Molecular dynamics simulations of cyclosporin A: The crystal structure and dynamic modelling of a structure in apolar solution based on NMR data

1987 ◽  
Vol 1 (3) ◽  
pp. 219-241 ◽  
Author(s):  
J. Lautz ◽  
H. Kessler ◽  
R. Kaptein ◽  
W. F. van Gunsteren
Keyword(s):  
Crystal Structure ◽  
Molecular Dynamics ◽  
Cyclosporin A ◽  
Molecular Dynamics Simulations ◽  
Dynamic Modelling ◽  
Nmr Data ◽  
Dynamics Simulations

scholarly journals Combined Use of Structure Analysis, Studies of Molecular Association in Solution, and Molecular Modelling to Understand the Different Propensities of Dihydroxybenzoic Acids to Form Solid Phases

Pharmaceutics ◽  
2021 ◽  
Vol 13 (5) ◽  
pp. 734
Author(s):  
Aija Trimdale ◽  
Anatoly Mishnev ◽  
Agris Bērziņš
Keyword(s):  
Crystal Structure ◽  
Molecular Dynamics ◽  
Molecular Dynamics Simulations ◽  
Structure Analysis ◽  
Crystal Structure Analysis ◽  
Molecular Association ◽  
Hydroxyl Groups ◽  
Solid Phases ◽  
Solvent Molecules ◽  
Dynamics Simulations

The arrangement of hydroxyl groups in the benzene ring has a significant effect on the propensity of dihydroxybenzoic acids (diOHBAs) to form different solid phases when crystallized from solution. All six diOHBAs were categorized into distinctive groups according to the solid phases obtained when crystallized from selected solvents. A combined study using crystal structure and molecule electrostatic potential surface analysis, as well as an exploration of molecular association in solution using spectroscopic methods and molecular dynamics simulations were used to determine the possible mechanism of how the location of the phenolic hydroxyl groups affect the diversity of solid phases formed by the diOHBAs. The crystal structure analysis showed that classical carboxylic acid homodimers and ring-like hydrogen bond motifs consisting of six diOHBA molecules are prominently present in almost all analyzed crystal structures. Both experimental spectroscopic investigations and molecular dynamics simulations indicated that the extent of intramolecular bonding between carboxyl and hydroxyl groups in solution has the most significant impact on the solid phases formed by the diOHBAs. Additionally, the extent of hydrogen bonding with solvent molecules and the mean lifetime of solute–solvent associates formed by diOHBAs and 2-propanol were also investigated.

Active site gate of M32 carboxypeptidases illuminated by crystal structure and molecular dynamics simulations

2017 ◽  
Vol 1865 (11) ◽  
pp. 1406-1415 ◽  
Author(s):  
Bhaskar Sharma ◽  
Sahayog N. Jamdar ◽  
Biplab Ghosh ◽  
Pooja Yadav ◽  
Ashwani Kumar ◽  
...  
Keyword(s):  
Crystal Structure ◽  
Molecular Dynamics ◽  
Molecular Dynamics Simulations ◽  
Active Site ◽  
Dynamics Simulations

Interaction of Water with the Model Ionic Liquid [bmim][BF4]: Molecular Dynamics Simulations and Comparison with NMR Data

2008 ◽  
Vol 112 (26) ◽  
pp. 7826-7836 ◽  
Author(s):  
Margherita Moreno ◽  
Franca Castiglione ◽  
Andrea Mele ◽  
Carlo Pasqui ◽  
Guido Raos
Keyword(s):  
Molecular Dynamics ◽  
Ionic Liquid ◽  
Molecular Dynamics Simulations ◽  
Nmr Data ◽  
Dynamics Simulations

scholarly journals Inter-helical conformational preferences of HIV-1 TAR-RNA from maximum occurrence analysis of NMR data and molecular dynamics simulations

2016 ◽  
Vol 18 (8) ◽  
pp. 5743-5752 ◽  
Author(s):  
Witold Andrałojć ◽  
Enrico Ravera ◽  
Loïc Salmon ◽  
Giacomo Parigi ◽  
Hashim M. Al-Hashimi ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulations ◽  
Conformational Space ◽  
Nmr Data ◽  
Conformational Preferences ◽  
Tar Rna ◽  
Dynamics Simulations ◽  
Maximum Occurrence ◽  
Hiv 1

Molecular dynamics simulations and maximum occurrence distribution identify the same most likely sampled conformations over the available conformational space.

scholarly journals [UO2(NH3)5]Br2·NH3: synthesis, crystal structure, and speciation in liquid ammonia solution by first-principles molecular dynamics simulations

2015 ◽  
Vol 44 (16) ◽  
pp. 7332-7337 ◽  
Author(s):  
Patrick Woidy ◽  
Michael Bühl ◽  
Florian Kraus
Keyword(s):  
Crystal Structure ◽  
Molecular Dynamics ◽  
Bond Strength ◽  
Molecular Dynamics Simulations ◽  
First Principles ◽  
Liquid Ammonia ◽  
Ammonia Solution ◽  
X Ray Diffraction ◽  
X Ray ◽  
Dynamics Simulations

X-Ray diffraction and Car–Parrinello molecular dynamics simulations furnish insights into the speciation of uranyl(vi) in liquid ammonia, calling special attention to the effect of solvation on the U–N bond length and bond strength.

scholarly journals Reducing Crystal Structure Overprediction of Ibuprofen with Large Scale Molecular Dynamics Simulations

2021 ◽  
Author(s):  
Nicholas Francia ◽  
Louise Price ◽  
Matteo Salvalaglio
Keyword(s):  
Crystal Structure ◽  
Molecular Dynamics ◽  
Molecular Dynamics Simulations ◽  
Crystal Structures ◽  
Finite Temperature ◽  
Structure Prediction ◽  
Large Scale ◽  
Lattice Energy ◽  
Racemic Mixture ◽  
Dynamics Simulations

<p>The control of the crystal form is a central issue in the pharmaceutical industry. The identification of putative polymorphs through Crystal Structure Prediction (CSP) methods is based on lattice energy calculations, which are known to significantly over-predict the number of plausible crystal structures. A valuable tool to reduce overprediction is to employ physics-based, dynamic simulations to coalesce lattice energy minima separated by small barriers into a smaller number of more stable geometries once thermal effects are introduced. Molecular dynamics simulations and enhanced sampling methods can be employed in this context to simulate crystal structures at finite temperature and pressure. </p><p>Here we demonstrate the applicability of approaches based on molecular dynamics to systematically process realistic CSP datasets containing several hundreds of crystal structures. The system investigated is ibuprofen, a conformationally flexible active pharmaceutical ingredient that crystallises both in enantiopure forms and as a racemic mixture. By introducing a hierarchical approach in the analysis of finite-temperature supercell configurations, we can post-process a dataset of 555 crystal structures, identifying 65% of the initial structures as labile, while maintaining all the experimentally known crystal structures in the final, reduced set. Moreover, the extensive nature of the initial dataset allows one to gain quantitative insight into the persistence and the propensity to transform of crystal structures containing common hydrogen-bonded intermolecular interaction motifs.</p>

Solvent-dependent conformation and hydrogen-bonding capacity of cyclosporin A: evidence from partition coefficients and molecular dynamics simulations

1993 ◽  
Vol 36 (24) ◽  
pp. 3757-3764 ◽  
Author(s):  
Nabil El Tayar ◽  
Alan E. Mark ◽  
Philippe Vallat ◽  
Roger M. Brunne ◽  
Bernard Testa ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Hydrogen Bonding ◽  
Cyclosporin A ◽  
Molecular Dynamics Simulations ◽  
Partition Coefficients ◽  
Dynamics Simulations
Sign in / Sign up

Export Citation Format

Share Document