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.

Kraitchman has shown that a single isotopic substitution on an atom is sufficient to determine directly the coordinates of that atom with respect to the principal axes of the original molecule. Kraitchman's formulas represent exact solutions of the equations for the equilibrium moments of inertia. However, the effects of the zero‐point vibrations are such that the coordinates obtained by substitution from the ground state moments of inertia I0 are systematically less than r0. These coordinates have here been called r (substitution) or rs, and it is found that rs≃(r0+re)/2, and Is= ∑ imirsi2≃(I0+Ie)/2.In the usual method of solution, the coordinate of one atom is determined from the equation for I0, and therefore the difference I0—Is must be made up by this one coordinate. This introduces a large error in the structures normally determined from ground state constants, and results in variations of 0.01 A in structures determined from different sets of isotopic species. If instead, we obtain the structure on...

A new criterion for the determination of molecular structures from ground state rotational constants

Flexible models for intramolecular motion, a versatile treatment and its application to glyoxal☆

The S1←S0 000 transitions of phenol and the hydrogen bonded phenol(H2O)1 cluster have been studied by high resolution fluorescence excitation spectroscopy. All lines in the monomer spectrum are split by 56±4 MHz due to the internal rotation of the −OH group about the a axis. The barrier for this internal motion is determined in the ground and excited states; V2″=1215 cm−1, and V2′=4710 cm−1. The rotational constants for the monomer in the ground state are in agreement with those reported in microwave studies. The excited state rotational constants were found to be A′=5313.7 MHz, B′=2620.5 MHz, and C′=1756.08 MHz. The region of the redshifted 000 transition of phenol(H2O)1 shows two distinct bands which are 0.85 cm−1 apart. Their splitting arises from a torsional motion which interchanges the two equivalent H atoms in the H2O moiety of the cluster. This assignment was confirmed by spin statistical considerations. Both bands could be fit to rigid rotor Hamiltonians. Due to the interaction between the overal...

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High resolution uv spectroscopy of phenol and the hydrogen bonded phenol/water cluster

The conformation and dynamical behavior of molecular systems is very often advantageously described in terms of physically well-adapted curvilinear coordinates. It is rather easy to show that the numerous analytical expressions of the kinetic energy operator of a molecular system described in terms of n curvilinear coordinates can all be transformed into the following more usable expression: (T) over cap=Sigma(ij)f(2)(ij)(q)partial derivative(2)/partial derivativeq(i)partial derivativeq(j)+Sigma(i)f(1)(i)(q)partial derivative/partial derivativeq(i)+nu(q), where f(2)(ij)(q), f(1)(i)(q), and nu(q) are functions of the curvilinear coordinates q=(...,q(i),...). If the advantages of curvilinear coordinates are unquestionable, they do have a major drawback: the sometimes awful complexity of the analytical expression of the kinetic operator (T) over cap for molecular systems with more than five atoms. Therefore, we develop an algorithm for computing (T) over cap for a given value of the n curvilinear coordinates q. The calculation of the functions f(2)(ij)(q), f(1)(i)(q), and nu(q) only requires the knowledge of the Cartesian coordinates and their derivatives in terms of the n curvilinear coordinates. This coordinate transformation (curvilinear-->Cartesian) is very easy to perform and is widely used in quantum chemistry codes resorting to a Z-matrix to define the curvilinear coordinates. Thus, the functions f(2)(ij)(q), f(1)(i)(q), and nu(q) can be evaluated numerically and exactly for a given value of q, which makes it possible to propagate wavepackets or to simulate the spectra of rather complex systems (constrained Hamiltonian). The accuracy of this numerical procedure is tested by comparing two calculations of the bending spectrum of HCN: the first one, performed by using the present numerical kinetic operator procedure, the second one, obtained in previous studies, by using an analytical kinetic operator. Finally, the ab initio computation of the internal rotation spectrum and wave functions of 2-methylpropanal by means of dimensionality reduction, is given as an original application. (C) 2002 American Institute of Physics.

A. Bauder

Papers

Internal rotation in acetaldehyde

Pure rotational spectrum of benzene-d1

Analysis of microwave and infrared transitions of phenol by rotation-internal rotation theory. Phenol-OD

Microwave spectrum, rotational constants and dipole moment of s-cis acrolein

The substitution structure, barrier to internal rotation, and low frequency vibrations of pyruvic acid