A scaled quantum mechanical force field for the alanine-alanine zwitterions in water based on scale factors for alanine, glycine, N-methylacetamide, acetate, formate, and methylamine

Journal of Molecular Structure

Volumn 697, Issue 1-3, 2004, Pages 81-95

  Williams, Robert W ^a   Bone, Ian ^a,b   Weir, Alan F ^a,c  

^a UNIFORMED SERVICES UNIVERSITY OF THE HEALTH SCIENCES   (United States)

^b ATTN: MCHB TS L ^*  (United States)

^c USACHPPM   (United States)

Author keywords

Ab initio; Acetate; Alanine; Drug development; Force field; Formate; Fourier transform infrared spectra; Glycine; Methylamine; N methylacetamide; Peptide; Quantum mechanical; Raman; Scale factors; Scaled quantum mechanical force field

Indexed keywords

ACETIC ACID; ALANINE; AMPHOLYTE; FORMIC ACID; GLYCINE; METHYLAMINE; N METHYLACETAMIDE;

AB INITIO CALCULATION; ANALYTIC METHOD; ARTICLE; CHEMICAL STRUCTURE; DENSITY FUNCTIONAL THEORY; FORCE; GEOMETRY; INFRARED SPECTROSCOPY; MOLECULAR MODEL; PH MEASUREMENT; QUANTUM MECHANICS; RAMAN SPECTROMETRY; VIBRATION;

EID: 2942598293     PISSN: 00222860     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.molstruc.2004.03.038     Document Type: Article

References (41)

1. Moult J., Fidelis K., Zemla A., Hubbard T. Proceedings of CASP5 - Fifth Meeting on the Critical Assessment of Techniques for Protein Structure Prediction, Pacific Grove, California, December 1-5. 2002
2. Baker D., Sali A. Protein structure prediction and structural genomics. Science. 294:(5540):2001;93-96
3. Neumaier A. Mathematical modeling of proteins and mathematical prediction of protein structure. SIAM Rev. 39:(3):1996;407-460
4. Kaminski G., Stern H.A., Berne B.J., Friesner R.A., Cao Y.X., Murphy R.B., Zhou R., Halgren T.A. Development of a polarizable force field for proteins via ab initio quantum chemistry: first generation model and gas phase tests. J. Comput. Chem. 23:(16):2002;1515-1531
5. Palmö K., Pietilä L.-O., Krimm S. Construction of molecular mechanics energy functions by mathematical transformation of ab initio force fields and structures. J. Comput. Chem. 12:1991;385-390
6. Palmo K., Mannfors B., Mirkin N.G., Krimm S. Potential energy functions: from consistent force fields to spectroscopically determined polarizable force fields. Biopolymers. 68:(3):2003;383-394
7. Allinger N.L., Yuh Y.H., Lii J.-H. Molecular mechanics. The mm3 Force Field for hydrocarbons. 1. J. Am. Chem. Soc. 111:1989;8551-8566
8. Lii J.-H., Allinger N.L. Molecular mechanics. The mm3 force field for hydrocarbons. 2. Vibrational frequencies and thermodynamics. J. Am. Chem. Soc. 111:1989;8566-8575
9. Soler J.M., Artacho E., Gale J.D., Garca A., Junquera J., Ordejn P., Sanchez-Portal D. The siesta method for ab initio order-n materials simulation. J. Phys.: Condens. Matter. 14:2002;2745-2779
10. Williams R.W., Weaver J.L., Lowrey A.H. Relation between calculated amide frequencies and solution structure in ala-x peptides. Biopolymers. 30:1990;599-608
11. Williams R.W., Weaver J.L. Amide iii frequencies of ala-x peptides depend on the x amino acid size. Biopolymers. 30:1990;593-597
12. Asher S.A., Ianoul A., Mix G., Boyden M.N., Karnoup A., Diem M., Schweitzer-Stenner R. Dihedral psi angle dependence of the amide iii vibration: a uniquely sensitive uv resonance raman secondary structural probe. J. Am. Chem. Soc. 123:(47):2001;11775-11781
13. Ianoul A., Boyden M.N., Asher S.A. Dependence of the peptide amide iii vibration on the phi dihedral angle. J. Am. Chem. Soc. 123:(30):2001;7433-7434
14. Eker F., Cao X., Nafie L., Schweitzer-Stenner R. Tripeptides adopt stable structures in water. A combined polarized visible raman, ftir, and vcd spectroscopic study. J. Am. Chem. Soc. 124:2002;14330-14341
15. Williams R.W., Lowrey A.H. Effects of hydration on scale factors for ab initio force constants. J. Comput. Chem. 12:1991;761-777
16. Lowrey A.H., Williams R.W. Effects of hydration on scale factors for ab initio force constants ii. J. Mol. Struct. (Theochem). 253:1992;35-56
17. Lowrey A.H., Williams R.W. Effects of hydration on scale factors for ab initio force constants iii: supermolecules. J. Mol. Struct. (Theochem). 253:1992;57-72
18. Williams R.W. Effects of hydration on scale factors for ab initio force constants iv: trans- and cis-n-methylacetamide. Biopolymers. 32:1992;829-847
19. Williams R.W., Cheh J.L., Lowrey A.H., Weir A.F. Effects of hydration on scale factors for ab-initio force constants ix: methanol. J. Phys. Chem. 99:1995;5299-5307
20. Lowrey A.H., Williams R.W. Computational and spectroscopic studies of hydrated molecules. Advances in Molecular Structure Research. vol. 1:1995;JAI Press, Greenwich, CT. pp. 227-260
21. Weir A.F., Lowrey A.H., Williams R.W. Scaled quantum mechanical force field for alanyl-alanine peptide in solution. Biopolymers. 58:2001;577-591
22. Chang C.-D., Meienhofer J. Int. J. Pept. Protein Res. 11:1978;246
23. Williams R.W. Protein secondary structure analysis using raman amide i and amide iii spectra. Hirs C.H.W., Timasheff S.N. Methods in Enzymology. Enzyme Structure. vol. 130:1986;311-331
24. Oboodi M.R., Alva C., Diem M. Solution-phase raman studies of alanyl dipeptides and various isotopomers: a reevaluation of the amide iii vibrational assignment. J. Phys. Chem. 88:1984;501-505
25. M.J. Frisch, G.W. Trucks, H.B. Schlegel, G.E. Scuseria, M.A. Robb, J.R. Cheeseman, V.G. Zakrzewski, J.A. Montgomery, R.E. Stratmann, J.C. Burant, S. Dapprich, J.M. Millam, A.D. Daniels, K.N. Kudin, M.C. Strain, O. Farkas, J. Tomasi, V. Barone, M. Cossi, R. Cammi, B. Mennucci, C. Pomelli, C. Adamo, S. Clifford, J. Ochterski, G.A. Petersson, P.Y. Ayala, Q. Cui, K. Morokuma, D.K. Malick, A.D. Rabuck, K. Raghavachari, J.B. Foresman, J. Cioslowski, J.V. Ortiz, B.B. Stefanov, G. Liu, A. Liashenko, P. Piskorz, I. Komaromi, R. Gomperts, R.L. Martin, D.J. Fox, T. Keith, M.A. Al-Laham, C.Y. Peng, A. Nanayakkara, C. Gonzalez, M. Challacombe, P.M.W. Gill, B.G. Johnson, W. Chen, M.W. Wong, J.L. Andres, M. Head-Gordon, E.S. Replogle, J.A. Pople, GAUSSIAN 98, Gaussian, Inc., Pittsburgh, PA, 1998.
26. M.J. Frisch, G.W. Trucks, H.B. Schlegel, P.M.W. Gill, B.G. Johnson, M.A. Robb, J.R. Cheeseman, T. Keith, G.A. Petersson, J.A. Montgomery, K. Raghavachari, M.A. Al-Laham, V.G. Zakrzewski, J.V. Ortiz, J.B. Foresman, C.Y. Peng, P.Y. Ayala, W. Chen, M.W. Wong, J.L. Andres, E.S. Replogle, R. Gomperts, R.L. Martin, D.J. Fox, J.S. Binkley, D.J. Defrees, J. Baker, J.P. Stewart, M. Head-Gordon, C. Gonzalez, J.A. Pople, GAUSSIAN 94, Revision B.3, Gaussian, Inc., Pittsburgh, PA, 1995.
27. The SQMFF program package is a series of related programs developed by Peter Pulay and co-workers in the 1970s at the Etvös University, Budapest; specifically, the BMAT program which handles internal coordinates was written by Peter Pulay and the SCALE2 program is due to Gabor Pongor. This methodology is described in Ref. [28].
28. Fogarasi G., Púlay P. Ab initio calculation of force fields and vibrational spectra. Vibrational Spectra and Structure: A Series of Advances. vol. 3:1985;Elsevier, Amsterdam. (chapter 3) pp. 125-219
29. D.F. McIntosh, M.R. Peterson, Qcmp012 general vibrational analysis programs utilizing the wilson gf matrix method for a general unsymmetrized molecule, Technical Report, University of Toronto, Toronto, Ontario, M5S 1a1 Canada, this is a report published by the published by the Quantum Chemistry Program Exchange, Indiana University Department of Chemistry, 7, 1977.
30. C.K. Johnson, Ortep-ii: a fortran thermal-ellipsoid plot program for crystal structure illustrations, Technical Report, Oak Ridge National Laboratory, oRNL-5138, 1976.
31. Lawson C.L., Hanson R.J. Solving Least Squared Problems. Prentice-Hall Series in Automatic Computation. 1975;Prentice-Hall, Englewood Cliffs, NJ
32. Lowrey A.H., Kalasinsky V.F., Williams R.W. Scaled quantum mechanical force field for glycine in basic solution. Struct. Chem. 4:1993;289-298
33. Williams R.W., Kalasinsky V.F., Lowrey A.H. Scaled quantum mechanical force field for cis- and trans-glycine in acidic solution. J. Mol. Struct. (Theochem). 281:1993;157-171
34. Pulay P., Fogarasi G., Pang F., Boggs J.E. J. Am. Chem. Soc. 101:1979;2550
35. S. Krimm, J. Bandekar, Vibrational spectroscopy and conformation of peptides, polypeptides, and proteins, in: C.B. Anfinsen, J.T. Edsall, F.M.Richards (Eds.), Advances in Protein Chemistry New York, 38 (1986) 181-364.
36. R.W. Williams, I. Bone, A.F. Weir, Complete experimental and calculated frequencies, potential energy distributions, scale factors, diagonal and selected interaction force constants for isotopomers of alanyl-alanine zwitterion in water, alanine, glycine, n-methylacetamide, acetate, formate, and methylamine, J. Mol. Struct. These tables have been deposited with the British Library Lending Division (BLLD) as Supplementary Publication number SUP 26701, 92p.
37. Weir A.F., Lowrey A.H., Williams R.W. Transferable scaled quantum mechanical scale factors for alanine. J. Mol. Struct. (Theochem). 362:1996;339-354
38. Panchenko Y.N. Vibrational spectra and scaled quantum-mechanical molecular force fields. J. Mol. Struct. 567/568:2001;217-230
39. Maple J.R., Hwang M.J., Jalkanen K.J., Stockfisch T.P., Hagler A.T. Derivation of class ii force fields: V. Quantum force field for amides, peptides, and related compounds. J. Comput. Chem. 19:1998;430-458
40. Maple J.R., Hwang M.J., Jalkanen K.J., Stockfisch T.P., Hagler A.T. Derivation of class ii force fields: Viii. Derivation of a general quantum mechanical force field for organic compunds. J. Comput. Chem. 19:2001;430-458
41. Zídek L., Novotny M.V., Stone M.J. Increased protein backbone conformational entropy upon hydrophobic ligand binding. Nat. Struct. Biol. 6:(12):1999;1118-1121