title: Elucidating Hyperconjugation from Electronegativity to Predict Drug Conformational Energy in a High Throughput Manner.
abstract: Computational chemists use structure-based drug design and molecular dynamics of drug/protein complexes which require an accurate description of the conformational space of drugs. Organic chemists use qualitative chemical principles such as the effect of electronegativity on hyperconjugation, the impact of steric clashes on stereochemical outcome of reactions, and the consequence of resonance on the shape of molecules to rationalize experimental observations. While computational chemists speak about electron densities and molecular orbitals, organic chemists speak about partial charges and localized molecular orbitals. Attempts to reconcile these two parallel approaches such as programs for natural bond orbitals and intrinsic atomic orbitals computing Lewis structures-like orbitals and reaction mechanism have appeared. In the past, we have shown that encoding and quantifying chemistry knowledge and qualitative principles can lead to predictive methods. In the same vein, we thought to understand the conformational behaviors of molecules and to encode this knowledge back into a molecular mechanics tool computing conformational potential energy and to develop an alternative to atom types and training of force fields on large sets of molecules. Herein, we describe a conceptually new approach to model torsion energies based on fundamental chemistry principles. To demonstrate our approach, torsional energy parameters were derived on-the-fly from atomic properties. When the torsional energy terms implemented in GAFF, Parm@Frosst, and MMFF94 were substituted by our method, the accuracy of these force fields to reproduce MP2-derived torsional energy profiles and their transferability to a variety of functional groups and drug fragments were overall improved. In addition, our method did not rely on atom types and consequently did not suffer from poor automated atom type assignments.
authors.affiliation: Department of Chemistry, McGill University , 801 Sherbrooke St. W., Montréal, QC, Canada H3A 0B8.
authors.forename: Zhaomin
authors.initials: Z
authors.lastname: Liu
authors.affiliation: Department of Chemistry, McGill University , 801 Sherbrooke St. W., Montréal, QC, Canada H3A 0B8.
authors.forename: Joshua
authors.initials: J
authors.lastname: Pottel
authors.affiliation: Department of Chemistry, McGill University , 801 Sherbrooke St. W., Montréal, QC, Canada H3A 0B8.
authors.forename: Moeed
authors.initials: M
authors.lastname: Shahamat
authors.affiliation: Department of Chemistry, McGill University , 801 Sherbrooke St. W., Montréal, QC, Canada H3A 0B8.
authors.forename: Anna
authors.initials: A
authors.lastname: Tomberg
authors.affiliation: Chemical Computing Group Inc. , 1010 Sherbrooke St. W., Montréal, QC, Canada H3A 2R7.
authors.forename: Paul
authors.initials: P
authors.lastname: Labute
authors.affiliation: Department of Chemistry, McGill University , 801 Sherbrooke St. W., Montréal, QC, Canada H3A 0B8.
authors.forename: Nicolas
authors.initials: N
authors.lastname: Moitessier
mesh_terms: D015195:Drug Design; D004583:Electrons; D008968:Molecular Conformation; D056004:Molecular Dynamics Simulation; D004364:Pharmaceutical Preparations / Q000737:chemistry*; D013816:Thermodynamics
chemical_list: D004364:Pharmaceutical Preparations