scholarly journals Efficiently Calculating Anharmonic Frequencies of Molecular Vibration by Molecular Dynamics Trajectory Analysis

ACS Omega ◽  
2019 ◽  
Vol 4 (5) ◽  
pp. 9271-9283 ◽  
Author(s):  
Shaoqing Wang
Keyword(s):  
Molecular Dynamics ◽  
Trajectory Analysis ◽  
Molecular Vibration ◽  
Anharmonic Frequencies ◽  
Molecular Dynamics Trajectory

scholarly journals Parallel performance of molecular dynamics trajectory analysis

2020 ◽  
Vol 32 (19) ◽  
Author(s):  
Mahzad Khoshlessan ◽  
Ioannis Paraskevakos ◽  
Geoffrey C. Fox ◽  
Shantenu Jha ◽  
Oliver Beckstein
Keyword(s):  
Molecular Dynamics ◽  
Trajectory Analysis ◽  
Parallel Performance ◽  
Molecular Dynamics Trajectory

scholarly journals Intrinsic molecular vibration and rigorous vibrational assignment of benzene by first-principles molecular dynamics

2020 ◽  
Vol 10 (1) ◽  
Author(s):  
Shaoqing Wang
Keyword(s):  
Molecular Dynamics ◽  
First Principles ◽  
Density Functional ◽  
Molecular Vibration ◽  
Vibrational Assignment ◽  
Considerable Uncertainty ◽  
Molecular Dynamics Trajectory ◽  
Trial And Error Method ◽  
Historical Issues ◽  
First Principles Molecular Dynamics

Abstract Vibrational assignment, which establishes the correspondence between vibrational modes and spectral frequencies, is a key step in any spectroscopic study. Due to the lack of experimental technique to directly observe the thermal vibration of atoms, the assignment is usually done by empirical trial-and-error method with considerable uncertainty. Here we demonstrate a successful study of intrinsic molecular vibration property based on first-principles molecular dynamics trajectory. A unified approach for calculating and assigning vibrational frequencies is developed and applied to solve some historical issues of benzene vibration. As a major achievement, the experimental frequencies of benzene a2g and b2u vibrations are reassigned, which breaks a deadlock in contemporary spectroscopic science and removes a cloud over the application of density-functional theory in organic chemistry. This work paves the way for the comprehensive realization of the first-principles spectroscopic research, and provides crucial clues to solve the century-old problems of Kekule resonance, π-deformation, and aromaticity.

Eucb: A C++ program for molecular dynamics trajectory analysis

2011 ◽  
Vol 182 (3) ◽  
pp. 834-841 ◽  
Author(s):  
Ioannis G. Tsoulos ◽  
Athanassios Stavrakoudis
Keyword(s):  
Molecular Dynamics ◽  
Trajectory Analysis ◽  
Molecular Dynamics Trajectory ◽  
C Program

A Thorough Theoretical Exploration of Intriguing Characteristics of Cyclo[18]carbon: Geometry, Bonding Nature, Aromaticity, Weak Interaction, Reactivity, Excited States, Vibrations, Molecular Dynamics and Various Molecular Properties

2019 ◽  
Author(s):  
Tian Lu ◽  
Qinxue Chen ◽  
Zeyu Liu
Keyword(s):  
Molecular Dynamics ◽  
Excited States ◽  
Electronic Excitation ◽  
Ring Structure ◽  
Molecular Properties ◽  
Molecular Vibration ◽  
Full Characterization ◽  
Long Time ◽  
Almost All

Although cyclo[18]carbon has been theoretically and experimentally investigated since long time ago, only very recently it was prepared and directly observed by means of STM/AFM in condensed phase (Kaiser et al., <i>Science</i>, <b>365</b>, 1299 (2019)). The unique ring structure and dual 18-center π delocalization feature bring a variety of unusual characteristics and properties to the cyclo[18]carbon, which are quite worth to be explored. In this work, we present an extremely comprehensive and detailed investigation on almost all aspects of the cyclo[18]carbon, including (1) Geometric characteristics (2) Bonding nature (3) Electron delocalization and aromaticity (4) Intermolecular interaction (5) Reactivity (6) Electronic excitation and UV/Vis spectrum (7) Molecular vibration and IR/Raman spectrum (8) Molecular dynamics (9) Response to external field (10) Electron ionization, affinity and accompanied process (11) Various molecular properties. We believe that our full characterization of the cyclo[18]carbon will greatly deepen researchers' understanding of this system, and thereby help them to utilize it in practice and design its various valuable derivatives.

A Thorough Theoretical Exploration of Intriguing Characteristics of Cyclo[18]carbon: Geometry, Bonding Nature, Aromaticity, Weak Interaction, Reactivity, Excited States, Vibrations, Molecular Dynamics and Various Molecular Properties

2019 ◽  
Author(s):  
Tian Lu ◽  
Qinxue Chen ◽  
Zeyu Liu
Keyword(s):  
Molecular Dynamics ◽  
Excited States ◽  
Electronic Excitation ◽  
Ring Structure ◽  
Molecular Properties ◽  
Molecular Vibration ◽  
Full Characterization ◽  
Long Time ◽  
Almost All

Although cyclo[18]carbon has been theoretically and experimentally investigated since long time ago, only very recently it was prepared and directly observed by means of STM/AFM in condensed phase (Kaiser et al., <i>Science</i>, <b>365</b>, 1299 (2019)). The unique ring structure and dual 18-center π delocalization feature bring a variety of unusual characteristics and properties to the cyclo[18]carbon, which are quite worth to be explored. In this work, we present an extremely comprehensive and detailed investigation on almost all aspects of the cyclo[18]carbon, including (1) Geometric characteristics (2) Bonding nature (3) Electron delocalization and aromaticity (4) Intermolecular interaction (5) Reactivity (6) Electronic excitation and UV/Vis spectrum (7) Molecular vibration and IR/Raman spectrum (8) Molecular dynamics (9) Response to external field (10) Electron ionization, affinity and accompanied process (11) Various molecular properties. We believe that our full characterization of the cyclo[18]carbon will greatly deepen researchers' understanding of this system, and thereby help them to utilize it in practice and design its various valuable derivatives.

A Nanosecond Molecular Dynamics Trajectory for a B DNA Double Helix: Evidence for Substates

1994 ◽  
Vol 116 (10) ◽  
pp. 4461-4462 ◽  
Author(s):  
K. J. McConnell ◽  
R Nirmala ◽  
M. A. Young ◽  
G. Ravishanker ◽  
D. L. Beveridge
Keyword(s):  
Molecular Dynamics ◽  
Double Helix ◽  
Molecular Dynamics Trajectory ◽  
Dna Double Helix
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