Carbonization in polyacrylonitrile (PAN) based carbon fibers studied by ReaxFF molecular dynamics simulations

B Saha, GC Schatz - The Journal of Physical Chemistry B, 2012 - ACS Publications
The carbonization mechanism in polyacrylonitrile (PAN) based carbon nanofibers is studied
using ReaxFF molecular dynamics simulations. Simulations are performed at two …

A proton-shuttle reaction mechanism for histone deacetylase 8 and the catalytic role of metal ions

R Wu, S Wang, N Zhou, Z Cao… - Journal of the American …, 2010 - ACS Publications
Zinc-dependent histone deacetylase 8 (HDAC8) catalyzes the removal of acetyl moieties
from histone tails, and is critically involved in regulating chromatin structure and gene …

Comparison of aromatic NH··· π, OH··· π, and CH··· π interactions of alanine using MP2, CCSD, and DFT methods

N Mohan, KP Vijayalakshmi, N Koga… - Journal of …, 2010 - Wiley Online Library
A comparison of the performance of various density functional methods including long‐
range corrected and dispersion corrected methods [MPW1PW91, B3LYP, B3PW91, B97‐D …

Zinc chelation with hydroxamate in histone deacetylases modulated by water access to the linker binding channel

R Wu, Z Lu, Z Cao, Y Zhang - Journal of the American Chemical …, 2011 - ACS Publications
It is of significant biological interest and medical importance to develop class-and isoform-
selective histone deacetylase (HDAC) modulators. The impact of the linker component on …

Theoretical molecular design of heteroacenes for singlet fission: Tuning the diradical character by modifying π-conjugation length and aromaticity

S Ito, M Nakano - The Journal of Physical Chemistry C, 2015 - ACS Publications
A theoretical molecular design for efficient singlet fission (SF) is performed for several
heteroacene models involving nitrogen (N) atoms based on the diradical character criterion …

Flexibility of catalytic zinc coordination in thermolysin and HDAC8: A Born− Oppenheimer ab initio QM/MM molecular dynamics study

R Wu, P Hu, S Wang, Z Cao… - Journal of chemical theory …, 2010 - ACS Publications
The different coordination modes and fast ligand exchange of zinc coordination has been
suggested to be one key catalytic feature of the zinc ion which makes it an invaluable metal …

Highly dissociative and concerted mechanism for the nicotinamide cleavage reaction in Sir2Tm enzyme suggested by ab initio QM/MM molecular dynamics …

P Hu, S Wang, Y Zhang - Journal of the American Chemical …, 2008 - ACS Publications
Sir2 enzymes catalyze the NAD+-dependent protein deacetylation and play critical roles in
epigenetics, cell death, and lifespan regulation. In spite of a current flurry of experimental …

To stack or not to stack: performance of a new density functional for the uracil and thymine dimers

J Gu, J Wang, J Leszczynski, Y Xie… - Chemical physics …, 2008 - Elsevier
The newly developed density functional M06-2x was used to predict the structures and
stacking interactions of the nucleic acid base dimers of uracil and thymine. This study …

A designed bithiopheneimide-based conjugated polymer for organic photovoltaic with ultrafast charge transfer at donor/PC71BM interface: theoretical study and …

SB Li, YA Duan, Y Geng, HB Li, JZ Zhang… - Physical Chemistry …, 2014 - pubs.rsc.org
In the current work, a series of bithiopheneimide (BTI)-based D–A copolymers were
investigated based on the reported PDTSBTI (1) to screen excellent molecules toward …

How do SET-domain protein lysine methyltransferases achieve the methylation state specificity? Revisited by Ab initio QM/MM molecular dynamics simulations

P Hu, S Wang, Y Zhang - Journal of the American Chemical …, 2008 - ACS Publications
A distinct protein lysine methyltransferase (PKMT) only transfers a certain number of methyl
group (s) to its target lysine residue in spite of the fact that a lysine residue can be either …