Harmonic Force Field for Glycine Oligopeptides EDDY J. BAUTISTA, 1 JORGE M. SEMINARIO 1,2 1 Department of Chemical Engineering, Texas A&M University, College Station, TX 2 Department of Electrical and Computer Engineering, Texas A&M University, College Station, TX Received 9 March 2007; accepted 3 April 2007 Published online 8 August 2007 in Wiley InterScience (www.interscience.wiley.com). DOI 10.1002/qua.21413 ABSTRACT: The need for much more useful molecular dynamics simulations of nanosized system requires precise and unambiguous methods to determine force field parameters avoiding fitting procedures in favor of first principles ones. We use a procedure FUERZA to calculate force constant parameters for glycine oligopeptides using as an input the Hessian tensor from an ab initio calculation. For a molecular system having n atoms, The FUERZA procedure reduces the 3n  3n problem to 3n 3  3 matrices representing atom-atom interactions. The procedure reproduces quite well most of the frequencies and as expected, it overestimates somehow stretching frequencies of bonds with terminal atoms such as hydrogens but it yields precise results for all other frequencies. A harmonic force field is reported for glycine oligopeptides. © 2007 Wiley Periodicals, Inc. Int J Quantum Chem 108: 180 –188, 2008 Key words: force field; glycine; DFT; harmonic constants; FUERZA 1. Introduction T here has been tremendous work to develop generalized force field parameters to perform molecular mechanics (MM) and molecular dynam- ics (MD) simulations in the literature. For instance, the widely used force field in the CHARMM pro- gram by Karplus et al [1]. was based on a strategic combination of experimental data, ab initio results, and further MD simulations using periodic bound- ary conditions. Thus to develop backbone energet- ics in proteins, Brooks and coworkers [2]. improved the treatment of the peptide backbone using quan- tum mechanical (QM) and molecular mechanical (MM) calculations on the alanine, glycine, and pra- line dipeptides, and the results from these calcula- tions were combined with MD simulations of pro- teins in crystal and aqueous environments where additional parameter optimization via Monte Carlo simulated annealing were used. Also ab initio force fields of glycine dipeptide in C 5 and C 7 conforma- tions [3] were calculated by Schafer and coworkers using ab initio optimized geometries for the glycine dipeptide of several conformations. An overview of empirical force fields for biological macromolecules was done by Mackerell [4]. The development of Correspondence to: J. M. Seminario; e-mail: seminario@ tamu.edu International Journal of Quantum Chemistry, Vol 108, 180 –188 (2008) © 2007 Wiley Periodicals, Inc.