scholarly journals Correction: Effective in silico prediction of new oxazolidinone antibiotics: force field simulations of the antibiotic–ribosome complex supervised by experiment and electronic structure methods

2016 ◽  
Vol 12 ◽  
pp. 608-610
Author(s):  
Jörg Grunenberg ◽  
Giuseppe Licari
Keyword(s):  
Electronic Structure ◽  
Force Field ◽  
In Silico ◽  
In Silico Prediction ◽  
Electronic Structure Methods

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

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 In silico prediction of annihilators for triplet–triplet annihilation upconversion via auxiliary-field quantum Monte Carlo

2021 ◽  
Author(s):  
John L. Weber ◽  
Emily M. Churchill ◽  
Steffen Jockusch ◽  
Evan J. Arthur ◽  
Andrew B. Pun ◽  
...  
Keyword(s):  
Monte Carlo ◽  
Electronic Structure ◽  
Excited State ◽  
Quantum Monte Carlo ◽  
In Silico ◽  
Auxiliary Field ◽  
In Silico Prediction ◽  
Organic Chromophores ◽  
Triplet Triplet Annihilation

Electronic structure theories such as AFQMC can accurately predict the low-lying excited state energetics of organic chromophores involved in triplet–triplet annihilation upconversion. A novel class of benzothiadiazole annihilators is discovered.

Performance of Electronic Structure Methods for the Description of Hückel-Möbius Interconversions in Extended π-Systems

2019 ◽  
Author(s):  
Tatiana Woller ◽  
Ambar Banerjee ◽  
Nitai Sylvetsky ◽  
Xavier Deraet ◽  
Frank De Proft ◽  
...  
Keyword(s):  
Electronic Structure ◽  
Basis Set ◽  
Dft Methods ◽  
Molecular Switching ◽  
Wide Range ◽  
Electronic Structure Methods ◽  
Explicitly Correlated ◽  
Relative Errors ◽  
The Stability ◽  
Basis Set Expansion

<p>Expanded porphyrins provide a versatile route to molecular switching devices due to their ability to shift between several π-conjugation topologies encoding distinct properties. Taking into account its size and huge conformational flexibility, DFT remains the workhorse for modeling such extended macrocycles. Nevertheless, the stability of Hückel and Möbius conformers depends on a complex interplay of different factors, such as hydrogen bonding, p···p stacking, steric effects, ring strain and electron delocalization. As a consequence, the selection of an exchange-correlation functional for describing the energy profile of topological switches is very difficult. For these reasons, we have examined the performance of a variety of wavefunction methods and density functionals for describing the thermochemistry and kinetics of topology interconversions across a wide range of macrocycles. Especially for hexa- and heptaphyrins, the Möbius structures have a pronouncedly stronger degree of static correlation than the Hückel and figure-eight structures, and as a result the relative energies of singly-twisted structures are a challenging test for electronic structure methods. Comparison of limited orbital space full CI calculations with CCSD(T) calculations within the same active spaces shows that post-CCSD(T) correlation contributions to relative energies are very minor. At the same time, relative energies are weakly sensitive to further basis set expansion, as proven by the minor energy differences between MP2/cc-pVDZ and explicitly correlated MP2-F12/cc-pVDZ-F12 calculations. Hence, our CCSD(T) reference values are reasonably well-converged in both 1-particle and n-particle spaces. While conventional MP2 and MP3 yield very poor results, SCS-MP2 and particularly SOS-MP2 and SCS-MP3 agree to better than 1 kcal mol<sup>-1</sup> with the CCSD(T) relative energies. Regarding DFT methods, only M06-2X provides relative errors close to chemical accuracy with a RMSD of 1.2 kcal mol<sup>-1</sup>. While the original DSD-PBEP86 double hybrid performs fairly poorly for these extended p-systems, the errors drop down to 2 kcal mol<sup>-1</sup> for the revised revDSD-PBEP86-NL, again showing that same-spin MP2-like correlation has a detrimental impact on performance like the SOS-MP2 results. </p>

Ideal–Gas Thermochemical Properties for Alkanolamine and Related Species Involved in Carbon Capture Applications

2020 ◽  
Author(s):  
Nayyereh hatefi ◽  
William Smith
Keyword(s):  
Heat Capacity ◽  
Electronic Structure ◽  
Co2 Capture ◽  
Carbon Capture ◽  
Ideal Gas ◽  
Thermochemical Properties ◽  
Temperature Range ◽  
Comparison Results ◽  
Electronic Structure Methods ◽  
Protonated Forms

<div>Ideal{gas thermochemical properties (enthalpy, entropy, Gibbs energy, and heat capacity, Cp) of 49 alkanolamines potentially suitable for CO2 capture applications and their carbamate and protonated forms were calculated using two high{order electronic structure methods, G4 and G3B3 (or G3//B3LYP). We also calculate for comparison results from the commonly used B3LYP/aug-cc-pVTZ method. This data is useful for the construction of molecular{based thermodynamic models of CO2 capture processes involving these species. The Cp data for each species over the temperature range 200 K{1500 K is presented as functions of temperature in the form of NASA seven-term polynomial expressions, permitting the set of thermochemical properties to be calculated over this temperature range. The accuracy of the G3B3 and G4 results is estimated to be 1 kcal/mol and the B3LYP/aug-cc-pVTZ results are of nferior quality..</div>

Speciation of cultivated temperate and tropical Pleurotus species –an in silico prediction using conserved sequences

2019 ◽  
Vol 28 (1) ◽  
Author(s):  
Anupam Barh ◽  
V P Sharma ◽  
Shwet Kamal ◽  
Mahantesh Shirur ◽  
Sudheer Kumar Annepu ◽  
...  
Keyword(s):  
In Silico ◽  
In Silico Prediction ◽  
Conserved Sequences ◽  
Pleurotus Species
Sign in / Sign up

Export Citation Format

Share Document