Molecular aggregation in liquid acetic acid: insight from molecular dynamics/quantum mechanics modelling of structural and NMR properties

2019 ◽  
Vol 21 (27) ◽  
pp. 14811-14820 ◽  
Author(s):  
Dovilė Lengvinaitė ◽  
Kęstutis Aidas ◽  
Liudvikas Kimtys
Keyword(s):  
Molecular Dynamics ◽  
Acetic Acid ◽  
Quantum Mechanics ◽  
Molecular Aggregation ◽  
Upfield Shift ◽  
Low Concentration ◽  
H Nmr ◽  
Nmr Properties

Quantum mechanics/molecular dynamics approaches have been applied to unveil the anomalous upfield shift of the 1H NMR signal of acetic acid by going from low-concentration solution in cyclohexane to the neat liquid.

A Conserved Asparagine in a Ubiquitin Conjugating Enzyme Positions the Substrate for Nucleophilic Attack

2018 ◽  
Author(s):  
Walker M. Jones ◽  
Aaron G. Davis ◽  
R. Hunter Wilson ◽  
Katherine L. Elliott ◽  
Isaiah Sumner
Keyword(s):  
Molecular Dynamics ◽  
Quantum Mechanics ◽  
Molecular Mechanics ◽  
Reaction Rates ◽  
Nucleophilic Attack ◽  
Classical Molecular Dynamics ◽  
Ubiquitin Conjugating Enzyme ◽  
Conjugating Enzyme

We present classical molecular dynamics (MD), Born-Oppenheimer molecular dynamics (BOMD), and hybrid quantum mechanics/molecular mechanics (QM/MM) data. MD was performed using the GPU accelerated pmemd module of the AMBER14MD package. BOMD was performed using CP2K version 2.6. The reaction rates in BOMD were accelerated using the Metadynamics method. QM/MM was performed using ONIOM in the Gaussian09 suite of programs. Relevant input files for BOMD and QM/MM are available.

scholarly journals Conformational energies and equilibria of cyclic dinucleotides in vacuo and in solution: computational chemistry vs. NMR experiments

2021 ◽  
Author(s):  
Ondrej Gutten ◽  
Petr Jurečka ◽  
Zahra Aliakbar Tehrani ◽  
Miloš Buděšínský ◽  
Jan Řezáč ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Quantum Mechanics ◽  
Computational Chemistry ◽  
Computational Error ◽  
Cyclic Dinucleotides ◽  
Error Bars ◽  
Conformational Energies

Computational “error bars” for modelling cyclic dinucleotides – NMR experiment vs. quantum mechanics and molecular dynamics.

scholarly journals Experimental and molecular dynamics studies of an ultra-fast sequential hydrogen plasma process for fabricating phosphorene-based sensors

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
M. Rajabali ◽  
H. Asgharyan ◽  
V. Fadaei Naeini ◽  
A. Boudaghi ◽  
B. Zabihi ◽  
...  
Keyword(s):  
Electron Microscopy ◽  
Molecular Dynamics ◽  
Field Effect ◽  
Field Effect Transistors ◽  
Hydrogen Plasma ◽  
Device Fabrication ◽  
Dynamics Simulation ◽  
Red Phosphorus ◽  
Large Area ◽  
Low Concentration

AbstractLow concentration phosphorene-based sensors have been fabricated using a facile and ultra-fast process which is based on an exfoliation-free sequential hydrogen plasma treatment to convert the amorphous phosphorus thin film into mono- or few-layered phosphorene sheets. These sheets have been realized directly on silicon substrates followed by the fabrication of field-effect transistors showing the low leakage current and reasonable mobility for the nano-sensors. Being capable of covering the whole surface of the silicon substrate, red phosphorus (RP) coated substrate has been employed to achieve large area phosphorene sheets. Unlike the available techniques including mechanical exfoliation, there is no need for any exfoliation and/or transfer step which is significant progress in shortening the device fabrication procedure. These phosphorene sheets have been examined using transmission electron microscopy (TEM), Scanning electron microscopy (SEM), Raman spectroscopy and atomic-force microscopy (AFM). Electrical output in different states of the crystallization as well as its correlation with the test parameters have been also extensively used to examine the evolution of the phosphorene sheets. By utilizing the fabricated devices, the sensitivity of the phosphorene based-field effect transistors to the soluble L-Cysteine in low concentrations has been studied by measuring the FET response to the different concentrations. At a gate voltage of − 2.5 V, the range of 0.07 to 0.60 mg/ml of the L-Cysteine has been distinguishably detected presenting a gate-controlled sensor for a low-concentration solution. A reactive molecular dynamics simulation has been also performed to track the details of this plasma-based crystallization. The obtained results showed that the imparted energy from hydrogen plasma resulted in a phase transition from a system containing red phosphorus atoms to the crystal one. Interestingly and according to the simulation results, there is a directional preference of crystal growth as the crystalline domains are being formed and RP atoms are more likely to re-locate in armchair than in zigzag direction.

scholarly journals Tautomerisation in 1-(4-Methylphenylazo)naphthalen-2-ol and 2-(4-Methylphenylazo)-4-methylphenol: A Crystallographic and 13C{1H}NMR Study

1999 ◽  
Vol 23 (3) ◽  
pp. 178-179
Author(s):  
Wendy I. Cross ◽  
Kevin R. Flower ◽  
Robin G. Pritchard
Keyword(s):  
Acetic Acid ◽  
Nmr Spectroscopy ◽  
Resonant Frequency ◽  
X Ray Diffraction ◽  
X Ray ◽  
H Nmr ◽  
Nmr Study ◽  
Acetic Acid Esters ◽  
Acid Esters ◽  
Equivalent Carbon

The acetic acid esters of 1-(4-methylphenylazo)naphthalen-2-ol 1 and 2-(4-methylphenylazo)-4-methylphenol 3 are prepared and characterised by single crystal X-ray diffraction studies and 13C{1H}NMR spectroscopy; the position of the C(2)13C resonance for the ester is used to predict the position of resonant frequency of the equivalent carbon in the parent alcohols and hence, calculate the position of the azo-hydrazone equilibrium in these compounds.

scholarly journals How Small Molecules Affect the Thermo-Oxidative Aging Mechanism of Polypropylene: A Reactive Molecular Dynamics Study

Polymers ◽  
2021 ◽  
Vol 13 (8) ◽  
pp. 1243
Author(s):  
Fan Zhang ◽  
Yufei Cao ◽  
Xuan Liu ◽  
Huan Xu ◽  
Diannan Lu ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Acetic Acid ◽  
Small Molecules ◽  
Aging Process ◽  
Experimental Studies ◽  
Hydroxyl Group ◽  
Oxidative Aging ◽  
Reactive Molecular Dynamics ◽  
Aging Mechanism ◽  
Effects Of Temperature

Understanding the aging mechanism of polypropylene (PP) is fundamental for the fabrication and application of PP-based materials. In this paper, we present our study in which we first used reactive molecular dynamics (RMD) simulations to explore the thermo-oxidative aging of PP in the presence of acetic acid or acetone. We studied the effects of temperature and oxygen on the aging process and discussed the formation pathways of typical small molecule products (H2, CO, CO2, CH4, C2H4, and C2H6). The effect of two infection agents, acetic acid and acetone, on the aging reaction was analyzed emphatically. The simulation results showed that acetone has a weak impact on accelerating the aging process, while acetic acid has a significant effect, consistent with previous experimental studies. By tracking the simulation trajectories, both acetic acid and acetone produced small active free radicals to further react with other fragment products, thus accelerating the aging process. The first reaction step of acetic acid is often the shedding of the H atom on the hydroxyl group, while the reaction of acetone is often the shedding of the H atom or the methyl. The latter requires higher energy at lower temperatures. This is why the acceleration effect of acetone for the thermo-oxidative aging of PP was not so significant compared to acetic acid in the experimental temperature (383.15 K).

scholarly journals Computational Methods for Ab Initio Molecular Dynamics

2018 ◽  
Vol 2018 ◽  
pp. 1-14 ◽  
Author(s):  
Eric Paquet ◽  
Herna L. Viktor
Keyword(s):  
Molecular Dynamics ◽  
Quantum Mechanics ◽  
Ab Initio ◽  
First Principles ◽  
Density Functional ◽  
Path Integrals ◽  
Ab Initio Molecular Dynamics ◽  
Molecular Systems ◽  
Hartree Fock ◽  
Computational Perspective

Ab initio molecular dynamics is an irreplaceable technique for the realistic simulation of complex molecular systems and processes from first principles. This paper proposes a comprehensive and self-contained review of ab initio molecular dynamics from a computational perspective and from first principles. Quantum mechanics is presented from a molecular dynamics perspective. Various approximations and formulations are proposed, including the Ehrenfest, Born–Oppenheimer, and Hartree–Fock molecular dynamics. Subsequently, the Kohn–Sham formulation of molecular dynamics is introduced as well as the afferent concept of density functional. As a result, Car–Parrinello molecular dynamics is discussed, together with its extension to isothermal and isobaric processes. Car–Parrinello molecular dynamics is then reformulated in terms of path integrals. Finally, some implementation issues are analysed, namely, the pseudopotential, the orbital functional basis, and hybrid molecular dynamics.

Synthesis of amino acid derivatives of indole-3-acetic acid

2005 ◽  
Vol 2005 (10) ◽  
pp. 640-642 ◽  
Author(s):  
Ying Liu ◽  
Liang Zhao ◽  
Liang Liu ◽  
Lin-Yi Wei ◽  
Lu-Hua Lai
Keyword(s):  
Acetic Acid ◽  
Amino Acid ◽  
Amino Acid Derivatives ◽  
H Nmr ◽  
Derivatives Of ◽  
Indole 3 Acetic Acid

Amino acid derivatives of a modified indole-3-acetic acid have been synthesised. Fourteen new dipeptide-like compounds 3–4 were obtained and their structures were elucidated based on the IR, 1H NMR, MS spectra.

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