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.

/pdf/glycam06-a-generalizable-biomolecular-force-field-2f07t7094q.pdf

GLYCAM06: a generalizable biomolecular force field. Carbohydrates.

Mise au point. Theorie des effets de couplage vibronique multimodes. Probleme a 2 etats. Couplage vibronique mettant en jeu des modes et des etats degeneres. Effets du couplage vibronique multimodes en spectroscopie. Comportement statistique des niveaux d'energie vibroniques. Intersections coniques et evolution temporelle de la fluorescence

Multimode molecular dynamics beyond the Born-Oppenheimer approximation

The convergence of ab initio predictions to the one- and n-particle limits has been systematically explored for several conformational energy prototypes: the inversion barriers of ammonia, water, and isocyanic acid, the torsional barrier of ethane, the E/Z rotamer separation of formic acid, and the barrier to linearity of silicon dicarbide. Explicit ab initio results were obtained with atomic-orbital basis sets as large as [7s6p5d4f3g2h1i/6s5p4d3f2g1h] and electron correlation treatments as extensive as fifth-order Mo/ller–Plesset perturbation theory (MP5), the full coupled-cluster method through triple excitations (CCSDT), and Brueckner doubles theory including perturbational corrections for both triple and quadruple excitations [BD(TQ)]. Subsequently, basis set and electron correlation extrapolation schemes were invoked to gauge any further variations in arriving at the ab initio limit. Physical effects which are tacitly neglected in most theoretical work have also been quantified by computations of non...

In pursuit of the ab initio limit for conformational energy prototypes

Multimode Molecular Dynamics Beyond the Born‐Oppenheimer Approximation

An inductive method for a systematic selection of energy functions of interatomic interactions in large families of molecules is suggested and is applied to the family of cycloalkane and n‐alkane molecules. Equilibrium conformations, vibrational frequencies, and excess enthalpies, including strain energies and vibrational enthalpies, are all derived from the same set of energy functions. The energy‐function parameters are optimized by a least‐squares algorithm to give the best possible agreement with a large amount and variety of observed data. Analytical derivatives of the various calculated quantities with respect to the energy parameters help to facilitate the computational procedures. The resulting agreement with experiment is used as a measure of success of the energy functions with optimized parameters, referred to as “consistent force field” (CFF). Different CFF's are compared and selected according to their relative success. Energy functions commonly used in conformational analysis are examined in...

Consistent Force Field for Calculations of Conformations, Vibrational Spectra, and Enthalpies of Cycloalkane and n‐Alkane Molecules

The infrared spectrum of carbon suboxide

Miscellaneous techniques for infrared prism spectroscopy are described in detail. These include: techniques for cleaving, cutting, and polishing alkali halide crystals for absorption cell windows; construction of absorption cells for liquids and gases, including some suitable for high and low temperatures and one of long path; the measurement of cell thickness; removal of atmospheric absorption; techniques useful for wavelengths above twenty-five microns; formulas for recording inks. A modified source-optical system and a method of calibration adjustment for Perkin-Elmer Model 12 instruments are also discussed.

Notes on the Practice of Infrared Spectroscopy

Vibrational spectra of CF3CCH, CF3CCD, and CF3CCCF3

Infrared and raman spectra of chromyl chloride

Improved infrared data have been obtained for benzene‐d6 from 300—3700 cm—1 for both vapor and liquid phases. The frequencies can be interpreted very completely and satisfactorily. Good evidence was found for assigning v14 and v15 to 1287 and 838 cm—1 in benzene‐d6. This provides valuable confirmation for Mair and Hornig's choice of 1310 and 1152 in benzene itself. All the fundamental frequencies for both benzene and benzene‐d6 now seem to be well established, aside from small uncertainties in a few cases where the values have been inferred from combination tones or from the product rule.The infrared spectrum of benzene vapor for the range 300—700 cm—1 is also given.

Foil A. Miller

Papers

The infrared spectrum of carbon suboxide

Notes on the Practice of Infrared Spectroscopy

Vibrational spectra of CF3CCH, CF3CCD, and CF3CCCF3

Infrared and raman spectra of chromyl chloride

Infrared Spectrum of Benzene‐d6