Critical assessment of performance of alternative molecular modeling methods depending on a specific object and goal of the investigation is a question of continuous interest. This prompted us to demonstrate the origin of the guidelines we have used for a rational choice and use of a proper low level calculation method (LLM) for an initial geometry optimization of generated conformers, with the aim of selecting a set for further optimization. What was performed herein was a comparison of LLMs: MM3, MM+, UFF, Dreiding, AM1, PM3, and PM6 on the optimization of conformers’ geometry of α-methoxyphenylacetic acid (MPA) 2-butyl esters as a set of typical diastereomeric esters of a chiral derivatizing agent. This set of esters calculated represents only compounds of this certain type in the current work. The LLM conformer energies were correlated with benchmark energies found by using higher level reference method B3LYP/6-311++G** on the geometries gained previously by optimization with LLMs. In an alternative treatment, the energy range to be covered and corresponding number of LLM optimized conformers obligatory for submitting to further optimization using a high level optimization cascade were considered on the basis of determination of the cut-off conformer (COFC). 1. Introduction Critical assessment of performance of different alternative molecular modeling methods depending on the particular objects and specific goals is a question of continuous interest [1–7]. The aim of the current work is to demonstrate how the guidelines are derived for a rational choice of a proper low level calculation method (LLM) for the initial geometry optimization of generated conformers in the total conformational analysis of diastereomeric esters. The LLM chosen should allow selecting of a reliable set of conformers for further higher level optimization. Having previously followed such guidelines in the total conformational analysis of several esters with up to 11 dihedrals in their structure, the initial optimization of thousands of conformers all together have afforded reliable sets of conformers. The following higher level optimization of the selected conformers has led to the results that, in turn, have allowed calculation of the molecular shielding models in exceptional accordance with differential shielding effects in the NMR spectra [8]. The properties of organic compounds are dependent on their three-dimensional structures. Knowing the prevailing conformer [1] of certain compounds or population of reactive conformers of molecules of another type is often a key to
References
[1]
R. Aav, T. Pehk, S. Tamp et al., “Theoretical prediction and assignment of vicinal1H-1H coupling constants of diastereomeric 3-alkoxy-6,7-epoxy-2-oxabicyclo[3.3.0]octanes,” Magnetic Resonance in Chemistry, vol. 49, no. 2, pp. 76–82, 2011.
[2]
K. W. Sattelmeyer, J. Tirado-Rives, and W. L. Jorgensen, “Comparison of SCC-DFTB and NDDO-based semiempirical molecular orbital methods for organic molecules,” Journal of Physical Chemistry A, vol. 110, no. 50, pp. 13551–13559, 2006.
[3]
K. Gkionis, J. G. Hill, S. P. Oldfield, and J. A. Platts, “Performance of Becke's half-and-half functional for non-covalent interactions: energetics, geometries and electron densities,” Journal of Molecular Modeling, vol. 15, no. 9, pp. 1051–1060, 2009.
[4]
R. S. Paton and J. M. Goodman, “Hydrogen bonding and π-stacking: how reliable are force fields? A critical evaluation of force field descriptions of nonbonded interactions,” Journal of Chemical Information and Modeling, vol. 49, no. 4, pp. 944–955, 2009.
[5]
G. L. Warren, C. W. Andrews, A.-M. Capelli et al., “A critical assessment of docking programs and scoring functions,” Journal of Medicinal Chemistry, vol. 49, no. 20, pp. 5912–5931, 2006.
[6]
R. Wang, Y. Lu, and S. Wang, “Comparative evaluation of 11 scoring functions for molecular docking,” Journal of Medicinal Chemistry, vol. 46, no. 12, pp. 2287–2303, 2003.
[7]
T. Cheng, X. Li, Y. Li, Z. Liu, and R. Wang, “Comparative assessment of scoring functions on a diverse test set,” Journal of Chemical Information and Modeling, vol. 49, no. 4, pp. 1079–1093, 2009.
[8]
S. Tamp, K. Danilas, M. Kreen et al., “A total conformational analysis of diastereomeric esters and calculation of their conformational shielding models,” Journal of Molecular Structure: THEOCHEM, vol. 851, no. 1–3, pp. 84–91, 2008.
[9]
R. G. Parr and W. Yang, Density-Functional Theory of Atoms and Molecules, Oxford University Press, Oxford, UK, 1989.
[10]
？. Alver, M. F. Kaya, M. Bilge, and C. Parlak, “Vibrational spectroscopic investigation and conformational analysis of methacrylamidoantipyrine: a comparative density functional study,” Journal of Theoretical Chemistry, vol. 2013, Article ID 386247, 10 pages, 2013.
[11]
Z. Weiqun, L. Baolong, C. Yang, Z. Yong, and L. L. Y. Xujie, “The structure and conformation analysis of N-2-fluorobenzoyl-N′-2-methoxyphenylthiourea,” Journal of Molecular Structure: THEOCHEM, vol. 715, no. 1–3, pp. 117–124, 2005.
[12]
M. W. Hill, K. B. Wiberg, H. Castrejon, W. F. Bailey, J. Ochterski, and J. M. Seminario, Recent Developments and Applications of Modern Density Functional Theory, Elsevier, London, UK, 1996.
[13]
O. T？ubrik, P. Burk, T. Pehk, and U. M？eorg, “Conformational analysis of 1-acetyl-2-methylhydrazine,” Journal of Molecular Structure: THEOCHEM, vol. 546, pp. 119–125, 2001.
[14]
A. Metsala, E. Usin, I. Vallikivi, L. Villo, T. Pehk, and O. Parve, “Quantum chemical evaluation of the yield of hydroxybenzophenones in the fries rearrangement of hydroxyphenyl benzoates,” Journal of Molecular Structure: THEOCHEM, vol. 712, no. 1–3, pp. 215–221, 2004.
[15]
T. D. Rasmussen and F. Jensen, “Force field modelling of conformational energies,” Molecular Simulation, vol. 30, no. 11-12, pp. 801–806, 2004.
[16]
M. Stahl, U. Schopfer, G. Frenking, and R. W. Hoffmann, “Conformational analysis with carbon-carbon coupling constants. A density functional and molecular mechanics study,” Journal of Organic Chemistry, vol. 62, no. 11, pp. 3702–3704, 1997.
[17]
E. Voloshina, J. Fleischhauer, and P. Kraft, “Conformational analysis and CD calculations of methyl-substituted 13-tridecano-13-lactones,” Helvetica Chimica Acta, vol. 88, no. 2, pp. 194–209, 2005.
[18]
A. Leach, Molecular Modeling: Principles and Applications, Prentice Hall, New York, NY, USA, 2nd edition, 2001.
[19]
B. M. Trost, J. L. Belletire, S. Godleski et al., “On the use of the O-methylmandelate ester for establishment of absolute configuration of secondary alcohols,” Journal of Organic Chemistry, vol. 51, no. 12, pp. 2370–2374, 1986.
[20]
T. Pehk, E. Lippmaa, M. Lopp, A. Paju, B. C. Borer, and R. J. K. Taylor, “Determination of the absolute configuration of chiral secondary alcohols; new advances using carbon-13 and 2D-NMR spectroscopy,” Tetrahedron: Asymmetry, vol. 4, no. 7, pp. 1527–1532, 1993.
[21]
J. M. Seco, E. Qui？oá, and R. Riguera, “The assignment of absolute configuration by NMR,” Chemical Reviews, vol. 104, no. 1, pp. 17–117, 2004.
[22]
J. W. Ponder, Program TINKER, (version 5.0), 2007, http://dasher.wustl.edu/tinker/.
[23]
R. V. Pappu, R. K. Hart, and J. W. Ponder, “Analysis and application of potential energy smoothing and search methods for global optimization,” Journal of Physical Chemistry B, vol. 102, no. 48, pp. 9725–9742, 1998.
[24]
D. C. Young, Computational Chemistry: A Practical Guide for Applying Techniques to Real-World Problems, John Wiley & Sons, New York, NY, USA, 2001.
[25]
M. J. Frisch, G. W. Trucks, H. B. Schlegel et al., Gaussian 03 (Revision E. 01), Gaussian Inc., Wallingford, Conn, USA, 2009.
[26]
S. Grimme, “Semiempirical GGA-type density functional constructed with a long-range dispersion correction,” Journal of Computational Chemistry, vol. 27, no. 15, pp. 1787–1799, 2006.
[27]
J. J. P. Stewart, “Optimization of parameters for semiempirical methods. II. Applications,” Journal of Computational Chemistry, vol. 109, pp. 221–264, 1998.
[28]
M. J. S. Dewar, E. G. Zoebisch, and E. F. Healy, “Development and use of quantum mechanical molecular models. 76. AM1: a new general purpose quantum mechanical molecular model,” Journal of the American Chemical Society, vol. 107, no. 13, pp. 3902–3909, 1985.
[29]
L. P. Davis, R. M. Guidry, J. R. Williams, M. J. S. Dewar, and H. S. Rzepa, “MNDO calculations for compounds containing aluminum and boron,” Journal of Computational Chemistry, vol. 2, pp. 433–445, 1981.
[30]
J. J. P. Stewart, “Optimization of parameters for semiempirical methods. I. Method,” Journal of Computational Chemistry, vol. 10, pp. 209–220, 1989.
[31]
J. J. P. Stewart, “Optimization of parameters for semiempirical methods V: modification of NDDO approximations and application to 70 elements,” Journal of Molecular Modeling, vol. 13, no. 12, pp. 1173–1213, 2007.
[32]
A. K. Rappé, C. J. Casewit, K. S. Colwell, W. A. Goddard III, and W. M. Skiff, “UFF, a full periodic table force field for molecular mechanics and molecular dynamics simulations,” Journal of the American Chemical Society, vol. 114, no. 25, pp. 10024–10035, 1992.
[33]
A. K. Rappé and W. A. Goddard III, “Charge equilibration for molecular dynamics simulations,” Journal of Physical Chemistry, vol. 95, no. 8, pp. 3358–3363, 1991.
[34]
S. L. Mayo, B. D. Olafson, and W. A. Goddard III, “DREIDING: a generic force field for molecular simulations,” Journal of Physical Chemistry, vol. 94, no. 26, pp. 8897–8909, 1990.
