scholarly journals 2019-nCoV vs. SARS-CoV: Which Truly Has a Higher ACE2 Affinity? A Quantum Chemical Perspective on Virus-Receptor Noncovalent Interactions

2020 ◽  
Author(s):  
Nitai Sylvetsky
Keyword(s):  
Molecular Dynamics ◽  
Electronic Structure ◽  
Force Field ◽  
Quantum Chemical ◽  
Noncovalent Interactions ◽  
Van Der Waals ◽  
Noncovalent Interaction ◽  
Van Der Waals Interactions ◽  
Virus Receptor ◽  
Electronic Structure Methods

Noncovalent interaction energetics associated with ACE2 affinity differences are investigated using electronic structure methods; Our results were found to challenge previous predictions – claiming a higher affinity for 2019-nCoV compared to SARS-CoV based merely on "chemical intuition". In addition, we demonstrate that a broadly-used classical molecular dynamics force field – MMFF94 – is clearly incapable of reproducing DFT-based noncovalent interaction energetics for the systems at hand (despite being specifically parameterized for van der Waals interactions).

scholarly journals 2019-nCoV vs. SARS-CoV: Which Truly Has a Higher ACE2 Affinity? A Quantum Chemical Perspective on Virus-Receptor Noncovalent Interactions

2020 ◽  
Author(s):  
Nitai Sylvetsky
Keyword(s):  
Molecular Dynamics ◽  
Electronic Structure ◽  
Force Field ◽  
Quantum Chemical ◽  
Noncovalent Interactions ◽  
Van Der Waals ◽  
Noncovalent Interaction ◽  
Van Der Waals Interactions ◽  
Virus Receptor ◽  
Electronic Structure Methods

Noncovalent interaction energetics associated with ACE2 affinity differences are investigated using electronic structure methods; Our results were found to challenge previous predictions – claiming a higher affinity for 2019-nCoV compared to SARS-CoV based merely on "chemical intuition". In addition, we demonstrate that a broadly-used classical molecular dynamics force field – MMFF94 – is clearly incapable of reproducing DFT-based noncovalent interaction energetics for the systems at hand (despite being specifically parameterized for van der Waals interactions).

scholarly journals A look at the density functional theory zoo with the advanced GMTKN55 database for general main group thermochemistry, kinetics and noncovalent interactions

2017 ◽  
Vol 19 (48) ◽  
pp. 32184-32215 ◽  
Author(s):  
Lars Goerigk ◽  
Andreas Hansen ◽  
Christoph Bauer ◽  
Stephan Ehrlich ◽  
Asim Najibi ◽  
...  
Keyword(s):  
Density Functional Theory ◽  
Electronic Structure ◽  
Density Functional ◽  
Noncovalent Interactions ◽  
Main Group ◽  
Density Functionals ◽  
Functional Theory ◽  
The Density Functional Theory ◽  
Benchmark Database ◽  
Electronic Structure Methods

We present the updated and extended GMTKN55 benchmark database for more accurate and extensive energetic evaluation of density functionals and other electronic structure methods with detailed guidelines for method users.

scholarly journals Theory and practice of modeling van der Waals interactions in electronic-structure calculations

2019 ◽  
Vol 48 (15) ◽  
pp. 4118-4154 ◽  
Author(s):  
Martin Stöhr ◽  
Troy Van Voorhis ◽  
Alexandre Tkatchenko
Keyword(s):  
Electronic Structure ◽  
Computational Modeling ◽  
State Of The Art ◽  
Van Der Waals ◽  
Electronic Structure Calculations ◽  
Black Box ◽  
Theory And Practice ◽  
Van Der Waals Interactions ◽  
Dispersion Interactions ◽  
Structure Calculations

Opening the black box of van der Waals-inclusive electronic structure calculations: a tutorial-style introduction to van der Waals dispersion interactions, state-of-the-art methods in computational modeling and complementary experimental techniques.

Study of 1,3-dimethylimidazolium chloride with electronic structure methods and force field approaches

2008 ◽  
Vol 129 (17) ◽  
pp. 174503 ◽  
Author(s):  
Christian Krekeler ◽  
Jochen Schmidt ◽  
Yuan Yuan Zhao ◽  
Baofu Qiao ◽  
Robert Berger ◽  
...  
Keyword(s):  
Electronic Structure ◽  
Force Field ◽  
Electronic Structure Methods ◽  
Field Approaches

Optimizing Protein–Protein van der Waals Interactions for the AMBER ff9x/ff12 Force Field

2013 ◽  
Vol 10 (1) ◽  
pp. 273-281 ◽  
Author(s):  
Dail E. Chapman ◽  
Jonathan K. Steck ◽  
Paul S. Nerenberg
Keyword(s):  
Force Field ◽  
Van Der Waals ◽  
Van Der Waals Interactions

MMPEP: Development and evaluation of peptide parameters for Allinger's MMP2(85) programme, including calculations on crambin and insulin

1988 ◽  
Vol 66 (11) ◽  
pp. 2687-2702 ◽  
Author(s):  
Saul Wolfe ◽  
Donald Fredric Weaver ◽  
Kiyull Yang
Keyword(s):  
Hydrogen Bonding ◽  
Force Field ◽  
Van Der Waals ◽  
Heavy Atom ◽  
Van Der Waals Interactions ◽  
Heavy Atoms ◽  
Minimization Procedure ◽  
Natural Result ◽  
Experimental Crystal ◽  
Initial Starting

Allinger's MMP2(85) program has been converted to an IBM environment, and the dimensions expanded to a current maximum of 999 atoms. Substantial additional expansion will be possible. An all-atom set of parameters, which permit Allinger's comprehensive force field to be applied to the molecular mechanics treatment of peptides, has been determined. These parameters, termed MMPEP, contain 21 atom types: 5 for carbon, 6 for hydrogen, 5 for nitrogen, 4 for oxygen, and 1 for sulfur, and are based on crystallographic heavy atom bond lengths and bond angles, vibrational and microwave spectra, and ab initio calculations. To minimize the conformational energy of a peptide from an initial starting geometry, all internally stored parameters are released, and replaced by PEPCON, a 360-line external file containing the MMPEP parameters.The ability of the MMPEP parameterization of MM85 to reproduce experimental crystal structures has been tested on several peptides and polypeptides, and the use of a dielectric constant ε = 78.5 D leads to the following results: Ala-Ala-Gly (rms = 0.261); Gly-Gly-Val (rms = 0.349); glutathione (rms = 0.417); crambin (327 heavy atoms; rms = 0.310 for all heavy atoms); insulin (389 heavy atoms; rms = 0.646 for all heavy atoms); the origins of deviations can be interpreted. No problems have been encountered in the application of the Newton–Raphson minimization procedure to such large molecules as crambin and insulin, even though all possible nonbonded interactions have been retained. On the IBM 3081 computer, real time minimization of trip)eptides requires 1–2 min, crambin requires 250 min, and insulin 200 min. Since hydrogen bonding in Allinger's force field is a natural result of electrostatic and van der Waals interactions, in MMPEP hydrogen bonding is taken into account through the large number of hydrogen atom types and their different bond moments and van der Waals radii.

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