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Lin M, Tian B, Huang R, Xiao C. Study on the Transport Properties of SO 2 and NO at the Interface of H 2O 2 Solutions Using Molecular Dynamics. J Phys Chem B 2024. [PMID: 38656112 DOI: 10.1021/acs.jpcb.4c00013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/26/2024]
Abstract
Gas-liquid interfaces have a unique structure different from the bulk phase due to the complex intermolecular interactions within them and are regarded as barriers that prevent gases from entering solution or as channels that affect gas reactions. In this study, the adsorption and mass-transfer mechanisms of sulfur dioxide and nitric oxide at the gas-liquid interface of a H2O2 solution were comprehensively analyzed using molecular dynamics (MD) simulations. The analysis on molecule angle showed that H2O molecules tended to align parallel to the solution surface on the surface of the H2O2 solution. Regardless of whether the gas was adsorbed on the surface of the solution or not, H2O2 molecules were always perpendicular to the interface of the solution. The analysis on molecule angle and radial distribution function revealed that the H atoms of H2O molecules had a corresponding turn, and SO2 molecules were greatly affected by the attraction of H2O2 molecules during the adsorption of gas molecules on the interface. Steered MD was utilized to investigate the mass-transfer process of SO2 and NO molecules across the gas-liquid interface. The S atoms of SO2 molecules were significantly influenced by H2O2 molecules, while the O atoms of NO molecules gradually transitioned from the gas phase to the liquid phase. The results provided information on how gas molecules interacted with the surface of the solution and the specific details of the molecular orientation at the solution surface.
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Affiliation(s)
- Mingqi Lin
- Department of Energy and Power Engineering, College of Electrical Engineering, Guizhou University, Huaxi District, Guiyang 550025, China
| | - Bobing Tian
- Department of Energy and Power Engineering, College of Electrical Engineering, Guizhou University, Huaxi District, Guiyang 550025, China
| | - Ren Huang
- Department of Energy and Power Engineering, College of Electrical Engineering, Guizhou University, Huaxi District, Guiyang 550025, China
| | - Chao Xiao
- Department of Energy and Power Engineering, College of Electrical Engineering, Guizhou University, Huaxi District, Guiyang 550025, China
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2
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Parida C, Chowdhuri S. Effects of Hydrogen Peroxide on the Hydrogen Bonding Structure and Dynamics of Water and Its Influence on the Aqueous Solvation of the Insulin Monomer. J Phys Chem B 2023; 127:10814-10823. [PMID: 38055728 DOI: 10.1021/acs.jpcb.3c05107] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/08/2023]
Abstract
The hydrogen bond structure and dynamics of water and hydrogen peroxide (H2O2) in their binary mixtures have been studied at 298 K by classical molecular dynamics simulations. Twelve different concentrations of aqueous-H2O2 solutions are considered for this study. We have analyzed the interactions between water and H2O2 by site-site pair correlation functions and observed that the probability of formation of OW···HP hydrogen bonds are higher compared to OP···HW. The second solvation shell of water is strongly affected by increasing H2O2 concentrations (XP > 0.50), which signifies the destruction of the tetrahedral network structure of water. The translational and rotational dynamics of water and H2O2 do not significantly change up to 25% of H2O2 in aqueous mixtures. The hydrogen bond lifetime of water-water, water-H2O2, and H2O2-H2O2 in the aqueous-H2O2 solutions shows a very minimal change with increasing H2O2 concentrations. In addition to this, we also investigated the effect of H2O2 on the insulin monomer and observed that higher concentrations of H2O2 (XP = 0.10) change the secondary structure. The influence of H2O2 is more on chain-B than that on chain-A in the insulin monomer. The H2O2 occupancy at the protein surface is higher for negatively charged (GLU) and polar (ASN and THR) amino acid residues compared with that for positively charged and neutral residues in the solutions.
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Affiliation(s)
- Chinmay Parida
- School of Basic Sciences, Indian Institute of Technology, Bhubaneswar 752050, India
| | - Snehasis Chowdhuri
- School of Basic Sciences, Indian Institute of Technology, Bhubaneswar 752050, India
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3
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Arismendi-Arrieta DJ, Sen A, Eriksson A, Broqvist P, Kullgren J, Hermansson K. H2O2(s) and H2O2·2H2O(s) crystals compared with ices: DFT functional assessment and D3 analysis. J Chem Phys 2023; 159:194701. [PMID: 37966002 DOI: 10.1063/5.0145203] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2023] [Accepted: 07/27/2023] [Indexed: 11/16/2023] Open
Abstract
The H2O and H2O2 molecules resemble each other in a multitude of ways as has been noted in the literature. Here, we present density functional theory (DFT) calculations for the H2O2(s) and H2O2·2H2O(s) crystals and make selected comparisons with ice polymorphs. The performance of a number of dispersion-corrected density functionals-both self-consistent and a posteriori ones-are assessed, and we give special attention to the D3 correction and its effects. The D3 correction to the lattice energies is large: for H2O2(s) the D3 correction constitutes about 25% of the lattice energy using PBE, much more for RPBE, much less for SCAN, and it primarily arises from non-H-bonded interactions out to about 5 Å.The large D3 corrections to the lattice energies are likely a consequence of several effects: correction for missing dispersion interaction, the ability of D3 to capture and correct various other kinds of limitations built into the underlying DFT functionals, and finally some degree of cell-contraction-induced polarization enhancement. We find that the overall best-performing functionals of the twelve examined are optPBEvdW and RPBE-D3. Comparisons with DFT assessments for ices in the literature show that where the same methods have been used, the assessments largely agree.
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Affiliation(s)
| | - Anik Sen
- Department of Chemistry-Ångström, Uppsala University, P.O. Box 530, S-75121 Uppsala, Sweden
| | - Anders Eriksson
- Department of Chemistry-Ångström, Uppsala University, P.O. Box 530, S-75121 Uppsala, Sweden
| | - Peter Broqvist
- Department of Chemistry-Ångström, Uppsala University, P.O. Box 530, S-75121 Uppsala, Sweden
| | - Jolla Kullgren
- Department of Chemistry-Ångström, Uppsala University, P.O. Box 530, S-75121 Uppsala, Sweden
| | - Kersti Hermansson
- Department of Chemistry-Ångström, Uppsala University, P.O. Box 530, S-75121 Uppsala, Sweden
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4
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Ghadirian F, Abbasi H, Bavi O, Naeimabadi A. How living cells are affected during the cold atmospheric pressure plasma treatment. Free Radic Biol Med 2023; 205:141-150. [PMID: 37295538 DOI: 10.1016/j.freeradbiomed.2023.06.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/13/2023] [Revised: 06/03/2023] [Accepted: 06/06/2023] [Indexed: 06/12/2023]
Abstract
When the electric discharge process is limited by high voltage electrodes shielding, the ionization measure would be controlled to less than one percent and the temperature to less than 37 °C even at atmospheric pressure, so-called cold atmospheric pressure plasma (CAP). CAP has been found to have profound medical applications in association with its reactive oxygen and nitrogen species (ROS/RNS). In this way that during plasma exposure, the subjected medium (e.g. cell cytoplasmic membrane in plasma therapy) interacts with ROS/RNS. Accordingly, a precise study of the mentioned interactions and their consequences on the cells' behavior changes, is necessary. The results lead to the reduction of possible risks and provide the opportunity of optimizing the efficacy of CAP before the development of CAP applications in the field of plasma medicine. In this report molecular dynamic (MD) simulation is used to investigate the mentioned interactions and a proper and compatible comparison with the experimental results is presented. Based on this, the effects of H2O2, NO and O2 on the living cell's membrane are investigated in biological conditions. Our results show that: i) The hydration of phospholipid polar heads would be enhanced associated with the H2O2 presence. ii) A new definition of the surface area assigned to each phospholipid (APL), more reliable and compatible with the physical expectations, is introduced. iii) The long-term behavior of NO and O2 is their penetration into the lipid bilayer and sometimes passing through the membrane into the cell. The latter would be an indication of internal cells' pathways activation leading to modification of cells' function.
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Affiliation(s)
- Fatemeh Ghadirian
- Faculty of Physics and Energy Engineering, Amirkabir University of Technology, P. O. Box, 15875-4413, Tehran, Iran
| | - Hossein Abbasi
- Faculty of Physics and Energy Engineering, Amirkabir University of Technology, P. O. Box, 15875-4413, Tehran, Iran.
| | - Omid Bavi
- Department of Mechanical Engineering, Shiraz University of Technology, Shiraz, Iran
| | - Aboutorab Naeimabadi
- Faculty of Physics and Energy Engineering, Amirkabir University of Technology, P. O. Box, 15875-4413, Tehran, Iran
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5
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Peralta A, Odriozola G. A Neural-Network-Optimized Hydrogen Peroxide Pairwise Additive Model for Classical Simulations. J Chem Theory Comput 2023; 19:4172-4181. [PMID: 37306692 PMCID: PMC10921400 DOI: 10.1021/acs.jctc.3c00287] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2023] [Indexed: 06/13/2023]
Abstract
We have developed an all-atom pairwise additive model for hydrogen peroxide using an optimization procedure based on artificial neural networks (ANNs). The model is based on experimental molecular geometry and includes a dihedral potential that hinders the cis-type configuration and allows for crossing the trans one, defined between the planes that have the two oxygen atoms and each hydrogen. The model's parametrization is achieved by training simple ANNs to minimize a target function that measures the differences between various thermodynamic and transport properties and the corresponding experimental values. Finally, we evaluated a range of properties for the optimized model and its mixtures with SPC/E water, including bulk-liquid properties (density, thermal expansion coefficient, adiabatic compressibility, etc.) and properties of systems at equilibrium (vapor and liquid density, vapor pressure and composition, surface tension, etc.). Overall, we obtained good agreement with experimental data.
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Affiliation(s)
- Alvaro
Ramos Peralta
- Área de Física de Procesos
Irreversibles, División de Ciencias Básicas e Ingeniería, Universidad Autónoma Metropolitana-Azcapotzalco, Av. San Pablo 180, 02200 Ciudad de México, Mexico
| | - Gerardo Odriozola
- Área de Física de Procesos
Irreversibles, División de Ciencias Básicas e Ingeniería, Universidad Autónoma Metropolitana-Azcapotzalco, Av. San Pablo 180, 02200 Ciudad de México, Mexico
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6
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Piatnytskyi DV, Volkov SN. Complexes of hydrogen peroxide molecules with DNA nucleic bases. J Biomol Struct Dyn 2023; 41:15003-15008. [PMID: 36995109 DOI: 10.1080/07391102.2023.2193986] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2022] [Accepted: 02/20/2023] [Indexed: 03/31/2023]
Abstract
The analysis of complexes formation of hydrogen peroxide molecule with DNA nucleic bases is carried out using methods of quantum chemistry. Optimized geometries of complexes are determined and the interaction energies that lead to complex formation are calculated. Comparison with the same calculations for water molecule is made. It is shown that complexes with hydrogen peroxide molecule are energetically more stable than the same complexes with water molecule. Such energetic advantage is achieved particularly due to geometrical properties of hydrogen peroxide molecule, especially presence of dihedral angle. Position of hydrogen peroxide molecule in close vicinity to DNA could lead to blocking of its recognition by proteins or direct damage via hydroxyl radical formation. These results can have significant impact in understanding of mechanisms of cancer therapy.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- D V Piatnytskyi
- Laboratory of Biophysics of Macromolecules, Bogolyubov Institute for Theoretical Physics, Kyiv, Ukraine
| | - S N Volkov
- Laboratory of Biophysics of Macromolecules, Bogolyubov Institute for Theoretical Physics, Kyiv, Ukraine
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7
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Donaldson DJ. Experimental Confirmation of H 2O 2 Adsorption at the Water-Air Interface. J Phys Chem A 2022; 126:5647-5653. [PMID: 35960909 PMCID: PMC9422982 DOI: 10.1021/acs.jpca.2c04373] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2022] [Revised: 08/01/2022] [Indexed: 11/28/2022]
Abstract
Recent work has reported that hydrogen peroxide is formed at the air-water interface. Given the reduced solvation environment there, this process could give rise to enhanced production of OH from H2O2 photolysis at the interface. These considerations give some importance to understanding the adsorption thermochemistry of hydrogen peroxide. Although there are two molecular dynamics studies that provide the adsorption free energy, to date there is no experimental verification that H2O2 adsorbs at the air-water interface. Here we use glancing-angle Raman spectroscopy to follow the surface adsorption behavior of this molecule. Using standard states of 1 mol L-1 for each of the bulk and surface phases yields a ΔG° of -5 kJ mol-1 at 293 K, comparable to that obtained for DMSO.
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Affiliation(s)
- D. James Donaldson
- Department
of Chemistry, University of Toronto, 80 St. George Street, Toronto, ON M5S
3H6, Canada
- Department
of Physical and Environmental Sciences, University of Toronto Scarborough, 1265 Military Trail, Toronto, ON M1C 1A4, Canada
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8
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Poštulka J, Slavíček P, Pysanenko A, Poterya V, Fárník M. Bimolecular reactions on sticky and slippery clusters: Electron-induced reactions of hydrogen peroxide. J Chem Phys 2022; 156:054306. [DOI: 10.1063/5.0079283] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023] Open
Affiliation(s)
- Jan Poštulka
- Department of Physical Chemistry, University of Chemistry and Technology, Prague, Technická 5, 16628 Prague, Czech Republic
| | - Petr Slavíček
- Department of Physical Chemistry, University of Chemistry and Technology, Prague, Technická 5, 16628 Prague, Czech Republic
| | - Andriy Pysanenko
- J. Heyrovský Institute of Physical Chemistry, Czech Academy of Sciences, Dolejškova 2155/3, Prague 8, Czech Republic
| | - Viktoriya Poterya
- J. Heyrovský Institute of Physical Chemistry, Czech Academy of Sciences, Dolejškova 2155/3, Prague 8, Czech Republic
| | - Michal Fárník
- J. Heyrovský Institute of Physical Chemistry, Czech Academy of Sciences, Dolejškova 2155/3, Prague 8, Czech Republic
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9
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Orabi EA, Öztürk TN, Bernhardt N, Faraldo-Gómez JD. Corrections in the CHARMM36 Parametrization of Chloride Interactions with Proteins, Lipids, and Alkali Cations, and Extension to Other Halide Anions. J Chem Theory Comput 2021; 17:6240-6261. [PMID: 34516741 DOI: 10.1021/acs.jctc.1c00550] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The nonpolarizable CHARMM force field is one of the most widely used energy functions for all-atom biomolecular simulations. Chloride is the only halide ion included in the latest version, CHARMM36m, and is used widely in simulation studies, often as an electrolyte ion but also as the biological substrate of transport proteins and enzymes. Here, we find that existing parameters systematically underestimate the interaction of Cl- with proteins and lipids. Accordingly, when examined in solution, little to no Cl-association can be observed with most components of the protein, including backbone, polar side chains and aromatic rings. The strength of the interaction with cationic side chains and with alkali ions is also incongruent with experimental measurements, specifically osmotic coefficients of concentrated solutions. Consistent with these findings, a 4-μs trajectory of the Cl--specific transport protein CLC-ec1 shows irreversible Cl- dissociation from the so-called Scen binding site, even in a 150 mM NaCl buffer. To correct for these deficiencies, we formulate a series of pair-specific Lennard-Jones parameters that override those resulting from the conventional Lorentz-Berthelot combination rules. These parameters, referred to as NBFIX, are systematically calibrated against available experimental data as well as ab initio geometry optimizations and energy evaluations, for a wide set of binary and ternary Cl- complexes with protein and lipid analogs and alkali cations. Analogously, we also formulate parameter sets for the other three biological halide ions, namely, fluoride, bromide, and iodide. The resulting parameters are used to calculate the potential of mean force defining the interaction of each anion and each of the protein and lipid analogues in bulk water, revealing association free energies in the range of -0.3 to -3.3 kcal/mol, with the F- complexes being the least stable. The NBFIX corrections also preserve the Cl- occupancy of CLC-ec1 in a second 4-μs trajectory. We posit that these optimized molecular-mechanics models provide a more realistic foundation for all-atom simulation studies of processes entailing changes in hydration, recognition, or transport of halide anions.
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Affiliation(s)
- Esam A Orabi
- Theoretical Molecular Biophysics Laboratory, National Heart, Lung and Blood Institute, National Institutes of Health, 10 Center Drive, Bethesda, Maryland 20814, United States
| | - Tuǧba N Öztürk
- Theoretical Molecular Biophysics Laboratory, National Heart, Lung and Blood Institute, National Institutes of Health, 10 Center Drive, Bethesda, Maryland 20814, United States.,Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St. Louis, Missouri 63110, United States
| | - Nathan Bernhardt
- Theoretical Molecular Biophysics Laboratory, National Heart, Lung and Blood Institute, National Institutes of Health, 10 Center Drive, Bethesda, Maryland 20814, United States
| | - José D Faraldo-Gómez
- Theoretical Molecular Biophysics Laboratory, National Heart, Lung and Blood Institute, National Institutes of Health, 10 Center Drive, Bethesda, Maryland 20814, United States
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10
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Orabi EA. Molecular dynamics investigation of the structural flexibility of H2O2 and H2S2 in response to medium polarity. J Mol Liq 2021. [DOI: 10.1016/j.molliq.2021.115469] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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11
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Molecular dynamics study of the competitive binding of hydrogen peroxide and water molecules with DNA phosphate groups. EUROPEAN BIOPHYSICS JOURNAL: EBJ 2021; 50:759-770. [PMID: 33834265 DOI: 10.1007/s00249-021-01522-8] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/01/2020] [Revised: 02/28/2021] [Accepted: 03/22/2021] [Indexed: 10/21/2022]
Abstract
The interaction of hydrogen peroxide molecules with the DNA double helix is of great interest for understanding the mechanisms of anticancer therapy utilising heavy ion beams. In the present work, a molecular dynamics study of competitive binding of hydrogen peroxide and water molecules with phosphate groups of the DNA double helix backbone was carried out. The system of DNA double helix in a water solution with hydrogen peroxide molecules and Na[Formula: see text] counterions was simulated. The results show that the hydrogen peroxide molecules bind to oxygen atoms of the phosphate groups of the double helix backbone replacing water molecules of its hydration shell. The complexes of hydrogen peroxide molecules with the phosphate groups are stabilized by one or two hydrogen bonds and by Na[Formula: see text] counterions, forming ion-mediated contacts between phosphate groups and hydrogen peroxide molecules. The complex characterized by one H-bond between the hydrogen peroxide molecule and phosphate group is dominant, the other complexes are rare. The hydrogen peroxide molecule bound to the phosphate group of the double helix backbone can inhibit the formation of hydrogen bonds indispensable for the DNA biological functioning.
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12
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Orabi EA, English AM. Modeling Shows that Rotation about the Peroxide O-O Bond Assists Protein and Lipid Functional Groups in Discriminating between H 2O 2 and H 2O. J Phys Chem B 2020; 125:137-147. [PMID: 33356279 DOI: 10.1021/acs.jpcb.0c10326] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Long associated with cell death, hydrogen peroxide (H2O2) is now known to perform many physiological roles. Unraveling its biological mechanisms of action requires atomic-level knowledge of its association with proteins and lipids, which we address here. High-level [MP2(full)/6-311++G(3df,3pd)] ab initio calculations reveal skew rotamers as the lowest-energy states of isolated H2O2 (ϕHOOH ∼ 112°) with minimum and maximum electrostatic potentials (kcal/mol) of -24.8 (Vs,min) and 36.5 (Vs,max), respectively. Transition-state, nonpolar trans rotamers (ϕHOOH ∼ 180°) at 1.2 kcal/mol higher in energy are poorer H-bond acceptors (Vs,min = -16.6) than the skew rotamers, while highly polar cis rotamers (ϕHOOH ∼ 0°) at 7.8 kcal/mol are much better H-bond donors (Vs,max = 52.7). Modeling H2O2 association with neutral and charged analogs of protein residues and lipid groups (e.g., ester, phosphate, choline) reveals that skew rotamers (ϕHOOH = 84-122°) are favored in the neutral and cationic complexes, which display gas-phase interaction energies (ECP, kcal/mol) of -1.5 to -18. The neutral and cationic complexes of H2O exhibit a similar range of stabilities (ECP ∼ -1 to -18). However, considerably higher energies (ECP ∼ -14 to -36) are found for the H2O2 complexes of the anionic ligands, which are stabilized by charge-assisted H-bond donation from cis and distorted cis rotamers (ϕHOOH = 0-60°). H2O is a much poorer H-bond donor (Vs,max = 33.4) than cis-H2O2, so its anionic complexes are significantly weaker (ECP ∼ -11 to -20). Thus, by dictating the rotamer preference of H2O2, functional groups in biomolecules can discriminate between H2O2 and H2O. Finally, exploiting the present ab initio data, we calibrated and validated our published molecular mechanics model for H2O2 (Orabi, E. A.; English, A. M. J. Chem. Theory Comput. 2018, 14, 2808-2821) to provide an important tool for simulating H2O2 in biology.
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Affiliation(s)
- Esam A Orabi
- Department of Chemistry, Faculty of Science, Assiut University, Assiut 71516, Egypt.,Department of Chemistry and Biochemistry, Concordia University, 7141 Sherbrooke Street West, Montréal, Québec H4B 1R6, Canada
| | - Ann M English
- Department of Chemistry and Biochemistry, Concordia University, 7141 Sherbrooke Street West, Montréal, Québec H4B 1R6, Canada.,Center for Research in Molecular Modeling (CERMM) and Quebec Network for Research on Protein Function, Engineering, and Applications (PROTEO), Concordia University, Montreal, Quebec H4B 1R6, Canada
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13
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Orabi EA, Faraldo-Gómez JD. New Molecular-Mechanics Model for Simulations of Hydrogen Fluoride in Chemistry and Biology. J Chem Theory Comput 2020; 16:5105-5126. [PMID: 32615034 DOI: 10.1021/acs.jctc.0c00247] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Hydrogen fluoride (HF) is the most polar diatomic molecule and one of the simplest molecules capable of hydrogen-bonding. HF deviates from ideality both in the gas phase and in solution and is thus of great interest from a fundamental standpoint. Pure and aqueous HF solutions are broadly used in chemical and industrial processes, despite their high toxicity. HF is a stable species also in some biological conditions, because it does not readily dissociate in water unlike other hydrogen halides; yet, little is known about how HF interacts with biomolecules. Here, we set out to develop a molecular-mechanics model to enable computer simulations of HF in chemical and biological applications. This model is based on a comprehensive high-level ab initio quantum chemical investigation of the structure and energetics of the HF monomer and dimer; (HF)n clusters, for n = 3-7; various clusters of HF and H2O; and complexes of HF with analogs of all 20 amino acids and of several commonly occurring lipids, both neutral and ionized. This systematic analysis explains the unique properties of this molecule: for example, that interacting HF molecules favor nonlinear geometries despite being diatomic and that HF is a strong H-bond donor but a poor acceptor. The ab initio data also enables us to calibrate a three-site molecular-mechanics model, with which we investigate the structure and thermodynamic properties of gaseous, liquid, and supercritical HF in a wide range of temperatures and pressures; the solvation structure of HF in water and of H2O in liquid HF; and the free diffusion of HF across a lipid bilayer, a key process underlying the high cytotoxicity of HF. Despite its inherent simplifications, the model presented significantly improves upon previous efforts to capture the properties of pure and aqueous HF fluids by molecular-mechanics methods and to our knowledge constitutes the first parameter set calibrated for biomolecular simulations.
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Affiliation(s)
- Esam A Orabi
- Theoretical Molecular Biophysics Laboratory, National Heart, Lung and Blood Institute, National Institutes of Health, 10 Center Drive, Bethesda, Maryland 20814, United States
| | - José D Faraldo-Gómez
- Theoretical Molecular Biophysics Laboratory, National Heart, Lung and Blood Institute, National Institutes of Health, 10 Center Drive, Bethesda, Maryland 20814, United States
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14
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Orabi EA, Peslherbe GH. Computational insight into hydrogen persulfide and a new additive model for chemical and biological simulations. Phys Chem Chem Phys 2019; 21:15988-16004. [PMID: 31297500 DOI: 10.1039/c9cp02998b] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
S-Sulfhydration of cysteine to the Cys-SSH persulfide is an oxidative post-translational modification that plays an important regulatory role in many physiological systems. Though hydrogen persulfide (H2S2) has recently been established as a signaling and cellular sulfhydration reagent, the chemistry and chemical biology of persulfides remain poorly explored. We first report an extensive high-level ab initio quantum chemical investigation of (H2S2)n, (H2S2)m·H2O, and (H2O)m·H2S2 clusters (n = 1-3 and m = 1, 2) and of H2S2 complexes with 19 compounds that model the side chains of naturally-occurring amino acids. The high polarizability of S necessitates the use of large, very diffuse, basis sets for proper description of H2S2 and its complexes. H2S2 possesses a skewed equilibrium geometry, with nonpolar trans and more polar cis conformers 6 and 8 kcal mol-1 higher in energy, respectively; the skewed conformation is preserved in all neutral and cationic complexes while a cis geometry prevails in some anionic complexes. H2S2 is found to be a better H-bond donor and a poorer acceptor than H2S, and that in complexes with H2O, alcohols and amines, H2S2 is a better H-bond donor. Radical delocalization on both S atoms stabilizes the perthiyl (HSS˙) over the thiyl (HS˙) radical and results in a ∼20 kcal mol-1 lower S-H homolytic bond dissociation in H2S2, making it a potential antioxidant. A simple additive model is optimized for H2S2 and used together with the TIP3P model and the CHARMM36 all-atom force field (FF) to investigate the structure and thermodynamic properties of liquid H2S2 and the solubility of H2S2 in water, and to model H2S2-protein interactions (for which new FF parameters are further developed). Very weak H-bonding characterizes liquid H2S2 and it is found immiscible in liquid water with a trend in H-bonding strengths between H2S2 and H2O in the order O-HO ≫ S-HO > O-HS. This work does not only provide a thorough description of the structure and energetics of H2S2 and its various complexes, but also yields a reliable FF for investigating H2S2 in chemistry and biology.
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Affiliation(s)
- Esam A Orabi
- Centre for Research in Molecular Modeling and Department of Chemistry and Biochemistry, Concordia University, 7141 Sherbrooke Street West, Montréal, Québec H4B 1R6, Canada.
| | - Gilles H Peslherbe
- Centre for Research in Molecular Modeling and Department of Chemistry and Biochemistry, Concordia University, 7141 Sherbrooke Street West, Montréal, Québec H4B 1R6, Canada.
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