Density functional tight binding: application to organic and biological molecules

M Gaus, Q Cui, M Elstner - Wiley Interdisciplinary Reviews …, 2014 - Wiley Online Library
In this work, we review recent extensions of the density functional tight binding (DFTB)
methodology and its application to organic and biological molecules. DFTB denotes a class …

Challenges in large scale quantum mechanical calculations

LE Ratcliff, S Mohr, G Huhs, T Deutsch… - Wiley …, 2017 - Wiley Online Library
During the past decades, quantum mechanical methods have undergone an amazing
transition from pioneering investigations of experts into a wide range of practical …

Conformational analysis of furanoside-containing mono-and oligosaccharides

HA Taha, MR Richards, TL Lowary - Chemical Reviews, 2013 - ACS Publications
D-arabinofuranose (2), as well as many plants, which produce polysaccharides rich in L-
arabinofuranose (3) 11− 14 and D-fructofuranose (4). 6 Other examples include the …

Multiscale QM/MM Simulations Identify the Roles of Asp239 and 1-OH···Nucleophile in Transition State Stabilization in Arabidopsis thaliana Cell-Wall Invertase 1

W Meelua, T Wanjai, N Thinkumrob… - Journal of Chemical …, 2023 - ACS Publications
Arabidopsis thaliana cell-wall invertase 1 (AtCWIN1), a key enzyme in sucrose metabolism
in plants, catalyzes the hydrolysis of sucrose into fructose and glucose. AtCWIN1 belongs to …

4′-C-Methoxy-2′-deoxy-2′-fluoro Modified Ribonucleotides Improve Metabolic Stability and Elicit Efficient RNAi-Mediated Gene Silencing

E Malek-Adamian, DC Guenther… - Journal of the …, 2017 - ACS Publications
We designed novel 4′-modified 2′-deoxy-2′-fluorouridine (2′-FU) analogues with the
aim to improve nuclease resistance and potency of therapeutic siRNAs by introducing 4′-C …

Adsorption of NO2, HCN, HCHO and CO on pristine and amine functionalized boron nitride nanotubes by self-consistent charge density functional tight-binding …

K Timsorn, C Wongchoosuk - Materials Research Express, 2020 - iopscience.iop.org
The adsorptions of toxic gases including NO 2, HCN, HCHO and CO molecules on the
pristine and amine functionalized (5, 0) single-wall boron nitride nanotubes (BNNTs) are …

Efficient predictions of formation energies and convex hulls from density functional tight binding calculations

A Kumar, ZA Ali, BM Wong - Journal of Materials Science & Technology, 2023 - Elsevier
Defects in materials significantly alter their electronic and structural properties, which affect
the performance of electronic devices, structural alloys, and functional materials. However …

Application of the SCC-DFTB method to hydroxide water clusters and aqueous hydroxide solutions

TH Choi, R Liang, CM Maupin… - The Journal of Physical …, 2013 - ACS Publications
The self-consistent charge density functional tight binding (SCC-DFTB) method has been
applied to hydroxide water clusters and a hydroxide ion in bulk water. To determine the …

Force fields and scoring functions for carbohydrate simulation

X Xiong, Z Chen, BP Cossins, Z Xu, Q Shao, K Ding… - Carbohydrate …, 2015 - Elsevier
Carbohydrate dynamics plays a vital role in many biological processes, but we are not
currently able to probe this with experimental approaches. The highly flexible nature of …

Improvement of DNA and RNA sugar pucker profiles from semiempirical quantum methods

M Huang, TJ Giese, TS Lee… - Journal of chemical theory …, 2014 - ACS Publications
Neglect of diatomic differential overlap (NDDO) and self-consistent density-functional tight-
binding (SCC-DFTB) semiempirical models commonly employed in combined quantum …