The path of chemical reactions - the IRC approach

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.

Graph theory and molecular orbitals. Total φ-electron energy of alternant hydrocarbons

Ranging from the physics of elementary particles to the structure of viruses, the subject matter of this book stresses the importance of optical activity and chirality in modern science and will be of interest to a wide range of scientists. Using classical and quantum methods with a strong emphasis on symmetry principles, the volume develops the theory of varied optical activity and related phenomena from the perspective of molecular scattering of polarized light. First Edition Hb (1983): 0-521-24602-4

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Molecular Light Scattering and Optical Activity

Structure, energetics, and dynamics of the nucleic Acid base pairs: nonempirical ab initio calculations.

Methanol and deuterated species: Infrared data, valence force field, rotamers, and conformation

Application of vibrational spectroscopy to the problem of structure determination of molecules of biological interest goes back to the early uses of raman and infrared spectroscopy in the study of organic molecules. For reviews of earlier work the reader is referred to compilations by Kohlrausch (1943) and by Jones and Sandorfy (1956), whereas more recently a comprehensive discussion has been presented by Bellamy (1975). These compilations accentuate the correlation of vibrational spectra with molecular structure from an essentially empirical point of view and culminate in the establishment of empirical correlation charts. For typical examples the reader is referred to Weast (1974) and Bellamy (1975). There have been many treatments of the theoretical basis of molecular vibrational spectroscopy. Among them the classical work by Herzberg (1945) and by Wilson et al. (1955) should be mentioned. Applications of infrared spectroscopy (IR) to structure problems of biological interest have been summarized by Susi (1969), Fraser and MacRae (1973), and Wallach and Winzler (1974). It was remarked quite eraly that relevant structural information about biological systems often requires study in aqueous solution, which forms the natural environment for most biologically important systems. Besides critical control of experimental conditions and samples the conventional methods of raman spectroscopy may be applied to aqueous solutions in a quite straightforward manner, cf. the contribution by Lord and Mendelson, Chapter 8.

Infrared membrane spectroscopy.

Relations between the simple form of MO-theory (two parameter theory) and the theory of spectra of graphs are investigated. By the use of some theorems of graph theory it is shown that the spectra of energy eigenvalues given by the simple MO-theory are determined besides of scale factors by the topology of the conjugated systems. Furthermore bond orders and charge orders are completely determined by the topology. A procedure for the calculation of the characteristic polynom and the characteristic vectors directly from the graph is given.

Zusammenhang von Graphentheorie und MO-Theorie von Molekeln mit Systemen konjugierter Bindungen

The dynamics and the Hamiltonian of a general asymmetric‐top molecule undergoing almost arbitrary deformations are discussed. s vector notations are used for translational, rotational, and internal‐velocity coordinates. The kinetic energy is formulated by generalizing the G‐matrix technique known from the theory of molecular vibrations. A geometrical definition of the rotational coordinates referring to the instantaneous principal axis system is compared with a dynamical definition involving the over‐all angular momentum. States of general internal motion are associated by definition with zero linear momentum and zero over‐all angular momentum.

Hs.H. Günthard

Papers

Methanol and deuterated species: Infrared data, valence force field, rotamers, and conformation

Infrared membrane spectroscopy.

Zusammenhang von Graphentheorie und MO-Theorie von Molekeln mit Systemen konjugierter Bindungen

General Internal Motion of Molecules, Classical and Quantum-Mechanical Hamiltonian

Solid state and gas infrared spectra and normal coordinate analysis of 5 isotopic species of acetaldehyde