We describe here a general Amber force field (GAFF) for organic molecules. GAFF is designed to be compatible with existing Amber force fields for proteins and nucleic acids, and has parameters for most organic and pharmaceutical molecules that are composed of H, C, N, O, S, P, and halogens. It uses a simple functional form and a limited number of atom types, but incorporates both empirical and heuristic models to estimate force constants and partial atomic charges. The performance of GAFF in test cases is encouraging. In test I, 74 crystallographic structures were compared to GAFF minimized structures, with a root-mean-square displacement of 0.26 A, which is comparable to that of the Tripos 5.2 force field (0.25 A) and better than those of MMFF 94 and CHARMm (0.47 and 0.44 A, respectively). In test II, gas phase minimizations were performed on 22 nucleic acid base pairs, and the minimized structures and intermolecular energies were compared to MP2/6-31G* results. The RMS of displacements and relative energies were 0.25 A and 1.2 kcal/mol, respectively. These data are comparable to results from Parm99/RESP (0.16 A and 1.18 kcal/mol, respectively), which were parameterized to these base pairs. Test III looked at the relative energies of 71 conformational pairs that were used in development of the Parm99 force field. The RMS error in relative energies (compared to experiment) is about 0.5 kcal/mol. GAFF can be applied to wide range of molecules in an automatic fashion, making it suitable for rational drug design and database searching.

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Development and testing of a general amber force field.

Heme-Containing Oxygenases

Asymmetric 1,3-Dipolar Cycloaddition Reactions

A self-consistent system of additive covalent radii, R(AB)=r(A) + r(B), is set up for the entire periodic table, Groups 1-18, Z=1-118. The primary bond lengths, R, are taken from experimental or theoretical data corresponding to chosen group valencies. All r(E) values are obtained from the same fit. Both E-E, E-H, and E-CH 3 data are incorporated for most elements, E. Many E-E' data inside the same group are included. For the late main groups, the system is close to that of Pauling. For other elements it is close to the methyl-based one of Suresh and Koga [J. Phys. Chem. A 2001, 105, 5940] and its predecessors. For the diatomic alkalis MM' and halides XX', separate fits give a very high accuracy. These primary data are then absorbed with the rest. The most notable exclusion are the transition-metal halides and chalcogenides which are regarded as partial multiple bonds. Other anomalies include H 2 and F 2 . The standard deviation for the 410 included data points is 2.8 pm.

Molecular single-bond covalent radii for elements 1-118.

Based on the modified Perdew and Wang exchange functional (MPW) and Becke's 1995 correlation functional (B95), we developed two hybrid meta density functional theory (HMDFT) methods, namely MPW1B95 and MPWB1K. In addition, based on the new X functional of Xin and Goddard, again combined with B95 correlation functional, we developed two other new HMDFT methods, X1B95 and XB1K. MPW1B95 and X1B95 were optimized against a representative database of six atomization energies (AE6). MPWB1K and XB1K were optimized against a kinetics database of three forward barrier heights, three reverse barrier heights, and three energies of reaction for the reactions in the BH6 representative barrier height database. We compared the newly developed methods to other HMDFT and hybrid DFT methods for atomization energies, ionization potentials, electron affinities, barrier heights, saddle point geometries, hydrogen bonding, and weak van der Waals weak interactions. In addition, we optimized scaling factors for calculating zero-po...

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Hybrid Meta Density Functional Theory Methods for Thermochemistry, Thermochemical Kinetics, and Noncovalent Interactions: The MPW1B95 and MPWB1K Models and Comparative Assessments for Hydrogen Bonding and van der Waals Interactions

Spectroscopic data related to the structures of polyatomic molecules in the gas phase have been reviewed, critically evaluated, and compiled. All reported bond distances and angles have been classified as equilibrium (re), average (rz), substitution (rs), or effective (ro) parameters, and have been given a quality rating which is a measure of the parameter uncertainty. The surveyed literature includes work from all of the areas of gas‐phase spectroscopy from which precise quantitative structural information can be derived. Introductory material includes definitions of the various types of parameters and a description of the evaluation procedure.

Molecular structures of gas‐phase polyatomic molecules determined by spectroscopic methods

The microwave spectra of the normal, 34S, D,, and D2 isotopic species of gaseous sulfuric acid have been assigned. Rotational and centrifugal distortion constants were obtained. A conformation with C, symmetry has been identified. Important structural parameters are r ( 0 H ) = 0.97 (1) A, r ( S O I ) = 1.574 (10) A, r(S0,) = 1.422 (10) A, LH,O,S = 108.5 (15), LOlSO18 = 101.3 (lo)’, LO2SO2< = 123.3 (lo)’. The torsional angle Ol8SOIH is -90.9 (10)’ and the two SOz planes form an angle of 88.4 (1)’. The dipole moment was determined to be 2.725 (15) D. A comparison of the derived structural parameters with related species is presented, and the possibility of the undetected existence of other stable conformations of sulfuric acid is discussed.

Microwave spectrum, structure, and dipole moment of sulfuric acid

The Mass and Microwave Spectra, Structures, and Dipole Moments of the Isomers of Sulfur Monofluoride

Microwave spectra, structures, and dipole moments of trimethylphosphine-borane and methylphosphine-borane

The authors report here that the epoxidation of trans-1-deuteriopropylene by a reconstituted cytochrome P-450 system proceeds with significant loss of the deuterium label. Further, the epoxidation of propylene by this enzymic system in D/sub 2/O affords predominantly trans-1-deuteriopropylene oxide.

Robert L. Kuczkowski

Papers

Molecular structures of gas‐phase polyatomic molecules determined by spectroscopic methods

Microwave spectrum, structure, and dipole moment of sulfuric acid

The Mass and Microwave Spectra, Structures, and Dipole Moments of the Isomers of Sulfur Monofluoride

Microwave spectra, structures, and dipole moments of trimethylphosphine-borane and methylphosphine-borane

Hydrogen-deuterium exchange during propylene epoxidation by cytochrome p-450