1
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Ho TH, Hien TD, Wilhelmsen Ø, Trinh TT. Thermophysical properties of polyethylene glycol oligomers via molecular dynamics simulations. RSC Adv 2024; 14:28125-28137. [PMID: 39228756 PMCID: PMC11369976 DOI: 10.1039/d4ra04898a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2024] [Accepted: 08/24/2024] [Indexed: 09/05/2024] Open
Abstract
Polyethylene glycol (PEG) is a versatile chemical with numerous applications in various fields, including biomedical research, pharmaceutical development, and industrial manufacturing. Molecular dynamics (MD) is a powerful tool for investigating the thermophysical properties of PEG molecules. In this study, we employ the General AMBER force field (GAFF) to perform MD simulations on various PEG oligomers, focusing on the calculation of density, self-diffusion coefficients, shear viscosity, and thermal conductivity. The results demonstrate excellent agreement with experimental data, where GAFF outperforms other force fields in reproducing thermophysical properties. For a PEG tetramer, the GAFF force field reproduces experimental data within 5% for the density, 5% for the diffusion coefficient, and 10% for the viscosity. In comparison, the OPLS force field displays significant deviations exceeding 80% for the diffusion coefficient and 400% for the viscosity. A detailed analysis of partial charge distributions and dihedral angles reveals that they significantly impact the structural behavior of PEG oligomers. The findings highlight the GAFF force field as one of the most accurate and reliable options for simulating systems with PEGs.
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Affiliation(s)
- Thi H Ho
- Laboratory for Computational Physics, Institute for Computational Science and Artificial Intelligence, Van Lang University Ho Chi Minh City Vietnam
- Faculty of Mechanical - Electrical and Computer Engineering, School of Technology, Van Lang University Ho Chi Minh City Vietnam
| | - Tong Duy Hien
- Faculty of Engineering, Vietnamese-German University (VGU) Thu Dau Mot City Binh Duong Province 75000 Vietnam
| | - Øivind Wilhelmsen
- Department of Chemistry, Porelab, Norwegian University of Science and Technology Trondheim Norway
| | - Thuat T Trinh
- Department of Chemistry, Porelab, Norwegian University of Science and Technology Trondheim Norway
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2
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Tang B, Bai Q, Fang YG, Francisco JS, Zhu C, Fang WH. Mechanistic Insights into N 2O 5-Halide Ions Chemistry at the Air-Water Interface. J Am Chem Soc 2024; 146:21742-21751. [PMID: 39074151 DOI: 10.1021/jacs.4c05850] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/31/2024]
Abstract
The activation of halogens (X = Cl, Br, I) by N2O5 is linked to NOx sources, ozone concentrations, NO3 reactivity, and the chemistry of halide-containing aerosol particles. However, a detailed chemical mechanism is still lacking. Herein, we explored the chemistry of the N2O5···X- systems at the air-water interface. Two different reaction pathways were identified for the reaction of N2O5 with X- at the air-water interface: the formation of XNO2 or XONO, along with NO3-. In the case of the Cl- system, the ClNO2 generation pathway is more favorable, while for the Br- and I- systems, the formation of BrONO and IONO is barrierless, making them the predominant products. Furthermore, the mechanisms of formation of X2 from XNO2 and XONO were also investigated. The high energy barriers of reactions and the high free energies of the products compared to those of the reactants indicate that ClNO2 is stable at the air-water interface. Contrary to the widely held belief regarding X2 producing from the reaction of XNO2 with X-, our calculations demonstrate that BrONO and IONO initially form stable BrONO···Br- and IONO···I- complexes, which then subsequently react with Br- and I- to form Br3- and I3-, respectively. Finally, Br3- and I3- decompose to form Br2 and I2. These findings have significant implications for experimental interpretation and offer new insights into halogen cycling in the atmosphere.
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Affiliation(s)
- Bo Tang
- Key Laboratory of Theoretical and Computational Photochemistry, Ministry of Education, College of Chemistry, Beijing Normal University, Beijing 100875, China
| | - Qi Bai
- Key Laboratory of Theoretical and Computational Photochemistry, Ministry of Education, College of Chemistry, Beijing Normal University, Beijing 100875, China
| | - Ye-Guang Fang
- Laboratory of Theoretical and Computational Nanoscience, CAS Key Laboratory of Nanosystem and Hierarchical Fabrication, CAS Center for Excellence in Nanoscience, National Center for Nanoscience and Technology, Beijing 100190, China
| | - Joseph S Francisco
- Department of Chemistry, University of Pennsylvania, Philadelphia, Pennsylvania 19104, United States
| | - Chongqin Zhu
- Key Laboratory of Theoretical and Computational Photochemistry, Ministry of Education, College of Chemistry, Beijing Normal University, Beijing 100875, China
| | - Wei-Hai Fang
- Key Laboratory of Theoretical and Computational Photochemistry, Ministry of Education, College of Chemistry, Beijing Normal University, Beijing 100875, China
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3
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Karwounopoulos J, Wu Z, Tkaczyk S, Wang S, Baskerville A, Ranasinghe K, Langer T, Wood GPF, Wieder M, Boresch S. Insights and Challenges in Correcting Force Field Based Solvation Free Energies Using a Neural Network Potential. J Phys Chem B 2024; 128:6693-6703. [PMID: 38976601 PMCID: PMC11264272 DOI: 10.1021/acs.jpcb.4c01417] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2024] [Revised: 05/31/2024] [Accepted: 06/14/2024] [Indexed: 07/10/2024]
Abstract
We present a comprehensive study investigating the potential gain in accuracy for calculating absolute solvation free energies (ASFE) using a neural network potential to describe the intramolecular energy of the solute. We calculated the ASFE for most compounds from the FreeSolv database using the Open Force Field (OpenFF) and compared them to earlier results obtained with the CHARMM General Force Field (CGenFF). By applying a nonequilibrium (NEQ) switching approach between the molecular mechanics (MM) description (either OpenFF or CGenFF) and the neural net potential (NNP)/MM level of theory (using ANI-2x as the NNP potential), we attempted to improve the accuracy of the calculated ASFEs. The predictive performance of the results did not change when this approach was applied to all 589 small molecules in the FreeSolv database that ANI-2x can describe. When selecting a subset of 156 molecules, focusing on compounds where the force fields performed poorly, we saw a slight improvement in the root-mean-square error (RMSE) and mean absolute error (MAE). The majority of our calculations utilized unidirectional NEQ protocols based on Jarzynski's equation. Additionally, we conducted bidirectional NEQ switching for a subset of 156 solutes. Notably, only a small fraction (10 out of 156) exhibited statistically significant discrepancies between unidirectional and bidirectional NEQ switching free energy estimates.
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Affiliation(s)
- Johannes Karwounopoulos
- Faculty
of Chemistry, Institute of Computational Biological Chemistry, University Vienna, Währingerstr. 17, 1090 Vienna, Austria
- Vienna
Doctoral School of Chemistry (DoSChem), University of Vienna, Währingerstr. 42, 1090 Vienna, Austria
| | - Zhiyi Wu
- Exscientia
plc, Schroedinger Building, Oxford OX4 4GE, United Kingdom
| | - Sara Tkaczyk
- Department
of Pharmaceutical Sciences, Pharmaceutical Chemistry Division, University of Vienna, Josef-Holaubek-Platz 2, 1090 Vienna, Austria
- Vienna
Doctoral School of Pharmaceutical, Nutritional and Sport Sciences
(PhaNuSpo),University of Vienna, Josef-Holaubek-Platz 2, 1090 Vienna, Austria
| | - Shuzhe Wang
- Exscientia
plc, Schroedinger Building, Oxford OX4 4GE, United Kingdom
| | - Adam Baskerville
- Exscientia
plc, Schroedinger Building, Oxford OX4 4GE, United Kingdom
| | | | - Thierry Langer
- Department
of Pharmaceutical Sciences, Pharmaceutical Chemistry Division, University of Vienna, Josef-Holaubek-Platz 2, 1090 Vienna, Austria
| | | | - Marcus Wieder
- Exscientia
plc, Schroedinger Building, Oxford OX4 4GE, United Kingdom
- Open
Molecular Software Foundation, Davis, California 95616, United States
| | - Stefan Boresch
- Faculty
of Chemistry, Institute of Computational Biological Chemistry, University Vienna, Währingerstr. 17, 1090 Vienna, Austria
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4
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Fang YG, Wei L, Francisco JS, Zhu C, Fang WH. Mechanistic Insights into Chloric Acid Production by Hydrolysis of Chlorine Trioxide at an Air-Water Interface. J Am Chem Soc 2024. [PMID: 39013148 DOI: 10.1021/jacs.4c06269] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/18/2024]
Abstract
Chlorine oxides play crucial roles in ozone depletion, and the final oxidation steps of chlorine oxide potentially result in the formation of chloric acid (HClO3) or perchloric acid (HClO4). Herein, the solvation and reactive uptake of three stable isomers of chlorine trioxide (Cl2O3), namely, ClOCl(O)O, ClClO3, and ClOOOCl, at the air-water interface were investigated using classical and hybrid quantum mechanics/molecular mechanics (QM/MM) molecular dynamics (MD) coupled with advanced free energy methods. Two distinct mechanisms were revealed for the hydrolysis of ClOCl(O)O and ClClO3: molecular and ionic mechanisms. A comparison of the computed free-energy profiles for the gaseous and air-water interfacial systems indicated that the air-water interface could markedly lower the free-energy barrier for ClO 3 - or HClO3 formation while stabilizing the product state. In particular, the hydrolysis of ClClO3 at the air-water interface was barrierless. In contrast, our calculations showed that the hydrolysis of ClOOOCl was very slow, indicating that ClOOOCl was inert to water at the air-water interface. This study provides theoretical evidence for the hypothesis that HClO3 is a sink for chlorine oxides and for the widespread distributions of HClO3 recently observed in the Arctic region.
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Affiliation(s)
- Ye-Guang Fang
- Key Laboratory of Theoretical and Computational Photochemistry, Ministry of Education, College of Chemistry, Beijing Normal University, Beijing 100875, PR China
- Laboratory of Theoretical and Computational Nanoscience, CAS Key Laboratory of Nanosystem and Hierarchical Fabrication, CAS Centre for Excellence in Nanoscience, National Centre for Nanoscience and Technology, Beijing 100190, PR China
| | - Laiyang Wei
- Key Laboratory of Theoretical and Computational Photochemistry, Ministry of Education, College of Chemistry, Beijing Normal University, Beijing 100875, PR China
| | - Joseph S Francisco
- Department of Chemistry, University of Pennsylvania, Philadelphia, Pennsylvania 19104, United States
| | - Chongqin Zhu
- Key Laboratory of Theoretical and Computational Photochemistry, Ministry of Education, College of Chemistry, Beijing Normal University, Beijing 100875, PR China
| | - Wei-Hai Fang
- Key Laboratory of Theoretical and Computational Photochemistry, Ministry of Education, College of Chemistry, Beijing Normal University, Beijing 100875, PR China
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5
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Beck PS, Leitão AG, Santana YB, Correa JR, Rodrigues CVS, Machado DFS, Matos GDR, Ramos LM, Gatto CC, Oliveira SCC, Andrade CKZ, Neto BAD. Revisiting Biginelli-like reactions: solvent effects, mechanisms, biological applications and correction of several literature reports. Org Biomol Chem 2024; 22:3630-3651. [PMID: 38652003 DOI: 10.1039/d4ob00272e] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/25/2024]
Abstract
This study critically reevaluates reported Biginelli-like reactions using a Kamlet-Abboud-Taft-based solvent effect model. Surprisingly, structural misassignments were discovered in certain multicomponent reactions, leading to the identification of pseudo three-component derivatives instead of the expected MCR adducts. Attempts to replicate literature conditions failed, prompting reconsideration of the described MCRs and proposed mechanisms. Electrospray ionization (tandem) mass spectrometry, NMR, melting points, elemental analyses and single-crystal X-ray analysis exposed inaccuracies in reported MCRs and allowed for the proposition of a complete catalytic cycle. Biological investigations using both pure and "contaminated" derivatives revealed distinctive features in assessed bioassays. A new cellular action mechanism was unveiled for a one obtained pseudo three-component adduct, suggesting similarity with the known dihydropyrimidinone Monastrol as Eg5 inhibitors, disrupting mitosis by forming monoastral mitotic spindles. Docking studies and RMSD analyses supported this hypothesis. The findings described herein underscore the necessity for a critical reexamination and potential corrections of structural assignments in several reports. This work emphasizes the significance of rigorous characterization and critical evaluation in synthetic chemistry, urging a careful reassessment of reported synthesis and biological activities associated with these compounds.
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Affiliation(s)
- Pedro S Beck
- University of Brasilia, Institute of Chemistry, Laboratory of Medicinal and Technological Chemistry. Campus Universitário Darcy Ribeiro, Brasília, DF, 70910-900, Brazil.
| | - Arthur G Leitão
- University of Brasilia, Institute of Chemistry, Laboratory of Medicinal and Technological Chemistry. Campus Universitário Darcy Ribeiro, Brasília, DF, 70910-900, Brazil.
| | - Yasmin B Santana
- University of Brasilia, Institute of Chemistry, Laboratory of Medicinal and Technological Chemistry. Campus Universitário Darcy Ribeiro, Brasília, DF, 70910-900, Brazil.
| | - José R Correa
- University of Brasilia, Institute of Chemistry, Laboratory of Medicinal and Technological Chemistry. Campus Universitário Darcy Ribeiro, Brasília, DF, 70910-900, Brazil.
| | - Carime V S Rodrigues
- University of Brasilia, Institute of Chemistry, Laboratory of Medicinal and Technological Chemistry. Campus Universitário Darcy Ribeiro, Brasília, DF, 70910-900, Brazil.
| | - Daniel F S Machado
- University of Brasilia, Institute of Chemistry, Laboratory of Medicinal and Technological Chemistry. Campus Universitário Darcy Ribeiro, Brasília, DF, 70910-900, Brazil.
| | - Guilherme D R Matos
- University of Brasilia, Institute of Chemistry, Laboratory of Medicinal and Technological Chemistry. Campus Universitário Darcy Ribeiro, Brasília, DF, 70910-900, Brazil.
| | - Luciana M Ramos
- Universidade Estadual de Goiás (UEG), Anápolis, Goiás, 75001-970, Brazil
| | - Claudia C Gatto
- University of Brasilia, Institute of Chemistry, Laboratory of Medicinal and Technological Chemistry. Campus Universitário Darcy Ribeiro, Brasília, DF, 70910-900, Brazil.
| | - Sarah C C Oliveira
- University of Brasilia, Institute of Biology, Laboratory of Allelopathy, Campus Universitário Darcy Ribeiro, Brasília, DF, 70910-900, Brazil
| | - Carlos K Z Andrade
- University of Brasilia, Institute of Chemistry, Laboratory of Medicinal and Technological Chemistry. Campus Universitário Darcy Ribeiro, Brasília, DF, 70910-900, Brazil.
| | - Brenno A D Neto
- University of Brasilia, Institute of Chemistry, Laboratory of Medicinal and Technological Chemistry. Campus Universitário Darcy Ribeiro, Brasília, DF, 70910-900, Brazil.
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6
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Haro Mares NB, Döller SC, Wissel T, Hoffmann M, Vogel M, Buntkowsky G. Structures and Dynamics of Complex Guest Molecules in Confinement, Revealed by Solid-State NMR, Molecular Dynamics, and Calorimetry. Molecules 2024; 29:1669. [PMID: 38611950 PMCID: PMC11013127 DOI: 10.3390/molecules29071669] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/29/2024] [Revised: 03/29/2024] [Accepted: 04/05/2024] [Indexed: 04/14/2024] Open
Abstract
This review gives an overview of current trends in the investigation of confined molecules such as water, small and higher alcohols, carbonic acids, ethylene glycol, and non-ionic surfactants, such as polyethylene glycol or Triton-X, as guest molecules in neat and functionalized mesoporous silica materials employing solid-state NMR spectroscopy, supported by calorimetry and molecular dynamics simulations. The combination of steric interactions, hydrogen bonds, and hydrophobic and hydrophilic interactions results in a fascinating phase behavior in the confinement. Combining solid-state NMR and relaxometry, DNP hyperpolarization, molecular dynamics simulations, and general physicochemical techniques, it is possible to monitor these confined molecules and gain deep insights into this phase behavior and the underlying molecular arrangements. In many cases, the competition between hydrogen bonding and electrostatic interactions between polar and non-polar moieties of the guests and the host leads to the formation of ordered structures, despite the cramped surroundings inside the pores.
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Affiliation(s)
- Nadia B. Haro Mares
- Eduard-Zintl-Institut für Anorganische und Physikalische Chemie, Technische Universität Darmstadt, Peter-Grünberg-Str. 8, D-64287 Darmstadt, Germany; (N.B.H.M.); (S.C.D.); (T.W.)
| | - Sonja C. Döller
- Eduard-Zintl-Institut für Anorganische und Physikalische Chemie, Technische Universität Darmstadt, Peter-Grünberg-Str. 8, D-64287 Darmstadt, Germany; (N.B.H.M.); (S.C.D.); (T.W.)
| | - Till Wissel
- Eduard-Zintl-Institut für Anorganische und Physikalische Chemie, Technische Universität Darmstadt, Peter-Grünberg-Str. 8, D-64287 Darmstadt, Germany; (N.B.H.M.); (S.C.D.); (T.W.)
| | - Markus Hoffmann
- Department of Chemistry and Biochemistry, State University of New York at Brockport, Brockport, NY 14420, USA
| | - Michael Vogel
- Institute for Condensed Matter Physics, Technische Universität Darmstadt, Hochschulstr. 6, D-64289 Darmstadt, Germany
| | - Gerd Buntkowsky
- Eduard-Zintl-Institut für Anorganische und Physikalische Chemie, Technische Universität Darmstadt, Peter-Grünberg-Str. 8, D-64287 Darmstadt, Germany; (N.B.H.M.); (S.C.D.); (T.W.)
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7
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Nkungli NK, Fouegue ADT, Tasheh SN, Bine FK, Hassan AU, Ghogomu JN. In silico investigation of falcipain-2 inhibition by hybrid benzimidazole-thiosemicarbazone antiplasmodial agents: A molecular docking, molecular dynamics simulation, and kinetics study. Mol Divers 2024; 28:475-496. [PMID: 36622482 PMCID: PMC9838286 DOI: 10.1007/s11030-022-10594-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2022] [Accepted: 12/20/2022] [Indexed: 01/10/2023]
Abstract
The emergence of artemisinin-resistant variants of Plasmodium falciparum necessitates the urgent search for novel antimalarial drugs. In this regard, an in silico study to screen antimalarial drug candidates from a series of benzimidazole-thiosemicarbazone hybrid molecules with interesting antiplasmodial properties and explore their falcipain-2 (FP2) inhibitory potentials has been undertaken herein. FP2 is a key cysteine protease that degrades hemoglobin in Plasmodium falciparum and is an important biomolecular target in the development of antimalarial drugs. Pharmacokinetic properties, ADMET profiles, MM/GBSA-based binding free energies, reaction mechanisms, and associated barrier heights have been investigated. DFT, molecular dynamics simulation, molecular docking, and ONIOM methods were used. From the results obtained, four 4N-substituted derivatives of the hybrid molecule (E)-2-(1-(5-chloro-1H-benzo[d]imidazol-2-yl)ethylidene)hydrazine-1-carbothioamide (1A) denoted 1B, 1C, 1D, and 1E are drug-like and promising inhibitors of FP2, exhibiting remarkably small inhibitory constants (5.94 × 10-14 - 2.59 × 10-04 n M) and favorable binding free energies (-30.32 to -17.17 kcal/mol). Moreover, the ONIOM results have revealed that 1B and possibly 1C and 1D may act as covalent inhibitors of FP2. The rate-determining step of the thermodynamically favorable covalent binding mechanism occurs across a surmountable barrier height of 24.18 kcal/mol in water and 28.42 kcal/mol in diethyl ether. Our findings are useful for further experimental investigations on the antimalarial activities of the hybrid molecules studied.
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Affiliation(s)
- Nyiang Kennet Nkungli
- Department of Chemistry, Faculty of Science, The University of Bamenda, Bambili, P. O. Box 39, Bamenda, Cameroon.
| | - Aymard Didier Tamafo Fouegue
- Department of Chemistry, Higher Teacher Training College Bertoua, University of Bertoua, P.O. Box 652, Bertoua, Cameroon
| | - Stanley Numbonui Tasheh
- Department of Chemistry, Faculty of Science, The University of Bamenda, Bambili, P. O. Box 39, Bamenda, Cameroon
- Department of Chemistry, Faculty of Science, University of Dschang, P. O. Box 67, Dschang, Cameroon
| | - Fritzgerald Kogge Bine
- Department of Chemistry, Faculty of Science, University of Dschang, P. O. Box 67, Dschang, Cameroon
| | - Abrar Ul Hassan
- Department of Chemistry, University of Gujrat, Gujrat, 54400, PK, Pakistan
| | - Julius Numbonui Ghogomu
- Department of Chemistry, Faculty of Science, The University of Bamenda, Bambili, P. O. Box 39, Bamenda, Cameroon
- Department of Chemistry, Faculty of Science, University of Dschang, P. O. Box 67, Dschang, Cameroon
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8
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Fang YG, Tang B, Yuan C, Wan Z, Zhao L, Zhu S, Francisco JS, Zhu C, Fang WH. Mechanistic insight into the competition between interfacial and bulk reactions in microdroplets through N 2O 5 ammonolysis and hydrolysis. Nat Commun 2024; 15:2347. [PMID: 38491022 PMCID: PMC10943240 DOI: 10.1038/s41467-024-46674-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2023] [Accepted: 02/28/2024] [Indexed: 03/18/2024] Open
Abstract
Reactive uptake of dinitrogen pentaoxide (N2O5) into aqueous aerosols is a major loss channel for NOx in the troposphere; however, a quantitative understanding of the uptake mechanism is lacking. Herein, a computational chemistry strategy is developed employing high-level quantum chemical methods; the method offers detailed molecular insight into the hydrolysis and ammonolysis mechanisms of N2O5 in microdroplets. Specifically, our calculations estimate the bulk and interfacial hydrolysis rates to be (2.3 ± 1.6) × 10-3 and (6.3 ± 4.2) × 10-7 ns-1, respectively, and ammonolysis competes with hydrolysis at NH3 concentrations above 1.9 × 10-4 mol L-1. The slow interfacial hydrolysis rate suggests that interfacial processes have negligible effect on the hydrolysis of N2O5 in liquid water. In contrast, N2O5 ammonolysis in liquid water is dominated by interfacial processes due to the high interfacial ammonolysis rate. Our findings and strategy are applicable to high-chemical complexity microdroplets.
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Affiliation(s)
- Ye-Guang Fang
- Key Laboratory of Theoretical and Computational Photochemistry, Ministry of Education, College of Chemistry, Beijing Normal University, Beijing, P. R. China
- Laboratory of Theoretical and Computational Nanoscience, CAS Key Laboratory of Nanosystem and Hierarchical Fabrication, CAS Centre for Excellence in Nanoscience, National Centre for Nanoscience and Technology, Beijing, P. R. China
| | - Bo Tang
- Key Laboratory of Theoretical and Computational Photochemistry, Ministry of Education, College of Chemistry, Beijing Normal University, Beijing, P. R. China
| | - Chang Yuan
- Key Laboratory of Theoretical and Computational Photochemistry, Ministry of Education, College of Chemistry, Beijing Normal University, Beijing, P. R. China
| | - Zhengyi Wan
- Department of Chemistry, University of Pennsylvania, Philadelphia, PA, USA
| | - Lei Zhao
- Key Laboratory of Theoretical and Computational Photochemistry, Ministry of Education, College of Chemistry, Beijing Normal University, Beijing, P. R. China
| | - Shuang Zhu
- Key Laboratory of Theoretical and Computational Photochemistry, Ministry of Education, College of Chemistry, Beijing Normal University, Beijing, P. R. China
| | - Joseph S Francisco
- Department of Chemistry, University of Pennsylvania, Philadelphia, PA, USA.
| | - Chongqin Zhu
- Key Laboratory of Theoretical and Computational Photochemistry, Ministry of Education, College of Chemistry, Beijing Normal University, Beijing, P. R. China.
| | - Wei-Hai Fang
- Key Laboratory of Theoretical and Computational Photochemistry, Ministry of Education, College of Chemistry, Beijing Normal University, Beijing, P. R. China
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9
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Rao Z, Fang YG, Pan Y, Yu W, Chen B, Francisco JS, Zhu C, Chu C. Accelerated Photolysis of H 2O 2 at the Air-Water Interface of a Microdroplet. J Am Chem Soc 2023. [PMID: 37914533 DOI: 10.1021/jacs.3c08101] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2023]
Abstract
Photochemical homolysis of hydrogen peroxide (H2O2) occurs widely in nature and is a key source of hydroxyl radicals (·OH). The kinetics of H2O2 photolysis play a pivotal role in determining the efficiency of ·OH production, which is currently mainly investigated in bulk systems. Here, we report considerably accelerated H2O2 photolysis at the air-water interface of microdroplets, with a rate 1.9 × 103 times faster than that in bulk water. Our simulations show that due to the trans quasiplanar conformational preference of H2O2 at the air-water interface compared to the bulk or gas phase, the absorption peak in the spectrum of H2O2 is significantly redshifted by 45 nm, corresponding to greater absorbance of photons in the sunlight spectrum and faster photolysis of H2O2. This discovery has great potential to solve current problems associated with ·OH-centered heterogeneous photochemical processes in aerosols. For instance, we show that accelerated H2O2 photolysis in microdroplets could lead to markedly enhanced oxidation of SO2 and volatile organic compounds.
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Affiliation(s)
- Zepeng Rao
- Department of Environmental Science, Zhejiang University, Hangzhou 310058, China
| | - Ye-Guang Fang
- College of Chemistry, Key Laboratory of Theoretical & Computational Photochemistry of Ministry of Education, Beijing Normal University, Beijing 100875 China
- Laboratory of Theoretical and Computational Nanoscience, CAS Key Laboratory of Nanosystem and Hierarchical Fabrication, CAS Center for Excellence in Nanoscience, National Center for Nanoscience and Technology, Beijing 100190 China
| | - Yishuai Pan
- Department of Environmental Science, Zhejiang University, Hangzhou 310058, China
| | - Wanchao Yu
- Department of Environmental Science, Zhejiang University, Hangzhou 310058, China
| | - Baoliang Chen
- Department of Environmental Science, Zhejiang University, Hangzhou 310058, China
| | - Joseph S Francisco
- Department of Earth and Environmental Science and Department of Chemistry, University of Pennsylvania, Philadelphia, Pennsylvania 19104, United States
| | - Chongqin Zhu
- College of Chemistry, Key Laboratory of Theoretical & Computational Photochemistry of Ministry of Education, Beijing Normal University, Beijing 100875 China
| | - Chiheng Chu
- Department of Environmental Science, Zhejiang University, Hangzhou 310058, China
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10
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Lundborg M, Lidmar J, Hess B. On the Path to Optimal Alchemistry. Protein J 2023; 42:477-489. [PMID: 37651042 PMCID: PMC10480267 DOI: 10.1007/s10930-023-10137-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/04/2023] [Indexed: 09/01/2023]
Abstract
Alchemical free energy calculations have become a standard and widely used tool, in particular for calculating and comparing binding affinities of drugs. Although methods to compute such free energies have improved significantly over the last decades, the choice of path between the end states of interest is usually still the same as two decades ago. We will show that there is a fundamentally arbitrary, implicit choice of parametrization of this path. To address this, the notion of the length of a path or a metric is required. A metric recently introduced in the context of the accelerated weight histogram method also proves to be very useful here. We demonstrate that this metric can not only improve the efficiency of sampling along a given path, but that it can also be used to improve the actual choice of path. For a set of relevant use cases, the combination of these improvements can increase the efficiency of alchemical free energy calculations by up to a factor 16.
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Affiliation(s)
| | - Jack Lidmar
- Department of Physics, KTH Royal Institute of Technology, 10691, Stockholm, Sweden
| | - Berk Hess
- Department of Applied Physics, KTH Royal Institute of Technology, 10691, Stockholm, Science for Life Laboratory, Solna, Sweden.
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11
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Rosalba TPF, Matos GDR, Salvador CEM, Andrade CKZ. Rational Design and Multicomponent Synthesis of Lipid-Peptoid Nanocomposites towards a Customized Drug Delivery System Assembly. Molecules 2023; 28:5725. [PMID: 37570698 PMCID: PMC10421149 DOI: 10.3390/molecules28155725] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2023] [Revised: 07/18/2023] [Accepted: 07/19/2023] [Indexed: 08/13/2023] Open
Abstract
Nanotechnology has assumed a significant role over the last decade in the development of various technologies applied to health sciences. This becomes even more evident with its application in controlled drug delivery systems. In this context, peptoids are a promising class of compounds for application as nanocarriers in drug delivery systems. These compounds can be obtained efficiently and with highly functionalized structural diversity via the Ugi 4-component reaction (U-4CR). Herein, we report the design of the process control strategy for the future development of lipid-peptoid-based customized drug delivery system assemblies. Over 20 lipid-peptoid nanocomposites were synthesized via the U-4CR in good to excellent yields. These products were successfully submitted to the nanoparticle formation by the emulsification-evaporation process from lipophilic solution and analyzed via Dynamic Light Scattering (DLS). Several molecules generated nanoparticles with a size ≤200 nm, making them good candidates for drug delivery systems, such as in cancer treatment.
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Affiliation(s)
- Thaissa Pasquali F. Rosalba
- Laboratório de Química Metodológica e Orgânica Sintética (LaQMOS), Instituto de Química, Universidade de Brasília, Campus Universitário Asa Norte, Brasilia 70904-970, Brazil
| | - Guilherme D. R. Matos
- Laboratório de Modelagem de Sistemas Complexos (LMSC), Instituto de Química, Universidade de Brasília, Campus Universitário Asa Norte, Brasilia 70904-970, Brazil
| | - Carlos Eduardo M. Salvador
- Laboratório de Química Metodológica e Orgânica Sintética (LaQMOS), Instituto de Química, Universidade de Brasília, Campus Universitário Asa Norte, Brasilia 70904-970, Brazil
| | - Carlos Kleber Z. Andrade
- Laboratório de Química Metodológica e Orgânica Sintética (LaQMOS), Instituto de Química, Universidade de Brasília, Campus Universitário Asa Norte, Brasilia 70904-970, Brazil
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12
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Rao Z, Li X, Fang YG, Francisco JS, Zhu C, Chu C. Spontaneous Oxidation of Thiols and Thioether at the Air-Water Interface of a Sea Spray Microdroplet. J Am Chem Soc 2023; 145:10839-10846. [PMID: 37133970 DOI: 10.1021/jacs.3c02334] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
The transport of dissolved organic sulfur, including thiols and thioethers, from the ocean surface to the atmosphere through sea spray aerosol (SSA) is of great importance for the global sulfur cycle. Thiol/thioether in SSA undergoes rapid oxidation that is historically linked to photochemical processes. Here, we report the discovery of a non-photochemical, spontaneous path of thiol/thioether oxidation in SSA. Among 10 investigated naturally abundant thiol/thioether, seven species displayed rapid oxidation in SSA, with disulfide, sulfoxide, and sulfone comprising the major products. We suggest that such spontaneous oxidation of thiol/thioether was mainly fueled by thiol/thioether enrichment at the air-water interface and generation of highly reactive radicals by the loss of an electron from ions (e.g., glutathionyl radical produced from ionization of deprotonated glutathione) at or near the surface of the water microdroplet. Our work sheds light on a ubiquitous but previously overlooked pathway of thiol/thioether oxidation, which could contribute to an accelerated sulfur cycle as well as related metal transformation (e.g., mercury) at ocean-atmosphere interfaces.
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Affiliation(s)
- Zepeng Rao
- Department of Environmental Science, Zhejiang University, Hangzhou 310058, China
| | - Xiaojiao Li
- College of Chemistry, Key Laboratory of Theoretical & Computational Photochemistry of Ministry of Education, Beijing Normal University, Beijing 100875, China
| | - Ye-Guang Fang
- Laboratory of Theoretical and Computational Nanoscience, CAS Key Laboratory of Nanosystem and Hierarchical Fabrication, CAS Center for Excellence in Nanoscience, National Center for Nanoscience and Technology, Beijing 100190, China
| | - Joseph S Francisco
- Department of Earth and Environmental Science and Department of Chemistry, University of Pennsylvania, Philadelphia, Pennsylvania 19104, United States
| | - Chongqin Zhu
- College of Chemistry, Key Laboratory of Theoretical & Computational Photochemistry of Ministry of Education, Beijing Normal University, Beijing 100875, China
| | - Chiheng Chu
- Department of Environmental Science, Zhejiang University, Hangzhou 310058, China
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13
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Jorge M, Barrera MC, Milne AW, Ringrose C, Cole DJ. What is the Optimal Dipole Moment for Nonpolarizable Models of Liquids? J Chem Theory Comput 2023; 19:1790-1804. [PMID: 36827585 PMCID: PMC10061682 DOI: 10.1021/acs.jctc.2c01123] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2022] [Indexed: 02/26/2023]
Abstract
In classical nonpolarizable models, electrostatic interactions are usually described by assigning fixed partial charges to interaction sites. Despite the multitude of methods and theories proposed over the years for partial charge assignment, a fundamental question remains─what is the correct degree of polarization that a fixed-charge model should possess to provide the best balance of interactions (including induction effects) and yield the best description of the potential energy surface of a liquid phase? We address this question by approaching it from two separate and independent viewpoints: the QUantum mechanical BEspoke (QUBE) approach, which assigns bespoke force field parameters for individual molecules from ab initio calculations with minimal empirical fitting, and the Polarization-Consistent Approach (PolCA) force field, based on empirical fitting of force field parameters with an emphasis on transferability by rigorously accounting for polarization effects in the parameterization process. We show that the two approaches yield consistent answers to the above question, namely, that the dipole moment of the model should be approximately halfway between those of the gas and the liquid phase. Crucially, however, the reference liquid-phase dipole needs to be estimated using methods that explicitly consider both mean-field and local contributions to polarization. In particular, continuum dielectric models are inadequate for this purpose because they cannot account for local effects and therefore significantly underestimate the degree of polarization of the molecule. These observations have profound consequences for the development, validation, and testing of nonpolarizable models.
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Affiliation(s)
- Miguel Jorge
- Department
of Chemical and Process Engineering, University
of Strathclyde, 75 Montrose Street, Glasgow G1 1XJ, United Kingdom
| | - Maria Cecilia Barrera
- Strathclyde
Institute of Pharmacy and Biomedical Sciences, University of Strathclyde, 161 Cathedral St, Glasgow G4 0RE, United Kingdom
| | - Andrew W. Milne
- Department
of Chemical and Process Engineering, University
of Strathclyde, 75 Montrose Street, Glasgow G1 1XJ, United Kingdom
| | - Chris Ringrose
- School
of Natural and Environmental Sciences, Newcastle
University, Newcastle
upon Tyne NE1 7RU, United Kingdom
| | - Daniel J. Cole
- School
of Natural and Environmental Sciences, Newcastle
University, Newcastle
upon Tyne NE1 7RU, United Kingdom
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14
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Hoffmann MM, Too MD, Paddock NA, Horstmann R, Kloth S, Vogel M, Buntkowsky G. On the Behavior of the Ethylene Glycol Components of Polydisperse Polyethylene Glycol PEG200. J Phys Chem B 2023; 127:1178-1196. [PMID: 36700884 PMCID: PMC9923754 DOI: 10.1021/acs.jpcb.2c06773] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
Molecular dynamics (MD) simulations are reported for [polyethylene glycol (PEG)200], a polydisperse mixture of ethylene glycol oligomers with an average molar weight of 200 g·mol-1. As a first step, available force fields for describing ethylene glycol oligomers were tested on how accurately they reproduced experimental properties. They were found to all fall short on either reproducing density, a static property, or the self-diffusion coefficient, a dynamic property. Discrepancies with the experimental data increased with the increasing size of the tested ethylene glycol oligomer. From the available force fields, the optimized potential for liquid simulation (OPLS) force field was used to further investigate which adjustments to the force field would improve the agreement of simulated physical properties with experimental ones. Two parameters were identified and adjusted, the (HO)-C-C-O proper dihedral potential and the polarity of the hydroxy group. The parameter adjustments depended on the size of the ethylene glycol oligomer. Next, PEG200 was simulated with the OPLS force field with and without modifications to inspect their effects on the simulation results. The modifications to the OPLS force field significantly decreased hydrogen bonding overall and increased the propensity of intramolecular hydrogen bond formation at the cost of intermolecular hydrogen bond formation. Moreover, some of the tri- and more so tetraethylene glycol formed intramolecular hydrogen bonds between the hydroxy end groups while still maintaining strong intramolecular interactions with the ether oxygen atoms. These observations allowed the interpretation of the obtained RDFs as well as structural properties such as the average end-to-end distances and the average radii of gyration. The MD simulations with and without the modifications showed no evidence of preferential association of like-oligomers to form clusters nor any evidence of long-range ordering such as a side-by-side stacking of ethylene glycol oligomers. Instead, the simulation results support the picture of PEG200 being a random mixture of its ethylene glycol oligomer components. Finally, additional MD simulations of a binary mixture of tri-and hexaethylene glycol with the same average molar weight as PEG200 revealed very similar structural and physical properties as for PEG200.
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Affiliation(s)
- Markus M. Hoffmann
- Department
of Chemistry and Biochemistry, State University
of New York College at Brockport, Brockport, New York14420, United States,. Phone: + 1(585) 395-5587. Fax: + 1(585) 395-5805
| | - Matthew D. Too
- Department
of Chemistry and Biochemistry, State University
of New York College at Brockport, Brockport, New York14420, United States
| | - Nathaniel A. Paddock
- Department
of Chemistry and Biochemistry, State University
of New York College at Brockport, Brockport, New York14420, United States
| | - Robin Horstmann
- Institute
of Condensed Matter Physics, Technical University
Darmstadt, Hochschulstraße
6, 64289Darmstadt, Germany
| | - Sebastian Kloth
- Institute
of Condensed Matter Physics, Technical University
Darmstadt, Hochschulstraße
6, 64289Darmstadt, Germany
| | - Michael Vogel
- Institute
of Condensed Matter Physics, Technical University
Darmstadt, Hochschulstraße
6, 64289Darmstadt, Germany
| | - Gerd Buntkowsky
- Institute
of Physical Chemistry, Technical University
Darmstadt, Alarich-Weiss-Straße
8, D-64287Darmstadt, Germany,. Phone: + 49 6151 16-21116. Fax: + 49 6151 16-21119
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15
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Wan Z, Fang Y, Liu Z, Francisco JS, Zhu C. Mechanistic Insights into the Reactive Uptake of Chlorine Nitrate at the Air-Water Interface. J Am Chem Soc 2023; 145:944-952. [PMID: 36595549 DOI: 10.1021/jacs.2c09837] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
It is well-known that the aqueous-phase processing of chlorine nitrate (ClONO2) plays a crucial role in ozone depletion. However, many of the physical and chemical properties of ClONO2 at the air-water interface or in bulk water are unknown or not understood on a microscopic scale. Here, the solvation and hydrolysis of ClONO2 at the air-water interface and in bulk water at 300 K were investigated by classical and ab initio molecular dynamics (AIMD) simulations combined with free energy methods. Our results revealed that ClONO2 prefers to accumulate at the air-water interface rather than in the bulk phase. Specifically, halogen bonding interactions (ClONO2)Cl···O(H2O) were found to be the predominant interactions between ClONO2 and H2O. Moreover, metadynamics-biased AIMD simulations revealed that ClONO2 hydrolysis is catalyzed at the air-water interface with an activation barrier of only ∼0.2 kcal/mol; additionally, the difference in free energy between the product and reactant is only ∼0.1 kcal/mol. Surprisingly, the near-barrierless reaction and the comparable free energies of the reactant and product suggested that the ClONO2 hydrolysis at the air-water interface is reversible. When the temperature is lowered from 300 to 200 K, the activation barrier for the ClONO2 hydrolysis at the air-water interface is increased to ∼5.4 kcal/mol. These findings have important implications for the interpretation of experiments.
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Affiliation(s)
- Zhengyi Wan
- Department of Chemistry, University of Pennsylvania, Philadelphia, Pennsylvania19104, United States
| | - Yeguang Fang
- College of Chemistry, Key Laboratory of Theoretical & Computational Photochemistry of Ministry of Education, Beijing Normal University, Beijing100190, People's Republic of China
| | - Ziao Liu
- Department of Chemistry, University of Pennsylvania, Philadelphia, Pennsylvania19104, United States
| | - Joseph S Francisco
- Department of Chemistry, University of Pennsylvania, Philadelphia, Pennsylvania19104, United States.,Department of Earth & Environmental Science, University of Pennsylvania, Philadelphia, Pennsylvania19104, United States
| | - Chongqin Zhu
- College of Chemistry, Key Laboratory of Theoretical & Computational Photochemistry of Ministry of Education, Beijing Normal University, Beijing100190, People's Republic of China
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16
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Yang H, Gladich I, Boucly A, Artiglia L, Ammann M. Orcinol and resorcinol induce local ordering of water molecules near the liquid-vapor interface. ENVIRONMENTAL SCIENCE: ATMOSPHERES 2022; 2:1277-1291. [PMID: 36561553 PMCID: PMC9648629 DOI: 10.1039/d2ea00015f] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/02/2022] [Accepted: 08/17/2022] [Indexed: 12/25/2022]
Abstract
Resorcinol and orcinol are simple members of the family of phenolic compounds present in particulate matter in the atmosphere; they are amphiphilic in nature and thus surface active in aqueous solution. Here, we used X-ray photoelectron spectroscopy to probe the concentration of resorcinol (benzene-1,3-diol) and orcinol (5-methylbenzene-1,3-diol) at the liquid-vapor interface of aqueous solutions. Qualitatively consistent surface propensity and preferential orientation was obtained by molecular dynamics simulations. Auger electron yield near-edge X-ray absorption fine structure (NEXAFS) spectroscopy was used to probe the hydrogen bonding (HB) structure, indicating that the local structure of water molecules near the surface of the resorcinol and orcinol solutions tends towards a larger fraction of tetrahedrally coordinated molecules than observed at the liquid-vapor interface of pure water. The order parameter obtained from the molecular dynamics simulations confirm these observations. This effect is being discussed in terms of the formation of an ordered structure of these molecules at the surface leading to patterns of hydrated OH groups with distances among them that are relatively close to those in ice. These results suggest that the self-assembly of phenolic species at the aqueous solution-air interface could induce freezing similar to the case of fatty alcohol monolayers and, thus, be of relevance for ice nucleation in the atmosphere. We also attempted at looking at the changes of the O 1b1, 3a2 and 1b2 molecular orbitals of liquid water, which are known to be sensitive to the HB structure as well, in response to the presence of resorcinol and orcinol. However, these changes remained negligible within uncertainty for both experimentally obtained valence spectra and theoretically calculated density of states.
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Affiliation(s)
- Huanyu Yang
- Laboratory of Environmental Chemistry, Paul Scherrer Institut5232 VilligenSwitzerland,Institute of Atmospheric and Climate Science, ETH Zürich8092 ZürichSwitzerland
| | - Ivan Gladich
- Qatar Environment & Energy Research Institute, Hamad Bin Khalifa UniversityP.O. Box 34110DohaQatar
| | - Anthony Boucly
- Laboratory of Environmental Chemistry, Paul Scherrer Institut5232 VilligenSwitzerland,Electrochemistry Laboratory, Paul Scherrer Institut5232 VilligenSwitzerland
| | - Luca Artiglia
- Laboratory of Environmental Chemistry, Paul Scherrer Institut5232 VilligenSwitzerland,Laboratory for Catalysis and Sustainable Chemistry, Paul Scherrer Institut5232 VilligenSwitzerland
| | - Markus Ammann
- Laboratory of Environmental Chemistry, Paul Scherrer Institut5232 VilligenSwitzerland
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17
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Oliveira MP, Gonçalves YMH, Ol Gheta SK, Rieder SR, Horta BAC, Hünenberger PH. Comparison of the United- and All-Atom Representations of (Halo)alkanes Based on Two Condensed-Phase Force Fields Optimized against the Same Experimental Data Set. J Chem Theory Comput 2022; 18:6757-6778. [PMID: 36190354 DOI: 10.1021/acs.jctc.2c00524] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The level of accuracy that can be achieved by a force field is influenced by choices made in the interaction-function representation and in the relevant simulation parameters. These choices, referred to here as functional-form variants (FFVs), include for example the model resolution, the charge-derivation procedure, the van der Waals combination rules, the cutoff distance, and the treatment of the long-range interactions. Ideally, assessing the effect of a given FFV on the intrinsic accuracy of the force-field representation requires that only the specific FFV is changed and that this change is performed at an optimal level of parametrization, a requirement that may prove extremely challenging to achieve in practice. Here, we present a first attempt at such a comparison for one specific FFV, namely the choice of a united-atom (UA) versus an all-atom (AA) resolution in a force field for saturated acyclic (halo)alkanes. Two force-field versions (UA vs AA) are optimized in an automated way using the CombiFF approach against 961 experimental values for the pure-liquid densities ρliq and vaporization enthalpies ΔHvap of 591 compounds. For the AA force field, the torsional and third-neighbor Lennard-Jones parameters are also refined based on quantum-mechanical rotational-energy profiles. The comparison between the UA and AA resolutions is also extended to properties that have not been included as parameterization targets, namely the surface-tension coefficient γ, the isothermal compressibility κT, the isobaric thermal-expansion coefficient αP, the isobaric heat capacity cP, the static relative dielectric permittivity ϵ, the self-diffusion coefficient D, the shear viscosity η, the hydration free energy ΔGwat, and the free energy of solvation ΔGche in cyclohexane. For the target properties ρliq and ΔHvap, the UA and AA resolutions reach very similar levels of accuracy after optimization. For the nine other properties, the AA representation leads to more accurate results in terms of η; comparably accurate results in terms of γ, κT, αP, ϵ, D, and ΔGche; and less accurate results in terms of cP and ΔGwat. This work also represents a first step toward the calibration of a GROMOS-compatible force field at the AA resolution.
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Affiliation(s)
- Marina P Oliveira
- Laboratorium für Physikalische Chemie, ETH Zürich, ETH-Hönggerberg, HCI, CH-8093 Zürich, Switzerland
| | - Yan M H Gonçalves
- Laboratorium für Physikalische Chemie, ETH Zürich, ETH-Hönggerberg, HCI, CH-8093 Zürich, Switzerland
| | - S Kashef Ol Gheta
- Laboratorium für Physikalische Chemie, ETH Zürich, ETH-Hönggerberg, HCI, CH-8093 Zürich, Switzerland
| | - Salomé R Rieder
- Laboratorium für Physikalische Chemie, ETH Zürich, ETH-Hönggerberg, HCI, CH-8093 Zürich, Switzerland
| | - Bruno A C Horta
- Laboratorium für Physikalische Chemie, ETH Zürich, ETH-Hönggerberg, HCI, CH-8093 Zürich, Switzerland
| | - Philippe H Hünenberger
- Laboratorium für Physikalische Chemie, ETH Zürich, ETH-Hönggerberg, HCI, CH-8093 Zürich, Switzerland
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18
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Abstract
Generalized force fields (FFs) act as extensions to biomolecular FFs to provide a wide coverage of organic molecules. However, their precise application to an arbitrary molecule presents a separate challenge. We show that MATCH assigns different atom types and bonded and nonbonded parameters than CGenFF, and the AM1-BCC charge model, commonly used with GAFF/GAFF2, does not exactly reproduce the performance of the RESP charge model. The results indicate the need for caution when employing FFs to ensure their integrity with respect to their implementation and validation.
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Affiliation(s)
- Asuka A. Orr
- Department of Pharmaceutical Sciences, University of Maryland, Baltimore, Maryland 21201, United States
| | - Suliman Sharif
- Department of Pharmaceutical Sciences, University of Maryland, Baltimore, Maryland 21201, United States
| | - Junmei Wang
- Department of Pharmaceutical Sciences and Computational Chemical Genomics Screening Center, University of Pittsburgh, Pittsburgh, Pennsylvania 15261, United States
| | - Alexander D. MacKerell
- Department of Pharmaceutical Sciences, University of Maryland, Baltimore, Maryland 21201, United States
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19
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Wang X, Liu S, Bao L, Zhang H, Yuan S, He M, Yuan S. Enhanced uptake of methacrolein at the acidic nanoparticle interface: Adsorption, heterogeneous reaction and impact for the secondary organic aerosol formation. THE SCIENCE OF THE TOTAL ENVIRONMENT 2021; 800:149532. [PMID: 34426310 DOI: 10.1016/j.scitotenv.2021.149532] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/23/2021] [Revised: 07/17/2021] [Accepted: 08/04/2021] [Indexed: 06/13/2023]
Abstract
Considering the moderate acidity of aerosols, the formation of secondary organic aerosols (SOA) through acid-catalyzed heterogeneous reactions has become a recent concern. However, the detailed information on the multiphase chemistry of organic compounds adsorbed onto acidic aerosols remains uncertain. In this work, we investigated the multiphase chemical processes between methacrolein (MACR) and sulfuric acid (SA) and their relationship with SOA formation. Results show that the aqueous nanoparticle interface, especially when it is an acidic nanoparticle interface, is a perfect area to adsorb and accommodate MACR. The occurrence percentage of MACR on the interface is more than 70%. With the increase of SA concentration, the first solvation shell changed from only water to the mixture of SA and water, which facilitates the heterogeneous hydration reaction of MACR. Compared with the neutral nanoparticle interface, the acidic nanoparticle interface exhibits a better ability to uptake and accommodate gaseous carbonyl species. Moreover, SA can catalyze the hydration reaction of MACR inside the aqueous media, and the resulting oligomers contribute to the formation and growth of SOA. The hydration reaction indirectly promotes the continuous adsorption of MACR at the acidic nanoparticle interface. The rate constant shows a positive altitude dependence, and acid-catalyzed reactions have an important impact on environmental chemistry, such as cloud SOA formation, within the range of about 2-6 km. This study reports a complete description of the heterogeneous interactions between unsaturated carbonyl species and acidic nanoparticles by using molecular dynamics and quantum chemistry methods, aiming to provide some insights for the further study on heterogeneous chemistry and its role in the formation of tropospheric SOA.
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Affiliation(s)
- Xueyu Wang
- Key Lab of Colloid and Interface Chemistry, Shandong University, Jinan 250100, China
| | - Shasha Liu
- School of Chemistry and Chemical Engineering, Qilu Normal University, Jinan 250100, China
| | - Lei Bao
- School of Chemical Sciences, University of the Chinese Academy of Sciences, Beijing 100049, China
| | - Heng Zhang
- Key Lab of Colloid and Interface Chemistry, Shandong University, Jinan 250100, China
| | - Shideng Yuan
- Key Lab of Colloid and Interface Chemistry, Shandong University, Jinan 250100, China
| | - Maoxia He
- Environment Research Institute, Shandong University, Qingdao 266237, China
| | - Shiling Yuan
- Key Lab of Colloid and Interface Chemistry, Shandong University, Jinan 250100, China.
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20
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Kong X, Castarède D, Thomson ES, Boucly A, Artiglia L, Ammann M, Gladich I, Pettersson JBC. A surface-promoted redox reaction occurs spontaneously on solvating inorganic aerosol surfaces. Science 2021; 374:747-752. [PMID: 34735230 DOI: 10.1126/science.abc5311] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
[Figure: see text].
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Affiliation(s)
- Xiangrui Kong
- Atmospheric Science Research Division, Department of Chemistry and Molecular Biology, University of Gothenburg, SE-41296 Gothenburg, Sweden
| | - Dimitri Castarède
- Atmospheric Science Research Division, Department of Chemistry and Molecular Biology, University of Gothenburg, SE-41296 Gothenburg, Sweden
| | - Erik S Thomson
- Atmospheric Science Research Division, Department of Chemistry and Molecular Biology, University of Gothenburg, SE-41296 Gothenburg, Sweden
| | - Anthony Boucly
- Laboratory of Environmental Chemistry, Paul Scherrer Institute, CH-5232 Villigen PSI, Switzerland
| | - Luca Artiglia
- Laboratory of Environmental Chemistry, Paul Scherrer Institute, CH-5232 Villigen PSI, Switzerland
| | - Markus Ammann
- Laboratory of Environmental Chemistry, Paul Scherrer Institute, CH-5232 Villigen PSI, Switzerland
| | - Ivan Gladich
- Qatar Environment and Energy Research Institute, Hamad Bin Khalifa University, P.O. Box 31110, Doha, Qatar
| | - Jan B C Pettersson
- Atmospheric Science Research Division, Department of Chemistry and Molecular Biology, University of Gothenburg, SE-41296 Gothenburg, Sweden
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21
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Kashefolgheta S, Wang S, Acree WE, Hünenberger PH. Evaluation of nine condensed-phase force fields of the GROMOS, CHARMM, OPLS, AMBER, and OpenFF families against experimental cross-solvation free energies. Phys Chem Chem Phys 2021; 23:13055-13074. [PMID: 34105547 PMCID: PMC8207520 DOI: 10.1039/d1cp00215e] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2021] [Accepted: 04/28/2021] [Indexed: 12/02/2022]
Abstract
Experimental solvation free energies are nowadays commonly included as target properties in the validation of condensed-phase force fields, sometimes even in their calibration. In a previous article [Kashefolgheta et al., J. Chem. Theory. Comput., 2020, 16, 7556-7580], we showed how the involved comparison between experimental and simulation results could be made more systematic by considering a full matrix of cross-solvation free energies . For a set of N molecules that are all in the liquid state under ambient conditions, such a matrix encompasses N×N entries for considering each of the N molecules either as solute (A) or as solvent (B). In the quoted study, a cross-solvation matrix of 25 × 25 experimental value was introduced, considering 25 small molecules representative for alkanes, chloroalkanes, ethers, ketones, esters, alcohols, amines, and amides. This experimental data was used to compare the relative accuracies of four popular condensed-phase force fields, namely GROMOS-2016H66, OPLS-AA, AMBER-GAFF, and CHARMM-CGenFF. In the present work, the comparison is extended to five additional force fields, namely GROMOS-54A7, GROMOS-ATB, OPLS-LBCC, AMBER-GAFF2, and OpenFF. Considering these nine force fields, the correlation coefficients between experimental values and simulation results range from 0.76 to 0.88, the root-mean-square errors (RMSEs) from 2.9 to 4.8 kJ mol-1, and average errors (AVEEs) from -1.5 to +1.0 kJ mol-1. In terms of RMSEs, GROMOS-2016H66 and OPLS-AA present the best accuracy (2.9 kJ mol-1), followed by OPLS-LBCC, AMBER-GAFF2, AMBER-GAFF, and OpenFF (3.3 to 3.6 kJ mol-1), and then by GROMOS-54A7, CHARM-CGenFF, and GROMOS-ATB (4.0 to 4.8 kJ mol-1). These differences are statistically significant but not very pronounced, and are distributed rather heterogeneously over the set of compounds within the different force fields.
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Affiliation(s)
- Sadra Kashefolgheta
- Laboratorium für Physikalische Chemie, ETH Zürich, ETH-Hönggerberg, HCICH-8093 ZürichSwitzerland+41 44 632 55 03
| | - Shuzhe Wang
- Laboratorium für Physikalische Chemie, ETH Zürich, ETH-Hönggerberg, HCICH-8093 ZürichSwitzerland+41 44 632 55 03
| | - William E. Acree
- Department of Chemistry, University of North Texas1155 Union Circle Drive #305070DentonTexas 76203USA
| | - Philippe H. Hünenberger
- Laboratorium für Physikalische Chemie, ETH Zürich, ETH-Hönggerberg, HCICH-8093 ZürichSwitzerland+41 44 632 55 03
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22
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Yin YY, Zhao J, Zhang LL, Xu XY, Liu JQ. Molecular mechanisms of inhibitor bindings to A-FABP deciphered by using molecular dynamics simulations and calculations of MM-GBSA. SAR AND QSAR IN ENVIRONMENTAL RESEARCH 2021; 32:293-315. [PMID: 33655818 DOI: 10.1080/1062936x.2021.1891966] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/10/2020] [Accepted: 02/15/2021] [Indexed: 06/12/2023]
Abstract
Adipocyte fatty-acid binding protein (A-FABP) plays a central role in many aspects of metabolic diseases. It is an important target in drug design for treatment of FABP-related diseases. In this study, molecular dynamics (MD) simulations followed by calculations of molecular mechanics generalized Born surface area (MM-GBSA) and principal components analysis (PCA) were implemented to decipher molecular mechanism correlating with binding of inhibitors 57Q, 57P and L96 to A-FABP. The results show that van der Waals interactions are the leading factors to control associations of 57Q, 57P, and L96 with A-FABP, which reveals an energetic basis for designing of clinically available inhibitors towards A-FABP. The information from PCA and cross-correlation analysis rationally unveils that inhibitor bindings affect conformational changes of A-FABP and change relative movements between residues. Decomposition of binding affinity into contributions of individual residues not only detects hot spots of inhibitor/A-FABP binding but also shows that polar interactions of the positively charged residue Arg126 with three inhibitors provide a significant contribution for stabilization of the inhibitor/A-FABP bindings. Furthermore, the binding strength of L96 to residues Ser55, Phe57 and Lys58 are stronger than that of inhibitors 57Q and 57P to these residues.
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Affiliation(s)
- Y Y Yin
- School of Science, Shandong Jiaotong University, Jinan, China
| | - J Zhao
- School of Science, Shandong Jiaotong University, Jinan, China
| | - L L Zhang
- School of Science, Shandong Jiaotong University, Jinan, China
| | - X Y Xu
- School of Science, Shandong Jiaotong University, Jinan, China
| | - J Q Liu
- School of Science, Shandong Jiaotong University, Jinan, China
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23
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Oliveira MP, Andrey M, Rieder SR, Kern L, Hahn DF, Riniker S, Horta BAC, Hünenberger PH. Systematic Optimization of a Fragment-Based Force Field against Experimental Pure-Liquid Properties Considering Large Compound Families: Application to Saturated Haloalkanes. J Chem Theory Comput 2020; 16:7525-7555. [DOI: 10.1021/acs.jctc.0c00683] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Affiliation(s)
- Marina P. Oliveira
- Laboratorium für Physikalische Chemie, ETH Zürich, ETH-Honggerberg, HCI, CH-8093 Zürich, Switzerland
| | - Maurice Andrey
- Laboratorium für Physikalische Chemie, ETH Zürich, ETH-Honggerberg, HCI, CH-8093 Zürich, Switzerland
| | - Salomé R. Rieder
- Laboratorium für Physikalische Chemie, ETH Zürich, ETH-Honggerberg, HCI, CH-8093 Zürich, Switzerland
| | - Leyla Kern
- Laboratorium für Physikalische Chemie, ETH Zürich, ETH-Honggerberg, HCI, CH-8093 Zürich, Switzerland
| | - David F. Hahn
- Laboratorium für Physikalische Chemie, ETH Zürich, ETH-Honggerberg, HCI, CH-8093 Zürich, Switzerland
| | - Sereina Riniker
- Laboratorium für Physikalische Chemie, ETH Zürich, ETH-Honggerberg, HCI, CH-8093 Zürich, Switzerland
| | - Bruno A. C. Horta
- Instituto de Química, Universidade Federal do Rio de Janeiro, Rio de Janeiro 21941-909, Brazil
| | - Philippe H. Hünenberger
- Laboratorium für Physikalische Chemie, ETH Zürich, ETH-Honggerberg, HCI, CH-8093 Zürich, Switzerland
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24
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Gladich I, Abotaleb A, Sinopoli A. Tuning CO 2 Capture at the Gas/Amine Solution Interface by Changing the Solvent Polarity. J Phys Chem B 2020; 124:10245-10256. [PMID: 33140965 DOI: 10.1021/acs.jpcb.0c06340] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Carbon dioxide scrubbing by aqueous amine solution is considered as a promising technology for post-combustion CO2 capture, while mitigating climate change. The lack of physicochemical details for this process, especially at the interface between the gas and the condensed phase, limits our capability in designing novel and more cost-effective scrubbing systems. Here, we present classical and first-principles molecular dynamics results on CO2 capture at the gas/amine solution interfaces using solvents of different polarities. Even if it is apolar, carbon dioxide is absorbed at the gas/monoethanolamine (MEA) aqueous solution interface, forming stable and interfacial [CO2·MEA] complexes, which are the first reaction intermediate toward the chemical conversion of CO2 to carbamate ions. We report that the stability of the interfacial [CO2·MEA] precomplex depends on the nature and polarity of the solution, as well as on the conformer population of MEA. By changing the polarity of the solvent, using chloroform, we observed a shift in the interfacial MEA population toward conformers that form more stable [CO2·MEA] complexes and, at the same time, a further stabilization of the complex induced by the solvent environment. Thus, while lowering the polarity of the solvent could decrease the solubility of MEA, at the same time, it favors conformers that are more prone to CO2 capture and mineralization. The results presented here offer a theoretical framework that helps in designing novel and more cost-effective solvents for CO2 scrubbing systems, while shedding further light on the intrinsic reaction mechanisms of interfacial environments in general.
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Affiliation(s)
- Ivan Gladich
- Qatar Environment and Energy Research Institute, Hamad Bin Khalifa University, P.O. Box 34110, Doha, Qatar
| | - Ahmed Abotaleb
- Qatar Environment and Energy Research Institute, Hamad Bin Khalifa University, P.O. Box 34110, Doha, Qatar
| | - Alessandro Sinopoli
- Qatar Environment and Energy Research Institute, Hamad Bin Khalifa University, P.O. Box 34110, Doha, Qatar
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25
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Kashefolgheta S, Oliveira MP, Rieder SR, Horta BAC, Acree WE, Hünenberger PH. Evaluating Classical Force Fields against Experimental Cross-Solvation Free Energies. J Chem Theory Comput 2020; 16:7556-7580. [DOI: 10.1021/acs.jctc.0c00688] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Affiliation(s)
- Sadra Kashefolgheta
- Laboratorium für Physikalische Chemie, ETH Zürich, ETH-Hönggerberg, HCI, CH-8093 Zürich, Switzerland
| | - Marina P. Oliveira
- Laboratorium für Physikalische Chemie, ETH Zürich, ETH-Hönggerberg, HCI, CH-8093 Zürich, Switzerland
| | - Salomé R. Rieder
- Laboratorium für Physikalische Chemie, ETH Zürich, ETH-Hönggerberg, HCI, CH-8093 Zürich, Switzerland
| | - Bruno A. C. Horta
- Instituto de Química, Universidade Federal do Rio de Janeiro, Rio de Janeiro 21941-909, Brazil
| | - William E. Acree
- Department of Chemistry, University of North Texas, 1155 Union Circle Drive #305070, Denton, Texas 76203, United States
| | - Philippe H. Hünenberger
- Laboratorium für Physikalische Chemie, ETH Zürich, ETH-Hönggerberg, HCI, CH-8093 Zürich, Switzerland
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26
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He X, Man VH, Yang W, Lee TS, Wang J. A fast and high-quality charge model for the next generation general AMBER force field. J Chem Phys 2020; 153:114502. [PMID: 32962378 DOI: 10.1063/5.0019056] [Citation(s) in RCA: 242] [Impact Index Per Article: 60.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
The General AMBER Force Field (GAFF) has been broadly used by researchers all over the world to perform in silico simulations and modelings on diverse scientific topics, especially in the field of computer-aided drug design whose primary task is to accurately predict the affinity and selectivity of receptor-ligand binding. The atomic partial charges in GAFF and the second generation of GAFF (GAFF2) were originally developed with the quantum mechanics derived restrained electrostatic potential charge, but in practice, users usually adopt an efficient charge method, Austin Model 1-bond charge corrections (AM1-BCC), based on which, without expensive ab initio calculations, the atomic charges could be efficiently and conveniently obtained with the ANTECHAMBER module implemented in the AMBER software package. In this work, we developed a new set of BCC parameters specifically for GAFF2 using 442 neutral organic solutes covering diverse functional groups in aqueous solution. Compared to the original BCC parameter set, the new parameter set significantly reduced the mean unsigned error (MUE) of hydration free energies from 1.03 kcal/mol to 0.37 kcal/mol. More excitingly, this new AM1-BCC model also showed excellent performance in the solvation free energy (SFE) calculation on diverse solutes in various organic solvents across a range of different dielectric constants. In this large-scale test with totally 895 neutral organic solvent-solute systems, the new parameter set led to accurate SFE predictions with the MUE and the root-mean-square-error of 0.51 kcal/mol and 0.65 kcal/mol, respectively. This newly developed charge model, ABCG2, paved a promising path for the next generation GAFF development.
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Affiliation(s)
- Xibing He
- Department of Pharmaceutical Sciences and Computational Chemical Genomics Screening Center, School of Pharmacy, University of Pittsburgh, Pittsburgh, Pennsylvania 15261, USA
| | - Viet H Man
- Department of Pharmaceutical Sciences and Computational Chemical Genomics Screening Center, School of Pharmacy, University of Pittsburgh, Pittsburgh, Pennsylvania 15261, USA
| | - Wei Yang
- Department of Chemistry and Biochemistry and Institute of Molecular Biophysics, Florida State University, Tallahassee, Florida 32306, USA
| | - Tai-Sung Lee
- Laboratory for Biomolecular Simulation Research, Center for Integrative Proteomics Research, and Department of Chemistry and Chemical Biology, Rutgers University, Piscataway, New Jersey 08854, USA
| | - Junmei Wang
- Department of Pharmaceutical Sciences and Computational Chemical Genomics Screening Center, School of Pharmacy, University of Pittsburgh, Pittsburgh, Pennsylvania 15261, USA
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27
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Zhu C, Zeng XC, Francisco JS, Gladich I. Hydration, Solvation, and Isomerization of Methylglyoxal at the Air/Water Interface: New Mechanistic Pathways. J Am Chem Soc 2020; 142:5574-5582. [PMID: 32091211 DOI: 10.1021/jacs.9b09870] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Aqueous-phase processing of methylglyoxal (MG) has been suggested to play a key role in the formation of secondary organic aerosols and catalyze particle growth in the atmosphere. However, the details of these processes remain speculative owing to the lack of a complete description of the physicochemical behavior of MG on atmospheric aerosols. Here, the solvation and hydrolysis of MG at the air/liquid water interface is studied via classical and first-principles molecular dynamics simulations combined with free-energy methods. Our results reveal that the polarity of the water solvent catalyzed the trans-to-cis isomerization of MG at the air/liquid water interface relative to the gas phase. Despite the presence of a hydrophobic group, MG often solvates with both the ketone and methyl groups parallel to the water interface. Analysis of the instantaneous water surface reveals that when MG is in the trans state, the methyl group repels interfacial water to maintain the planarity of the molecule, indicating that lateral and temporal inhomogeneities of interfacial environments are important for fully characterizing the solvation of MG. The counterintuitive behavior of the hydrophobic group is ascribed to a tendency to maximize the number of hydrogen bonds between MG and interfacial water while minimizing the torsional free energy. This drives MG hydration, and our simulations indicate that the formation of MG diol is catalyzed at the air/liquid water interface compared to the gas phase and occurs through nucleophilic attack of water on the carbonyl carbon.
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Affiliation(s)
- Chongqin Zhu
- Department of Chemistry, University of Nebraska-Lincoln, Lincoln, Nebraska 68588, United States.,Department of Earth and Environmental Science and Department of Chemistry, University of Pennsylvania, Philadelphia, Pennsylvania 19104, United States
| | - Xiao Cheng Zeng
- Department of Chemistry, University of Nebraska-Lincoln, Lincoln, Nebraska 68588, United States
| | - Joseph S Francisco
- Department of Chemistry, University of Nebraska-Lincoln, Lincoln, Nebraska 68588, United States.,Department of Earth and Environmental Science and Department of Chemistry, University of Pennsylvania, Philadelphia, Pennsylvania 19104, United States
| | - Ivan Gladich
- Qatar Environment and Energy Research Institute, Hamad Bin Khalifa University, P.O. Box 5825, Doha, Qatar.,European Centre for Living Technology (ECLT), Ca' Bottacin, Dorsoduro 3911, Calle Crosera, 30124 Venice, Italy
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28
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Applicability of a thermodynamic cycle approach for a force field parametrization targeting non-aqueous solvation free energies. J Comput Aided Mol Des 2019; 34:71-82. [PMID: 31781991 DOI: 10.1007/s10822-019-00261-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2019] [Accepted: 11/21/2019] [Indexed: 10/25/2022]
Abstract
Accurate solvation free energy ΔGsolv predictions require well parametrized force fields. In order to refit Lennard-Jones (LJ) parameters for improved ΔGsolv predictions for a variety of compound classes and chemical environments, a large number of ΔGsolv calculations is required. As the calculation of ΔGsolv is computational expensive, there is need for efficient but precise calculation methods. In this work, we focus on the computation of non-aqueous solvation free energies. We compare ΔGsolv results from highly precise reference simulations for transferring a solute from the vacuum into a condensed phase and results obtained from a thermodynamic cycle implementation. As test systems, we alter LJ parameters ε and σ of widely used GAFF atom types ca, cl, n1, oh and os in various solute/solvent combinations. We examine the degree of configurational space overlap and find an impact by hydrogen bonds and the solvent accessible surface area. We conclude that the application of a thermodynamic cycle for the parametrization of force fields targeting ΔGsolv is useful if the adaptation of LJ parameters is limited to atom types in the solute or if only ε is changed.
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29
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Bhadra P, Siu SWI. Refined Empirical Force Field to Model Protein-Self-Assembled Monolayer Interactions Based on AMBER14 and GAFF. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2019; 35:9622-9633. [PMID: 31246036 DOI: 10.1021/acs.langmuir.9b01367] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Understanding protein interaction with material surfaces is important for the development of nanotechnological devices. The structures and dynamics of proteins can be studied via molecular dynamics (MD) if the protein-surface interactions can be accurately modeled. To answer this question, we computed the adsorption free energies of peptides (representing eleven different amino acids) on a hydrophobic self-assembled monolayer (CH3-SAM) and compared them to the benchmark experimental data set. Our result revealed that existing biomolecular force fields, GAFF and AMBER ff14sb, cannot reproduce the experimental peptide adsorption free energies by Wei and Latour (Langmuir, 2009, 25, 5637-5646). To obtain the improved force fields, we systematically tuned the Lennard-Jones parameters of selected amino acid sidechains and the functional group of SAM with repeated metadynamics and umbrella sampling simulations. The final parameter set has yielded a significant improvement in the free energy values with R = 0.83 and MSE = 0.65 kcal/mol. We applied the refined force field to predict the initial adsorption orientation of lysozyme on CH3-SAM. Two major orientations-face-down and face-up-were predicted. Our analysis on the protein structure, solvent accessible surface area, and binding of native ligand NAG3 suggested that lysozyme in the face-up orientation can remain active after initial adsorption. However, because of its weaker affinity (ΔΔG = 7.86 kcal/mol) for the ligand, the bioactivity of the protein is expected to reduce. Our work facilitates the use of MD for the study of protein-SAM systems. The refined force field compatible with GROMACS is available at https://cbbio.cis.um.edu.mo/software/SAMFF .
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Affiliation(s)
- Pratiti Bhadra
- Department of Computer and Information Science , University of Macau , Avenida da Universidade , Taipa , Macau
| | - Shirley W I Siu
- Department of Computer and Information Science , University of Macau , Avenida da Universidade , Taipa , Macau
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30
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Hahn DF, Milić JV, Hünenberger PH. Vase
‐
Kite
Equilibrium of Resorcin[4]arene Cavitands Investigated Using Molecular Dynamics Simulations with Ball‐and‐Stick Local Elevation Umbrella Sampling. Helv Chim Acta 2019. [DOI: 10.1002/hlca.201900060] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- David F. Hahn
- Laboratory of Physical Chemistry, Department of Chemistry and Applied BiosciencesETH Zürich Vladimir-Prelog-Weg 2 CH-8093 Zürich Switzerland
| | - Jovana V. Milić
- Laboratory of Photonics and InterfacesÉcole Polytechnique Fédérale de Lausanne, EPFL SB ISIC LPI, Station 6 CH-1015 Lausanne Switzerland
| | - Philippe H. Hünenberger
- Laboratory of Physical Chemistry, Department of Chemistry and Applied BiosciencesETH Zürich Vladimir-Prelog-Weg 2 CH-8093 Zürich Switzerland
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31
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Gonçalves YMH, Senac C, Fuchs PFJ, Hünenberger PH, Horta BAC. Influence of the Treatment of Nonbonded Interactions on the Thermodynamic and Transport Properties of Pure Liquids Calculated Using the 2016H66 Force Field. J Chem Theory Comput 2019; 15:1806-1826. [DOI: 10.1021/acs.jctc.8b00425] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Affiliation(s)
- Yan M. H. Gonçalves
- Instituto de Química, Universidade Federal do Rio de Janeiro, Rio de Janeiro 21941-909, Brazil
| | - Caroline Senac
- Sorbonne
Université,
CNRS, INSERM, Laboratoire d’Imagerie Biomédicale (LIB), F-75006 Paris, France
| | - Patrick F. J. Fuchs
- Sorbonne Université,
École normale supérieure, PSL University, CNRS, Laboratoire
des biomolécules, LBM, 75005 Paris, France
- Université
Paris Diderot, 75013 Paris, France
| | | | - Bruno A. C. Horta
- Instituto de Química, Universidade Federal do Rio de Janeiro, Rio de Janeiro 21941-909, Brazil
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32
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Glova AD, Volgin IV, Nazarychev VM, Larin SV, Lyulin SV, Gurtovenko AA. Toward realistic computer modeling of paraffin-based composite materials: critical assessment of atomic-scale models of paraffins. RSC Adv 2019; 9:38834-38847. [PMID: 35540183 PMCID: PMC9076000 DOI: 10.1039/c9ra07325f] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2019] [Revised: 08/24/2020] [Accepted: 11/19/2019] [Indexed: 11/30/2022] Open
Abstract
Paraffin-based composites represent a promising class of materials with numerous practical applications such as e.g. heat storage. Computer modeling of these complex multicomponent systems requires a proper theoretical description of both the n-alkane matrix and the non-alkane filler molecules. The latter can be modeled with the use of a state-of-the-art general-purpose force field such as GAFF, CHARMM, OPLS-AA and GROMOS, while the paraffin matrix is traditionally described in the frame of relatively old, alkane-specific force fields (TraPPE, NERD, and PYS). In this paper we link these two types of models and evaluate the performance of several general-purpose force fields in computer modeling of paraffin by their systematic comparison with earlier alkane-specific models as well as with experimental data. To this end, we have performed molecular dynamics simulations of n-eicosane bulk samples with the use of 10 different force fields: TraPPE, NERD, PYS, OPLS-UA, GROMOS, GAFF, GAFF2, OPLS-AA, L-OPLS-AA, and CHARMM36. For each force field we calculated several thermal, structural and dynamic characteristics of n-eicosane over a wide temperature range. Overall, our findings show that the general-purpose force fields such as CHARMM36, L-OPLS-AA and GAFF/GAFF2 are able to provide a realistic description of n-eicosane samples. While alkane-specific models outperform most general-purpose force fields as far as the temperature dependence of mass density, the coefficient of volumetric thermal expansion in the liquid state, and the crystallization temperature are concerned, L-OPLS-AA, CHARMM36 and GAFF2 force fields provide a better match with experiment for the shear viscosity and the diffusion coefficient in melt. Furthermore, we show that most general-purpose force fields are able to reproduce qualitatively the experimental triclinic crystal structure of n-eicosane at low temperatures. Atomic-scale computational models of paraffins are critically assessed and compared.![]()
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Affiliation(s)
- Artyom D. Glova
- Institute of Macromolecular Compounds
- Russian Academy of Sciences
- St. Petersburg
- Russia
| | - Igor V. Volgin
- Institute of Macromolecular Compounds
- Russian Academy of Sciences
- St. Petersburg
- Russia
| | - Victor M. Nazarychev
- Institute of Macromolecular Compounds
- Russian Academy of Sciences
- St. Petersburg
- Russia
| | - Sergey V. Larin
- Institute of Macromolecular Compounds
- Russian Academy of Sciences
- St. Petersburg
- Russia
| | - Sergey V. Lyulin
- Institute of Macromolecular Compounds
- Russian Academy of Sciences
- St. Petersburg
- Russia
- Faculty of Physics
| | - Andrey A. Gurtovenko
- Institute of Macromolecular Compounds
- Russian Academy of Sciences
- St. Petersburg
- Russia
- Faculty of Physics
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33
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Hagler AT. Force field development phase II: Relaxation of physics-based criteria… or inclusion of more rigorous physics into the representation of molecular energetics. J Comput Aided Mol Des 2018; 33:205-264. [DOI: 10.1007/s10822-018-0134-x] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2018] [Accepted: 07/18/2018] [Indexed: 01/04/2023]
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34
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Zhong J, Carignano MA, Kais S, Zeng XC, Francisco JS, Gladich I. Tuning the Stereoselectivity and Solvation Selectivity at Interfacial and Bulk Environments by Changing Solvent Polarity: Isomerization of Glyoxal in Different Solvent Environments. J Am Chem Soc 2018; 140:5535-5543. [DOI: 10.1021/jacs.8b01503] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Jie Zhong
- Department of Chemistry, University of Nebraska—Lincoln, Lincoln, Nebraska 68588, United States
| | - Marcelo A. Carignano
- Qatar Environment and Energy Research Institute, Hamad Bin Khalifa University, P.O. Box 31110, Doha, Qatar
| | - Sabre Kais
- Department of Chemistry, Department of Physics and Birck Nanotechnology Center, Purdue University, West Lafayette, Indiana 47907, United States
| | - Xiao Cheng Zeng
- Department of Chemistry, University of Nebraska—Lincoln, Lincoln, Nebraska 68588, United States
| | - Joseph S. Francisco
- Department of Chemistry, University of Nebraska—Lincoln, Lincoln, Nebraska 68588, United States
| | - Ivan Gladich
- Qatar Environment and Energy Research Institute, Hamad Bin Khalifa University, P.O. Box 31110, Doha, Qatar
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35
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Chandramouli B, Del Galdo S, Mancini G, Tasinato N, Barone V. Tailor-made computational protocols for precise characterization of small biological building blocks using QM and MM approaches. Biopolymers 2018. [DOI: 10.1002/bip.23109] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Affiliation(s)
- Balasubramanian Chandramouli
- Scuola Normale Superiore, Piazza dei Cavalieri 7; Pisa 56126 Italy
- Compunet, Istituto Italiano di Tecnologia, via Morego 30; Genova Italy
| | - Sara Del Galdo
- Scuola Normale Superiore, Piazza dei Cavalieri 7; Pisa 56126 Italy
| | - Giordano Mancini
- Scuola Normale Superiore, Piazza dei Cavalieri 7; Pisa 56126 Italy
- Istituto Nazionale di Fisica Nucleare (INFN) sezione di Pisa, Largo Bruno Pontecorvo 3; Pisa 56127 Italy
| | - Nicola Tasinato
- Scuola Normale Superiore, Piazza dei Cavalieri 7; Pisa 56126 Italy
| | - Vincenzo Barone
- Scuola Normale Superiore, Piazza dei Cavalieri 7; Pisa 56126 Italy
- Istituto Nazionale di Fisica Nucleare (INFN) sezione di Pisa, Largo Bruno Pontecorvo 3; Pisa 56127 Italy
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36
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Matos GDR, Kyu DY, Loeffler HH, Chodera JD, Shirts MR, Mobley DL. Approaches for calculating solvation free energies and enthalpies demonstrated with an update of the FreeSolv database. JOURNAL OF CHEMICAL AND ENGINEERING DATA 2017; 62:1559-1569. [PMID: 29056756 PMCID: PMC5648357 DOI: 10.1021/acs.jced.7b00104] [Citation(s) in RCA: 129] [Impact Index Per Article: 18.4] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/27/2023]
Abstract
Solvation free energies can now be calculated precisely from molecular simulations, providing a valuable test of the energy functions underlying these simulations. Here, we briefly review "alchemical" approaches for calculating the solvation free energies of small, neutral organic molecules from molecular simulations, and illustrate by applying them to calculate aqueous solvation free energies (hydration free energies). These approaches use a non-physical pathway to compute free energy differences from a simulation or set of simulations and appear to be a particularly robust and general-purpose approach for this task. We also present an update (version 0.5) to our FreeSolv database of experimental and calculated hydration free energies of neutral compounds and provide input files in formats for several simulation packages. This revision to FreeSolv provides calculated values generated with a single protocol and software version, rather than the heterogeneous protocols used in the prior version of the database. We also further update the database to provide calculated enthalpies and entropies of hydration and some experimental enthalpies and entropies, as well as electrostatic and nonpolar components of solvation free energies.
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Affiliation(s)
- Guilherme Duarte Ramos Matos
- Department of Chemistry, University of California, Irvine, Department of Pharmaceutical Sciences, University of California, Irvine, Scientific Computing Department, STFC, UK, Computational and Systems Biology Program, Sloan Kettering Institute, Department of Chemical and Biological Engineering, University of Colorado Boulder, Boulder, and Departments of Pharmaceutical Sciences and Chemistry, University of California, Irvine
| | - Daisy Y Kyu
- Department of Chemistry, University of California, Irvine, Department of Pharmaceutical Sciences, University of California, Irvine, Scientific Computing Department, STFC, UK, Computational and Systems Biology Program, Sloan Kettering Institute, Department of Chemical and Biological Engineering, University of Colorado Boulder, Boulder, and Departments of Pharmaceutical Sciences and Chemistry, University of California, Irvine
| | - Hannes H Loeffler
- Department of Chemistry, University of California, Irvine, Department of Pharmaceutical Sciences, University of California, Irvine, Scientific Computing Department, STFC, UK, Computational and Systems Biology Program, Sloan Kettering Institute, Department of Chemical and Biological Engineering, University of Colorado Boulder, Boulder, and Departments of Pharmaceutical Sciences and Chemistry, University of California, Irvine
| | - John D Chodera
- Department of Chemistry, University of California, Irvine, Department of Pharmaceutical Sciences, University of California, Irvine, Scientific Computing Department, STFC, UK, Computational and Systems Biology Program, Sloan Kettering Institute, Department of Chemical and Biological Engineering, University of Colorado Boulder, Boulder, and Departments of Pharmaceutical Sciences and Chemistry, University of California, Irvine
| | - Michael R Shirts
- Department of Chemistry, University of California, Irvine, Department of Pharmaceutical Sciences, University of California, Irvine, Scientific Computing Department, STFC, UK, Computational and Systems Biology Program, Sloan Kettering Institute, Department of Chemical and Biological Engineering, University of Colorado Boulder, Boulder, and Departments of Pharmaceutical Sciences and Chemistry, University of California, Irvine
| | - David L Mobley
- Department of Chemistry, University of California, Irvine, Department of Pharmaceutical Sciences, University of California, Irvine, Scientific Computing Department, STFC, UK, Computational and Systems Biology Program, Sloan Kettering Institute, Department of Chemical and Biological Engineering, University of Colorado Boulder, Boulder, and Departments of Pharmaceutical Sciences and Chemistry, University of California, Irvine
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37
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Deepak V, Wang B, Koot D, Kasonga A, Stander XX, Coetzee M, Stander A. In silico design and bioevaluation of selective benzotriazepine BRD4 inhibitors with potent antiosteoclastogenic activity. Chem Biol Drug Des 2017; 90:97-111. [DOI: 10.1111/cbdd.12930] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2016] [Revised: 11/16/2016] [Accepted: 12/01/2016] [Indexed: 01/05/2023]
Affiliation(s)
- Vishwa Deepak
- Department of Physiology; Faculty of Health Sciences; University of Pretoria; Pretoria South Africa
| | | | - Dwayne Koot
- Department of Chemistry; Faculty of Natural and Agricultural Sciences; University of Pretoria; Pretoria South Africa
| | - Abe Kasonga
- Department of Physiology; Faculty of Health Sciences; University of Pretoria; Pretoria South Africa
| | - Xiao Xing Stander
- Department of General Surgery; Faculty of Health Sciences; University of Pretoria; Pretoria South Africa
| | - Magdalena Coetzee
- Department of Physiology; Faculty of Health Sciences; University of Pretoria; Pretoria South Africa
- Institute for Food; Nutrition and Well-being; University of Pretoria; Pretoria South Africa
| | - Andre Stander
- Department of Physiology; Faculty of Health Sciences; University of Pretoria; Pretoria South Africa
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38
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Mohamed NA, Bradshaw RT, Essex JW. Evaluation of solvation free energies for small molecules with the AMOEBA polarizable force field. J Comput Chem 2016; 37:2749-2758. [PMID: 27757978 PMCID: PMC5111595 DOI: 10.1002/jcc.24500] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2016] [Revised: 09/05/2016] [Accepted: 09/07/2016] [Indexed: 01/24/2023]
Abstract
The effects of electronic polarization in biomolecular interactions will differ depending on the local dielectric constant of the environment, such as in solvent, DNA, proteins, and membranes. Here the performance of the AMOEBA polarizable force field is evaluated under nonaqueous conditions by calculating the solvation free energies of small molecules in four common organic solvents. Results are compared with experimental data and equivalent simulations performed with the GAFF pairwise-additive force field. Although AMOEBA results give mean errors close to "chemical accuracy," GAFF performs surprisingly well, with statistically significantly more accurate results than AMOEBA in some solvents. However, for both models, free energies calculated in chloroform show worst agreement to experiment and individual solutes are consistently poor performers, suggesting non-potential-specific errors also contribute to inaccuracy. Scope for the improvement of both potentials remains limited by the lack of high quality experimental data across multiple solvents, particularly those of high dielectric constant. © 2016 The Authors. Journal of Computational Chemistry Published by Wiley Periodicals, Inc.
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Affiliation(s)
- Noor Asidah Mohamed
- Computational Systems Chemistry, School of ChemistryUniversity of SouthamptonHighfieldSouthamptonSO17 1BJUK
| | - Richard T. Bradshaw
- Computational Systems Chemistry, School of ChemistryUniversity of SouthamptonHighfieldSouthamptonSO17 1BJUK
| | - Jonathan W. Essex
- Computational Systems Chemistry, School of ChemistryUniversity of SouthamptonHighfieldSouthamptonSO17 1BJUK
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39
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Horta BAC, Merz PT, Fuchs PFJ, Dolenc J, Riniker S, Hünenberger PH. A GROMOS-Compatible Force Field for Small Organic Molecules in the Condensed Phase: The 2016H66 Parameter Set. J Chem Theory Comput 2016; 12:3825-50. [DOI: 10.1021/acs.jctc.6b00187] [Citation(s) in RCA: 88] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Bruno A. C. Horta
- Laboratory
of Physical Chemistry, ETH Zürich, CH-8093 Zürich, Switzerland
- Instituto de Química, Universidade Federal do Rio de Janeiro, Rio de Janeiro 21941-909, Brazil
| | - Pascal T. Merz
- Laboratory
of Physical Chemistry, ETH Zürich, CH-8093 Zürich, Switzerland
| | - Patrick F. J. Fuchs
- Institut Jacques Monod, UMR 7592 CNRS, Université Paris-Diderot, Sorbonne Paris Cité, F-75205 Paris, France
| | - Jozica Dolenc
- Laboratory
of Physical Chemistry, ETH Zürich, CH-8093 Zürich, Switzerland
- Chemistry,
Biology and Pharmacy Information Center, ETH Zürich, CH-8093 Zürich, Switzerland
| | - Sereina Riniker
- Laboratory
of Physical Chemistry, ETH Zürich, CH-8093 Zürich, Switzerland
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40
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Liu S, Cao S, Hoang K, Young KL, Paluch AS, Mobley DL. Using MD Simulations To Calculate How Solvents Modulate Solubility. J Chem Theory Comput 2016; 12:1930-41. [PMID: 26878198 DOI: 10.1021/acs.jctc.5b00934] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Here, our interest is in predicting solubility in general, and we focus particularly on predicting how the solubility of particular solutes is modulated by the solvent environment. Solubility in general is extremely important, both for theoretical reasons - it provides an important probe of the balance between solute-solute and solute-solvent interactions - and for more practical reasons, such as how to control the solubility of a given solute via modulation of its environment, as in process chemistry and separations. Here, we study how the change of solvent affects the solubility of a given compound. That is, we calculate relative solubilities. We use MD simulations to calculate relative solubility and compare our calculated values with experiment as well as with results from several other methods, SMD and UNIFAC, the latter of which is commonly used in chemical engineering design. We find that straightforward solubility calculations based on molecular simulations using a general small-molecule force field outperform SMD and UNIFAC both in terms of accuracy and coverage of the relevant chemical space.
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Affiliation(s)
| | | | | | - Kayla L Young
- Department of Chemical, Paper and Biomedical Engineering, Miami University , Oxford, Ohio 45056, United States
| | - Andrew S Paluch
- Department of Chemical, Paper and Biomedical Engineering, Miami University , Oxford, Ohio 45056, United States
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41
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Hansen N, van Gunsteren WF. Practical Aspects of Free-Energy Calculations: A Review. J Chem Theory Comput 2014; 10:2632-47. [PMID: 26586503 DOI: 10.1021/ct500161f] [Citation(s) in RCA: 289] [Impact Index Per Article: 28.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Free-energy calculations in the framework of classical molecular dynamics simulations are nowadays used in a wide range of research areas including solvation thermodynamics, molecular recognition, and protein folding. The basic components of a free-energy calculation, that is, a suitable model Hamiltonian, a sampling protocol, and an estimator for the free energy, are independent of the specific application. However, the attention that one has to pay to these components depends considerably on the specific application. Here, we review six different areas of application and discuss the relative importance of the three main components to provide the reader with an organigram and to make nonexperts aware of the many pitfalls present in free energy calculations.
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Affiliation(s)
- Niels Hansen
- Institute of Thermodynamics and Thermal Process Engineering, University of Stuttgart , D-70569 Stuttgart, Germany.,Laboratory of Physical Chemistry, Swiss Federal Institute of Technology, ETH , CH-8093 Zürich, Switzerland
| | - Wilfred F van Gunsteren
- Laboratory of Physical Chemistry, Swiss Federal Institute of Technology, ETH , CH-8093 Zürich, Switzerland
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42
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Chodera JD, Noé F. Markov state models of biomolecular conformational dynamics. Curr Opin Struct Biol 2014; 25:135-44. [PMID: 24836551 DOI: 10.1016/j.sbi.2014.04.002] [Citation(s) in RCA: 511] [Impact Index Per Article: 51.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2014] [Revised: 04/08/2014] [Accepted: 04/12/2014] [Indexed: 10/25/2022]
Abstract
It has recently become practical to construct Markov state models (MSMs) that reproduce the long-time statistical conformational dynamics of biomolecules using data from molecular dynamics simulations. MSMs can predict both stationary and kinetic quantities on long timescales (e.g. milliseconds) using a set of atomistic molecular dynamics simulations that are individually much shorter, thus addressing the well-known sampling problem in molecular dynamics simulation. In addition to providing predictive quantitative models, MSMs greatly facilitate both the extraction of insight into biomolecular mechanism (such as folding and functional dynamics) and quantitative comparison with single-molecule and ensemble kinetics experiments. A variety of methodological advances and software packages now bring the construction of these models closer to routine practice. Here, we review recent progress in this field, considering theoretical and methodological advances, new software tools, and recent applications of these approaches in several domains of biochemistry and biophysics, commenting on remaining challenges.
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Affiliation(s)
- John D Chodera
- Computational Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA.
| | - Frank Noé
- Department of Mathematics and Computer Science, Freie Universität Berlin, Arnimallee 6, 14195 Berlin, Germany.
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