scholarly journals Conformational dynamics of carbohydrates: Raman optical activity of d-glucuronic acid and N-acetyl-d-glucosamine using a combined molecular dynamics and quantum chemical approach

2015 ◽  
Vol 17 (8) ◽  
pp. 6016-6027 ◽  
Author(s):  
Shaun T. Mutter ◽  
François Zielinski ◽  
James R. Cheeseman ◽  
Christian Johannessen ◽  
Paul L. A. Popelier ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Optical Activity ◽  
Quantum Chemical ◽  
Glucuronic Acid ◽  
State Of The Art ◽  
Conformational Dynamics ◽  
Conformational Space ◽  
Computational Approaches ◽  
Raman Optical Activity ◽  
Quantum Chemical Approach

Raman optical activity combined with state-of-the-art computational approaches successfully probes the conformational space of two important carbohydrates.

Raman optical activity of tetra-alanine in the poly(l-proline) II type peptide conformation

2017 ◽  
Vol 19 (3) ◽  
pp. 2078-2086 ◽  
Author(s):  
Masakazu Furuta ◽  
Tomotsumi Fujisawa ◽  
Hiroyasu Urago ◽  
Takahiro Eguchi ◽  
Takahito Shingae ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulations ◽  
Quantum Chemical Calculations ◽  
Optical Activity ◽  
Quantum Chemical ◽  
Peptide Conformation ◽  
Raman Optical Activity ◽  
Dynamics Simulations

Raman optical activity spectra of tetra-alanine was characterized by quantum chemical calculations combined with molecular dynamics simulations.

scholarly journals Establishing the link between fibril formation and Raman optical activity spectra of insulin

2017 ◽  
Vol 19 (21) ◽  
pp. 13614-13621 ◽  
Author(s):  
Jiří Kessler ◽  
Shigeki Yamamoto ◽  
Petr Bouř
Keyword(s):  
Molecular Dynamics ◽  
Optical Activity ◽  
Density Functional ◽  
Fibril Formation ◽  
Raman Optical Activity ◽  
Insulin Fibrils

Molecular dynamics and density functional simulations are used to explain changes in Raman optical activity accompanying the formation of insulin fibrils.

Rational design of novel fluorescent analogues of cholesterol: a “step-by-step” computational study

2019 ◽  
Vol 21 (28) ◽  
pp. 15487-15503 ◽  
Author(s):  
Andrea Bonvicini ◽  
Peter Reinholdt ◽  
Vincent Tognetti ◽  
Laurent Joubert ◽  
Daniel Wüstner ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulations ◽  
Quantum Chemical ◽  
Rational Design ◽  
State Of The Art ◽  
Computational Study ◽  
Dynamics Simulations ◽  
Fluorescent Analogues

State-of-the-art quantum chemical and molecular dynamics simulations are used as guidelines in design of novel fluorescent analogues of cholesterol.

AB INITIO PATH INTEGRAL STUDY ON ISOTOPE EFFECT OF AMMONIA MOLECULE

2005 ◽  
Vol 04 (01) ◽  
pp. 175-181 ◽  
Author(s):  
MASANORI TACHIKAWA ◽  
MOTOYUKI SHIGA
Keyword(s):  
Molecular Dynamics ◽  
Ab Initio ◽  
Isotope Effect ◽  
Path Integral ◽  
Quantum Chemical ◽  
Degrees Of Freedom ◽  
Dynamics Simulation ◽  
Ammonia Molecule ◽  
Quantum Chemical Approach ◽  
Quantum Feature

We have applied ab initio path integral molecular dynamics simulation to study the quantum feature and proton/deuteron isotope effect of ammonia molecule. This method treats all the rotational and vibrational degrees of freedom fully quantum mechanically, while the potential energies of the respective molecular configurations are calculated "on the fly" using ab initio quantum chemical approach. The differences on the geometry and the electronic structure between NH 3 and ND 3 molecules are investigated in detail.

scholarly journals Conformational Analysis of Cinhonine and Cinhonidine by Tensor Decomposition of Molecular Dynamics Trajectories

2019 ◽  
Vol 92 (2) ◽  
pp. 259-267
Author(s):  
Karlo Sović ◽  
Tea Ostojić ◽  
Ines Primožič ◽  
Tomica Hrenar ◽  
Mirjana Skočibušić ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Principal Component Analysis ◽  
Conformational Analysis ◽  
Molecular Dynamics Simulations ◽  
Quantum Chemical ◽  
Principal Component ◽  
Conformational Space ◽  
Cartesian Coordinates ◽  
Dynamics Simulations ◽  
Quantum Chemical Molecular Dynamics

Full conformational space of cinchonine and cinchonidine has been investigated by means of statistical analysis of quantum chemical molecular dynamics simulations. Recently developed procedure comprising principal component analysis of molecular dynamics trajectories was applied on cinchonine and cinchonidine as well as on their protonated and methylated quaternary derivatives. The method for full conformational analysis includes Cartesian coordinates sampling through quantum chemical molecular dynamics simulations, reduction of dimensionality by principal component analysis, determination of probability distributions in a reduced space of Cartesian coordinates and search for all the strict extrema points in probability distribution functions. In order to gain crucial insight in the understanding of chirality induction of these alkaloids, comparison of the determined conformational spaces of pseudo-enantiomers has been made. It was shown that protonation of the quinuclidine nitrogen atom stabilizes the conformers with the intramolecular 1N–H∙∙∙9O hydrogen bond whereas methylation on the same position results in the reduction of the domain of internal coordinates responsible for the conformational space.

scholarly journals Paving the way to conformationally unravel complex glycopeptide antibiotics by means of Raman optical activity

2021 ◽  
Vol 12 (16) ◽  
pp. 5952-5964
Author(s):  
Roy Aerts ◽  
Jente Vanhove ◽  
Wouter Herrebout ◽  
Christian Johannessen
Keyword(s):  
Optical Activity ◽  
Conformational Space ◽  
Glycopeptide Antibiotics ◽  
Raman Optical Activity ◽  
The Way

Raman optical activity tackles the complex conformational space of glycopeptide antibiotics.

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