Universal QM/MM approaches for general nanoscale applications
Quantum mechanics/molecular mechanics (QM/MM) hybrid models allow one to address
chemical phenomena in complex molecular environments. Whereas this modeling approach …
chemical phenomena in complex molecular environments. Whereas this modeling approach …
High-resolution reversible folding of hyperstable RNA tetraloops using molecular dynamics simulations
We report the de novo folding of three hyperstable RNA tetraloops to 1–3 Å rmsd from their
experimentally determined structures using molecular dynamics simulations initialized in the …
experimentally determined structures using molecular dynamics simulations initialized in the …
Performance of M06, M06-2X, and M06-HF density functionals for conformationally flexible anionic clusters: M06 functionals perform better than B3LYP for a model …
We present a comparative assessment of the performance of the M06 suite of density
functionals (M06, M06-2X, and M06-HF) against an MP2 benchmark for calculating the …
functionals (M06, M06-2X, and M06-HF) against an MP2 benchmark for calculating the …
RNA force field with accuracy comparable to state-of-the-art protein force fields
Molecular dynamics (MD) simulation has become a powerful tool for characterizing at an
atomic level of detail the conformational changes undergone by proteins. The application of …
atomic level of detail the conformational changes undergone by proteins. The application of …
DNA–protein π-interactions in nature: abundance, structure, composition and strength of contacts between aromatic amino acids and DNA nucleobases or …
KA Wilson, JL Kellie, SD Wetmore - Nucleic acids research, 2014 - academic.oup.com
Four hundred twenty-eight high-resolution DNA–protein complexes were chosen for a
bioinformatics study. Although 164 crystal structures (38% of those searched) contained no …
bioinformatics study. Although 164 crystal structures (38% of those searched) contained no …
Predicting rate constants of reactive chlorine species toward organic compounds by combining machine learning and quantum chemical calculation
S Zheng, W Qin, H Ji, W Guo… - Environmental Science & …, 2023 - ACS Publications
Reactive chlorine species (RCS), such as chlorine (HOCl/OCl–), chlorine dioxide (ClO2),
chlorine atom (Cl•), and dichlorine radical (Cl2•–), play a crucial role in oxidation and …
chlorine atom (Cl•), and dichlorine radical (Cl2•–), play a crucial role in oxidation and …
Nature and magnitude of aromatic base stacking in DNA and RNA: Quantum chemistry, molecular mechanics, and experiment
J Šponer, JE Šponer, A Mládek, P Jurečka… - …, 2013 - Wiley Online Library
Base stacking is a major interaction shaping up and stabilizing nucleic acids. During the last
decades, base stacking has been extensively studied by experimental and theoretical …
decades, base stacking has been extensively studied by experimental and theoretical …
Stacking in RNA: NMR of four tetramers benchmark molecular dynamics
DE Condon, SD Kennedy, BC Mort… - Journal of chemical …, 2015 - ACS Publications
Molecular dynamics (MD) simulations for RNA tetramers r (AAAA), r (CAAU), r (GACC), and r
(UUUU) are benchmarked against 1H–1H NOESY distances and 3 J scalar couplings to test …
(UUUU) are benchmarked against 1H–1H NOESY distances and 3 J scalar couplings to test …
Spin splitting energy of transition metals: A new, more affordable wave function benchmark method and its use to test density functional theory
D Zhang, DG Truhlar - Journal of Chemical Theory and …, 2020 - ACS Publications
Accurately predicting the spin splitting energy of chemical species is important for
understanding their reactivity and magnetic properties, but it is very challenging, especially …
understanding their reactivity and magnetic properties, but it is very challenging, especially …
Chitosan derivatives as effective nanocarriers for ocular release of timolol drug
PI Siafaka, A Titopoulou, EN Koukaras… - International journal of …, 2015 - Elsevier
The aim of the present study was to evaluate the effectiveness of neat chitosan (CS) and its
derivatives with succinic anhydride (CSUC) and 2-carboxybenzaldehyde (CBCS) as …
derivatives with succinic anhydride (CSUC) and 2-carboxybenzaldehyde (CBCS) as …