[HTML][HTML] RNA structural dynamics as captured by molecular simulations: a comprehensive overview

J Šponer, G Bussi, M Krepl, P Banáš… - Chemical …, 2018‏ - pmc.ncbi.nlm.nih.gov
With both catalytic and genetic functions, ribonucleic acid (RNA) is perhaps the most
pluripotent chemical species in molecular biology, and its functions are intimately linked to …

Metal ion modeling using classical mechanics

P Li, KM Merz Jr - Chemical reviews, 2017‏ - ACS Publications
Metal ions play significant roles in numerous fields including chemistry, geochemistry,
biochemistry, and materials science. With computational tools increasingly becoming …

RNA structural dynamics as captured by molecular simulations: a comprehensive overview

J Sponer, G Bussi, M Krepl, P Banáš, S Bottaro… - Chemical …, 2018‏ - ACS Publications
With both catalytic and genetic functions, ribonucleic acid (RNA) is perhaps the most
pluripotent chemical species in molecular biology, and its functions are intimately linked to …

Parameterization of monovalent ions for the OPC3, OPC, TIP3P-FB, and TIP4P-FB water models

A Sengupta, Z Li, LF Song, P Li… - Journal of chemical …, 2021‏ - ACS Publications
Monovalent ions play significant roles in various biological and material systems. Recently,
four new water models (OPC3, OPC, TIP3P-FB, and TIP4P-FB), with significantly improved …

Systematic parameterization of monovalent ions employing the nonbonded model

P Li, LF Song, KM Merz Jr - Journal of chemical theory and …, 2015‏ - ACS Publications
Monovalent ions play fundamental roles in many biological processes in organisms.
Modeling these ions in molecular simulations continues to be a challenging problem. The 12 …

Parameterization of highly charged metal ions using the 12-6-4 LJ-type nonbonded model in explicit water

P Li, LF Song, KM Merz Jr - The Journal of Physical Chemistry B, 2015‏ - ACS Publications
Highly charged metal ions act as catalytic centers and structural elements in a broad range
of chemical complexes. The nonbonded model for metal ions is extensively used in …

A practical guide to biologically relevant molecular simulations with charge scaling for electronic polarization

E Duboue-Dijon, M Javanainen, P Delcroix… - The Journal of …, 2020‏ - pubs.aip.org
Molecular simulations can elucidate atomistic-level mechanisms of key biological
processes, which are often hardly accessible to experiment. However, the results of the …

Systematic parametrization of divalent metal ions for the OPC3, OPC, TIP3P-FB, and TIP4P-FB water models

Z Li, LF Song, P Li, KM Merz Jr - Journal of chemical theory and …, 2020‏ - ACS Publications
Divalent metal ions play important roles in biological and materials systems. Molecular
dynamics simulation is an efficient tool to investigate these systems at the microscopic level …

Unlocking the computational design of metal–organic cages

A Tarzia, KE Jelfs - Chemical Communications, 2022‏ - pubs.rsc.org
Metal–organic cages are macrocyclic structures that can possess an intrinsic void that can
hold molecules for encapsulation, adsorption, sensing, and catalysis applications. As metal …

Parametrization of DFTB3/3OB for magnesium and zinc for chemical and biological applications

X Lu, M Gaus, M Elstner, Q Cui - The Journal of Physical …, 2015‏ - ACS Publications
We report the parametrization of the approximate density functional theory, DFTB3, for
magnesium and zinc for chemical and biological applications. The parametrization strategy …