PAPQMD parametrization of molecular systems with cyclopropyl rings: Conformational study of homopeptides constituted by 1-aminocyclopropane-1-carboxylic acid

The suitability of ab initio, semiempirical and density functional methods as sources of stretching and bending parameters has been explored using the PAPQMD (Program for Approximate Parametrization from Quantum Mechanical Data) strategy. Results show that semiempirical methods provide parameters comparable to those compiled on empirical force fields. In this respect the AM1 method seems to be a good method to obtain parameters at a minimum computational cost. On the other hand, harmonic force fields initially developed for proteins and DNA have been extended to include compounds containing highly strained three-membered rings, like 1-aminocyclopropane-1-carboxylic acid. For this purpose the cyclopropyl ring has been explicitly parametrized at the AM1 level considering different chemical environments. Finally, the new set of parameters has been used to investigate the conformational preferences of homopeptides constituted by 1-aminocyclopropane-1-carboxylic acid. Results indicate that such compounds tend to adopt a helical conformation stabilized by intramolecular hydrogen bonds between residues i and i+3. This conformation allows the arrangement of the cyclic side chains without steric clashes.

[1]  W. Ashman,et al.  Molecular mechanics parameterization: Bond lengths and angles for nitrogen and phosphorus containing compounds , 1990 .

[2]  M. Karplus,et al.  Proteins: A Theoretical Perspective of Dynamics, Structure, and Thermodynamics , 1988 .

[3]  Norman L. Allinger,et al.  Conformational analysis. 130. MM2. A hydrocarbon force field utilizing V1 and V2 torsional terms , 1977 .

[4]  H. Scheraga,et al.  Energy parameters in polypeptides. VII. Geometric parameters, partial atomic charges, nonbonded interactions, hydrogen bond interactions, and intrinsic torsional potentials for the naturally occurring amino acids , 1975 .

[5]  Jenn-Huei Lii,et al.  The MM3 force field for amides, polypeptides and proteins , 1991 .

[6]  M. Dewar,et al.  Ground States of Molecules. 38. The MNDO Method. Approximations and Parameters , 1977 .

[7]  Arnold T. Hagler,et al.  Direct evaluation of nonbonding interactions from ab initio calculations , 1989 .

[8]  H. Berendsen,et al.  A consistent empirical potential for water–protein interactions , 1984 .

[9]  Henry F. Schaefer,et al.  A systematic theoretical study of harmonic vibrational frequencies: The ammonium ion NH4+ and other simple molecules , 1980 .

[10]  William L. Jorgensen,et al.  Relative partition coefficients for organic solutes from fluid simulations , 1990 .

[11]  C. Alemán,et al.  A molecular mechanical study of the structure of poly(α‐aminoisobutyric acid) , 1992 .

[12]  J. Pople,et al.  Self—Consistent Molecular Orbital Methods. XII. Further Extensions of Gaussian—Type Basis Sets for Use in Molecular Orbital Studies of Organic Molecules , 1972 .

[13]  P. Pulay,et al.  A systematic study of the convergence and additivity of correlation and basis set effects on the force constants of small molecules: HF, HCN, and NH3 , 1983 .

[14]  S. Lifson,et al.  Energy functions for peptides and proteins. I. Derivation of a consistent force field including the hydrogen bond from amide crystals. , 1974, Journal of the American Chemical Society.

[15]  P. Pulay,et al.  AB Initio Vibrational Force Fields , 1984 .

[16]  C. Alemán,et al.  A new strategy for the evaluation of force parameters from quantum mechanical computations , 1991 .

[17]  M. Challacombe,et al.  Coordinate transformations of cubic force constants and transferability of anharmonic force constants in internal coordinates , 1991 .

[18]  A. T. Hagler,et al.  A novel decomposition of torsional potentials into pairwise interactions: A study of energy second derivatives , 1990 .

[19]  Carlos Alemán,et al.  CONFORMATIONAL PROPERTIES OF ALPHA -AMINO ACIDS DISUBSTITUTED AT THE ALPHA-CARBON , 1997 .

[20]  M. Karplus,et al.  Molecular dynamics simulations in biology , 1990, Nature.

[21]  F. Javier Luque,et al.  Comparison of NDDO and quasi‐ab initio approaches to compute semiempirical molecular electrostatic potentials , 1994, J. Comput. Chem..

[22]  P. C. Hariharan,et al.  Accuracy of AH n equilibrium geometries by single determinant molecular orbital theory , 1974 .

[23]  A. Lombardi,et al.  Noncoded residues as building blocks in the design of specific secondary structures: Symmetrically disubstituted glycines and β‐alanine , 1993, Biopolymers.

[24]  J. Stewart.  Optimization of parameters for semiempirical methods II. Applications , 1989 .

[25]  C. Toniolo,et al.  Structures of polypeptides from α-amino acids disubstituted at the α-carbon , 1991 .

[26]  H. Berendsen,et al.  COMPUTER-SIMULATION OF MOLECULAR-DYNAMICS - METHODOLOGY, APPLICATIONS, AND PERSPECTIVES IN CHEMISTRY , 1990 .

[27]  A. Lowrey,et al.  Effects of hydration on scale factors for ab initio force constants , 1991 .

[28]  D. Case,et al.  Langevin modes of macromolecules: Applications to crambin and DNA hexamers , 1990, Biopolymers.

[29]  P. Kollman,et al.  An all atom force field for simulations of proteins and nucleic acids , 1986, Journal of computational chemistry.

[30]  Erik De Clercq,et al.  Toward improved anti-HIV chemotherapy: therapeutic strategies for intervention with HIV infections. , 1995 .

[31]  Carlos Aleman,et al.  Suitability of the PM3‐derived molecular electrostatic potentials , 1993, J. Comput. Chem..

[32]  J. Hermans,et al.  310 HELIX VERSUS ALPHA -HELIX : A MOLECULAR DYNAMICS STUDY OF CONFORMATIONAL PREFERENCES OF AIB AND ALANINE , 1994 .

[33]  Ming-Jing Hwang,et al.  Derivation of Class II Force Fields. 2. Derivation and Characterization of a Class II Force Field, CFF93, for the Alkyl Functional Group and Alkane Molecules , 1994 .

[34]  C. Alemán,et al.  A conformational study of the dehydroalanine: Dipeptide and homopolypeptide , 1993, Biopolymers.

[35]  Parr,et al.  Development of the Colle-Salvetti correlation-energy formula into a functional of the electron density. , 1988, Physical review. B, Condensed matter.

[36]  Eamonn F. Healy,et al.  Development and use of quantum mechanical molecular models. 76. AM1: a new general purpose quantum mechanical molecular model , 1985 .

[37]  C. Tanford.  Macromolecules , 1994, Nature.

[38]  Harold A. Scheraga,et al.  Determination of net atomic charges using a modified partial equalization of orbital electronegativity method. IV. Application to hypervalent sulfur‐ and phosphorus‐containing molecules , 1995, J. Comput. Chem..

[39]  W. Thiel,et al.  Semiempirical treatment of electrostatic potentials and partial charges in combined quantum mechanical and molecular mechanical approaches , 1996, J. Comput. Chem..

[40]  Modesto Orozco,et al.  Effect of electron correlation on the electrostatic potential distribution of molecules , 1991 .

[41]  Jordi Casanovas,et al.  Ab initio SCF and force-field calculations on low-energy conformers of 2-acetylamino-2,N-dimethylpropanamide , 1994 .

[42]  G. Marshall,et al.  THE MOLTEN HELIX : EFFECTS OF SOLVATION ON THE ALPHA - TO 310-HELICAL TRANSITION , 1995 .

[43]  M. Nakata,et al.  Geometrical structure of cyclopropane as studied by gas electron diffraction and spectroscopic data , 1985 .

[44]  P. Pulay,et al.  Cubic force constants and equilibrium geometry of methane from Hartree–Fock and correlated wavefunctions , 1978 .

[45]  A. Becke,et al.  Density-functional exchange-energy approximation with correct asymptotic behavior. , 1988, Physical review. A, General physics.

[46]  G. Burns,et al.  The force field and normal coordinates of cyclopropane-H6 and -D6 , 1969 .

[47]  William L. Jorgensen,et al.  OPLS potential functions for nucleotide bases. Relative association constants of hydrogen-bonded base pairs in chloroform , 1991 .

[48]  P. Bagus,et al.  Force constants for the symmetric stretch motions of acetylene: Accurate ab initio calculations , 1977 .

[49]  Erik De Clercq,et al.  HIV‐1‐specific RT inhibitors: Highly selective inhibitors of human immunodeficiency virus type 1 that are specifically targeted at the viral reverse transcriptase , 1993, Medicinal research reviews.

[50]  C. Alemán,et al.  PAPQMD/AM1 Parametrization of the bonded term of aromatic biomolecules , 1994 .

[51]  Modesto Orozco,et al.  On the use of AM1 and MNDO wave functions to compute accurate electrostatic charges , 1990 .

[52]  R. Meyer,et al.  Methanol and deuterated species: Infrared data, valence force field, rotamers, and conformation , 1974 .

[53]  György G. Ferenczy,et al.  Semiempirical AM1 electrostatic potentials and AM1 electrostatic potential derived charges: A comparison with ab initio values , 1989 .

[54]  C. Alemán,et al.  Retromodified Residues: Small Peptides and Polymers. Interactions, Force-Field Parametrization and Conformational Analyses , 1995 .

[55]  C. Bock,et al.  Effect of basic set quality and electron correlation on the scale factors of a harmonic force field , 1990 .

[56]  Michael J. S. Dewar,et al.  Ground states of molecules. XXV. MINDO/3. Improved version of the MINDO semiempirical SCF-MO method , 1975 .

[57]  C. Toniolo,et al.  Structural versatility of peptides from Cα,αdialkylated glycines: Linear Ac3c homo‐oligopeptides , 1989 .

[58]  R. Cramer,et al.  Validation of the general purpose tripos 5.2 force field , 1989 .

[59]  Jonathan W. Essex,et al.  Atomic charges for variable molecular conformations , 1992 .

[60]  P. Kollman,et al.  A Second Generation Force Field for the Simulation of Proteins, Nucleic Acids, and Organic Molecules , 1995 .

[61]  Norman L. Allinger,et al.  Molecular mechanics. The MM3 force field for hydrocarbons. 1 , 1989 .