activation of Rhizomucor miehei lipase involves the displacement of an α-helical lid (residues 82–96) away from the active site on moving from water (high dielectric) to lipid (low dielectric). The presence of two media of very different dielectric properties suggests that electrostatic interactions play an important role in this process. We have used linearized Poisson–Boltzmann calculations to examine the key electrostatic interactions which contribute to lid stability in the closed and open states. It is the two charged residues of the lid, Arg86 and Asp91, that form the strongest electrostatic interactions with the rest of the protein. We identify key residues whose interactions with the lid are significantly perturbed by the change in the dielectric of the medium: Asp61, Arg80, Lys109, Glu117 and the active-site residues Asp203 and Asp256, all of which lie within approximately 20 ? of the lid. We suggest that these residues are good candidates for site-specific mutation studies, which could help elucidate their role in the lipase activation mechanism. Received: 27 May 1998 / Accepted: 17 September 1998 / Published online: 7 December 1998     

Diatomic potential well depths from analyses of high-resolution electron energy spectra for autoionizing collision complexes

High-resolution energy spectra of electrons released in Penning ionization collisions of metastable rare gas atoms Rg*(ns) (Rg = He, Ne, Ar, Kr, Xe) with several open-shell and closed-shell atoms are analyzed to determine the well depth of the potential energy curve which describes the respective autoionizing collision complex. We thereby elucidate trends in the chemical interaction of Rg* with closed-shell target atoms A(ns ²) and establish a basis for detailed comparison with the respective interactions involving open-shell, ground state alkali atoms A(ns). From electron energy spectra due to␣associative ionization (RgH⁺ formation) in Rg* + H(1s) collisions, we determine binding energies for the RgH⁺(¹Σ) ground state potential (Rg = Ne, Ar, Kr, Xe) with uncertainties around 0.03 eV. Received: 30 June 1998 / Accepted: 5 August 1998 / Published online: 28 October 1998     

Examining ligand-protein interactions with binding-energy landscapes

Binding-energy landscapes are used to investigate the thermodynamics of molecular recognition for the pteridine ring, a recognition anchor in binding with dihydrofolate reductase, and two molecules with the same shape but different heteroatom substitutions. The relative importance of hydrogen bonding and hydrophobic interactions in this system is analyzed by comparing these three different decorations of the pteridine scaffold. Received: 5 May 1998 / Accepted: 3 September 1998 / Published online: 17 December 1998     

Ab initio MO study of ethylene insertion into the Sm–C bond of H2SiCp2SmCH3

Ethylene insertion into the Sm–C bond of H₂SiCp₂SmCH₃, a model reaction of an olefin polymerization propagation step, has been studied by ab initio molecular orbital methods. The small electronegativity of the Sm atom makes the Sm–C bond ionic, the methyl group being negatively charged by −0.75. The reaction passes through a loose ethylene complex with a binding energy of 15 kcal/mol and then a tight four-centered transition state with an agostic interaction between the Sm atom and one of the methyl CH bonds. A small activation energy of 14 kcal/mol is required to pass through this transition state, indicating that this is an easy reaction. Compared with the reactions with group 4 cationic silylene-bridged metallocenes the activation energy is higher and the reaction is less exothermic. The origin of these differences is discussed. The results of molecular mechanics calculations on regio- and stereoselectivities in the insertion reaction of propylene are also reported. Received: 13 July 1998 / Accepted: 28 August 1998 / Published online: 2 November 1998     

Recent advances in molecular dynamics simulation towards the realistic representation of biomolecules in solution

Coupled advances in empirical force fields and classical molecular dynamics simulation methodologies, combined with the availability of faster computers, has lead to significant progress towards accurately representing the structure and dynamics of biomolecular systems, such as proteins, nucleic acids, and lipids in their native environments. Thanks to these advances, simulation results are moving beyond merely evaluating force fields, displaying expected structural fluctuations, or demonstrating low root-mean-squared deviations from experimental structures and now provide believable structural insight into a variety of processes such as the stabilization of A-DNA in mixed water and ethanol solution or reversible β-peptide folding in methanol. The purpose of this overview is to take stock of these recent advances in biomolecular simulation and point out some common deficiencies exposed in longer simulations. The most significant methodological advances relate to the development of fast methods to properly treat long-range electrostatic interactions, and in this regard the fast Ewald methods are becoming the de facto standard. Received: 9 April 1998 / Accepted: 21 May 1998 / Published online: 13 August 1998     

Prediction of 13C NMR chemical shifts in substituted naphthalenes

The prediction of the ¹³C NMR signals for derivatives of naphthalene has been investigated using mathematical modeling techniques. Two empirical multiple regression models which utilize the field, resonance, and Charton's steric parameters together with molar refractivity were developed, one for α- and the other for β-substituted naphthalene derivatives. In the α case the model had a correlation coefficient of observed versus predicted line positions of r = 0.973 with a standard deviation of 2.2 ppm while in the β case r = 0.979 with the standard deviation being 2.3 ppm. The database consisted of 3152 signals from 394 naphthalene derivatives. We also report the use of the Taft steric parameter in place of the Charton steric parameter in the above- mentioned prediction equations. Received: 19 June 1998 / Accepted: 20 October 1998 / Published online: 16 March 1999     

Electron affinities, excitation energies and ionization potentials of the transition metals (I) Sc and Ti

The electron affinities of the Sc and Ti atoms have been obtained by configuration interaction calculations. Energy convergence with respect to the systematic expansion of both the one-electron basis set and the configuration space was investigated for valence electrons, and the inclusion of correlation contributions from core electrons and relativistic effects gave the electron affinities of 0.181 eV and 0.163 eV for Sc and Ti, respectively. These are in excellent agreement with the observed values of 0.189 ± 0.020 eV and 0.080 eV. The same approach was applied for the first excited states and positive ions of both atoms. Excellent agreement with the experimental results was also obtained for these states. Received: 16 February 1998 / Accepted: 2 April 1998 / Published online: 23 June 1998