A new molecular-dynamics based approach for molecular crystal structure search

2005 ◽  
Vol 123 (5) ◽  
pp. 051108 ◽  
Author(s):  
V. Buch ◽  
R. Martoňák ◽  
M. Parrinello
Keyword(s):  
Crystal Structure ◽  
Molecular Dynamics ◽  
Molecular Crystal ◽  
Structure Search

A Heuristic Molecular-Dynamics Approach for the Prediction of a Molecular Crystal Structure

1995 ◽  
Vol 68 (2) ◽  
pp. 519-527 ◽  
Author(s):  
Nobuo Tajima ◽  
Takayuki Tanaka ◽  
Tomoko Arikawa ◽  
Takashi Sakurai ◽  
Shoichi Teramae ◽  
...  
Keyword(s):  
Crystal Structure ◽  
Molecular Dynamics ◽  
Molecular Crystal

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.

scholarly journals Surface Chemistry, Crystal Structure, Size and Topography Role in the Albumin Adsorption Process on TiO2 Anatase Crystallographic Faces and Its 3D-Nanocrystal: A Molecular Dynamics Study

Coatings ◽  
2021 ◽  
Vol 11 (4) ◽  
pp. 420
Author(s):  
Giuseppina Raffaini
Keyword(s):  
Crystal Structure ◽  
Molecular Dynamics ◽  
Surface Chemistry ◽  
Protein Adsorption ◽  
Adsorption Process ◽  
Sol Gel ◽  
Interaction Strength ◽  
Theoretical Work ◽  
Blood Protein ◽  
Tio2 Anatase

TiO2 is widely used in biomaterial implants. The topography, chemical and structural properties of titania surfaces are an important aspect to study. The size of TiO2 nanoparticles synthetized by sol–gel method can influence the responses in the biological environment, and by using appropriate heat treatments different contents of different polymorphs can be formed. Protein adsorption is a crucial step for the biological responses, involving, in particular, albumin, the most abundant blood protein. In this theoretical work, using molecular mechanics and molecular dynamics methods, the adsorption process of an albumin subdomain is reported both onto specific different crystallographic faces of TiO2 anatase and also on its ideal three-dimensional nanosized crystal, using the simulation protocol proposed in my previous theoretical studies about the adsorption process on hydrophobic ordered graphene-like or hydrophilic amorphous polymeric surfaces. The different surface chemistry of anatase crystalline faces and the nanocrystal topography influence the adsorption process, in particular the interaction strength and protein fragment conformation, then its biological activity. This theoretical study can be a useful tool to better understand how the surface chemistry, crystal structure, size and topography play a key role in protein adsorption process onto anatase surface so widely used as biomaterial.

scholarly journals The crystal structure of the first ether solvate of hexaphenyldistannane [(Ph3Sn)2 • 2 THF]

2020 ◽  
Vol 43 (1) ◽  
pp. 1-6 ◽  
Author(s):  
Jonathan O. Bauer
Keyword(s):  
Crystal Structure ◽  
Inclusion Compounds ◽  
Molecular Crystal ◽  
Structural Features ◽  
Structural Investigations ◽  
Crystal Solvates

AbstractStructural investigations of molecular crystal solvates can provide important information for the targeted crystallization of particular inclusion compounds. Here, the crystal structure of the first ether solvate of hexaphenyldistannane [(Ph3Sn)2 • 2 THF] is reported. Structural features in terms of host-guest interactions and in the context of the previously reported polymorphs and solvates of (Ph3Sn)2 are discussed.

WHICH IS THE PROTON-SHUTTLE IN ISOXANTHOPTERIN DEAMINASE? QM/MM MD UNDERSTANDING

2013 ◽  
Vol 12 (08) ◽  
pp. 1341002 ◽  
Author(s):  
XIN ZHANG ◽  
MING LEI
Keyword(s):  
Crystal Structure ◽  
Molecular Dynamics ◽  
Hydrogen Bonds ◽  
Proton Transfer ◽  
Glutamic Acid ◽  
Active Site ◽  
Nucleophilic Attack ◽  
Zinc Ions ◽  
Initial Model ◽  
Dynamics Simulations

The deamination process of isoxanthopterin catalyzed by isoxanthopterin deaminase was determined using the combined QM(PM3)/MM molecular dynamics simulations. In this paper, the updated PM3 parameters were employed for zinc ions and the initial model was built up based on the crystal structure. Proton transfer and following steps have been investigated in two paths: Asp336 and His285 serve as the proton shuttle, respectively. Our simulations showed that His285 is more effective than Aap336 in proton transfer for deamination of isoxanthopterin. As hydrogen bonds between the substrate and surrounding residues play a key role in nucleophilic attack, we suggested mutating Thr195 to glutamic acid, which could enhance the hydrogen bonds and help isoxanthopterin get close to the active site. The simulations which change the substrate to pterin 6-carboxylate also performed for comparison. Our results provide reference for understanding of the mechanism of deaminase and for enhancing the deamination rate of isoxanthopterin deaminase.

Molecular-crystal structure of DL-?-(5-bromo-1-uracilyl)-?-alanine

1981 ◽  
Vol 17 (3) ◽  
pp. 299-301
Author(s):  
A. F. Mishnev ◽  
Ya. Ya. Bleidelis ◽  
V. �. Krishane ◽  
R. A. Pa�gle ◽  
M. Yu. Lidak
Keyword(s):  
Crystal Structure ◽  
Molecular Crystal

scholarly journals Car–Parrinello and path integral molecular dynamics study of the intramolecular hydrogen bonds in the crystals of benzoylacetone and dideuterobenzoylacetone

2014 ◽  
Vol 16 (42) ◽  
pp. 23026-23037 ◽  
Author(s):  
Piotr Durlak ◽  
Zdzisław Latajka
Keyword(s):  
Molecular Dynamics ◽  
Hydrogen Bond ◽  
Hydrogen Bonds ◽  
Ab Initio ◽  
Path Integral ◽  
Molecular Crystal ◽  
Short Hydrogen Bond ◽  
Deuterated Analogue ◽  
Dynamics Simulations ◽  
Intramolecular Hydrogen

The dynamics of the intramolecular short hydrogen bond in the molecular crystal of benzoylacetone and its deuterated analogue are investigated using ab initio molecular dynamics simulations.

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