A comprehensive study of the rotational energy profiles of organic systems by ab initio MO theory, forming a basis for peptide torsional parameters

Ab initio molecular orbital calculations have been carried out on over 50 model organic molecules and ions to provide the data necessary in the determination of torsional parameters for a force field involving polypeptides. The rotational energy profiles were obtained at the HF/6‐31G*//HF/6‐31G* level. The results were supported, in many cases, by full geometry optimizations and with consideration of correlation corrections at the MP2 level. With the exception of the dihedral angle being studied, all of the molecules were fully optimized with C1 symmetry. © 1995 by John Wiley & Sons, Inc.

[1]  William L. Jorgensen,et al.  Cis-trans energy difference for the peptide bond in the gas phase and in aqueous solution , 1988 .

[2]  U. Singh,et al.  A NEW FORCE FIELD FOR MOLECULAR MECHANICAL SIMULATION OF NUCLEIC ACIDS AND PROTEINS , 1984 .

[3]  W. L. Jorgensen,et al.  The OPLS [optimized potentials for liquid simulations] potential functions for proteins, energy minimizations for crystals of cyclic peptides and crambin. , 1988, Journal of the American Chemical Society.

[4]  David A. Dixon,et al.  Ab initio conformational analysis of cyclohexane , 1990 .

[5]  Victor J. Hruby,et al.  Ab Initio Molecular Orbital Studies of the Rotational Barriers and the 33S and 13C Chemical Shieldings for Dimethyl Disulfide , 1992 .

[6]  Kenneth S. Pitzer,et al.  The Molecular Structure and Thermodynamics of Propane The Vibration Frequencies, Barrier to Internal Rotation, Entropy, and Heat Capacity , 1944 .

[7]  Alice Chung-Phillips,et al.  Torsional energy levels and wave functions , 1992 .

[8]  William F. Murphy,et al.  Rotational isomerism. XI. Raman spectra of n-butane, 2-methylbutane, and 2, 3-dimethylbutane , 1974 .

[9]  L. Bartell,et al.  Molecular structure of n-butane: calculation of vibrational shrinkages and an electron diffraction re-investigation , 1977 .

[10]  W G Richards,et al.  Histamine tautomerism and its mode of action. , 1990, Biochimica et biophysica acta.

[11]  T. A. Wildman,et al.  STO-3G MO calculations on structures and internal rotational barriers of phenol, benzoyl X(X = H, F, CH3, CN, OCH3), acetyl fluoride, acetyl cyanide, and carbonyl cyanide , 1982 .

[12]  Brian F. Yates,et al.  The syn rotational barrier in butane , 1990 .

[13]  Norman L. Allinger,et al.  Conformational analysis—CXXIII: Carboxylic acids and esters in force field calculations , 1977 .

[14]  Kenneth S. Pitzer,et al.  Chemical Equilibria, Free Energies, and Heat Contents for Gaseous Hydrocarbons. , 1940 .

[15]  Louis Pierce,et al.  Microwave Spectrum, Dipole Moment, Structure, and Internal Rotation of Dimethyl Sulfide , 1961 .

[16]  Saulo A. Vázquez,et al.  A molecular mechanics study of conformational trends in simple alcohols and ethers. Part I: Geometric trends , 1991 .

[17]  William L. Jorgensen,et al.  Molecular dynamics and Monte Carlo simulations favor the .alpha.-helical form for alanine-based peptides in water , 1993 .

[18]  Mark A. Murcko,et al.  Rotational barriers. 2. Energies of alkane rotamers. An examination of gauche interactions , 1988 .

[19]  Martin Karplus,et al.  Empirical force field study of geometries and conformational transitions of some organic molecules , 1992 .

[20]  Akira Tsuboyama,et al.  Ab Initio Gradient Calculation of the Molecular Structures of Dimethyl Ether and Dimethyl Sulfide , 1984 .

[21]  Mark A. Murcko,et al.  Barriers to rotation adjacent to double bonds. 4. Effect of basis set on structures, and of electron correlation on relative energies , 1988 .

[22]  Salvatore Profeta,et al.  Rotation around the C1C2 bond of propylamine, an ab initio study , 1988 .

[23]  F. Bernardi,et al.  Conformational studies by dynamic NMR. 7. Stereochemical processes in 2,3-dimethylbutane , 1977 .

[24]  M. Karplus,et al.  CHARMM: A program for macromolecular energy, minimization, and dynamics calculations , 1983 .

[25]  Harold A. Scheraga,et al.  Low frequency Raman spectra of dimethyl, methyl ethyl, and diethyl disulfides, and rotational isomerism about their carbon-sulfur bonds , 1976 .

[26]  Imre G. Csizmadia,et al.  An ab initio molecular orbital study of the protonation of amines , 1974 .

[27]  Ming-Jing Hwang,et al.  Derivation of class II force fields. I. Methodology and quantum force field for the alkyl functional group and alkane molecules , 1994, J. Comput. Chem..

[28]  Cornelis Altona,et al.  The anomeric effect: Ab‐initio studies on molecules of the type XCH2OCH3 , 1990 .

[29]  J Tirado-Rives,et al.  Molecular dynamics simulations of the unfolding of an alpha-helical analogue of ribonuclease A S-peptide in water. , 1991, Biochemistry.

[30]  Jill E. Gready,et al.  Guanidinium‐Type resonance stabilization and its biological implications. I. the guanidine and extended‐guanidine series , 1989 .

[31]  David Feller,et al.  Ab initio study of hydrogen bonding in the phenol–water system , 1993, J. Comput. Chem..

[32]  William L. Jorgensen,et al.  Do denaturants interact with aromatic hydrocarbons in water , 1993 .

[33]  William L. Jorgensen,et al.  Molecular dynamics of proteins with the OPLS potential functions. Simulation of the third domain of silver pheasant ovomucoid in water , 1990 .

[34]  Ulrich Burkert,et al.  Calculation of alcohol conformations by molecular mechanics , 1979 .

[35]  M Levitt.  Protein conformation, dynamics, and folding by computer simulation. , 1982, Annual review of biophysics and bioengineering.

[36]  W G Richards,et al.  Theoretical calculation of tautomer equilibria in solution: 4-(5-)methylimidazole. , 1989, Biochimica et biophysica acta.

[37]  Warren J. Hehre,et al.  AB INITIO Molecular Orbital Theory , 1986 .

[38]  Charles Bender,et al.  Molecular mechanics (MM2) calculations on peptides and on the protein Crambin using the CYBER 205 , 1989 .

[39]  M Karplus,et al.  Side-chain torsional potentials: effect of dipeptide, protein, and solvent environment. , 1979, Biochemistry.

[40]  Ramesh K. Kakar,et al.  Microwave rotational spectrum and internal rotation in gauche ethyl alcohol , 1980 .

[41]  E. Fischer,et al.  The microwave spectrum of gauche-ethylamine , 1984 .

[42]  W. J. Orville-Thomas,et al.  Internal rotation in molecules , 1974 .

[43]  Donald B. Boyd,et al.  Conformational analysis—CXVII , 1976 .

[44]  Kazutoshi Tanabe,et al.  Basis set and electron correlation effects on the internal rotational barrier heights of formamide and acetamide , 1991 .

[45]  William L. Jorgensen,et al.  Solvent effects on the barrier to isomerization for a tertiary amide from ab initio and Monte Carlo calculations , 1992 .

[46]  William F. Murphy,et al.  Low-frequency Raman spectrum and asymmetric potential function for internal rotation of gaseous n-butane , 1980 .

[47]  Charles J. Wurrey,et al.  Raman spectra of gases. XVI - Torsional transitions in ethanol and ethanethiol , 1975 .

[48]  Lothar Schäfer,et al.  Ab initio studies of structural features not easily amenable to experiment. 30. Conformational analysis and molecular structures of propanal and butanal , 1984 .

[49]  K B Wiberg,et al.  Barriers to rotation adjacent to double bonds. 2. n-Propyl versus isopropyl groups. , 1986, Journal of the American Chemical Society.

[50]  Bernard Testa,et al.  Principles of organic stereochemistry , 1979 .

[51]  Jonathan W. Essex,et al.  Theoretical Calculation of a Solution Phase Torsional Free Energy Profile. π-Ethylimidazole in Water , 1993 .

[52]  P. Kollman,et al.  Application of RESP charges to calculate conformational energies, hydrogen bond energies, and free energies of solvation , 1993 .

[53]  E. Fischer,et al.  The microwave spectrum of trans-ethylamine , 1982 .

[54]  F. Nicolaisen,et al.  Far-infrared gas spectra of phenol, 4-fluorophenol, thiophenol and some deuterated species: barrier to internal rotation , 1974 .

[55]  W. L. Jorgensen,et al.  Molecular dynamics simulations of the unfolding of apomyoglobin in water. , 1993, Biochemistry.

[56]  Norman L. Allinger,et al.  Ab initio calculations of the rotational potential functions for propylamine and ethylmethylamine , 1980 .

[57]  Kenneth B. Wiberg,et al.  Barriers to rotation adjacent to double bonds. 3. The carbon-oxygen barrier in formic acid, methyl formate, acetic acid, and methyl acetate. The origin of ester and amide resonance , 1987 .

[58]  Krishnan Raghavachari,et al.  Rotational potential surface for alkanes: Basis set and electron correlation effects on the conformations of n‐butane , 1984 .