Semiempirical quantum mechanical methods for noncovalent interactions for chemical and biochemical applications

AS Christensen, T Kubar, Q Cui, M Elstner - Chemical reviews, 2016 - ACS Publications
Semiempirical (SE) methods can be derived from either Hartree–Fock or density functional
theory by applying systematic approximations, leading to efficient computational schemes …

[HTML][HTML] Enhanced semiempirical QM methods for biomolecular interactions

ND Yilmazer, M Korth - Computational and structural biotechnology journal, 2015 - Elsevier
Recent successes and failures of the application of 'enhanced'semiempirical QM (SQM)
methods are reviewed in the light of the benefits and backdraws of adding dispersion (D) …

Extension of the self-consistent-charge density-functional tight-binding method: third-order expansion of the density functional theory total energy and introduction of a …

Y Yang, H Yu, D York, Q Cui… - The Journal of Physical …, 2007 - ACS Publications
The standard self-consistent-charge density-functional-tight-binding (SCC-DFTB) method
(Phys. Rev. B 1998, 58, 7260) is derived by a second-order expansion of the density …

A transferable H-bonding correction for semiempirical quantum-chemical methods

M Korth, M Pitonak, J Rezac… - Journal of chemical theory …, 2010 - ACS Publications
Semiempirical methods could offer a feasible compromise between ab initio and empirical
approaches for the calculation of large molecules with biological relevance. A key problem …

Third-generation hydrogen-bonding corrections for semiempirical QM methods and force fields

M Korth - Journal of Chemical Theory and Computation, 2010 - ACS Publications
Computational modeling of biological systems is a rapidly evolving field that calls for
methods that are able to allow for extensive sampling with systems consisting of thousands …

PDDG/PM3 and PDDG/MNDO: improved semiempirical methods

MP Repasky, J Chandrasekhar… - Journal of …, 2002 - Wiley Online Library
Two new semiempirical methods employing a Pairwise Distance Directed Gaussian
modification have been developed: PDDG/PM3 and PDDG/MNDO; they are easily …

An efficient linear-scaling Ewald method for long-range electrostatic interactions in combined QM/MM calculations

K Nam, J Gao, DM York - Journal of Chemical Theory and …, 2005 - ACS Publications
A method is presented for the efficient evaluation of long-range electrostatic forces in
combined quantum mechanical and molecular mechanical (QM/MM) calculations of periodic …

A critical assessment of two-body and three-body interactions in water

GR Medders, V Babin, F Paesani - Journal of chemical theory and …, 2013 - ACS Publications
The microscopic behavior of water under different conditions and in different environments
remains the subject of intense debate. A great number of the controversies arise due to the …

Specific reaction parametrization of the AM1/d Hamiltonian for phosphoryl transfer reactions: H, O, and P atoms

K Nam, Q Cui, J Gao, DM York - Journal of Chemical Theory and …, 2007 - ACS Publications
A semiempirical AM1/d Hamiltonian is developed to model phosphoryl transfer reactions
catalyzed by enzymes and ribozymes for use in linear-scaling calculations and combined …

Structure, energy, vibrational spectrum, and Bader's analysis of π⋯ H hydrogen bonds and H− δ⋯ H+ δ dihydrogen bonds

BG de Oliveira - Physical Chemistry Chemical Physics, 2013 - pubs.rsc.org
In this paper, the intermolecular structural study asserted by the vibrational analysis in the
stretch frequencies of hydrogen bonds (π⋯ H) and dihydrogen bonds (H− δ⋯ H+ δ) have …