scholarly journals Quantum mechanical synthon interaction energies

2017 ◽  
Vol 73 (a2) ◽  
pp. C682-C682
Author(s):  
Dylan Jayatilaka ◽  
Samuel Thompson ◽  
Sajesh Thomas ◽  
Peter Spackman ◽  
Mark Spackman
Keyword(s):  
Quantum Mechanical ◽  
Interaction Energies

scholarly journals Interactions between large molecules pose a puzzle for reference quantum mechanical methods

2021 ◽  
Vol 12 (1) ◽  
Author(s):  
Yasmine S. Al-Hamdani ◽  
Péter R. Nagy ◽  
Andrea Zen ◽  
Dennis Barton ◽  
Mihály Kállay ◽  
...  
Keyword(s):  
Experimental Information ◽  
Quantum Mechanical ◽  
Interaction Energies ◽  
Small Organic Molecules ◽  
Large Molecules ◽  
Reference Information ◽  
Mechanical Methods ◽  
Non Covalent Interactions ◽  
Semi Empirical ◽  
Covalent Interactions

AbstractQuantum-mechanical methods are used for understanding molecular interactions throughout the natural sciences. Quantum diffusion Monte Carlo (DMC) and coupled cluster with single, double, and perturbative triple excitations [CCSD(T)] are state-of-the-art trusted wavefunction methods that have been shown to yield accurate interaction energies for small organic molecules. These methods provide valuable reference information for widely-used semi-empirical and machine learning potentials, especially where experimental information is scarce. However, agreement for systems beyond small molecules is a crucial remaining milestone for cementing the benchmark accuracy of these methods. We show that CCSD(T) and DMC interaction energies are not consistent for a set of polarizable supramolecules. Whilst there is agreement for some of the complexes, in a few key systems disagreements of up to 8 kcal mol−1 remain. These findings thus indicate that more caution is required when aiming at reproducible non-covalent interactions between extended molecules.

Free energies of solvation with quantum mechanical interaction energies from classical mechanical simulations

1999 ◽  
Vol 110 (3) ◽  
pp. 1329-1337 ◽  
Author(s):  
Robert H. Wood ◽  
Eric M. Yezdimer ◽  
Shinichi Sakane ◽  
Jose A. Barriocanal ◽  
Douglas J. Doren
Keyword(s):  
Quantum Mechanical ◽  
Interaction Energies ◽  
Free Energies ◽  
Mechanical Interaction

scholarly journals Microscopic Factors Modulating the Interactions Between the SARS-Cov-2 Main Protease and α−Ketoamide Inhibitors

2020 ◽  
Author(s):  
Luigi Genovese ◽  
William Dawson ◽  
Takahito Nakajima ◽  
Viviana Cristiglio ◽  
Valérie Vallet ◽  
...  
Keyword(s):  
Aqueous Solution ◽  
Catalytic Domain ◽  
Covalent Bonding ◽  
Quantum Mechanical ◽  
Interaction Energies ◽  
Multi Scale ◽  
Main Protease ◽  
Catalytic Cysteine ◽  
The Mean ◽  
Dynamics Simulations

<p>We performed 10 ns scale molecular dynamics simulations of 6 SARS-Cov-2 main protease/􀀀ketoamide inhibitor complexes in aqueous solution, in the phase before the inhibitor covalently binds to the protease's catalytic cysteine, using a polarizable multi-scale molecular modeling approach. For each simulation, 100 Mpro/inhibitor snapshots</p><p>(about 4 800 atoms) were extracted along the last 2 ns simulation segments. They were post processed using a fully quantum mechanical O(N) approach to decompose the protease in sets of fragments from which we computed the mean local interaction energies between the inhibitors and the different pockets of the protease catalytic domain. Contrary to earlier results, our analysis shows that the protease pocket S2 to be a key anchoring site able to lock within the catalytic domain an alpha-ketoamide inhibitor even before covalent bonding to the protease catalytic cysteine occurs. To target that pocket our computations suggest to consider hydrophobic groups, like cyclo-propyl or cyclo-hexyl.</p>

scholarly journals Microscopic Factors Modulating the Interactions Between the SARS-CoV-2 Main Protease and α−Ketoamide Inhibitors

2020 ◽  
Author(s):  
Luigi Genovese ◽  
William Dawson ◽  
Takahito Nakajima ◽  
Viviana Cristiglio ◽  
Valérie Vallet ◽  
...  
Keyword(s):  
Aqueous Solution ◽  
Catalytic Domain ◽  
Covalent Bonding ◽  
Quantum Mechanical ◽  
Interaction Energies ◽  
Multi Scale ◽  
Main Protease ◽  
Catalytic Cysteine ◽  
The Mean ◽  
Dynamics Simulations

<p>We performed 10 ns scale molecular dynamics simulations of 6 SARS-CoV-2 main protease/alpha-ketoamide inhibitor complexes in aqueous solution, in the phase before the inhibitor covalently binds to the protease's catalytic cysteine, using a polarizable multi-scale molecular modeling approach. For each simulation, 100 Mpro/inhibitor snapshots</p><p>(about 4 800 atoms) were extracted along the last 2 ns simulation segments. They were post processed using a fully quantum mechanical O(N) approach to decompose the protease in sets of fragments from which we computed the mean local interaction energies between the inhibitors and the different pockets of the protease catalytic domain. Contrary to earlier results, our analysis shows that the protease pocket S2 to be a key anchoring site able to lock within the catalytic domain an alpha-ketoamide inhibitor even before covalent bonding to the protease catalytic cysteine occurs. To target that pocket our computations suggest to consider hydrophobic groups, like cyclo-propyl or cyclo-hexyl.</p>

Pairwise Decomposition of Residue Interaction Energies Using Semiempirical Quantum Mechanical Methods in Studies of Protein−Ligand Interaction

2005 ◽  
Vol 127 (18) ◽  
pp. 6583-6594 ◽  
Author(s):  
Kaushik Raha ◽  
Arjan J. van der Vaart ◽  
Kevin E. Riley ◽  
Martin B. Peters ◽  
Lance M. Westerhoff ◽  
...  
Keyword(s):  
Quantum Mechanical ◽  
Interaction Energies ◽  
Ligand Interaction ◽  
Residue Interaction ◽  
Mechanical Methods ◽  
Protein Ligand Interaction

scholarly journals THEORETICAL STUDY ON 15-CROWN-5 COMPLEX WITH SOME METAL CATIONS

2012 ◽  
Vol 12 (2) ◽  
pp. 135-140 ◽  
Author(s):  
Yahmin Yahmin ◽  
Harno Dwi Pranowo ◽  
Ria Armunanto
Keyword(s):  
Gas Phase ◽  
Metal Binding ◽  
Theoretical Study ◽  
Metal Cations ◽  
Quantum Mechanical ◽  
Interaction Energies ◽  
Mechanical Method ◽  
Binding Properties ◽  
Quantum Mechanical Method ◽  
Binding Capability

The capability of 15-crown-5 ethers to form complexes with some metal cations (Li+, Na+, K+, Zn2+, Cd2+ and Hg2+) was investigated by an ab initio quantum mechanical method. The calculations were performed at the RHF/lanl2mb level of theory. The interaction energies were used to evaluate the metal binding capability of the crown ether. The effect of nature of the metal on the binding properties was also studied. The results of the calculations showed that the interaction energy of the complexes increased in proportion with the ratio of ion charge, electronegativity and ionization potential to the cation diameter. In addition, based on the extraction distribution coefficient in the gas phase, it is found that the 15-crown-5 could not extract metal cations investigated.

scholarly journals Microscopic Factors Modulating the Interactions Between the SARS-CoV-2 Main Protease and α−Ketoamide Inhibitors

2020 ◽  
Author(s):  
Luigi Genovese ◽  
William Dawson ◽  
Takahito Nakajima ◽  
Viviana Cristiglio ◽  
Valérie Vallet ◽  
...  
Keyword(s):  
Aqueous Solution ◽  
Catalytic Domain ◽  
Covalent Bonding ◽  
Quantum Mechanical ◽  
Interaction Energies ◽  
Multi Scale ◽  
Main Protease ◽  
Catalytic Cysteine ◽  
The Mean ◽  
Dynamics Simulations

<p>We performed 10 ns scale molecular dynamics simulations of 6 SARS-CoV-2 main protease/alpha-ketoamide inhibitor complexes in aqueous solution, in the phase before the inhibitor covalently binds to the protease's catalytic cysteine, using a polarizable multi-scale molecular modeling approach. For each simulation, 100 Mpro/inhibitor snapshots</p><p>(about 4 800 atoms) were extracted along the last 2 ns simulation segments. They were post processed using a fully quantum mechanical O(N) approach to decompose the protease in sets of fragments from which we computed the mean local interaction energies between the inhibitors and the different pockets of the protease catalytic domain. Contrary to earlier results, our analysis shows that the protease pocket S2 to be a key anchoring site able to lock within the catalytic domain an alpha-ketoamide inhibitor even before covalent bonding to the protease catalytic cysteine occurs. To target that pocket our computations suggest to consider hydrophobic groups, like cyclo-propyl or cyclo-hexyl.</p>

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