New Advance in Computational Chemistry:  Full Quantum Mechanical ab Initio Computation of Streptavidin−Biotin Interaction Energy

2003 ◽  
Vol 107 (44) ◽  
pp. 12039-12041 ◽  
Author(s):  
Da W. Zhang ◽  
Yun Xiang ◽  
John Z. H. Zhang
Keyword(s):  
Ab Initio ◽  
Computational Chemistry ◽  
Interaction Energy ◽  
Quantum Mechanical ◽  
Ab Initio Computation ◽  
Full Quantum

Ab initio computation of the interaction energy curves for some low-lying states of CO which dissociate to ground-state3 P O and3 P C atoms

1992 ◽  
Vol 82 (1-2) ◽  
pp. 153-163 ◽  
Author(s):  
M. E. Rosenkrantz ◽  
J. E. Bohr ◽  
D. D. Konowalow
Keyword(s):  
Ab Initio ◽  
Interaction Energy ◽  
Ab Initio Computation

Molecular caps for full quantum mechanical computation of peptide-water interaction energy

2003 ◽  
Vol 24 (15) ◽  
pp. 1846-1852 ◽  
Author(s):  
D. W. Zhang ◽  
X. H. Chen ◽  
J. Z. H. Zhang
Keyword(s):  
Interaction Energy ◽  
Quantum Mechanical ◽  
Water Interaction ◽  
Quantum Mechanical Computation ◽  
Full Quantum

FULL AB INITIO COMPUTATION OF PROTEIN-WATER INTERACTION ENERGIES

2004 ◽  
Vol 03 (01) ◽  
pp. 43-49 ◽  
Author(s):  
D. W. ZHANG ◽  
J. Z. H. ZHANG
Keyword(s):  
Ab Initio ◽  
Interaction Energy ◽  
Ab Initio Calculation ◽  
Density Functional ◽  
Protein Molecule ◽  
Interaction Energies ◽  
Hartree Fock ◽  
Ab Initio Computation ◽  
Moller Plesset ◽  
High Degree

A method to perform full quantum mechanical (ab initio) calculation of interaction energy involving a macromolecule like protein has recently been developed. This new scheme, named molecular fractionation with conjugate caps (MFCC), decomposes a protein molecule into amino acid-based fragments. These individual fragments are properly treated to preserve the chemical property of the bonds that are cut. Through proper combination of interaction energies between the molecule and individual fragments and their conjugate caps, the full protein-molecule interaction energy can be obtained to a high degree-of-accuracy by full ab initio calculations. Here we report a benchmark full ab initio calculation of interaction energy between a HIV-1 gp41 protein (with 982 atoms) and a water molecule at various geometries using HF (Hartree Fock), DFT (density functional theory) and MP2 (second-order Moller-Plesset perturbation theory) methods on a standard workstation.

Quantum Mechanical Interpretation of the Ultra-Low Energy Methyl-Rotation Dynamics in Porous Metal-Organic Frameworks Probed by Low-Frequency Vibrational Spectroscopy and ab initio Simulations

2018 ◽  
Author(s):  
Qi Li ◽  
Adam J. Zaczek ◽  
Timothy M. Korter ◽  
J. Axel Zeitler ◽  
Michael T. Ruggiero
Keyword(s):  
Ab Initio ◽  
Metal Organic Frameworks ◽  
Low Frequency ◽  
Rotor Dynamics ◽  
Quantum Mechanical ◽  
Valuable Insight ◽  
Void Space ◽  
Ab Initio Simulations ◽  
Metal Organic ◽  
Insight Into

<div>Understanding the nature of the interatomic interactions present within the pores of metal-organic frameworks</div><div>is critical in order to design and utilize advanced materials</div><div>with desirable applications. In ZIF-8 and its cobalt analogue</div><div>ZIF-67, the imidazolate methyl-groups, which point directly</div><div>into the void space, have been shown to freely rotate - even</div><div>down to cryogenic temperatures. Using a combination of ex-</div><div>perimental terahertz time-domain spectroscopy, low-frequency</div><div>Raman spectroscopy, and state-of-the-art ab initio simulations,</div><div>the methyl-rotor dynamics in ZIF-8 and ZIF-67 are fully charac-</div><div>terized within the context of a quantum-mechanical hindered-</div><div>rotor model. The results lend insight into the fundamental</div><div>origins of the experimentally observed methyl-rotor dynamics,</div><div>and provide valuable insight into the nature of the weak inter-</div><div>actions present within this important class of materials.</div>

scholarly journals A Review on Combination of Ab Initio Molecular Dynamics and NMR Parameters Calculations

2021 ◽  
Vol 22 (9) ◽  
pp. 4378
Author(s):  
Anna Helena Mazurek ◽  
Łukasz Szeleszczuk ◽  
Dariusz Maciej Pisklak
Keyword(s):  
Molecular Dynamics ◽  
Ab Initio ◽  
Small Amplitude ◽  
Ab Initio Molecular Dynamics ◽  
Quantum Mechanical ◽  
Time Step ◽  
Noticeable Effect ◽  
Nmr Parameters ◽  
Mechanical Methods ◽  
Simulation Time

This review focuses on a combination of ab initio molecular dynamics (aiMD) and NMR parameters calculations using quantum mechanical methods. The advantages of such an approach in comparison to the commonly applied computations for the structures optimized at 0 K are presented. This article was designed as a convenient overview of the applied parameters such as the aiMD type, DFT functional, time step, or total simulation time, as well as examples of previously studied systems. From the analysis of the published works describing the applications of such combinations, it was concluded that including fast, small-amplitude motions through aiMD has a noticeable effect on the accuracy of NMR parameters calculations.

Quantitative Prediction of Aggregation‐Induced Emission: A Full Quantum Mechanical Approach to the Optical Spectra

2020 ◽  
Vol 132 (28) ◽  
pp. 11647-11652
Author(s):  
Wei Zhang ◽  
Jinfeng Liu ◽  
Xinsheng Jin ◽  
Xinggui Gu ◽  
Xiao Cheng Zeng ◽  
...  
Keyword(s):  
Optical Spectra ◽  
Quantitative Prediction ◽  
Quantum Mechanical ◽  
Aggregation Induced Emission ◽  
Mechanical Approach ◽  
Quantum Mechanical Approach ◽  
Full Quantum

Efficient ab initio quantum mechanical simulations of structural stability and vibrational properties of bulk, monolayer and ( n ,0) nanotubes: Yttrium sesquioxide Y 2 O 3

2019 ◽  
Vol 51 (2) ◽  
pp. 232-242 ◽  
Author(s):  
Tarek Larbi ◽  
Khaled E. El‐Kelany ◽  
Klaus Doll ◽  
Mosbah Amlouk
Keyword(s):  
Ab Initio ◽  
Structural Stability ◽  
Quantum Mechanical ◽  
Vibrational Properties

Ab initio computation of interband contribution to the optical conductivity of YBa2Cu3O7−x

1988 ◽  
Vol 153-155 ◽  
pp. 1239-1240
Author(s):  
S.T. Chui ◽  
Robert V. Kasowski ◽  
William Y. Hsu
Keyword(s):  
Ab Initio ◽  
Optical Conductivity ◽  
Ab Initio Computation
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