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Proton network flexibility enables robustness and large electric fields in the ketosteroid isomerase active site [article]

Lu Wang, Stephen D. Fried, Thomas E. Markland
2017 arXiv   pre-print
We demonstrate that these properties arise from the network's ability to respond to a perturbation by shifting proton positions and redistributing electronic charge density.  ...  Here we combine electronic structure calculations and ab initio path integral molecular dynamics simulations, which incorporate both nuclear and electronic quantum effects, to show why the network of short  ...  (b) Comparison of ∆∆pKa obtained from AI-PIMD simulations and UV-Vis experiments. 33 The theoretical and experimental error bars are 0.03 and 0.10, respectively.  ... 
arXiv:1708.04734v1 fatcat:oymmd2n7izgejfulckmcw2r62i

Prediction of Organic Reaction Products: Determining the Best Reaction Conditions

Marco Durante, Guido Sello
2000 Journal of chemical information and computer sciences  
Some results will be presented to illustrate the power of the method.  ...  Consequently, we need the descriptions of the transition state and of the state solvation.  ...  APPENDIX Examples of program results for reactions from the REACCS database are given in Table 26 .  ... 
doi:10.1021/ci990430c pmid:10761122 fatcat:a73zkcx3xffnjphymnfnemzr34

Optical properties of wine pigments: theoretical guidelines with new methodological perspectives

Patrick Trouillas, Florent Di Meo, Johannes Gierschner, Mathieu Linares, Juan Carlos Sancho-García, Michal Otyepka
2015 Tetrahedron  
Molecular modelling (quantum mechanics and molecular dynamics) is more and more adapted to understand wine chemistry and pigmentation.  ...  and charge transfer excited states.  ...  Scheme 1 summarizes the hierarchy of this wide array of methods. Scheme 1: Hierarchy of quantum methods to deal with π-conjugated systems and non-covalent interactions (H-bonding and π-stacking).  ... 
doi:10.1016/j.tet.2014.10.046 fatcat:q3cml7m67fhcfging6fs3myqjm

Estimating the Roles of Protonation and Electronic Polarization in Absolute Binding Affinity Simulations [article]

Edward King, Ruxi Qi, Han Li, Ray Luo, Erick Aitchison
2021 arXiv   pre-print
Comparison of binding energy prediction at various protonation states indicates that proper electrostatic setup is also crucial in binding affinity prediction of charged systems, prompting us to propose  ...  With the advent of GPU acceleration, absolute alchemical methods, which simulate the removal of ligand electrostatics and van der Waals interactions with the protein, have become routinely accessible and  ...  Acknowledgements This work was supported by National Institute of Health/NIGMS (Grant Nos. GM093040 and GM130367)  ... 
arXiv:2103.08731v1 fatcat:waye4nvsezh7boq7psiifny3di

Testing Geometrical Discrimination within an Enzyme Active Site: Constrained Hydrogen Bonding in the Ketosteroid Isomerase Oxyanion Hole

Paul A. Sigala, Daniel A. Kraut, Jose M. M. Caaveiro, Brandon Pybus, Eliza A. Ruben, Dagmar Ringe, Gregory A. Petsko, Daniel Herschlag
2008 Journal of the American Chemical Society  
We bring together 1.2-1.5 Å resolution X-ray crystallography, 1 H and 19 F NMR spectroscopy, quantum mechanical calculations, and transition-state analogue binding measurements to test the distance scale  ...  Further, this constraint has substantial energetic effects on ligand binding and stabilization of negative charge within the oxyanion hole.  ...  Quantum Mechanical Calculations.  ... 
doi:10.1021/ja803928m pmid:18808119 pmcid:PMC2700827 fatcat:2x2a7umub5cwjnnbffqr47wsgy

Molecular Mechanism of a Green-Shifted, pH-Dependent Red Fluorescent Protein mKate Variant

Qi Wang, Laura J. Byrnes, Bo Shui, Ute F. Röhrig, Avtar Singh, Dmitriy M. Chudakov, Sergey Lukyanov, Warren R. Zipfel, Michael I. Kotlikoff, Holger Sondermann, Maria Gasset
2011 PLoS ONE  
Based on optical spectra and crystal structures of GmKate in its green and red states, the reversible color transition is attributed to the different protonation states of the cis-chromophore, an interpretation  ...  that was confirmed by quantum chemical calculations.  ...  We thank Stephen Perry for his assistance with quantum yield and photostability measurements. Author Contributions  ... 
doi:10.1371/journal.pone.0023513 pmid:21887263 pmcid:PMC3161743 fatcat:off6osrxyjdalkbu7mrttb4tm4

Thiol redox biochemistry: insights from computer simulations

Ari Zeida, Carlos M. Guardia, Pablo Lichtig, Laura L. Perissinotti, Lucas A. Defelipe, Adrián Turjanski, Rafael Radi, Madia Trujillo, Darío A. Estrin
2014 Biophysical Reviews  
In this work we review the application of classical and quantum-mechanical atomistic simulation tools to the investigation of selected relevant issues in thiol redox biochemistry, such as investigations  ...  of disulfide bonds and thiol−disulfide exchange, (4) formation of sulfenamides, (5) formation of nitrosothiols and transnitrosation reactions, and (6) oneelectron oxidation pathways.  ...  RR and MT acknowledge the financial support of the Howard Hughes Medical Institute, National Institutes of Health, Agencia Nacional de Investigación e Innovación (ANII, Uruguay) and Comisión Sectorial  ... 
doi:10.1007/s12551-013-0127-x pmid:28509962 pmcid:PMC5427810 fatcat:ikjci7caufbspl5lfjoldnswvy

Simulating solvation and acidity in complex mixtures with first-principles accuracy: the case of CH_3SO_3H and H_2O_2 in phenol [article]

Kevin Rossi, Veronika Juraskova, Raphael Wischert, Laurent Garel, Clemence Corminboeuf, Michele Ceriotti
2020 arXiv   pre-print
In order to address the challenges posed by the complexity of the problem, we resort to a set of data-driven methods and enhanced sampling algorithms.  ...  _3H in phenol as an example.  ...  Supporting Information Available The following files are available free of charge. Supplementary  ... 
arXiv:2006.12597v1 fatcat:6qes5bgrafaqfmlayz6f2albhm

Photo-isomerization upshifts the pKa of the Photoactive Yellow Protein chromophore to contribute to photocycle propagation

Sadia Naseem, Adèle D. Laurent, Elizabeth C. Carroll, Mikas Vengris, Masato Kumauchi, Wouter D. Hoff, Anna I. Krylov, Delmar S. Larsen
2013 Journal of Photochemistry and Photobiology A: Chemistry  
Formation of the pCA thioester reduces the pK a of the phenolic group by 0.3 units (from 9.5 ± 0.15 to 9.2 ± 0.16).  ...  the pK a of the phenolate group by 0.6 units (to 10.1 ± 0.22).  ...  The computational part of this study was conducted under the auspices of the iOpenShell Center for Computational Studies of Electronic Structure and Spectroscopy of Open-Shell and Electronically Excited  ... 
doi:10.1016/j.jphotochem.2013.06.019 fatcat:6iogjeig2ncprleaepteuxmszy

Deuterium Isotope Effects on Acid-Base Equilibrium of Organic Compounds

Meiyi Liu, Jiali Gao
2021 Molecules  
Although the average ΔpKa change from Model 1 was found to be in reasonable agreement with the experimental average result, the pKaH2O dependence of the solvent isotope effects is absent.  ...  Deuterium isotope effects on acid–base equilibrium have been investigated using a combined path integral and free-energy perturbation simulation method.  ...  Conflicts of Interest: The authors declare no conflict of interest. Sample Availability: Computational input samples are available from the authors.  ... 
doi:10.3390/molecules26247687 pmid:34946769 pmcid:PMC8705040 fatcat:wtkz7qxe4bffxixumqxmecslri

Protective Effects of [6]-Gingerol Against Chemical Carcinogens: Mechanistic Insights

Furlan, Bren
2020 International Journal of Molecular Sciences  
Moreover, our quantum mechanical study of the alkylation reactions of chemical carcinogens with [6]-gingerol and glutathione provide valuable insights in the reaction mechanisms and the geometries of the  ...  Finally, the obtained results also point to the applicability of quantum chemical methods to studies of alkylation reactions related to chemical carcinogenesis.  ...  At physiological conditions, the predicted pKa value for the phenol group of [6]-gingerol was slightly lower (by 0.1) than for the thiol group of glutathione resulting in a 1% higher abundance of simulated  ... 
doi:10.3390/ijms21030695 pmid:31973096 pmcid:PMC7037038 fatcat:3gmnmsac6be7dpnyxqd3sk6htq

Plant-Derived and Dietary Hydroxybenzoic Acids—A Comprehensive Study of Structural, Anti-/Pro-Oxidant, Lipophilic, Antimicrobial, and Cytotoxic Activity in MDA-MB-231 and MCF-7 Cell Lines

Monika Kalinowska, Ewelina Gołębiewska, Grzegorz Świderski, Sylwia Męczyńska-Wielgosz, Hanna Lewandowska, Anna Pietryczuk, Adam Cudowski, Aleksander Astel, Renata Świsłocka, Mariola Samsonowicz, Anna Barbara Złowodzka, Waldemar Priebe (+1 others)
2021 Nutrients  
Moreover, the structure of HBAs was studied by means of experimental (FTIR, 1H, and 13C NMR) and quantum chemical DFT methods (the NBO and CHelpG charges, electrostatic potential maps, and electronic parameters  ...  The biological activity of hydroxybenzoic acids was discussed in relation to their geometry, the electronic charge distribution in their molecules, their lipophilicity, and their acidity.  ...  Data Availability Statement: The data presented in this study are available on request from the corresponding author. Conflicts of Interest: The authors declare no conflict of interest.  ... 
doi:10.3390/nu13093107 pmid:34578985 pmcid:PMC8466373 fatcat:qqljrn2tpzealcnyix3i355c5u

Development of constant-pH simulation methods in implicit solvent and applications in biomolecular systems

Fernando Luís Barroso daSilva, Luis Gustavo Dias
2017 Biophysical Reviews  
Due to the quantum nature of the process, involving the forming and breaking of chemical bonds, quantum methods should ideally by employed.  ...  Simplified methods based on Monte Carlo sampling have been devised and will be reviewed here, highlighting the updated state-ofthe-art of this field, advantages, and limitations of different theoretical  ...  At present, practical alternatives disregard the solvent and solute quantum mechanical nature, or better, only a few atoms are treated as quantum mechanics objects while the neighbors are approximated  ... 
doi:10.1007/s12551-017-0311-5 pmid:28921104 pmcid:PMC5662048 fatcat:t2lxac7tgfabpkvney64yelvwu

How does the protein environment optimize the thermodynamics of thiol sulfenylation? Insights from model systems to QM/MM calculations on human 2-Cys peroxiredoxin

Julianna Oláh, Laura van Bergen, Frank De Proft, Goedele Roos
2014 Journal of Biomolecular Structure and Dynamics  
Here, insights into the thiol sulfenylation thermodynamics is obtained from model calculations on small systems and from a quantum mechanics/molecular mechanics (QM/MM) analysis on human 2-Cys peroxiredoxin  ...  To study thiol sulfenylation in Tpx-B, our recently developed computational method to determine reduction potentials relatively compared to a reference system and based on reaction energies (REE) is updated  ...  JO acknowledges the financial support of a EU Marie Curie ERG Fellowship (Project "Oestrometab"), of a Bolyai János Research Fellowship and of the New Széchenyi Plan (TÁMOP-4.2.2/B-10/1-2010-0009).  ... 
doi:10.1080/07391102.2014.907543 pmid:24762169 fatcat:v7xpitpcxfanzcr6nfwz4jgruq

Hydrogen Atomic Positions of O–H···O Hydrogen Bonds in Solution and in the Solid State: The Synergy of Quantum Chemical Calculations with 1H-NMR Chemical Shifts and X-ray Diffraction Methods

Michael Siskos, M. Choudhary, Ioannis Gerothanassis
2017 Molecules  
The exact knowledge of hydrogen atomic positions of O-H···O hydrogen bonds in solution and in the solid state has been a major challenge in structural and physical organic chemistry.  ...  has been determined by X-ray from single crystals or from powders; (ii) 1 H-NMR chemical shifts as constraints in DFT calculations, and (iii) use of root-mean-square deviation between experimentally determined  ...  Acknowledgments: We are grateful to the Greek Community support Framework III, Regional Operational Program of Epirus (2000-2006) (MIS91629) for supporting the purchase of an Avance 500 LC-NMR instrument  ... 
doi:10.3390/molecules22030415 pmid:28272366 fatcat:ewngeamfrrcrvfkp22x3z4nliu
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