Evidence for substrate binding-induced zwitterion formation in the catalytic Cys-His dyad of the SARS-CoV main protease

A Paasche, A Zipper, S Schäfer, J Ziebuhr… - Biochemistry, 2014 - ACS Publications
The coronavirus main protease (Mpro) represents an attractive drug target for antiviral
therapy of coronavirus (CoV) infections, including severe acute respiratory syndrome …

Why an integrated approach between search algorithms and chemical intuition is necessary?

VS Thimmakondu, A Sinjari, D Inostroza… - Physical Chemistry …, 2022 - pubs.rsc.org
Though search algorithms are appropriate tools for identifying low-energy isomers, fixing
several constraints seems to be a fundamental prerequisite to successfully running any …

A tabu-search based strategy for modeling molecular aggregates and binary reactions

S Nandi, SR McAnanama-Brereton, MP Waller… - Computational and …, 2017 - Elsevier
Modern day computational chemistry is moving towards studying complex chemical
systems, and global optimization algorithms are becoming increasingly important in …

Si 2 C 5 H 2 isomers–search algorithms versus chemical intuition

K Thirumoorthy, AL Cooksy… - Physical Chemistry …, 2020 - pubs.rsc.org
The pros and cons of using search algorithms alone in identifying new geometries have
been discussed by using the Si2C5H2 elemental composition as an example. Within 30 kcal …

Six Low-Lying Isomers of C11H8 Are Unidentified in the Laboratory–A Theoretical Study

T Roy, S Ghosal, VS Thimmakondu - The Journal of Physical …, 2021 - ACS Publications
Isomers of C11H8 have been theoretically examined using density functional theory and
coupled-cluster methods. The current investigation reveals that 2 a H-cyclopenta [cd] indene …

Interfacial water at the trialanine hydrophilic surface: a DFT electronic structure and bottom-up investigation

G Lanza, MA Chiacchio - Physical Chemistry Chemical Physics, 2015 - pubs.rsc.org
DFT-M062X quantum chemical computations on the Ala3H+· nH2O (n up to 37) complexes
have been performed to model for hydration effects on the molecular properties of …

Hybrid metaheuristic approach for nonlocal optimization of molecular systems

T Dresselhaus, J Yang, S Kumbhar… - Journal of Chemical …, 2013 - ACS Publications
Accurate modeling of molecular systems requires a good knowledge of the structure;
therefore, conformation searching/optimization is a routine necessity in computational …

QM/MM studies of structure and reactivity of cytochrome P450 enzymes: Methodology and selected applications

S Shaik, H Chen, D Usharani… - Drug metabolism …, 2014 - books.google.com
The incorporation of oxygen into biochemical processes has brought about an evolutionary
leap whereby many organisms have evolved to use oxygen as part of the life sustaining …

PathOpt—A global transition state search approach: Outline of algorithm

C Grebner, LP Pason, B Engels - Journal of Computational …, 2013 - Wiley Online Library
We propose a new algorithm to determine reaction paths and test its capability for Ar12 and
Ar13 clusters. Its main ingredient is a search for the local minima on a (n− 1) dimensional …

QM/MM investigations of organic chemistry oriented questions

TC Schmidt, A Paasche, C Grebner, K Ansorg… - Electronic Effects in …, 2014 - Springer
About 35 years after its first suggestion, QM/MM became the standard theoretical approach
to investigate enzymatic structures and processes. The success is due to the ability of …