scholarly journals Revealing Quantum Mechanical Effects in Enzyme Catalysis with Large-Scale Electronic Structure Simulation

2018 ◽  
Author(s):  
Zhongyue Yang ◽  
Rimsha Mehmood ◽  
Mengyi Wang ◽  
Helena W. Qi ◽  
Adam H. Steeves ◽  
...  
Keyword(s):  
Electronic Structure ◽  
Active Sites ◽  
Dna Methyltransferase ◽  
Enzyme Mechanism ◽  
Quantum Mechanical ◽  
Valuable Insight ◽  
Relative Importance ◽  
Non Covalent Interactions ◽  
Covalent Interactions ◽  
Structure Properties

<div><div><div><p>Enzymes have evolved to facilitate challenging reactions at ambient conditions with specificity seldom matched by other catalysts. Computational modeling provides valuable insight into catalytic mechanism, and the large size of enzymes mandates multi-scale, quantum mechanical-molecular mechanical (QM/MM) simulations. Although QM/MM plays an essential role in balancing simulation cost to enable sampling with full QM treatment needed to understand electronic structure in enzyme active sites, the relative importance of these two strategies for understanding enzyme mechanism is not well known. We explore challenges in QM/MM for studying the reactivity and stability of three diverse enzymes: i) Mg2+-dependent catechol O-methyltransferase (COMT), ii) radical enzyme choline trimethylamine lyase (CutC), and iii) DNA methyltransferase (DNMT1), which has structural Zn2+ binding sites. In COMT, strong non-covalent interactions lead to long range coupling of electronic structure properties across the active site, but the more isolated nature of the metallocofactor in DNMT1 leads to faster convergence of some properties. We quantify these effects in COMT by computing covariance matrices of by-residue electronic structure properties during dynamics and along the reaction coordinate. In CutC, we observe spontaneous bond cleavage following initiation events, highlighting the importance of sampling and dynamics. We use electronic structure analysis to quantify the relative importance of CHO and OHO non-covalent interactions in imparting reactivity. These three diverse cases enable us to provide some general recommendations regarding QM/MM simulation of enzymes.</p></div></div></div>

scholarly journals Revealing Quantum Mechanical Effects in Enzyme Catalysis with Large-Scale Electronic Structure Simulation

2018 ◽  
Author(s):  
Zhongyue Yang ◽  
Rimsha Mehmood ◽  
Mengyi Wang ◽  
Helena W. Qi ◽  
Adam H. Steeves ◽  
...  
Keyword(s):  
Electronic Structure ◽  
Active Sites ◽  
Dna Methyltransferase ◽  
Enzyme Mechanism ◽  
Quantum Mechanical ◽  
Valuable Insight ◽  
Relative Importance ◽  
Non Covalent Interactions ◽  
Covalent Interactions ◽  
Structure Properties

<div><div><div><p>Enzymes have evolved to facilitate challenging reactions at ambient conditions with specificity seldom matched by other catalysts. Computational modeling provides valuable insight into catalytic mechanism, and the large size of enzymes mandates multi-scale, quantum mechanical-molecular mechanical (QM/MM) simulations. Although QM/MM plays an essential role in balancing simulation cost to enable sampling with full QM treatment needed to understand electronic structure in enzyme active sites, the relative importance of these two strategies for understanding enzyme mechanism is not well known. We explore challenges in QM/MM for studying the reactivity and stability of three diverse enzymes: i) Mg2+-dependent catechol O-methyltransferase (COMT), ii) radical enzyme choline trimethylamine lyase (CutC), and iii) DNA methyltransferase (DNMT1), which has structural Zn2+ binding sites. In COMT, strong non-covalent interactions lead to long range coupling of electronic structure properties across the active site, but the more isolated nature of the metallocofactor in DNMT1 leads to faster convergence of some properties. We quantify these effects in COMT by computing covariance matrices of by-residue electronic structure properties during dynamics and along the reaction coordinate. In CutC, we observe spontaneous bond cleavage following initiation events, highlighting the importance of sampling and dynamics. We use electronic structure analysis to quantify the relative importance of CHO and OHO non-covalent interactions in imparting reactivity. These three diverse cases enable us to provide some general recommendations regarding QM/MM simulation of enzymes.</p></div></div></div>

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.

Co-operativity in non-covalent interactions in ternary complexes: a comprehensive electronic structure theory based investigation

2018 ◽  
Vol 24 (9) ◽  
Author(s):  
Shyam Vinod Kumar Panneer ◽  
Mahesh Kumar Ravva ◽  
Brijesh Kumar Mishra ◽  
Venkatesan Subramanian ◽  
Narayanasami Sathyamurthy
Keyword(s):  
Electronic Structure ◽  
Ternary Complexes ◽  
Electronic Structure Theory ◽  
Structure Theory ◽  
Non Covalent Interactions ◽  
Covalent Interactions

AFM Research in Catalysis and Medicine

2020 ◽  
Vol 7 (3) ◽  
pp. 248-255
Author(s):  
Ludmila Matienko ◽  
Mil Elena Mickhailovna ◽  
Binyukov Vladimir Ivanovich ◽  
Goloshchapov Alexandr Nikolaevich
Keyword(s):  
Hydrogen Bonds ◽  
Active Sites ◽  
Morphological Changes ◽  
Iron Complexes ◽  
Supramolecular Structures ◽  
Intermolecular Hydrogen Bonds ◽  
Force Microscopy ◽  
Atomic Force ◽  
Non Covalent Interactions ◽  
Covalent Interactions

Background: In this study, we show that the AFM method not only allows monitoring the morphological changes in biological structures fixed on the surface due to H-bonds, but also makes it possible to study the self-organization of metal complexes by simulating the active center of enzymes due to intermolecular H-bonds into stable nanostructures; the sizes of which are much smaller than the studied biological objects. The possible role of intermolecular hydrogen bonds in the formation of stable supramolecular metal complexes, which are effective catalysts for the oxidation of alkyl arenes to hydroperoxides by molecular oxygen and mimic the selective active sites of enzymes, was first studied by AFM. Methods and Results: The formation of supramolecular structures due to intermolecular hydrogen bonds and, possibly, other non-covalent interactions, based on homogenous catalysts and models of active centers enzymes, heteroligand nickel and iron complexes, was proven by AFM-technique. AFM studies of supramolecular structures were carried out using NSG30 cantilever with a radius of curvature of 2 nm, in the tapping mode. To form nanostructures on the surface of a hydrophobic, chemically modified silicon surface as a substrate, the sample was prepared using a spin-coating process from solutions of the nickel and iron complexes. The composition and the structure of the complex Ni2(acac)(OAc)3·NMP·2H2O were determined in earlier works using various methods: mass spectrometry, UV- and IR-spectroscopy, elemental analysis, and polarography. Self-assembly of supramolecular structures is due to intermolecular interactions with a certain coordination of these interactions, which may be a consequence of the properties of the components themselves, the participation of hydrogen bonds and other non-covalent interactions, as well as the balance of the interaction of these components with the surface. Using AFM, approaches have been developed for fixing on the surface and quantifying parameters of cells. Conclusion: This study summarizes the authors' achievements in using the atomic force microscopy (AFM) method to study the role of intermolecular hydrogen bonds (and other non-covalent interactions) and supramolecular structures in the mechanisms of catalysis. The data obtained from AFM based on nickel and iron complexes, which are effective catalysts and models of active sites of enzymes, indicate a high probability of the formation of supramolecular structures in real conditions of catalytic oxidation, and can bring us closer to understanding enzymes activity. With a sensitive AFM method, it is possible to observe the self-organization of model systems into stable nanostructures due to H-bonds and possibly other non-covalent interactions, which can be considered as a step towards modeling the active sites of enzymes. Methodical approaches of atomic force microscopy for the study of morphological changes of cells have been developed.

scholarly journals Revealing quantum mechanical effects in enzyme catalysis with large-scale electronic structure simulation

2019 ◽  
Vol 4 (2) ◽  
pp. 298-315 ◽  
Author(s):  
Zhongyue Yang ◽  
Rimsha Mehmood ◽  
Mengyi Wang ◽  
Helena W. Qi ◽  
Adam H. Steeves ◽  
...  
Keyword(s):  
Electronic Structure ◽  
Enzyme Catalysis ◽  
Active Sites ◽  
Large Scale ◽  
Quantum Mechanical ◽  
Length Scales ◽  
Mechanical Simulation ◽  
Mechanical Effects ◽  
Structure Simulation ◽  
Quantum Mechanical Effects

Large scale quantum mechanical simulation systematically reveals length scales over which electronically driven interactions occur at enzyme active sites.

scholarly journals Targeted Oxidation Strategy (TOS) for Potential Inhibition of Coronaviruses by Disulfiram — a 70-Year Old Anti-Alcoholism Drug

2020 ◽  
Author(s):  
Luyan Xu ◽  
Jiahui Tong ◽  
Yiran Wu ◽  
Suwen Zhao ◽  
Bo-Lin Lin
Keyword(s):  
Clinical Trial ◽  
New Drugs ◽  
Phase Iii ◽  
Quantum Mechanical ◽  
Quantum Mechanical Calculations ◽  
Phase Iii Clinical Trial ◽  
Drug Candidates ◽  
Thiol Proteases ◽  
Non Covalent Interactions ◽  
Covalent Interactions

<p>In the new millennium, the outbreak of new coronavirus has happened three times: SARS-CoV, MERS-CoV, and 2019-nCoV. Unfortunately, we still have no pharmaceutical weapons against the diseases caused by these viruses. The pandemic of 2019-nCoV reminds us of the urgency to search new drugs with totally different mechanism that may target the weaknesses specific to coronaviruses. Herein, we disclose a new targeted oxidation strategy (TOS II) leveraging non-covalent interactions potentially to oxidize and inhibit the activities of cytosolic thiol proteins via thiol/thiolate oxidation to disulfide (TOD). Quantum mechanical calculations show encouraging results supporting the feasibility to selectively oxidize thiol of targeted proteins via TOS II even in relatively reducing cytosolic microenvironments. Molecular docking against the two thiol proteases M<sup>pro</sup> and PL<sup>pro</sup> of 2019-nCoV provide evidence to support a TOS II mechanism for two experimentally identified anti-2019-nCoV disulfide oxidants: disulfiram and PX-12. Remarkably, disulfiram is an anti-alcoholism drug approved by FDA 70 years ago, thus it can be immediately used in phase III clinical trial for anti-2019-nCoV treatment. Finally, a preliminary list of promising TOS II drug candidates targeting the two thiol proteases of 2019-nCoV are proposed upon virtual screening of 32143 disulfides.</p>

scholarly journals The intermolecular interactions in the aminonitromethylbenzenes

2011 ◽  
Vol 9 (1) ◽  
pp. 94-105 ◽  
Author(s):  
Rafal Kruszynski ◽  
Tomasz Sieranski
Keyword(s):  
Hydrogen Bonds ◽  
Lone Pair ◽  
Quantum Mechanical ◽  
Stacking Interactions ◽  
Quantum Mechanical Calculations ◽  
Charge Redistribution ◽  
Intermolecular Hydrogen Bonds ◽  
Non Covalent Interactions ◽  
The One ◽  
Covalent Interactions

AbstractThe intermolecular non-covalent interactions in aminonitromethylbenzenes namely 2-methyl-4-nitroaniline, 4-methyl-3-nitroaniline, 2-methyl-6-nitroaniline, 4-amino-2,6-dinitrotoluene, 2-methyl-5-nitroaniline, 4-methyl-2-nitroaniline, 2,3-dimethyl-6-nitroaniline, 4,5-dimethyl-2-nitroaniline and 2-methyl-3,5-dinitroaniline were studied by quantum mechanical calculations at RHF/311++G(3df,2p) and B3LYP/311++G(3df,2p) level of theory. The calculations prove that solely geometrical study of hydrogen bonding can be very misleading because not all short distances (classified as hydrogen bonds on the basis of interaction geometry) are bonding in character. For studied compounds interaction energy ranges from 0.23 kcal mol−1 to 5.59 kcal mol−1. The creation of intermolecular hydrogen bonds leads to charge redistribution in donors and acceptors. The Natural Bonding Orbitals analysis shows that hydrogen bonds are created by transfer of electron density from the lone pair orbitals of the H-bond acceptor to the antibonding molecular orbitals of the H-bond donor and Rydberg orbitals of the hydrogen atom. The stacking interactions are the interactions of delocalized molecular π-orbitals of the one molecule with delocalized antibonding molecular π-orbitals and the antibonding molecular σ-orbital created between the carbon atoms of the second aromatic ring and vice versa.

scholarly journals Targeted Oxidation Strategy (TOS) for Potential Inhibition of Coronaviruses by Disulfiram — a 70-Year Old Anti-Alcoholism Drug

2020 ◽  
Author(s):  
Luyan Xu ◽  
Jiahui Tong ◽  
Yiran Wu ◽  
Suwen Zhao ◽  
Bo-Lin Lin
Keyword(s):  
Clinical Trial ◽  
New Drugs ◽  
Phase Iii ◽  
Quantum Mechanical ◽  
Quantum Mechanical Calculations ◽  
Phase Iii Clinical Trial ◽  
Drug Candidates ◽  
Thiol Proteases ◽  
Non Covalent Interactions ◽  
Covalent Interactions

<p>In the new millennium, the outbreak of new coronavirus has happened three times: SARS-CoV, MERS-CoV, and 2019-nCoV. Unfortunately, we still have no pharmaceutical weapons against the diseases caused by these viruses. The pandemic of 2019-nCoV reminds us of the urgency to search new drugs with totally different mechanism that may target the weaknesses specific to coronaviruses. Herein, we disclose a new targeted oxidation strategy (TOS II) leveraging non-covalent interactions potentially to oxidize and inhibit the activities of cytosolic thiol proteins via thiol/thiolate oxidation to disulfide (TOD). Quantum mechanical calculations show encouraging results supporting the feasibility to selectively oxidize thiol of targeted proteins via TOS II even in relatively reducing cytosolic microenvironments. Molecular docking against the two thiol proteases M<sup>pro</sup> and PL<sup>pro</sup> of 2019-nCoV provide evidence to support a TOS II mechanism for two experimentally identified anti-2019-nCoV disulfide oxidants: disulfiram and PX-12. Remarkably, disulfiram is an anti-alcoholism drug approved by FDA 70 years ago, thus it can be immediately used in phase III clinical trial for anti-2019-nCoV treatment. Finally, a preliminary list of promising TOS II drug candidates targeting the two thiol proteases of 2019-nCoV are proposed upon virtual screening of 32143 disulfides.</p>

A novel ligand with –NH2 and –COOH-decorated Co/Fe-based oxide for an efficient overall water splitting: dual modulation roles of active sites and local electronic structure

2020 ◽  
Vol 10 (18) ◽  
pp. 6266-6273
Author(s):  
Yalan Zhang ◽  
Zebin Yu ◽  
Ronghua Jiang ◽  
Jung Huang ◽  
Yanping Hou ◽  
...  
Keyword(s):  
Electronic Structure ◽  
Water Splitting ◽  
Energy Demand ◽  
Active Sites ◽  
Electrode Materials ◽  
Global Energy ◽  
Overall Water Splitting ◽  
Local Electronic Structure ◽  
Electrochemical Water Splitting

Excellent electrochemical water splitting with remarkable durability can provide a solution to satisfy the increasing global energy demand in which the electrode materials play an important role.

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