Mixed quantum mechanical/molecular mechanical molecular dynamics simulations of biological systems in ground and electronically excited states
E Brunk, U Rothlisberger - Chemical reviews, 2015 - ACS Publications
The quantum nature of electrons and nuclei is manifested in countless biological events
including the rearrangements of electrons in biochemical reactions, electron and proton …
including the rearrangements of electrons in biochemical reactions, electron and proton …
QM/MM calculations with deMon2k
The density functional code deMon2k employs a fitted density throughout (Auxiliary Density
Functional Theory), which offers a great speed advantage without sacrificing necessary …
Functional Theory), which offers a great speed advantage without sacrificing necessary …
Automated parametrization of biomolecular force fields from quantum mechanics/molecular mechanics (QM/MM) simulations through force matching
P Maurer, A Laio, HW Hugosson… - Journal of Chemical …, 2007 - ACS Publications
We introduce a novel procedure to parametrize biomolecular force fields. We perform finite-
temperature quantum mechanics/molecular mechanics (QM/MM) molecular dynamics …
temperature quantum mechanics/molecular mechanics (QM/MM) molecular dynamics …
Glycine in aqueous solution: solvation shells, interfacial water, and vibrational spectroscopy from ab initio molecular dynamics
J Sun, D Bousquet, H Forbert, D Marx - The Journal of chemical …, 2010 - pubs.aip.org
An aqueous glycine solution is studied with ab initio molecular dynamics to investigate the
structural aspects of the different solvation shells within the zwitterion and their impact on the …
structural aspects of the different solvation shells within the zwitterion and their impact on the …
On the zwitterionic nature of gas-phase peptides and protein ions
R Marchese, R Grandori, P Carloni… - PLoS computational …, 2010 - journals.plos.org
Determining the total number of charged residues corresponding to a given value of net
charge for peptides and proteins in gas phase is crucial for the interpretation of mass …
charge for peptides and proteins in gas phase is crucial for the interpretation of mass …
Resonant infrared multiphoton dissociation spectroscopy of gas-phase protonated peptides. Experiments and Car–Parrinello dynamics at 300 K
The gas-phase structures of protonated peptides are studied by means of resonant infrared
multiphoton dissociation spectroscopy (R-IRMPD) performed with a free electron laser. The …
multiphoton dissociation spectroscopy (R-IRMPD) performed with a free electron laser. The …
A quantum mechanical/molecular dynamics/mean field study of acrolein in aqueous solution: Analysis of H bonding and bulk effects on spectroscopic properties
A novel molecular dynamics methodology recently proposed by our group [Rega et al,
Chem. Phys. Lett. 422, 367 (2006)], which is based on an integrated hybrid potential rooted …
Chem. Phys. Lett. 422, 367 (2006)], which is based on an integrated hybrid potential rooted …
Change in a protein's electronic structure induced by an explicit solvent: An ab initio fragment molecular orbital study of ubiquitin
Y Komeiji, T Ishida, DG Fedorov… - Journal of …, 2007 - Wiley Online Library
The effect of solvation on the electronic structure of the ubiqutin protein was analyzed using
the ab initio fragment molecular orbital (FMO) method. FMO calculations were performed for …
the ab initio fragment molecular orbital (FMO) method. FMO calculations were performed for …
Lysine based dipeptides-molecular rectifiers with very high rectification ratio and their application towards designing logic gates
RS Sawhney, G Sikri - Physica E: Low-dimensional Systems and …, 2024 - Elsevier
In this research paper, we have enquired the dipeptides (ie, smallest peptides) consisting of
oppositely charged amino acids namely, Lysine-Aspartic and Lysine-Glutamic, where l …
oppositely charged amino acids namely, Lysine-Aspartic and Lysine-Glutamic, where l …
Conformational Analysis of l-Prolines in Water
AE Aliev, D Courtier-Murias - The Journal of Physical Chemistry B, 2007 - ACS Publications
The results of the ring conformational analysis of l-proline, N-acetyl-l-proline, and trans-4-
hydroxy-l-proline by NMR combined with calculations using density functional theory (DFT) …
hydroxy-l-proline by NMR combined with calculations using density functional theory (DFT) …