1
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Loudermilk A, Dixon DA. Prediction of the p Ka's of Hydrated Metal Carbonates and Bicarbonates for Mg, Ca, Mn, Fe, Co, Ni, Cu, and Zn Dications. J Phys Chem A 2024; 128:5331-5343. [PMID: 38950028 DOI: 10.1021/acs.jpca.4c02879] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/03/2024]
Abstract
The gas- and aqueous-phase acidities of hydrated metal dication carbonates, bicarbonates, and hydroxide complexes M(CO3)(H2O)n for n = 1 to 3, M(HCO3)2, M(HCO3)2(H2O)2, M(HCO3)(OH), and M(HCO3)(H2O)2(OH) for M = Mg, Ca, Mn, Fe, Co, Ni, Cu, and Zn were calculated at the CCSD(T)/aug-cc-pwCVDZ/cc-pwCVDZ level in the gas phase and at the B3LYP/aug-cc-pVTZ/cc-pVTZ(-PP) level with the COSMO self-consistent reaction field (SCRF) method in the aqueous phase. The composite correlated molecular orbital theory G3(MP2) and G3(MP2)B3 methods were used to predict the pKa's of the Mg structures and cis-cis carbonic acid to provide additional benchmarks. Using values scaled to experiment for H2CO3, the pKa's of bicarbonate ligands in group 2 and transition-metal complexes were compared to carbonic acid to gauge the effect of the metal complex on the bicarbonate. The group 2 metal complexes M(HCO3)2 and M(HCO3)(OH) decreased the acidity of the bicarbonate ligands, whereas their dihydrates were even less acidic. The transition-metal di-bicarbonate and bicarbonate hydroxide complexes generally made the bicarbonate more acidic especially when reduction of the metal occurs consistent with electron donation from the ligands; this is accompanied by spin transfer which typically increases in the order Mn < Fe < Co < Ni < Cu. The transition-metal dihydrates were less acidic than carbonic acid. Using values scaled to experiment for hydrated metal dications, the pKa's of water coordinated to group 2 and transition-metal complexes were generally more acidic than the hydrated metal dications, with the exception of Ca bicarbonate dihydrate, Co carbonate, Ni di-bicarbonate dihydrate, and Cu bicarbonate hydroxide di-bicarbonate.
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Affiliation(s)
- Amanda Loudermilk
- Department of Chemistry and Biochemistry, The University of Alabama, Shelby Hall, Tuscaloosa, Alabama 35487-0336, United States
| | - David A Dixon
- Department of Chemistry and Biochemistry, The University of Alabama, Shelby Hall, Tuscaloosa, Alabama 35487-0336, United States
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2
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Wang K, Li D, Zhao H, Li X, Sheng X. Unraveling the synergic effect of H2O in CO2 capture by aminoalcohols. COMPUT THEOR CHEM 2022. [DOI: 10.1016/j.comptc.2022.113905] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
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3
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Roet S, Daub CD, Riccardi E. Chemistrees: Data-Driven Identification of Reaction Pathways via Machine Learning. J Chem Theory Comput 2021; 17:6193-6202. [PMID: 34555907 PMCID: PMC8515787 DOI: 10.1021/acs.jctc.1c00458] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/03/2022]
Abstract
![]()
We propose to analyze
molecular dynamics (MD) output via a supervised machine
learning (ML) algorithm, the decision tree.
The approach aims to identify the predominant geometric features which
correlate with trajectories that transition between two arbitrarily
defined states. The data-driven algorithm aims to identify these features
without the bias of human “chemical intuition”. We demonstrate
the method by analyzing the proton exchange reactions in formic acid
solvated in small water clusters. The simulations were performed with ab initio MD combined with a method to efficiently sample
the rare event, path sampling. Our ML analysis identified relevant
geometric variables involved in the proton transfer reaction and how
they may change as the number of solvating water molecules changes.
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Affiliation(s)
- Sander Roet
- Department of Chemistry, Norwegian University of Science and Technology, Høgskoleringen 5, 7491 Trondheim, Norway
| | - Christopher D Daub
- Department of Chemistry, University of Helsinki, P.O. Box 55, FI-00014 Helsinki, Finland
| | - Enrico Riccardi
- Department of Informatics, UiO, Gaustadalléen 23B, 0373 Oslo, Norway
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4
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Polino D, Grifoni E, Rousseau R, Parrinello M, Glezakou VA. How Collective Phenomena Impact CO2 Reactivity and Speciation in Different Media. J Phys Chem A 2020; 124:3963-3975. [DOI: 10.1021/acs.jpca.9b11744] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Daniela Polino
- Department of Chemistry and Applied Biosciences, ETH Zurich, c/o USI Campus Via Giuseppe Buffi 13, CH-6900 Lugano, Switzerland
- Facoltà di Informatica, Istituto di Scienze Computazionali, Università della Svizzera Italiana,Via Giuseppe Buffi 13, CH-6900 Lugano, Switzerland
| | - Emanuele Grifoni
- Department of Chemistry and Applied Biosciences, ETH Zurich, c/o USI Campus Via Giuseppe Buffi 13, CH-6900 Lugano, Switzerland
- Facoltà di Informatica, Istituto di Scienze Computazionali, Università della Svizzera Italiana,Via Giuseppe Buffi 13, CH-6900 Lugano, Switzerland
| | - Roger Rousseau
- Pacific Northwest National Laboratory, 902 Battelle Blvd., P.O. Box 999, MSIN K1-83, Richland, Washington 99352, United States
| | - Michele Parrinello
- Department of Chemistry and Applied Biosciences, ETH Zurich, c/o USI Campus Via Giuseppe Buffi 13, CH-6900 Lugano, Switzerland
- Facoltà di Informatica, Istituto di Scienze Computazionali, Università della Svizzera Italiana,Via Giuseppe Buffi 13, CH-6900 Lugano, Switzerland
- Istituto Italiano di Tecnologia, Via Morego 30, 16163 Genova, Italy
| | - Vassiliki-Alexandra Glezakou
- Pacific Northwest National Laboratory, 902 Battelle Blvd., P.O. Box 999, MSIN K1-83, Richland, Washington 99352, United States
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5
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Daub CD, Halonen L. Ab Initio Molecular Dynamics Simulations of the Influence of Lithium Bromide Salt on the Deprotonation of Formic Acid in Aqueous Solution. J Phys Chem B 2019; 123:6823-6829. [PMID: 31310529 PMCID: PMC6750841 DOI: 10.1021/acs.jpcb.9b04618] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Abstract
The deprotonation of formic acid is investigated using metadynamics in tandem with Born-Oppenheimer molecular dynamics simulations. We compare our findings for formic acid in pure water with previous studies before examining formic acid in aqueous solutions of lithium bromide. We carefully consider different definitions for the collective variable(s) used to drive the metadynamics, emphasizing that the variables used must include all of the possible reactive atoms in the system, in this case carboxylate oxygens and water hydrogens. This ensures that all the various possible proton exchange events can be accommodated and the collective variable(s) can distinguish the protonated and deprotonated states, even over rather long ab initio simulation runs (ca. 200-300 ps). Our findings show that the formic acid deprotonation barrier and the free energy of the deprotonated state are higher in concentrated lithium bromide, in agreement with the available experimental data for acids in salt solution. We show that the presence of Br- in proximity to the formic acid hydroxyl group effectively inhibits deprotonation. Our study extends previous work on acid deprotonation in pure water and at air-water interfaces to more complex multicomponent systems of importance in atmospheric and marine chemistry.
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Affiliation(s)
- Christopher D Daub
- Department of Chemistry , University of Helsinki , P.O. Box 55, Helsinki FIN-00014 , Finland
| | - Lauri Halonen
- Department of Chemistry , University of Helsinki , P.O. Box 55, Helsinki FIN-00014 , Finland
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6
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Arunachalam V, Tummanapelli AK, Vasudevan S. The multiple dissociation constants of glutathione disulfide: interpreting experimental pH-titration curves with ab initio MD simulations. Phys Chem Chem Phys 2019; 21:9212-9217. [PMID: 30993274 DOI: 10.1039/c9cp00761j] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
The hexapeptide glutathione disulfide (GSSG) has six ionizable groups with six associated dissociation constants. The experimentally measured pH-titration curve, however, does not exhibit the six corresponding equivalence points and bears little resemblance to standard textbook examples of acid-base pH-titration curves. The curve highlights the difficulties in determining multiple pKa values of polyprotic acids - typically proteins and peptides - from experiment. The six pKa values of GSSG can, however, be estimated using Car-Parrinello molecular dynamics (CPMD) simulations in conjunction with metadynamics sampling of the underlying free energy landscape of the dissociation reactions. Ab initio MD simulations were performed on a GSSG molecule solvated by 200 water molecules. Using the estimated pKa values the theoretical titration curve was calculated and found to be in good agreement with experiment. The results clearly highlight how dissociation constants estimated from ab initio MD simulations can facilitate the interpretation of the pH-titration curves of complex chemical and biological systems.
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7
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Thomas DA, Mucha E, Lettow M, Meijer G, Rossi M, von Helden G. Characterization of a trans-trans Carbonic Acid-Fluoride Complex by Infrared Action Spectroscopy in Helium Nanodroplets. J Am Chem Soc 2019; 141:5815-5823. [PMID: 30883095 PMCID: PMC6727381 DOI: 10.1021/jacs.8b13542] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
![]()
The high Lewis basicity
and small ionic radius of fluoride promote
the formation of strong ionic hydrogen bonds in the complexation of
fluoride with protic molecules. Herein, we report that carbonic acid,
a thermodynamically disfavored species that is challenging to investigate
experimentally, forms a complex with fluoride in the gas phase. Intriguingly,
this complex is highly stable and is observed in abundance upon nanoelectrospray
ionization of an aqueous sodium fluoride solution in the presence
of gas-phase carbon dioxide. We characterize the structure and properties
of the carbonic acid–fluoride complex, F–(H2CO3), and its deuterated isotopologue, F–(D2CO3), by helium nanodroplet
infrared action spectroscopy in the photon energy range of 390–2800
cm–1. The complex adopts a C2v symmetry structure with the carbonic acid
in a planar trans–trans conformation and both OH groups forming
ionic hydrogen bonds with the fluoride. Substantial vibrational anharmonic
effects are observed in the infrared spectra, most notably a strong
blue shift of the symmetric hydrogen stretching fundamental relative
to predictions from the harmonic approximation or vibrational second-order
perturbation theory. Ab initio thermostated ring-polymer molecular
dynamics simulations indicate that this blue shift originates from
strong coupling between the hydrogen stretching and bending vibrations,
resulting in an effective weakening of the OH···F– ionic hydrogen bonds.
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Affiliation(s)
- Daniel A Thomas
- Fritz-Haber-Institut der Max-Planck-Gesellschaft , Faradayweg 4-6 , 14195 Berlin , Germany
| | - Eike Mucha
- Fritz-Haber-Institut der Max-Planck-Gesellschaft , Faradayweg 4-6 , 14195 Berlin , Germany
| | - Maike Lettow
- Fritz-Haber-Institut der Max-Planck-Gesellschaft , Faradayweg 4-6 , 14195 Berlin , Germany
| | - Gerard Meijer
- Fritz-Haber-Institut der Max-Planck-Gesellschaft , Faradayweg 4-6 , 14195 Berlin , Germany
| | - Mariana Rossi
- Fritz-Haber-Institut der Max-Planck-Gesellschaft , Faradayweg 4-6 , 14195 Berlin , Germany
| | - Gert von Helden
- Fritz-Haber-Institut der Max-Planck-Gesellschaft , Faradayweg 4-6 , 14195 Berlin , Germany
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8
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Moqadam M, Lervik A, Riccardi E, Venkatraman V, Alsberg BK, van Erp TS. Local initiation conditions for water autoionization. Proc Natl Acad Sci U S A 2018; 115:E4569-E4576. [PMID: 29712836 PMCID: PMC5960278 DOI: 10.1073/pnas.1714070115] [Citation(s) in RCA: 44] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The pH of liquid water is determined by the infrequent process in which water molecules split into short-lived hydroxide and hydronium ions. This reaction is difficult to probe experimentally and challenging to simulate. One of the open questions is whether the local water structure around a slightly stretched OH bond is actually initiating the eventual breakage of this bond or whether this event is driven by a global ordering that involves many water molecules far away from the reaction center. Here, we investigated the self-ionization of water at room temperature by rare-event ab initio molecular dynamics and obtained autoionization rates and activation energies in good agreement with experiments. Based on the analysis of thousands of molecular trajectories, we identified a couple of local order parameters and show that if a bond stretch occurs when all these parameters are around their ideal range, the chance for the first dissociation step (double-proton jump) increases from [Formula: see text] to 0.4. Understanding these initiation triggers might ultimately allow the steering of chemical reactions.
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Affiliation(s)
- Mahmoud Moqadam
- Department of Chemistry, Norwegian University of Science and Technology, N-7491 Trondheim, Norway
| | - Anders Lervik
- Department of Chemistry, Norwegian University of Science and Technology, N-7491 Trondheim, Norway;
| | - Enrico Riccardi
- Department of Chemistry, Norwegian University of Science and Technology, N-7491 Trondheim, Norway
| | - Vishwesh Venkatraman
- Department of Chemistry, Norwegian University of Science and Technology, N-7491 Trondheim, Norway
| | - Bjørn Kåre Alsberg
- Department of Chemistry, Norwegian University of Science and Technology, N-7491 Trondheim, Norway
| | - Titus S van Erp
- Department of Chemistry, Norwegian University of Science and Technology, N-7491 Trondheim, Norway;
- Center for Molecular Modeling, Ghent University, B9000 Ghent, Belgium
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9
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Sakti AW, Nishimura Y, Nakai H. Rigorous pKa Estimation of Amine Species Using Density-Functional Tight-Binding-Based Metadynamics Simulations. J Chem Theory Comput 2017; 14:351-356. [DOI: 10.1021/acs.jctc.7b00855] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Aditya Wibawa Sakti
- Department
of Chemistry and Biochemistry, School of Advanced Science and Engineering, Waseda University, Tokyo 169-8555, Japan
| | - Yoshifumi Nishimura
- Research
Institute for Science and Engineering, Waseda University, Tokyo 169-8555, Japan
| | - Hiromi Nakai
- Department
of Chemistry and Biochemistry, School of Advanced Science and Engineering, Waseda University, Tokyo 169-8555, Japan
- Research
Institute for Science and Engineering, Waseda University, Tokyo 169-8555, Japan
- Core
Research for Evolutional Science and Technology (CREST), Japan Science and Technology Agency (JST), Saitama 332-0012, Japan
- Elements
Strategy Initiative for Catalysts and Batteries (ESICB), Kyoto University, Kyoto 615-8520, Japan
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10
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Denegri B, Matić M, Kronja O. The Role of Negative Hyperconjugation in Decomposition of Bicarbonate and Organic Carbonate Anions. ChemistrySelect 2016. [DOI: 10.1002/slct.201601357] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
- Bernard Denegri
- University of Zagreb; Faculty of Pharmacy and Biochemistry; Ante Kovačića 1 10000 Zagreb Croatia
| | - Mirela Matić
- University of Zagreb; Faculty of Pharmacy and Biochemistry; Ante Kovačića 1 10000 Zagreb Croatia
| | - Olga Kronja
- University of Zagreb; Faculty of Pharmacy and Biochemistry; Ante Kovačića 1 10000 Zagreb Croatia
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11
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Ions interacting in solution: Moving from intrinsic to collective properties. Curr Opin Colloid Interface Sci 2016. [DOI: 10.1016/j.cocis.2016.05.009] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
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12
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Daschakraborty S, Kiefer PM, Miller Y, Motro Y, Pines D, Pines E, Hynes JT. Reaction Mechanism for Direct Proton Transfer from Carbonic Acid to a Strong Base in Aqueous Solution I: Acid and Base Coordinate and Charge Dynamics. J Phys Chem B 2016; 120:2271-80. [PMID: 26879554 DOI: 10.1021/acs.jpcb.5b12742] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Protonation by carbonic acid H2CO3 of the strong base methylamine CH3NH2 in a neutral contact pair in aqueous solution is followed via Car-Parrinello molecular dynamics simulations. Proton transfer (PT) occurs to form an aqueous solvent-stabilized contact ion pair within 100 fs, a fast time scale associated with the compression of the acid-base hydrogen-bond (H-bond), a key reaction coordinate. This rapid barrierless PT is consistent with the carbonic acid-protonated base pKa difference that considerably favors the PT, and supports the view of intact carbonic acid as potentially important proton donor in assorted biological and environmental contexts. The charge redistribution within the H-bonded complex during PT supports a Mulliken picture of charge transfer from the nitrogen base to carbonic acid without altering the transferring hydrogen's charge from approximately midway between that of a hydrogen atom and that of a proton.
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Affiliation(s)
- Snehasis Daschakraborty
- Department of Chemistry and Biochemistry, University of Colorado , Boulder, Colorado 80309-0215, United States
| | - Philip M Kiefer
- Department of Chemistry and Biochemistry, University of Colorado , Boulder, Colorado 80309-0215, United States
| | - Yifat Miller
- Department of Chemistry, Ben-Gurion University of the Negev , P.O. Box 653, Beer-Sheva 84105, Israel
| | - Yair Motro
- Department of Chemistry, Ben-Gurion University of the Negev , P.O. Box 653, Beer-Sheva 84105, Israel
| | - Dina Pines
- Department of Chemistry, Ben-Gurion University of the Negev , P.O. Box 653, Beer-Sheva 84105, Israel
| | - Ehud Pines
- Department of Chemistry, Ben-Gurion University of the Negev , P.O. Box 653, Beer-Sheva 84105, Israel
| | - James T Hynes
- Department of Chemistry and Biochemistry, University of Colorado , Boulder, Colorado 80309-0215, United States.,Ecole Normale Supérieure-PSL Research University, Chemistry Department, Sorbonne Universités-UPMC University Paris 06, CNRS UMR 8640 Pasteur, 24 rue Lhomond, 75005 Paris, France
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13
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Pines D, Ditkovich J, Mukra T, Miller Y, Kiefer PM, Daschakraborty S, Hynes JT, Pines E. How Acidic Is Carbonic Acid? J Phys Chem B 2016; 120:2440-51. [PMID: 26862781 DOI: 10.1021/acs.jpcb.5b12428] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Carbonic, lactic, and pyruvic acids have been generated in aqueous solution by the transient protonation of their corresponding conjugate bases by a tailor-made photoacid, the 6-hydroxy-1-sulfonate pyrene sodium salt molecule. A particular goal is to establish the pK(a) of carbonic acid H2CO3. The on-contact proton transfer (PT) reaction rate from the optically excited photoacid to the carboxylic bases was derived, with unprecedented precision, from time-correlated single-photon-counting measurements of the fluorescence lifetime of the photoacid in the presence of the proton acceptors. The time-dependent diffusion-assisted PT rate was analyzed using the Szabo-Collins-Kimball equation with a radiation boundary condition. The on-contact PT rates were found to follow the acidity order of the carboxylic acids: the stronger was the acid, the slower was the PT reaction to its conjugate base. The pK(a) of carbonic acid was found to be 3.49 ± 0.05 using both the Marcus and Kiefer-Hynes free energy correlations. This establishes H2CO3 as being 0.37 pK(a) units stronger and about 1 pK(a) unit weaker, respectively, than the physiologically important lactic and pyruvic acids. The considerable acid strength of intact carbonic acid indicates that it is an important protonation agent under physiological conditions.
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Affiliation(s)
- Dina Pines
- Department of Chemistry, Ben-Gurion University of the Negev , P. O. Box 653, Beer-Sheva 84105, Israel
| | - Julia Ditkovich
- Department of Chemistry, Ben-Gurion University of the Negev , P. O. Box 653, Beer-Sheva 84105, Israel
| | - Tzach Mukra
- Department of Chemistry, Ben-Gurion University of the Negev , P. O. Box 653, Beer-Sheva 84105, Israel
| | - Yifat Miller
- Department of Chemistry, Ben-Gurion University of the Negev , P. O. Box 653, Beer-Sheva 84105, Israel
| | - Philip M Kiefer
- Department of Chemistry and Biochemistry, University of Colorado , Boulder, Colorado 80309-0215, United States
| | - Snehasis Daschakraborty
- Department of Chemistry and Biochemistry, University of Colorado , Boulder, Colorado 80309-0215, United States
| | - James T Hynes
- Department of Chemistry and Biochemistry, University of Colorado , Boulder, Colorado 80309-0215, United States.,Ecole Normale Supérieure-PSL Research University, Chemistry Department, Sorbonne Universités-UPMC University Paris 06, CNRS UMR 8640 Pasteur, 24 rue Lhomond, 75005 Paris, France
| | - Ehud Pines
- Department of Chemistry, Ben-Gurion University of the Negev , P. O. Box 653, Beer-Sheva 84105, Israel
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14
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Bandyopadhyay B, Biswas P, Kumar P. Ammonia as an efficient catalyst for decomposition of carbonic acid: a quantum chemical investigation. Phys Chem Chem Phys 2016; 18:15995-6004. [DOI: 10.1039/c6cp02407f] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Electronic structure calculations using M06-2X, MP2 and CCSD(T) methods have been employed to show ammonia as an efficient catalyst for decomposition of carbonic acid.
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Affiliation(s)
- Biman Bandyopadhyay
- Department of Chemistry
- Malaviya National Institute of Technology Jaipur
- Jaipur – 302017
- India
| | - Partha Biswas
- Department of Chemistry
- Scottish Church College
- Kolkata-700006
- India
| | - Pradeep Kumar
- Department of Chemistry
- Malaviya National Institute of Technology Jaipur
- Jaipur – 302017
- India
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15
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Tummanapelli AK, Vasudevan S. Ab Initio MD Simulations of the Brønsted Acidity of Glutathione in Aqueous Solutions: Predicting pKa Shifts of the Cysteine Residue. J Phys Chem B 2015; 119:15353-8. [PMID: 26550841 DOI: 10.1021/acs.jpcb.5b10093] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The tripeptide glutathione (GSH) is one of the most abundant peptides and the major repository for nonprotein sulfur in both animal and plant cells. It plays a critical role in intracellular oxidative stress management by the reversible formation of glutathione disulfide with the thiol-disulfide pair acting as a redox buffer. The state of charge of the ionizable groups of GSH can influence the redox couple, and hence the pKa value of the cysteine residue of GSH is critical to its functioning. Here we report ab initio Car-Parrinello molecular dynamics simulations of glutathione solvated by 200 water molecules, all of which are considered in the simulation. We show that the free-energy landscape for the protonation-deprotonation reaction of the cysteine residue of GSH computed using metadynamics sampling provides accurate estimates of the pKa and correctly predicts the shift in the dissociation constant values as compared with the isolated cysteine amino acid.
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Affiliation(s)
- Anil Kumar Tummanapelli
- Department of Inorganic and Physical Chemistry, Indian Institute of Science , Bangalore 560012, India
| | - Sukumaran Vasudevan
- Department of Inorganic and Physical Chemistry, Indian Institute of Science , Bangalore 560012, India
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16
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Tummanapelli AK, Vasudevan S. Ab Initio Molecular Dynamics Simulations of Amino Acids in Aqueous Solutions: Estimating pKa Values from Metadynamics Sampling. J Phys Chem B 2015; 119:12249-55. [PMID: 26331783 DOI: 10.1021/acs.jpcb.5b05211] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Changes in the protonation and deprotonation of amino acid residues in proteins play a key role in many biological processes and pathways. Here, we report calculations of the free-energy profile for the protonation-deprotonation reaction of the 20 canonical α amino acids in aqueous solutions using ab initio Car-Parrinello molecular dynamics simulations coupled with metadynamics sampling. We show here that the calculated change in free energy of the dissociation reaction provides estimates of the multiple pKa values of the amino acids that are in good agreement with experiment. We use the bond-length-dependent number of the protons coordinated to the hydroxyl oxygen of the carboxylic and the amine groups as the collective variables to explore the free-energy profiles of the Bronsted acid-base chemistry of amino acids in aqueous solutions. We ensure that the amino acid undergoing dissociation is solvated by at least three hydrations shells with all water molecules included in the simulations. The method works equally well for amino acids with neutral, acidic and basic side chains and provides estimates of the multiple pKa values with a mean relative error, with respect to experimental results, of 0.2 pKa units.
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Affiliation(s)
- Anil Kumar Tummanapelli
- Department of Inorganic and Physical Chemistry, Indian Institute of Science , Bangalore 560012, India
| | - Sukumaran Vasudevan
- Department of Inorganic and Physical Chemistry, Indian Institute of Science , Bangalore 560012, India
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17
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Tummanapelli AK, Vasudevan S. Estimating successive pKa values of polyprotic acids from ab initio molecular dynamics using metadynamics: the dissociation of phthalic acid and its isomers. Phys Chem Chem Phys 2015; 17:6383-8. [DOI: 10.1039/c4cp06000h] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
pKa values of polyprotic acids estimated from ab initio molecular dynamics computation of the change in free energy upon dissociation.
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Affiliation(s)
- Anil Kumar Tummanapelli
- Department of Inorganic and Physical Chemistry
- Indian Institute of Science
- Bangalore 560012
- India
| | - Sukumaran Vasudevan
- Department of Inorganic and Physical Chemistry
- Indian Institute of Science
- Bangalore 560012
- India
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18
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Tummanapelli AK, Vasudevan S. Dissociation Constants of Weak Acids from ab Initio Molecular Dynamics Using Metadynamics: Influence of the Inductive Effect and Hydrogen Bonding on pKa Values. J Phys Chem B 2014; 118:13651-7. [DOI: 10.1021/jp5088898] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Affiliation(s)
- Anil Kumar Tummanapelli
- Department of Inorganic and
Physical Chemistry, Indian Institute of Science, Bangalore 560012, India
| | - Sukumaran Vasudevan
- Department of Inorganic and
Physical Chemistry, Indian Institute of Science, Bangalore 560012, India
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19
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Lam RK, England AH, Sheardy AT, Shih O, Smith JW, Rizzuto AM, Prendergast D, Saykally RJ. The hydration structure of aqueous carbonic acid from X-ray absorption spectroscopy. Chem Phys Lett 2014. [DOI: 10.1016/j.cplett.2014.09.052] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
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20
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Capobianco RM, Gruszkiewicz MS, Bodnar RJ, Donald Rimstidt J. Conductivity Measurements on H2O-Bearing CO2-Rich Fluids. J SOLUTION CHEM 2014. [DOI: 10.1007/s10953-014-0219-7] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
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21
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Sadhukhan T, Latif IA, Datta SN. Solvation of CO2 in water: effect of RuBP on CO2 concentration in bundle sheath of C4 plants. J Phys Chem B 2014; 118:8782-91. [PMID: 24960074 DOI: 10.1021/jp505237s] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
An understanding of the temperature-dependence of solubility of carbon dioxide (CO2) in water is important for many industrial processes. Voluminous work has been done by both quantum chemical methods and molecular dynamics (MD) simulations on the interaction between CO2 and water, but a quantitative evaluation of solubility remains elusive. In this work, we have approached the problem by considering quantum chemically calculated total energies and thermal energies, and incorporating the effects of mixing, hydrogen bonding, and phonon modes. An overall equation relating the calculated free energy and entropy of mixing with the gas-solution equilibrium constant has been derived. This equation has been iteratively solved to obtain the solubility as functions of temperature and dielectric constant. The calculated solubility versus temperature plot excellently matches the observed plot. Solubility has been shown to increase with dielectric constant, for example, by addition of electrolytes. We have also found that at the experimentally reported concentration of enzyme RuBP in bundle sheath cells of chloroplast in C4 green plants, the concentration of CO2 can effectively increase by as much as a factor of 7.1-38.5. This stands in agreement with the observed effective rise in concentration by as much as 10 times.
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Affiliation(s)
- Tumpa Sadhukhan
- Department of Chemistry, Indian Institute of Technology - Bombay , Powai, Mumbai - 400 076, India
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22
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Galib M, Hanna G. The Role of Hydrogen Bonding in the Decomposition of H2CO3 in Water: Mechanistic Insights from Ab Initio Metadynamics Studies of Aqueous Clusters. J Phys Chem B 2014; 118:5983-93. [DOI: 10.1021/jp5029195] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Mirza Galib
- Department
of Chemistry, University of Alberta, Edmonton, Alberta T6G 2G2, Canada
| | - Gabriel Hanna
- Department
of Chemistry, University of Alberta, Edmonton, Alberta T6G 2G2, Canada
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23
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Galib M, Hanna G. Molecular dynamics simulations predict an accelerated dissociation of H2CO3 at the air–water interface. Phys Chem Chem Phys 2014; 16:25573-82. [DOI: 10.1039/c4cp03302g] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Ab initio molecular dynamics simulations of carbonic acid (H2CO3) at the air–water interface yield a lower dissociation barrier than in bulk water.
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Affiliation(s)
- Mirza Galib
- Department of Chemistry
- University of Alberta
- Edmonton, Canada
| | - Gabriel Hanna
- Department of Chemistry
- University of Alberta
- Edmonton, Canada
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24
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Reddy SK, Balasubramanian S. Carbonic acid: molecule, crystal and aqueous solution. Chem Commun (Camb) 2014; 50:503-14. [DOI: 10.1039/c3cc45174g] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
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25
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LIANG JINXIA, WANG BINJU, CAO ZEXING. THE MECHANISM OF ACID-CATALYZED DECARBOXYLATION OF PYRROLE-2-CARBOXYLIC ACID: INSIGHTS FROM CLUSTER-CONTINUUM MODEL CALCULATIONS. JOURNAL OF THEORETICAL & COMPUTATIONAL CHEMISTRY 2013. [DOI: 10.1142/s021963361350017x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
The decarboxylation of pyrrole-2-carboxylic acid comprises the addition of water to the carboxyl group and the C–C bond cleavage leading to the protonated carbonic acid. Herein possible concerted and stepwise mechanisms for the C-protonated and O-protonated pathways were extensively investigated by using the cluster-continuum model. The calculated results indicate that the initial hydration or the nucleophilic attack of water at the carbonyl group of both C- and O-protonated derivatives is the rate-determining step for the overall reaction, and the O-protonated pathway will dominate the whole reaction. The predicted activation Gibbs energies for the overall reaction initialized by the O-protonated species fall in the range of 83.3 ∼ 123.0 kJ/mol, showing good agreement with experimental values of 91.6 ∼ 101.3 kJ/mol. On the basis of extensive calculations, the remarkable dependence of the predicted mechanisms and thermodynamic values on the number of explicit water molecules in the cluster-continuum model was discussed.
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Affiliation(s)
- JINXIA LIANG
- State Key Laboratory of Physical Chemistry of Solid Surfaces and Fujian Provincial, Key Laboratory of Theoretical and Computational Chemistry, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 360015, P. R. China
| | - BINJU WANG
- State Key Laboratory of Physical Chemistry of Solid Surfaces and Fujian Provincial, Key Laboratory of Theoretical and Computational Chemistry, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 360015, P. R. China
| | - ZEXING CAO
- State Key Laboratory of Physical Chemistry of Solid Surfaces and Fujian Provincial, Key Laboratory of Theoretical and Computational Chemistry, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 360015, P. R. China
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26
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da Silva PL, Guimarães L, Pliego JR. Revisiting the mechanism of neutral hydrolysis of esters: water autoionization mechanisms with acid or base initiation pathways. J Phys Chem B 2013; 117:6487-97. [PMID: 23642004 DOI: 10.1021/jp311504d] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
The mechanism of neutral hydrolysis of ester has long been explored by theoretical studies. However, reliable theoretical calculations show that the usual bifunctional catalysis mechanism reported by different authors cannot explain the experimental kinetics. An important advance was recently reported by Gunaydin and Houk, suggesting that ions are involved in the mechanism and the process initiates by water autoionization followed by protonation of the ester (W(AI)A mechanism). However, this mechanism does not explain the hydrolysis of activated esters. In this work, we have used ab initio calculations, continuum solvation models, and intrinsic reaction coordinate method to support the W(AI)A mechanism for normal ester. In the case of activated esters, the process can also be viewed as water autoionization with formation of hydroxide ion aided by a second water molecule acting as a general base (W(AI)B mechanism). This is the mechanism that was proposed by Jencks and Carriuolo 50 years ago. Our analysis point out that the usual method for exploring mechanisms, searching for saddle points, may not work for problems like the present one, since there are no saddle points on the reaction pathway. Rather, the formation of a pair of ions from a neutral species may have an asymptotic barrier. The approach used in this paper allows the calculation of the free energy profile and enable us to explain the mechanism and kinetics of the neutral hydrolysis of normal (methyl acetate) and activated (methyl trifluoroacetate) esters. In addition, the present study suggests that formation of a pair of ions should always be considered in reactions in aqueous solution.
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Affiliation(s)
- Poliana Lima da Silva
- Departamento de Ciências Naturais, Universidade Federal de São João del-Rei, 36301-160, São João del-Rei, MG, Brazil
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27
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Rovira C. The description of electronic processes inside proteins from Car-Parrinello molecular dynamics: chemical transformations. WILEY INTERDISCIPLINARY REVIEWS-COMPUTATIONAL MOLECULAR SCIENCE 2013. [DOI: 10.1002/wcms.1153] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
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28
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STIRLING A. SO2 Hydrolysis: Ab initio MD Study of the Formation of Bisulfite Ion. JOURNAL OF COMPUTER CHEMISTRY-JAPAN 2013. [DOI: 10.2477/jccj.2012-0020] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
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29
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Wright LB, Rodger PM, Walsh TR. Aqueous citrate: a first-principles and force-field molecular dynamics study. RSC Adv 2013. [DOI: 10.1039/c3ra42437e] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
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30
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Wang B, Cao Z. How water molecules modulate the hydration of CO2in water solution: Insight from the cluster-continuum model calculations. J Comput Chem 2012; 34:372-8. [DOI: 10.1002/jcc.23144] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2012] [Revised: 09/03/2012] [Accepted: 09/12/2012] [Indexed: 11/10/2022]
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31
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Gallet GA, Pietrucci F, Andreoni W. Bridging Static and Dynamical Descriptions of Chemical Reactions: An ab Initio Study of CO2 Interacting with Water Molecules. J Chem Theory Comput 2012; 8:4029-39. [DOI: 10.1021/ct300581n] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Affiliation(s)
- Grégoire A. Gallet
- Centre Européen
de Calcul
Atomique et Moléculaire (CECAM), Ecole Polytechnique Fédérale
de Lausanne, Switzerland
| | - Fabio Pietrucci
- Centre Européen
de Calcul
Atomique et Moléculaire (CECAM), Ecole Polytechnique Fédérale
de Lausanne, Switzerland
| | - Wanda Andreoni
- Centre Européen
de Calcul
Atomique et Moléculaire (CECAM), Ecole Polytechnique Fédérale
de Lausanne, Switzerland
- Institut de Théorie des
Phénomènes Physiques, Ecole Polytechnique Fédérale
de Lausanne, Switzerland
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