scholarly journals Predicting accurate absolute binding energies in aqueous solution: thermodynamic considerations for electronic structure methods

2015 ◽  
Vol 17 (19) ◽  
pp. 12441-12451 ◽  
Author(s):  
Jan H. Jensen
Keyword(s):  
Aqueous Solution ◽  
Electronic Structure ◽  
Computational Chemistry ◽  
Binding Energies ◽  
Free Energies ◽  
Holy Grail ◽  
Electronic Structure Methods ◽  
Binding Free Energies

Binding free energies: a holy grail of computational chemistry.

scholarly journals A simple model for predicting the free energy of binding between anthracycline antibiotics and DNA.

2000 ◽  
Vol 47 (1) ◽  
pp. 1-9 ◽  
Author(s):  
W R Rudnicki ◽  
M Kurzepa ◽  
T Szczepanik ◽  
W Priebe ◽  
B Lesyng
Keyword(s):  
Free Energy ◽  
Theoretical Model ◽  
Density Functional ◽  
Binding Free Energy ◽  
Binding Energies ◽  
Free Energies ◽  
Anthracycline Antibiotics ◽  
Free Energy Of Binding ◽  
Derivatives Of ◽  
Binding Free Energies

A theoretical model for predicting the free energy of binding between anthracycline antibiotics and DNA was developed using the electron density functional (DFT) and molecular mechanics (MM) methods. Partial DFT-ESP charges were used in calculating the MM binding energies for complexes formed between anthracycline antibiotics and oligodeoxynucleotides. These energies were then compared with experimental binding free energies. The good correlation between the experimental and theoretical energies allowed us to propose a model for predicting the binding free energy for derivatives of anthracycline antibiotics and for quickly screening new anthracycline derivatives.

scholarly journals Omicron: A heavily mutated SARS-CoV-2 variant exhibits stronger binding to ACE2 and potently escape approved COVID-19 therapeutic antibodies

2021 ◽  
Author(s):  
Masaud Shah ◽  
Hyun Goo Woo
Keyword(s):  
South Africa ◽  
Electrostatic Potential ◽  
Binding Energies ◽  
Phase Iii ◽  
Therapeutic Antibodies ◽  
Free Energies ◽  
Significant Drop ◽  
Phase Iii Clinical Trials ◽  
Computational Mutagenesis ◽  
Binding Free Energies

AbstractThe new SARS-CoV-2 variant of concern “Omicron” was recently (Nov. 24th. 2021) spotted in South Africa and already spread around the world due to its enhanced transmissibility. The variant became conspicuous as it harbors more than thirty mutations in the spike protein with 15 mutations in the RBD region alone, potentially dampening the potency of therapeutic antibodies and enhancing the ACE2 binding. More worrying, Omicron infections have been reported in individuals who have received vaccines jabs in South Africa and Hong Kong. Here, we investigated the binding strength of Omicron with ACE2 and seven monoclonal antibodies that are either approved by FDA for COVID-19 therapy or undergoing phase III clinical trials. Computational mutagenesis and binding free energies could confirm that Omicron Spike binds ACE2 stronger than prototype SARS-CoV-2. Notably, three substitutions, i.e., T478K, Q493K, and Q498R, significantly contribute to the binding energies and doubled electrostatic potential of the RBDOmic-ACE2 complex. Instead of E484K substitution that helped neutralization escape of Beta, Gamma, and Mu variants, Omicron harbors E484A substitution. Together, T478K, Q493K, Q498R, and E484A substitutions contribute to a significant drop in the electrostatic potential energies between RBDOmic-mAbs, particularly in Etesevimab, Bamlanivimab, and CT-p59. CDR diversification could help regain the neutralization strength of these antibodies; however, we could not conduct this analysis to this end. Conclusively, our findings suggest that Omicron binds ACE2 with greater affinity, enhancing its infectivity and transmissibility. Mutations in the Spike are prudently devised by the virus that enhances the receptor binding and weakens the mAbs binding to escape the immune response.

Identifying MurI uncompetitive inhibitors by correlating decomposed binding energies with bioactivity

RSC Advances ◽  
2015 ◽  
Vol 5 (51) ◽  
pp. 40536-40545 ◽  
Author(s):  
Xiu Le ◽  
Qiong Gu ◽  
Jun Xu
Keyword(s):  
Binding Energies ◽  
New Method ◽  
Free Energies ◽  
Binding Free Energies

MurI uncompetitive inhibitors can be virtually identified by a new method that correlates decomposed binding free energies with the bioactivity.

Computational Chemistry Using Modern Electronic Structure Methods

2007 ◽  
Vol 84 (8) ◽  
pp. 1364 ◽  
Author(s):  
Robert Withnall ◽  
Babur Z. Chowdhry ◽  
Stephen Bell ◽  
Trevor J. Dines
Keyword(s):  
Electronic Structure ◽  
Computational Chemistry ◽  
Electronic Structure Methods

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>

Oxidation of ethylenediphosphinetetraacetate anions

1983 ◽  
Vol 48 (9) ◽  
pp. 2604-2608
Author(s):  
Jana Podlahová ◽  
Jaroslav Podlaha
Keyword(s):  
Aqueous Solution ◽  
Hydrogen Peroxide ◽  
Electronic Structure ◽  
Acid Solutions ◽  
Tetraacetic Acid ◽  
Single Product ◽  
Weakly Acid ◽  
Inhibiting Effect ◽  
Oxidation By Molecular Oxygen ◽  
Protonated Forms

The oxidation of the ethylenediphosphinetetraacetate anion and its protonated forms by iodine, periodate, hydrogen peroxide, and oxygen has been studied in aqueous solution. The oxidation by the first three reagents is fast and yields a single product, bis(phosphine oxide), which has been isolated and characterized as ethylenebis(phosphinyl)tetraacetic acid. The oxidation by molecular oxygen proceeds considerably more slowly; in weakly acid solutions its rate is determined by the properties of the oxygen rather than by the electronic structure of the various protonated substrate species. The inhibiting effect of the phosphonium structures takes place only in strongly acid solutions.

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