Semiempirical quantum–chemical methods

W Thiel - Wiley Interdisciplinary Reviews: Computational …, 2014 - Wiley Online Library
The semiempirical methods of quantum chemistry are reviewed, with emphasis on
established neglect of diatomic differential overlap‐based methods (MNDO, AM 1, PM 3) …

Molecular modeling of organic and biomolecular systems using BOSS and MCPRO

WL Jorgensen, J Tirado–Rives - Journal of Computational …, 2005 - Wiley Online Library
An overview is provided of the capabilities for the current versions of the BOSS and MCPRO
programs for molecular modeling of organic and biomolecular systems. Recent applications …

Performance of B3LYP density functional methods for a large set of organic molecules

J Tirado-Rives, WL Jorgensen - Journal of chemical theory and …, 2008 - ACS Publications
Testing of the commonly used hybrid density functional B3LYP with the 6-31G (d), 6-31G (d,
p), and 6-31+ G (d, p) basis sets has been carried out for 622 neutral, closed-shell organic …

The DBH24/08 database and its use to assess electronic structure model chemistries for chemical reaction barrier heights

J Zheng, Y Zhao, DG Truhlar - Journal of Chemical Theory and …, 2009 - ACS Publications
The diverse barrier height database DBH24 is updated by using W4 and W3. 2 data (Karton,
A.; Tarnopolsky, A.; Lamère, J.-F.; Schatz, GC; Martin, JMLJ Phys. Chem. A 2008, 112 …

Mechanisms and free energies of enzymatic reactions

J Gao, S Ma, DT Major, K Nam, J Pu… - Chemical …, 2006 - ACS Publications
Most enzymatic reactions have very large and remarkably similar apparent second-order
rate constants, kcat/KM, at mean values of about 107 M-1 s-1 with kcat in the range of 10 …

Semiempirical quantum-chemical orthogonalization-corrected methods: theory, implementation, and parameters

PO Dral, X Wu, L Spörkel, A Koslowski… - Journal of chemical …, 2016 - ACS Publications
Semiempirical orthogonalization-corrected methods (OM1, OM2, and OM3) go beyond the
standard MNDO model by explicitly including additional interactions into the Fock matrix in …

Advances in quantum and molecular mechanical (QM/MM) simulations for organic and enzymatic reactions

O Acevedo, WL Jorgensen - Accounts of chemical research, 2010 - ACS Publications
Application of combined quantum and molecular mechanical (QM/MM) methods focuses on
predicting activation barriers and the structures of stationary points for organic and …

The origins of femtomolar protein− ligand binding: hydrogen-bond cooperativity and desolvation energetics in the biotin−(strept) avidin binding site

J DeChancie, KN Houk - Journal of the American Chemical …, 2007 - ACS Publications
The unusually strong reversible binding of biotin by avidin and streptavidin has been
investigated by density functional and MP2 ab initio quantum mechanical methods. The …

Representative benchmark suites for barrier heights of diverse reaction types and assessment of electronic structure methods for thermochemical kinetics

J Zheng, Y Zhao, DG Truhlar - Journal of chemical theory and …, 2007 - ACS Publications
We propose three small sets of barrier heights for heavy-atom transfer, nucleophilic
substitution, and unimolecular and association reactions as benchmarks for comparing and …

Semiempirical quantum-chemical methods with orthogonalization and dispersion corrections

PO Dral, X Wu, W Thiel - Journal of Chemical Theory and …, 2019 - ACS Publications
We present two new semiempirical quantum-chemical methods with orthogonalization and
dispersion corrections: ODM2 and ODM3 (ODM x). They employ the same electronic …