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 …

Theory and simulation of the ultrafast double-bond isomerization of biological chromophores

S Gozem, HL Luk, I Schapiro, M Olivucci - Chemical reviews, 2017 - ACS Publications
Ultrafast processes in light-absorbing proteins have been implicated in the primary step in
the light-to-energy conversion and the initialization of photoresponsive biological functions …

An overview of molecular modeling for drug discovery with specific illustrative examples of applications

M Aminpour, C Montemagno, JA Tuszynski - Molecules, 2019 - mdpi.com
In this paper we review the current status of high-performance computing applications in the
general area of drug discovery. We provide an introduction to the methodologies applied at …

G protein–coupled receptor rhodopsin

K Palczewski - Annu. Rev. Biochem., 2006 - annualreviews.org
The rhodopsin crystal structure provides a structural basis for understanding the function of
this and other G protein–coupled receptors (GPCRs). The major structural motifs observed …

Identification Of Two Distinct Inactive Conformations Of The Beta-2 Adrenergic Receptor Reconciles Structural And Biochemical Observations

RO Dror, DH Arlow, DW Borhani, M Jensen… - Biophysical Journal, 2009 - cell.com
Diane Lynch1, Dow Hurst1, Patti Reggio1, Alan Grossfield2, Mike Pitman3. 1University of
North Carolina, Greensboro, Greensboro, NC, USA, 2University of Rochester School of …

Trajectory‐based nonadiabatic dynamics with time‐dependent density functional theory

BFE Curchod, U Rothlisberger, I Tavernelli - ChemPhysChem, 2013 - Wiley Online Library
Understanding the fate of an electronically excited molecule constitutes an important task for
theoretical chemistry, and practical implications range from the interpretation of atto‐and …

A solvent-driven molecular spring

Z Zhang, C Han, G Yu, F Huang - Chemical Science, 2012 - pubs.rsc.org
A solvent-driven doubly threaded rotaxane dimer based on an amino-modified copillar [5]
arene was prepared using bis (trifluoromethyl) phenyl isocyanate as stoppers. By …

Tracking the excited-state time evolution of the visual pigment with multiconfigurational quantum chemistry

LM Frutos, T Andruniów, F Santoro… - Proceedings of the …, 2007 - National Acad Sciences
The primary event that initiates vision is the photoinduced isomerization of retinal in the
visual pigment rhodopsin (Rh). Here, we use a scaled quantum mechanics/molecular …

Structure, initial excited-state relaxation, and energy storage of rhodopsin resolved at the multiconfigurational perturbation theory level

T Andruniów, N Ferré… - Proceedings of the …, 2004 - National Acad Sciences
We demonstrate that a “brute force” quantum chemical calculation based on an ab initio
multiconfigurational second order perturbation theory approach implemented in a quantum …

T-ray sensing and imaging

W Withayachumnankul, GM Png, X Yin… - Proceedings of the …, 2007 - ieeexplore.ieee.org
T-ray wavelengths are long enough to pass through dry, nonpolar objects opaque at visible
wavelengths, but short enough to be manipulated by optical components to form an image …