Polarizable force fields for molecular dynamics simulations of biomolecules

CM Baker - Wiley Interdisciplinary Reviews: Computational …, 2015 - Wiley Online Library
Molecular dynamics simulations are well established for the study of biomolecular systems.
Within these simulations, energy functions known as force fields are used to determine the …

Comparisons of different force fields in conformational analysis and searching of organic molecules: A review

T Lewis-Atwell, PA Townsend, MN Grayson - Tetrahedron, 2021 - Elsevier
This review aims to examine literature where different force fields are compared by their
performances in conformational analysis and searching of organic molecules …

Neutral peptides in the gas phase: conformation and aggregation issues

E Gloaguen, M Mons, K Schwing… - Chemical Reviews, 2020 - ACS Publications
Combined IR and UV laser spectroscopic techniques in molecular beams merged with
theoretical approaches have proven to be an ideal tool to elucidate intrinsic structural …

Evaluation of common theoretical methods for predicting infrared multiphotonic dissociation vibrational spectra of intramolecular hydrogen-bonded ions

AF Rodrigues-Oliveira, FW M. Ribeiro, G Cervi… - ACS …, 2018 - ACS Publications
Infrared photodissociation analyses are supported by theoretical calculations that allow a
trustworthy interpretation of experimental spectra of gaseous ions. B3LYP calculations are …

Investigations on isolated peptides by combined IR/UV spectroscopy in a molecular beam–structure, aggregation, solvation and molecular recognition

K Schwing, M Gerhards - International Reviews in Physical …, 2016 - Taylor & Francis
The well-known correlation between structure and functionality has motivated generations of
scientists to intensively investigate the structural behaviour of peptide and protein systems …

Single-conformation infrared spectra of model peptides in the amide I and amide II regions: Experiment-based determination of local mode frequencies and inter …

EG Buchanan, WH James, SH Choi, L Guo… - The Journal of …, 2012 - pubs.aip.org
Single-conformation infrared spectra in the amide I and amide II regions have been
recorded for a total of 34 conformations of three α-peptides, three β-peptides, four α/β …

Spectroscopic studies of kinetically trapped conformations in the gas phase: the case of triply protonated bradykinin

L Voronina, TR Rizzo - Physical Chemistry Chemical Physics, 2015 - pubs.rsc.org
Understanding the relation between the gas-phase structure of biological molecules and
their solution-phase structure is important when attempting to use gas-phase techniques to …

Surrogate based genetic algorithm method for efficient identification of low-energy peptide structures

J Villard, M Kılıç, U Rothlisberger - Journal of Chemical Theory …, 2023 - ACS Publications
Identification of the most stable structure (s) of a system is a prerequisite for the calculation of
any of its properties from first-principles. However, even for relatively small molecules …

Conformational structures of a decapeptide validated by first principles calculations and cold ion spectroscopy

TK Roy, V Kopysov, NS Nagornova, TR Rizzo… - …, 2015 - Wiley Online Library
Calculated structures of the two most stable conformers of a protonated decapeptide
gramicidin S in the gas phase have been validated by comparing the vibrational spectra …

A General Picture of Cucurbit [8] uril Host–Guest Binding: Recalibrating Bonded Interactions

Z Sun, Q He, Z Gong, P Kalhor, Z Huai, Z Liu - Molecules, 2023 - mdpi.com
Atomic-level understanding of the dynamic feature of host–guest interactions remains a
central challenge in supramolecular chemistry. The remarkable guest binding behavior of …