Theoretical Study of Iron Heterogeneous Growth on the Surface of C60 Molecule

2014 ◽  
Vol 1081 ◽  
pp. 115-118
Author(s):  
Qi Cheng Liu ◽  
Yun Fang Li
Keyword(s):  
Crystallization Process ◽  
Theoretical Study ◽  
Covalent Bond ◽  
Md Simulations ◽  
Nucleation And Growth ◽  
Bond Forming ◽  
Regular Icosahedron ◽  
Molecule Dynamics ◽  
Molecule Surface ◽  
Regular Closed

Direct molecule dynamics (MD) simulations have also been performed to study heterogeneous nucleation and growth of iron on C60 molecule. The grown mechanism of this crystallization process was explored. The results indicate that 92 iron atoms attach to C60 molecule surface can form new covalent bond, forming a closed regular icosahedron. More atoms grow in layer to form bigger regular closed clathrate base on the structure of former one. As increase of atoms number, there will appear some crystal faces.

Structural insights into the repair mechanism of AGT for methyl-induced DNA damage

2021 ◽  
Vol 0 (0) ◽  
Author(s):  
Rajendra P. Koirala ◽  
Rudramani Pokhrel ◽  
Prabin Baral ◽  
Purushottam B. Tiwari ◽  
Prem P. Chapagain ◽  
...  
Keyword(s):  
Covalent Bond ◽  
Cancer Therapeutics ◽  
Md Simulations ◽  
Structural Features ◽  
Umbrella Sampling ◽  
Repair Mechanism ◽  
Structural Investigations ◽  
Methylated Dna ◽  
Dna Base ◽  
Dna Alkyltransferase

Abstract Methylation induced DNA base-pairing damage is one of the major causes of cancer. O6-alkylguanine-DNA alkyltransferase (AGT) is considered a demethylation agent of the methylated DNA. Structural investigations with thermodynamic properties of the AGT-DNA complex are still lacking. In this report, we modeled two catalytic states of AGT-DNA interactions and an AGT-DNA covalent complex and explored structural features using molecular dynamics (MD) simulations. We utilized the umbrella sampling method to investigate the changes in the free energy of the interactions in two different AGT-DNA catalytic states, one with methylated GUA in DNA and the other with methylated CYS145 in AGT. These non-covalent complexes represent the pre- and post-repair complexes. Therefore, our study encompasses the process of recognition, complex formation, and separation of the AGT and the damaged (methylated) DNA base. We believe that the use of parameters for the amino acid and nucleotide modifications and for the protein-DNA covalent bond will allow investigations of the DNA repair mechanism as well as the exploration of cancer therapeutics targeting the AGT-DNA complexes at various functional states as well as explorations via stabilization of the complex.

scholarly journals Molecular Dynamics Simulations of Crystal Nucleation near Interfaces in Incompatible Polymer Blends

Polymers ◽  
2021 ◽  
Vol 13 (3) ◽  
pp. 347
Author(s):  
Wenlin Zhang ◽  
Lingyi Zou
Keyword(s):  
Molecular Dynamics ◽  
Polymer Blends ◽  
Md Simulations ◽  
Nucleation And Growth ◽  
Crystal Nucleation ◽  
Crystalline Order ◽  
Mobile Species ◽  
Deep Supercooling ◽  
Crystallizable Polymer ◽  
Dynamics Simulations

We apply molecular dynamics (MD) simulations to investigate crystal nucleation in incompatible polymer blends under deep supercooling conditions. Simulations of isothermal nucleation are performed for phase-separated blends with different degrees of incompatibility. In weakly segregated blends, slow and incompatible chains in crystallizable polymer domains can significantly hinder the crystal nucleation and growth. When a crystallizable polymer is blended with a more mobile species in interfacial regions, enhanced molecular mobility leads to the fast growth of crystalline order. However, the incubation time remains the same as that in pure samples. By inducing anisotropic alignment near the interfaces of strongly segregated blends, phase separation also promotes crystalline order to grow near interfaces between different polymer domains.

Rietveld refinement of the cocrystal 2,4-dihydroxybenzoic acid–N′-(propan-2-ylidene)nicotinohydrazide (1/1)

2012 ◽  
Vol 68 (9) ◽  
pp. o335-o337 ◽  
Author(s):  
Saul H. Lapidus ◽  
Andreas Lemmerer ◽  
Joel Bernstein ◽  
Peter W. Stephens
Keyword(s):  
Hydrogen Bond ◽  
Hydrogen Bonding ◽  
Powder Diffraction ◽  
Supramolecular Assembly ◽  
Covalent Bond ◽  
Analytical Tool ◽  
Powder Diffraction Data ◽  
Dihydroxybenzoic Acid ◽  
Bond Forming ◽  
Hydrogen Bond Interactions

A further example of using a covalent-bond-forming reaction to alter supramolecular assembly by modification of hydrogen-bonding possibilities is presented. This concept was introduced by Lemmerer, Bernstein & Kahlenberg [CrystEngComm(2011),13, 55–59]. The title structure, C9H11N3O·C7H6O4, which consists of a reacted niazid molecule,viz.N′-(propan-2-ylidene)nicotinohydrazide, and 2,4-dihydroxybenzoic acid, was solved from powder diffraction data using simulated annealing. The results further demonstrate the relevance and utility of powder diffraction as an analytical tool in the study of cocrystals and their hydrogen-bond interactions.

Glass Transition in Sub-nanometer Confinement

1998 ◽  
Vol 543 ◽  
Author(s):  
A. Huwe ◽  
F. Kremer ◽  
M. Arndt ◽  
P. Behrens ◽  
W. Schwieger ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Relaxation Rate ◽  
Pore Size ◽  
Coordination Number ◽  
Single Molecule ◽  
Bulk Liquid ◽  
Bond Forming ◽  
Broadband Dielectric Spectroscopy ◽  
Molecule Dynamics

AbstractBroadband dielectric spectroscopy (10−2 Hz - 109Hz) is employed to study the molecular dynamics of low-molecular-weight glassforming liquids being confined to nanopores. For the H-bond forming liquid propylene glycol being confined to (uncoated and silanized) nanopores (pore size: 2.5 nm, 5.0 nm and 7.5 nm) a molecular dynamics is observed which is comparable to that of the bulk liquid. Due to surface effects in uncoated nanopores the relaxation time distribution is broadened on the long term side and the mean relaxation rate is decreased by about half a decade. This effect can be counterbalanced by lubricating the inner surfaces of the pores resulting in a relaxation rate which is slightly faster compared to the bulk liquid. For the H-bonded liquid ethylene glycol (EG) embedded in zeolites of different pore size and topology one observes a sharp transition from a single-molecule dynamics to that of a liquid depending on the coordination number of the confined molecules. While EG in silicalite (showing a single molecule relaxation) has four neighboring molecules, EG in zeolite beta or AIPO4-5 has a coordination number of five and behaves like a bulk liquid.

The Stimulated Crystallization of Amorphous SiO2 Films on Si Substrates Induced By Laser and Thermal Treatments

1988 ◽  
Vol 116 ◽  
Author(s):  
Felix Edelman
Keyword(s):  
Incubation Time ◽  
Crystallization Process ◽  
Laser Flash ◽  
Nucleation And Growth ◽  
Point Of View ◽  
Growth Theory ◽  
Thermal Treatments ◽  
Kinetic Characteristics ◽  
Amorphous Sio2 ◽  
Si Substrates

AbstractThe transformation of amorphous to crystal (a-c) structure of Si02 layers, thermally grown on both (100) and (111) Si substrates, was carried out by CO2 laser, flash-lamp, and furnace heat: treatments. All the treatments resulted in S102 crystallization according to two different mechanisms: normal and self-sustained growth processes. The kinetic characteristics of the S102 crystallization process such as incubation time, rates of nucleation and growth, and the microstructure of the Si-Si02 interface were investigated and are discussed from the point of view of growth theory. The a-c transformation in Si3N4 and SixOyNz films on Si substrates is also discussed.

Modeling of Silicon Nanodots Nucleation and Growth Deposited by LPCVD on SiO2 : From Molecule/surface Interactions to Reactor Scale Simulations

2006 ◽  
Vol 959 ◽  
Author(s):  
Ilyes Zahi ◽  
Hugues Vergnes ◽  
Brigitte Caussat ◽  
Alain Esteve ◽  
Mehdi Djafari Rouhani ◽  
...  
Keyword(s):  
Chemical Vapor Deposition ◽  
Vapor Deposition ◽  
Deposition Time ◽  
Chemical Vapor ◽  
Surface Interactions ◽  
Nucleation And Growth ◽  
High Dilution ◽  
First Results ◽  
Pressure Chemical ◽  
Molecule Surface

ABSTRACTWe present first results combining models at continuum and atomistic (DFT) levels to improve understanding of key mechanisms involved in silicon nanodots (NDs) synthesis on SiO2 by Low Pressure Chemical Vapor Deposition (LPCVD) from silane SiH4. In particular, by simulating an industrial LPCVD reactor using the CFD code Fluent, we find that the deposition time could be increased and then the reproducibility and uniformity of NDs deposition could be improved when highly diluting silane in a carrier gas. A consequence of this high dilution seems to be that the contribution to deposition of unsaturated species such as silylene SiH2 highly increases. This result is important since our first DFT calculations have shown that silicon chemisorption on silanol Si-OH or siloxane Si-O-Si bonds present on SiO2 substrates could only proceed from silylene (and probably from other unsaturated species). The silane saturated molecule could only contribute to NDs growth, i.e. silicon chemisorption on already deposited silicon bonds. Increasing silylene contribution to deposition in highly diluting silane could then also exalt silicon nucleation on SiO2 substrates and then increase NDs density.

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