1
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Kacenauskaite L, Moncada Cohen M, Van Wyck SJ, Fayer MD. Fast Structural Dynamics in Concentrated HCl Solutions: From Proton Hopping to the Bulk Viscosity. J Am Chem Soc 2024; 146:12355-12364. [PMID: 38682723 DOI: 10.1021/jacs.3c11620] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/01/2024]
Abstract
Concentrated acid solutions, particularly HCl, have been studied extensively to examine the proton hopping and infrared spectral signatures of hydronium ions. Much less attention has been given to the structural dynamics of concentrated HCl solutions. Here, we apply optical heterodyne detected-optical Kerr effect (OHD-OKE) measurements to examine HCl concentration-dependent dynamics from moderate (0.8 m) to very high (15.5 m) concentrations and compare the results to the dynamics of NaCl solutions, as Na+ is similar in size to the hydronium cation. Both HCl and NaCl OHD-OKE signals decay as triexponentials at all concentrations, in contrast to pure water, which decays as a biexponential. Two remarkable features of the HCl dynamics are the following: (1) the bulk viscosity is linearly related to the slowest decay constant, t3, and (2) the concentration-dependent proton hopping times, determined by ab initio MD simulations and 2D IR chemical exchange experiments, both obtained from the literature, fall on the same line as the slowest structural dynamics relaxation time, t3, within experimental error. The structural dynamics of hydronium/chloride/water clusters, with relaxation times t3, are responsible for the concentration dependence of microscopic property of proton hopping and the macroscopic bulk viscosity. The slowest time constant (t3), which does not have a counterpart in pure water, is 3 ps at 0.8 m and increases by a factor of ∼2 by 15.5 m. The two fastest HCl decay constants, t1 and t2, are similar to those of pure water and increase mildly with the concentration.
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Affiliation(s)
- Laura Kacenauskaite
- Department of Chemistry, Stanford University, Stanford, California 94305, United States
- Nano-Science Center & Department of Chemistry, University of Copenhagen, Copenhagen 2100, Denmark
| | - Max Moncada Cohen
- Department of Chemistry, Stanford University, Stanford, California 94305, United States
| | - Stephen J Van Wyck
- Department of Chemistry, Stanford University, Stanford, California 94305, United States
| | - Michael D Fayer
- Department of Chemistry, Stanford University, Stanford, California 94305, United States
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2
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Piskulich ZA, Laage D, Thompson WH. A structure-dynamics relationship enables prediction of the water hydrogen bond exchange activation energy from experimental data. Chem Sci 2024; 15:2197-2204. [PMID: 38332825 PMCID: PMC10848719 DOI: 10.1039/d3sc04495e] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2023] [Accepted: 12/23/2023] [Indexed: 02/10/2024] Open
Abstract
It has long been understood that the structural features of water are determined by hydrogen bonding (H-bonding) and that the exchange of, or "jumps" between, H-bond partners underlies many of the dynamical processes in water. Despite the importance of H-bond exchanges there is, as yet, no direct method for experimentally measuring the timescale of the process or its associated activation energy. Here, we identify and exploit relationships between water's structural and dynamical properties that provide an indirect route for determining the H-bond exchange activation energy from experimental data. Specifically, we show that the enthalpy and entropy determining the radial distribution function in liquid water are linearly correlated with the activation energies for H-bond jumps, OH reorientation, and diffusion. Using temperature-dependent measurements of the radial distribution function from the literature, we demonstrate how these correlations allow us to infer the value of the jump activation energy, Ea,0, from experimental results. This analysis gives Ea,0 = 3.43 kcal mol-1, which is in good agreement with that predicted by the TIP4P/2005 water model. We also illustrate other approaches for estimating this activation energy consistent with these estimates.
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Affiliation(s)
- Zeke A Piskulich
- Department of Chemistry, University of Kansas Lawrence KS 66045 USA
| | - Damien Laage
- PASTEUR, Départment de Chimie, École Normale Supérieure, PSL University, Sorbonne Université, CNRS Paris 75005 France
| | - Ward H Thompson
- Department of Chemistry, University of Kansas Lawrence KS 66045 USA
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3
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Morishita M, Okumura Y, Fukushima R, Yamamoto H, Yanagita H. Hydrogen evolution reaction following the Slater-Pauling curve: acceleration of rate processes induced from dipole interaction between protons and ferromagnetic catalysts. RSC Adv 2023; 13:12941-12950. [PMID: 37114021 PMCID: PMC10128105 DOI: 10.1039/d2ra07865a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2022] [Accepted: 04/11/2023] [Indexed: 04/29/2023] Open
Abstract
Developing new concepts to design noble-metal-free catalysts is necessary to achieve the hydrogen economy and reduce global CO2 emissions. Here, we provide novel insights into the design of catalysts with internal magnetic fields by investigating the relationship between the hydrogen evolution reaction (HER) and the Slater-Pauling rule. This rule states that adding an element to a metal reduces the alloy's saturation magnetization by an amount proportional to the number of valence electrons outside the d shell of the added element. We observed that rapid hydrogen evolution occurred when the magnetic moment of the catalyst was high, as predicted by the Slater-Pauling rule. Numerical simulation of the dipole interaction revealed a critical distance, r C, at which the proton trajectory changes from a Brownian random walk to a close-approach orbit towards the ferromagnetic catalyst. The calculated r C was proportional to the magnetic moment, consistent with the experimental data. Interestingly, r C was proportional to the number of protons contributing to the HER and accurately reflected the migration length for the proton dissociation and hydration and the O-H bond length in water. The magnetic dipole interaction between the nuclear spin of the proton and the electronic spin of the magnetic catalyst is verified for the first time. The findings of this study will open a new direction in catalyst design aided by an internal magnetic field.
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Affiliation(s)
- Masao Morishita
- Department of Chemical Engineering and Materials Science, University of Hyogo 2167 Shosha Himeji 671-2201 Japan
| | - Yuki Okumura
- Department of Chemical Engineering and Materials Science, University of Hyogo 2167 Shosha Himeji 671-2201 Japan
| | - Ramu Fukushima
- Department of Chemical Engineering and Materials Science, University of Hyogo 2167 Shosha Himeji 671-2201 Japan
| | - Hiroaki Yamamoto
- Department of Chemical Engineering and Materials Science, University of Hyogo 2167 Shosha Himeji 671-2201 Japan
| | - Hidefumi Yanagita
- Sanalloy Industry Co., Ltd. 290-44 Takahashi Fukusaki-cho Kanzaki 679-2216 Japan
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4
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Ekimova M, Kleine C, Ludwig J, Ochmann M, Agrenius TEG, Kozari E, Pines D, Pines E, Huse N, Wernet P, Odelius M, Nibbering ETJ. From Local Covalent Bonding to Extended Electric Field Interactions in Proton Hydration. Angew Chem Int Ed Engl 2022; 61:e202211066. [PMID: 36102247 PMCID: PMC9827956 DOI: 10.1002/anie.202211066] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2022] [Indexed: 01/12/2023]
Abstract
Seemingly simple yet surprisingly difficult to probe, excess protons in water constitute complex quantum objects with strong interactions with the extended and dynamically changing hydrogen-bonding network of the liquid. Proton hydration plays pivotal roles in energy transport in hydrogen fuel cells and signal transduction in transmembrane proteins. While geometries and stoichiometry have been widely addressed in both experiment and theory, the electronic structure of these specific hydrated proton complexes has remained elusive. Here we show, layer by layer, how utilizing novel flatjet technology for accurate x-ray spectroscopic measurements and combining infrared spectral analysis and calculations, we find orbital-specific markers that distinguish two main electronic-structure effects: Local orbital interactions determine covalent bonding between the proton and neigbouring water molecules, while orbital-energy shifts measure the strength of the extended electric field of the proton.
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Affiliation(s)
- Maria Ekimova
- Max Born Institut für Nichtlineare Optik und KurzzeitspektroskopieMax Born Strasse 2A12489BerlinGermany
| | - Carlo Kleine
- Max Born Institut für Nichtlineare Optik und KurzzeitspektroskopieMax Born Strasse 2A12489BerlinGermany
| | - Jan Ludwig
- Max Born Institut für Nichtlineare Optik und KurzzeitspektroskopieMax Born Strasse 2A12489BerlinGermany
| | - Miguel Ochmann
- Institute for Nanostructure and Solid State Physics, Center for Free-Electron Laser ScienceLuruper Chaussee 14922761HamburgGermany
| | - Thomas E. G. Agrenius
- Department of PhysicsStockholm UniversityAlbaNova University Center106 91StockholmSweden
| | - Eve Kozari
- Department of ChemistryBen Gurion University of the NegevP.O.B. 653Beersheva84105Israel
| | - Dina Pines
- Department of ChemistryBen Gurion University of the NegevP.O.B. 653Beersheva84105Israel
| | - Ehud Pines
- Department of ChemistryBen Gurion University of the NegevP.O.B. 653Beersheva84105Israel
| | - Nils Huse
- Institute for Nanostructure and Solid State Physics, Center for Free-Electron Laser ScienceLuruper Chaussee 14922761HamburgGermany
| | - Philippe Wernet
- Department of Physics and AstronomyUppsala UniversityBox 516 Lägerhyddsvägen 1751 20UppsalaSweden
| | - Michael Odelius
- Department of PhysicsStockholm UniversityAlbaNova University Center106 91StockholmSweden
| | - Erik T. J. Nibbering
- Max Born Institut für Nichtlineare Optik und KurzzeitspektroskopieMax Born Strasse 2A12489BerlinGermany
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5
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Lazaridis T, Sepehri A. Amino acid deprotonation rates from classical force fields. J Chem Phys 2022; 157:085101. [DOI: 10.1063/5.0101960] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Acid ionization constants (pKa's) of titratable amino acid side chains have received a large amount of experimental and theoretical attention. In many situations, however, the rates of protonation and deprotonation, kon & koff, may also be important, for example in understanding the mechanism of action of proton channels or membrane proteins that couple proton transport to other processes. Protonation and deprotonation involve making and breaking of covalent bonds, which cannot be studied by classical force fields. However, environment effects on the rates should be captured by such methods. Here we present an approach for estimating deprotonation rates based on Warshel's extension of Marcus's theory of electron transfer, with input from molecular simulations. The missing bond dissociation energy is represented by a constant term determined by fitting the pKa value in solution. The statistics of the energy gap between protonated and deprotonated states is used to compute free energy curves of the two states and thus free energy barriers, from which the rate can be deduced. The method is applied to Glu, Asp, and His in bulk solution and select membrane proteins: the M2 proton channel, bacteriorhodopsin, and cytochrome c oxidase.
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Affiliation(s)
- Themis Lazaridis
- Department of Chemistry, City College of New York, United States of America
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6
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Joutsuka T. Molecular Mechanism of Autodissociation in Liquid Water: Ab Initio Molecular Dynamics Simulations. J Phys Chem B 2022; 126:4565-4571. [PMID: 35694850 DOI: 10.1021/acs.jpcb.2c01971] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Autodissociation in liquid water is one of the most important processes in various topics of physical chemistry, such as acid-base chemistry. Molecular simulations have elucidated most of the molecular mechanisms at the atomic level, yet quantitative analysis to compare with experiments using the potential of mean force (PMF) remains a hurdle, including the definition of reaction coordinates and the accuracy of liquid structures by ab initio molecular dynamics (AIMD) simulations with density functional theory (DFT) methods. Here, we perform AIMD simulations with the revPBE-D3 exchange-correlation functional to compute the PMF profiles of autoionization, or proton transfer (PT), in liquid water. For the quantitative analysis with physically meaningful reaction coordinates, we employ a PT coordinate, donor-acceptor (OH--H3O+) distance, and hydrogen (H)-bond number. The one-dimensional (1D) PMF profile along the PT coordinate shows no local minimum in the product state of PT (OH- and H3O+), which is necessary to accurately compute the acid dissociation constant (or pKa). On the other hand, the 2D PMF profiles along the PT coordinate and donor-acceptor distance show local minima in the product state and reaction barriers, and the computed pKw is comparable to the experiment. In addition, the 2D PMF profiles along the PT coordinate and the H-bond number reveal the molecular mechanism of the H-bond rearrangement concomitant with PT, in which the H-bond breaking before PT is slightly preferable. These findings indicate that an accurate evaluation of pKa by MD simulations requires the donor-acceptor distance in addition to the conventional PT coordinate.
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Affiliation(s)
- Tatsuya Joutsuka
- Institute of Quantum Beam Science, Graduate School of Science and Engineering, Ibaraki University, Hitachi 316-8511 Ibaraki, Japan.,Frontier Research Center for Applied Atomic Sciences, Ibaraki University, 162-1 Shirakata, Tokai, 319-1106 Ibaraki, Japan
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7
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Usmani A, Watthaisong P, Grisdanurak N, Suthirakun S. Insight into the effect of alkali treatment on enhancing adsorptivity of activated carbon for HCl removal in H2 feedstock. CHEMICAL PAPERS 2022. [DOI: 10.1007/s11696-022-02111-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
Abstract
AbstractThe removal of contaminated HCl gas in the petrochemical plants is essential to prevent corrosion problems, catalysts poisoning, and downstream contamination. Alkali-treated activated carbon (AC) was proposed as an effective adsorbent for HCl removal. Understanding the underlying mechanism of HCl adsorption on modified AC is key to design promising strategies for removal of HCl and other chlorinated hydrocarbon gases in the H2 feedstock. Here, a combined experimental and computational approach was used to study the role of alkali treatment on the adsorption behavior of HCl on the AC surfaces. We find that an interplay between alkali ions and oxygen-containing functional groups on the AC surface plays a crucial role in stabilizing the adsorbed HCl. The origin of such stable adsorbed configurations can be attributed to the dissociative adsorption of HCl leading to a formation of low energy species such as water, OH– and Cl– anions. These anions are electrostatically stabilized by the alkali ions resulting in a strong adsorption of −3.61 eV and −3.69 eV for Na+ and K+, respectively. Close investigation on charge analysis reveals that the epoxy functional group facilitates adsorbent-surface charge transfer where O and Cl atoms gain more charges of 0.37 e and 0.58 e which is in good correlation with the improved adsorption strength. The calculated results are consistence with the experimental observations that the Langmuir adsorptivity has been enhanced upon alkali modification. The maximum adsorption capacity of AC has been improved approximately by 4 times from 78.9 to 188.9 mg/g upon treatment.
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8
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Ohmine I, Saito S. Dynamical Behavior of Water; Fluctuation, Reactions and Phase Transitions. BULLETIN OF THE CHEMICAL SOCIETY OF JAPAN 2021. [DOI: 10.1246/bcsj.20210269] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Affiliation(s)
- Iwao Ohmine
- Institute for Molecular Science, Myodaiji, Okazaki, Aichi 444-8585, Japan
| | - Shinji Saito
- Institute for Molecular Science, Myodaiji, Okazaki, Aichi 444-8585, Japan
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9
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Kiefer PM, Daschakraborty S, Pines D, Pines E, Hynes JT. Electron Flow Characterization of Charge Transfer for Carbonic Acid to Strong Base Proton Transfer in Aqueous Solution. J Phys Chem B 2021; 125:11473-11490. [PMID: 34623157 DOI: 10.1021/acs.jpcb.1c05824] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Protonation of the strong base methylamine CH3NH2 by carbonic acid H2CO3 in aqueous solution, HOCOOH···NH2CH3 → HOCOO-···+HNH2CH3, has been previously studied ( J. Phys. Chem. B 2016, 109, 2271-2280; J. Phys. Chem. B 2016, 109, 2281-2290) via Car-Parinnello molecular dynamics. This proton transfer (PT) reaction within a hydrogen (H)-bonded complex was found to be barrierless and very rapid, with key reaction coordinates comprising the proton coordinate, the H-bond separation RON, and a solvent coordinate, reflecting the water solvent rearrangement involved in the neutral to ion pair conversion. In the present work, the reaction's charge flow aspects are analyzed in detail, especially a description via Mulliken charge transfer for PT (MCTPT). A natural bond orbital analysis and some extensions of them are employed for the complex's electronic structure during the reaction trajectories. Results demonstrate that consistent with the MCTPT picture, the charge transfer (CT) occurs from a methylamine base nonbonding orbital to a carbonic acid antibonding orbital. A complementary MCTPT reaction product perspective of CT from the antibonding orbital of the HN+ moiety to the nonbonding orbital of the oxygen in the H-bond complex is also presented. σOH and σHN+ bond order expressions show this CT to occur within the H-bond OHN triad, an aspect key for simultaneous bond-breaking and -forming in the PT reaction.
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Affiliation(s)
- Philip M Kiefer
- Department of Chemistry, University of Colorado, Boulder, Colorado 80309-0215, United States
| | - Snehasis Daschakraborty
- Department of Chemistry, University of Colorado, Boulder, Colorado 80309-0215, United States
| | - 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, University of Colorado, Boulder, Colorado 80309-0215, United States.,PASTEUR, Department of Chemistry, École Normale Supérieure, PSL University, Sorbonne Université, CNRS, 75005 Paris, France
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10
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Joutsuka T, Ando K. Efficient Free-energy Calculation of Proton Transfer by Constrained Density Functional Theory and Geometrically Restrained Molecular Dynamics Simulation. CHEM LETT 2021. [DOI: 10.1246/cl.210132] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Affiliation(s)
- Tatsuya Joutsuka
- Institute of Quantum Beam Science, Graduate School of Science and Engineering, Ibaraki University, Hitachi, Ibaraki 316-8511, Japan
| | - Koji Ando
- Department of Information and Sciences, Tokyo Woman’s Christian University, 2-6-1 Zenpukuji, Suginami-ku, Tokyo 167-8585, Japan
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11
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Sachar HS, Chava BS, Pial TH, Das S. Hydrogen Bonding and Its Effect on the Orientational Dynamics of Water Molecules inside Polyelectrolyte Brush-Induced Soft and Active Nanoconfinement. Macromolecules 2021. [DOI: 10.1021/acs.macromol.0c02813] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Affiliation(s)
- Harnoor Singh Sachar
- Department of Mechanical Engineering, University of Maryland, College Park, Maryland 20742, United States
| | - Bhargav Sai Chava
- Department of Mechanical Engineering, University of Maryland, College Park, Maryland 20742, United States
| | - Turash Haque Pial
- Department of Mechanical Engineering, University of Maryland, College Park, Maryland 20742, United States
| | - Siddhartha Das
- Department of Mechanical Engineering, University of Maryland, College Park, Maryland 20742, United States
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12
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Joutsuka T, Ando K. Constrained Density Functional Theory Molecular Dynamics Simulation of Deprotonation in Aqueous Silicic Acid. J Phys Chem B 2020; 124:8323-8330. [PMID: 32856917 DOI: 10.1021/acs.jpcb.0c05096] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The solubility of silicic acid in water is so low that the molecular mechanism behind the physical properties such as pKa remains poorly understood, despite the importance in fields such as chemistry and geology. Theoretical calculations provide the molecular-level information on such a rare chemical species yet face difficulties in the selection of reaction coordinates and the rare-event sampling of proton transfers (PTs) in condensed phases. We propose a straightforward calculation scheme of pKa with ab initio molecular dynamics (MD) simulation and the constrained density functional theory (CDFT), which provides structural and dynamical properties such as radial distribution functions, vibrational spectra, and reaction paths. The calculated reaction free energies of deprotonations agreed with experiments within a few kcal/mol. Analysis of the solvation structure shows that, after deprotonation, the hydronium ion D3O+ repels away from the deprotonated silicic acid SiO(OD)3- without forming a stable contact-ion pair. The calculated vibrational spectra are consistent with the spectroscopic measurements, and the dynamical analysis of the reaction path quantifies the couplings of the OD stretch vibrations of silicic acid and water to the PT reaction in terms of the vertical energy-gap coordinate that includes both the solute and the solvent components.
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Affiliation(s)
- Tatsuya Joutsuka
- Institute of Quantum Beam Science, Graduate School of Science and Engineering, Ibaraki University, Hitachi 316-8511 Ibaraki, Japan
| | - Koji Ando
- Department of Information and Sciences, Tokyo Womans Christian University, 2-6-1 Zenpukuji, Suginami-ku, Tokyo 167-8585, Japan
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13
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Novelli F, Guchhait B, Havenith M. Towards Intense THz Spectroscopy on Water: Characterization of Optical Rectification by GaP, OH1, and DSTMS at OPA Wavelengths. MATERIALS (BASEL, SWITZERLAND) 2020; 13:E1311. [PMID: 32183131 PMCID: PMC7143731 DOI: 10.3390/ma13061311] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/11/2020] [Revised: 03/05/2020] [Accepted: 03/10/2020] [Indexed: 12/02/2022]
Abstract
Water is the most prominent solvent. The unique properties of water are rooted in the dynamical hydrogen-bonded network. While TeraHertz (THz) radiation can probe directly the collective molecular network, several open issues remain about the interpretation of these highly anharmonic, coupled bands. In order to address this problem, we need intense THz radiation able to drive the liquid into the nonlinear response regime. Firstly, in this study, we summarize the available brilliant THz sources and compare their emission properties. Secondly, we characterize the THz emission by Gallium Phosphide (GaP), 2-{3-(4-hydroxystyryl)-5,5-dimethylcyclohex-2-enylidene}malononitrile (OH1), and 4-N,N-dimethylamino-4'-N'-methyl-stilbazolium 2,4,6-trimethylbenzenesulfonate (DSTMS) crystals pumped by an amplified near-infrared (NIR) laser with tunable wavelength. We found that both OH1 as well as DSTMS could convert NIR laser radiation between 1200 and 2500 nm into THz radiation with high efficiency (> 2 × 10-4), resulting in THz peak fields exceeding 0.1 MV/cm for modest pump excitation (~ mJ/cm2). DSTMS emits the broadest spectrum, covering the entire bandwidth of our detector from ca. 0.5 to ~7 THz, also at a laser wavelength of 2100 nm. Future improvements will require handling the photothermal damage of these delicate organic crystals, and increasing the THz frequency.
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Affiliation(s)
- Fabio Novelli
- Department of Physical Chemistry II, Ruhr University Bochum, 44801 Bochum, Germany;
| | - Biswajit Guchhait
- Department of Physical Chemistry II, Ruhr University Bochum, 44801 Bochum, Germany;
- Department of Chemistry, School of Natural Sciences, Shiv Nadar University, Greater Noida, Uttar Pradesh 201314, India
| | - Martina Havenith
- Department of Physical Chemistry II, Ruhr University Bochum, 44801 Bochum, Germany;
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14
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15
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Multistate Reactive Molecular Dynamics Simulations of Proton Diffusion in Water Clusters and in the Bulk. J Phys Chem B 2019; 123:9846-9861. [PMID: 31647873 DOI: 10.1021/acs.jpcb.9b03258] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
The molecular mechanics with proton transfer (MMPT) force field is combined with multistate adiabatic reactive molecular dynamics (MS-ARMD) to describe proton transport in the condensed phase. Parametrization for small protonated water clusters based on electronic structure calculations at the MP2/6-311+G(2d,2p) level of theory and refinement by comparing with infrared spectra for a protonated water tetramer yields a force field which faithfully describes the minimum energy structures of small protonated water clusters. In protonated water clusters up to (H2O)100H+, the proton hopping rate is around 100 hops/ns. This rate converges for 21 ≤ n ≤ 31, and no further speedup in bulk water is found. This indicates that bulklike behavior requires the solvation of a Zundel motif by ∼25 water molecules, which corresponds to the second solvation sphere. For smaller cluster sizes, the number of available states (i.e., the number of proton acceptors) is too small and slows down proton-transfer rates. The cluster simulations confirm that the excess proton is typically located on the surface. The free-energy surface as a function of the weights of the two lowest states and a configurational parameter suggests that the "special pair" plays a central role in rapid proton transport. The barriers between this minimum-energy structure and the Zundel and Eigen minima are sufficiently low (∼1 kcal/mol, consistent with recent experiments and commensurate with a hopping rate of ∼100/ns or 1 every 10 ps), leading to a highly dynamic environment. These findings are also consistent with recent experiments which find that Zundel-type hydration geometries are prevalent in bulk water.
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16
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Mendis CH, Piskulich ZA, Thompson WH. Tests of the Stokes–Einstein Relation through the Shear Viscosity Activation Energy of Water. J Phys Chem B 2019; 123:5857-5865. [DOI: 10.1021/acs.jpcb.9b04647] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Affiliation(s)
- Camina H. Mendis
- Department of Chemistry, University of Kansas, Lawrence, Kansas 66045, United States
| | - Zeke A. Piskulich
- Department of Chemistry, University of Kansas, Lawrence, Kansas 66045, United States
| | - Ward H. Thompson
- Department of Chemistry, University of Kansas, Lawrence, Kansas 66045, United States
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17
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Kundu A, Dahms F, Fingerhut BP, Nibbering ETJ, Pines E, Elsaesser T. Hydrated Excess Protons in Acetonitrile/Water Mixtures: Solvation Species and Ultrafast Proton Motions. J Phys Chem Lett 2019; 10:2287-2294. [PMID: 30999753 DOI: 10.1021/acs.jpclett.9b00756] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
The solvation structure of protons in aqueous media is highly relevant to electric properties and to proton transport in liquids and membranes. At ambient temperature, polar liquids display structural fluctuations on femto- to picosecond time scales with a direct impact on proton solvation. We use two-dimensional infrared (2D-IR) spectroscopy to follow proton dynamics in acetonitrile/water mixtures with the Zundel cation H5O2+ prepared in neat acetonitrile as a benchmark. The 2D-IR spectra of the proton transfer mode of H5O2+ demonstrate stochastic large-amplitude motions in the double-minimum proton potential, driven by fluctuating electric fields. In all cases, the excess proton is embedded in a water dimer, forming an H5O2+ complex as the major solvation species. This observation is rationalized by quantum mechanics/molecular mechanics molecular dynamics simulations including up to four water molecules embedded in acetonitrile. The Zundel motif interacts with its closest water neighbor in an H7O3+ unit without persistent proton localization.
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Affiliation(s)
- Achintya Kundu
- Max-Born-Institut für Nichtlineare Optik und Kurzzeitspektroskopie , Berlin 12489 , Germany
| | - Fabian Dahms
- Max-Born-Institut für Nichtlineare Optik und Kurzzeitspektroskopie , Berlin 12489 , Germany
| | - Benjamin P Fingerhut
- Max-Born-Institut für Nichtlineare Optik und Kurzzeitspektroskopie , Berlin 12489 , Germany
| | - Erik T J Nibbering
- Max-Born-Institut für Nichtlineare Optik und Kurzzeitspektroskopie , Berlin 12489 , Germany
| | - Ehud Pines
- Department of Chemistry , Ben Gurion University of the Negev , Beer-Sheva 84105 , Israel
| | - Thomas Elsaesser
- Max-Born-Institut für Nichtlineare Optik und Kurzzeitspektroskopie , Berlin 12489 , Germany
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18
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Sun CQ. Unprecedented O:⇔:O compression and H↔H fragilization in Lewis solutions. Phys Chem Chem Phys 2019; 21:2234-2250. [DOI: 10.1039/c8cp06910g] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
Charge injection in terms of protons, lone pairs, cations and anions by acid and base solvation mediates the HB network and properties of Lewis solutions through H↔H fragilization, O:⇔:O compression and polarization, ionic polarization and hydrating H2O dipolar screen shielding, anion–anion repulsion, compressed solvent H–O bond elongation and undercoordinated solute H–O bond contraction.
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Affiliation(s)
- Chang Q. Sun
- EBEAM
- Yangtze Normal University
- Chongqing 408100
- China
- NOVITUS
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19
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Sun CQ. Aqueous charge injection: solvation bonding dynamics, molecular nonbond interactions, and extraordinary solute capabilities. INT REV PHYS CHEM 2018. [DOI: 10.1080/0144235x.2018.1544446] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Affiliation(s)
- Chang Q. Sun
- EBEAM, Yangtze Normal University, Chongqing, People's Republic of China
- NOVITAS, EEE, Nanyang Technological University, Singapore, Singapore
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20
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Kundu A, Dahms F, Fingerhut BP, Nibbering ET, Pines E, Elsaesser T. Ultrafast vibrational relaxation and energy dissipation of hydrated excess protons in polar solvents. Chem Phys Lett 2018. [DOI: 10.1016/j.cplett.2018.10.030] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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21
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Piskulich ZA, Thompson WH. The activation energy for water reorientation differs between IR pump-probe and NMR measurements. J Chem Phys 2018; 149:164504. [DOI: 10.1063/1.5050203] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- Zeke A. Piskulich
- Department of Chemistry, University of Kansas, Lawrence, Kansas 66045, USA
- Center for Environmentally Beneficial Catalysis, University of Kansas, Lawrence, Kansas 66047, USA
| | - Ward H. Thompson
- Department of Chemistry, University of Kansas, Lawrence, Kansas 66045, USA
- Center for Environmentally Beneficial Catalysis, University of Kansas, Lawrence, Kansas 66047, USA
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22
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Dubey V, Kumar N, Daschakraborty S. Importance of Solvents’ Translational–Rotational Coupling for Translational Jump of a Small Hydrophobic Solute in Supercooled Water. J Phys Chem B 2018; 122:7569-7583. [DOI: 10.1021/acs.jpcb.8b03177] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Vikas Dubey
- Department of Chemistry, Indian Institute of Technology Patna, Patna 801103, Bihar, India
| | - Nitesh Kumar
- Department of Chemistry, Indian Institute of Technology Patna, Patna 801103, Bihar, India
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23
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Biswas R, Carpenter W, Fournier JA, Voth GA, Tokmakoff A. IR spectral assignments for the hydrated excess proton in liquid water. J Chem Phys 2018; 146:154507. [PMID: 28433032 DOI: 10.1063/1.4980121] [Citation(s) in RCA: 51] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
The local environmental sensitivity of infrared (IR) spectroscopy to a hydrogen-bonding structure makes it a powerful tool for investigating the structure and dynamics of excess protons in water. Although of significant interest, the line broadening that results from the ultrafast evolution of different solvated proton-water structures makes the assignment of liquid-phase IR spectra a challenging task. In this work, we apply a normal mode analysis using density functional theory of thousands of proton-water clusters taken from reactive molecular dynamics trajectories of the latest generation multistate empirical valence bond proton model (MS-EVB 3.2). These calculations are used to obtain a vibrational density of states and IR spectral density, which are decomposed on the basis of solvated proton structure and the frequency dependent mode character. Decompositions are presented on the basis of the proton sharing parameter δ, often used to distinguish Eigen and Zundel species, the stretch and bend character of the modes, the mode delocalization, and the vibrational mode symmetry. We find there is a wide distribution of vibrational frequencies spanning 1200-3000 cm-1 for every local proton configuration, with the region 2000-2600 cm-1 being mostly governed by the distorted Eigen-like configuration. We find a continuous red shift of the special-pair O⋯H+⋯O stretching frequency, and an increase in the flanking water bending intensity with decreasing δ. Also, we find that the flanking water stretch mode of the Zundel-like species is strongly mixed with the flanking water bend, and the special pair proton oscillation band is strongly coupled with the bend modes of the central H5O2+moiety.
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Affiliation(s)
- Rajib Biswas
- Department of Chemistry, James Franck Institute, and Institute for Biophysical Dynamics, The University of Chicago, Chicago, Illinois 60637, USA
| | - William Carpenter
- Department of Chemistry, James Franck Institute, and Institute for Biophysical Dynamics, The University of Chicago, Chicago, Illinois 60637, USA
| | - Joseph A Fournier
- Department of Chemistry, James Franck Institute, and Institute for Biophysical Dynamics, The University of Chicago, Chicago, Illinois 60637, USA
| | - Gregory A Voth
- Department of Chemistry, James Franck Institute, and Institute for Biophysical Dynamics, The University of Chicago, Chicago, Illinois 60637, USA
| | - Andrei Tokmakoff
- Department of Chemistry, James Franck Institute, and Institute for Biophysical Dynamics, The University of Chicago, Chicago, Illinois 60637, USA
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25
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Wick CD. A comparison of sodium and hydrogen halides at the air-water interface. J Chem Phys 2017; 147:161703. [PMID: 29096503 PMCID: PMC5648577 DOI: 10.1063/1.4984114] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2017] [Accepted: 05/12/2017] [Indexed: 11/14/2022] Open
Abstract
New molecular models, parameterized to ab initio calculations, were developed to describe HBr and HI at the air-water interface. These were used to compare how the air-water interface influenced dissociation of NaX and HX, with X being Cl, Br, or I, and also their propensity for the interface. The polarizable multistate empirical valence bond method, which explicitly describes proton sharing, was used to model HX. Results showed that the air-water interface suppressed HX dissociation from a contact ion pair to a solvent separated to a greater degree than NaX dissociation. Furthermore, HX had a greater propensity for the interface than NaX, which was a consequence of the hydronium ion having a greatest interfacial activity of all species studied. As a consequence of this, the average configuration of dissociated HX, while in both contact ion and solvent separated ion pairs near the air-water interface, is with the dissociated hydrogen oriented more towards the air than the X atom.
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Affiliation(s)
- Collin D Wick
- Louisiana Tech University, Ruston, Louisiana 71270, USA
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26
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Indra S, Daschakraborty S. Mechanism of translational jump of a hydrophobic solute in supercooled water: Importance of presolvation. Chem Phys Lett 2017. [DOI: 10.1016/j.cplett.2017.07.084] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
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27
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28
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Duboué-Dijon E, Pluhařová E, Domin D, Sen K, Fogarty AC, Chéron N, Laage D. Coupled Valence-Bond State Molecular Dynamics Description of an Enzyme-Catalyzed Reaction in a Non-Aqueous Organic Solvent. J Phys Chem B 2017; 121:7027-7041. [PMID: 28675789 DOI: 10.1021/acs.jpcb.7b03102] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Enzymes are widely used in nonaqueous solvents to catalyze non-natural reactions. While experimental measurements showed that the solvent nature has a strong effect on the reaction kinetics, the molecular details of the catalytic mechanism in nonaqueous solvents have remained largely elusive. Here we study the transesterification reaction catalyzed by the paradigm subtilisin Carlsberg serine protease in an organic apolar solvent. The rate-limiting acylation step involves a proton transfer between active-site residues and the nucleophilic attack of the substrate to form a tetrahedral intermediate. We design the first coupled valence-bond state model that simultaneously describes both reactions in the enzymatic active site. We develop a new systematic procedure to parametrize this model on high-level ab initio QM/MM free energy calculations that account for the molecular details of the active site and for both substrate and protein conformational fluctuations. Our calculations show that the reaction energy barrier changes dramatically with the solvent and protein conformational fluctuations. We find that the mechanism of the tetrahedral intermediate formation during the acylation step is similar to that determined under aqueous conditions, and that the proton transfer and nucleophilic attack reactions occur concertedly. We identify the reaction coordinate to be mostly due to the rearrangement of some residual water molecules close to the active site.
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Affiliation(s)
- Elise Duboué-Dijon
- École Normale Supérieure - PSL Research University , Département de Chimie, Sorbonne Universités - UPMC Univ Paris 06, CNRS UMR 8640 PASTEUR, 24 rue Lhomond, 75005 Paris, France
| | - Eva Pluhařová
- École Normale Supérieure - PSL Research University , Département de Chimie, Sorbonne Universités - UPMC Univ Paris 06, CNRS UMR 8640 PASTEUR, 24 rue Lhomond, 75005 Paris, France
| | - Dominik Domin
- École Normale Supérieure - PSL Research University , Département de Chimie, Sorbonne Universités - UPMC Univ Paris 06, CNRS UMR 8640 PASTEUR, 24 rue Lhomond, 75005 Paris, France
| | - Kakali Sen
- École Normale Supérieure - PSL Research University , Département de Chimie, Sorbonne Universités - UPMC Univ Paris 06, CNRS UMR 8640 PASTEUR, 24 rue Lhomond, 75005 Paris, France
| | - Aoife C Fogarty
- École Normale Supérieure - PSL Research University , Département de Chimie, Sorbonne Universités - UPMC Univ Paris 06, CNRS UMR 8640 PASTEUR, 24 rue Lhomond, 75005 Paris, France
| | - Nicolas Chéron
- École Normale Supérieure - PSL Research University , Département de Chimie, Sorbonne Universités - UPMC Univ Paris 06, CNRS UMR 8640 PASTEUR, 24 rue Lhomond, 75005 Paris, France
| | - Damien Laage
- École Normale Supérieure - PSL Research University , Département de Chimie, Sorbonne Universités - UPMC Univ Paris 06, CNRS UMR 8640 PASTEUR, 24 rue Lhomond, 75005 Paris, France
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29
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Dahms F, Fingerhut BP, Nibbering ETJ, Pines E, Elsaesser T. Large-amplitude transfer motion of hydrated excess protons mapped by ultrafast 2D IR spectroscopy. Science 2017; 357:491-495. [DOI: 10.1126/science.aan5144] [Citation(s) in RCA: 99] [Impact Index Per Article: 14.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2017] [Accepted: 06/27/2017] [Indexed: 11/02/2022]
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30
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Zhang W, van Duin ACT. Second-Generation ReaxFF Water Force Field: Improvements in the Description of Water Density and OH-Anion Diffusion. J Phys Chem B 2017; 121:6021-6032. [DOI: 10.1021/acs.jpcb.7b02548] [Citation(s) in RCA: 63] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Weiwei Zhang
- Department of Mechanical
and Nuclear Engineering, Pennsylvania State University, University Park, Pennsylvania 16802, United States
| | - Adri C. T. van Duin
- Department of Mechanical
and Nuclear Engineering, Pennsylvania State University, University Park, Pennsylvania 16802, United States
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31
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Biswas R, Carpenter W, Voth GA, Tokmakoff A. Molecular modeling and assignment of IR spectra of the hydrated excess proton in isotopically dilute water. J Chem Phys 2017; 145:154504. [PMID: 27782492 DOI: 10.1063/1.4964723] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Infrared (IR) spectroscopy of the water O-H stretch has been widely used to probe both the local hydrogen-bonding structure and dynamics of aqueous systems. Although of significant interest, the IR spectroscopy of excess protons in water remains difficult to assign as a result of extensive and strong intermolecular interactions in hydrated proton complexes. As an alternate approach, we develop a mixed quantum-classical model for the vibrational spectroscopy of the excess proton in isotopically dilute water that draws on frozen proton-water clusters taken from reactive molecular dynamics trajectories of the latest generation multi-state empirical valence bond proton model (MS-EVB 3.2). A semi-empirical single oscillator spectroscopic map for the instantaneous transition frequency and transition dipole moment is constructed using potential energy surfaces for the O-H stretch coordinate of the excess proton using electronic structure calculations. Calculated spectra are compared with experimental spectra of dilute H+ in D2O obtained from double-difference FTIR to demonstrate the validity of the map. The model is also used to decompose IR spectra into contributions from different aqueous proton configurations. We find that the O-H transition frequency continuously decreases as the oxygen-oxygen length for a special pair proton decreases, shifting from Eigen- to Zundel-like configurations. The same shift is accompanied by a shift of the flanking water stretches of the Zundel complex to higher frequency than the hydronium O-H vibrations.
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Affiliation(s)
- Rajib Biswas
- Department of Chemistry, James Franck Institute, and Institute for Biophysical Dynamics, The University of Chicago, Chicago, Illinois 60637, USA
| | - William Carpenter
- Department of Chemistry, James Franck Institute, and Institute for Biophysical Dynamics, The University of Chicago, Chicago, Illinois 60637, USA
| | - Gregory A Voth
- Department of Chemistry, James Franck Institute, and Institute for Biophysical Dynamics, The University of Chicago, Chicago, Illinois 60637, USA
| | - Andrei Tokmakoff
- Department of Chemistry, James Franck Institute, and Institute for Biophysical Dynamics, The University of Chicago, Chicago, Illinois 60637, USA
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33
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Boda M, Naresh Patwari G. Insights into acid dissociation of HCl and HBr with internal electric fields. Phys Chem Chem Phys 2017; 19:7461-7464. [DOI: 10.1039/c6cp08870h] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
A critical electric field exerted by the solvent on the ionizable group leads to acid dissociation.
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Affiliation(s)
- Manjusha Boda
- Department of Chemistry
- Indian Institute of Technology Bombay
- Mumbai 400076
- India
| | - G. Naresh Patwari
- Department of Chemistry
- Indian Institute of Technology Bombay
- Mumbai 400076
- India
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34
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Carreón YJ, Mercado-Uribe H. Dielectric spectroscopy of biomolecules at low frequencies: Evidence of proton wires. J Mol Liq 2016. [DOI: 10.1016/j.molliq.2016.08.025] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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35
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Xu Y, Zhang J, Wang D. Investigation of the CH3Cl + CN(-) reaction in water: Multilevel quantum mechanics/molecular mechanics study. J Chem Phys 2016; 142:244505. [PMID: 26133439 DOI: 10.1063/1.4922938] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
The CH3Cl + CN(-) reaction in water was studied using a multilevel quantum mechanics/molecular mechanics (MM) method with the multilevels, electrostatic potential, density functional theory (DFT) and coupled-cluster single double triple (CCSD(T)), for the solute region. The detailed, back-side attack SN2 reaction mechanism was mapped along the reaction pathway. The potentials of mean force were calculated under both the DFT and CCSD(T) levels for the reaction region. The CCSD(T)/MM level of theory presents a free energy activation barrier height at 20.3 kcal/mol, which agrees very well with the experiment value at 21.6 kcal/mol. The results show that the aqueous solution has a dominant role in shaping the potential of mean force. The solvation effect and the polarization effect together increase the activation barrier height by ∼11.4 kcal/mol: the solvation effect plays a major role by providing about 75% of the contribution, while polarization effect only contributes 25% to the activation barrier height. Our calculated potential of mean force under the CCSD(T)/MM also has a good agreement with the one estimated using data from previous gas-phase studies.
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Affiliation(s)
- Yulong Xu
- School of Science, Qilu University of Technology, Jinan 250353, China
| | - Jingxue Zhang
- College of Physics and Electronics, Shandong Normal University, Jinan 250014, China
| | - Dunyou Wang
- College of Physics and Electronics, Shandong Normal University, Jinan 250014, China
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36
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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 II: Solvent Coordinate-Dependent Reaction Path. J Phys Chem B 2016; 120:2281-90. [PMID: 26876428 DOI: 10.1021/acs.jpcb.5b12744] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The protonation of methylamine base CH3NH2 by carbonic acid H2CO3 within a hydrogen (H)-bonded complex in aqueous solution was studied via Car-Parrinello dynamics in the preceding paper (Daschakraborty, S.; Kiefer, P. M.; Miller, Y.; Motro, Y.; Pines, D.; Pines, E.; Hynes, J. T. J. Phys. Chem. B 2016, DOI: 10.1021/acs.jpcb.5b12742). Here some important further details of the reaction path are presented, with specific emphasis on the water solvent's role. The overall reaction is barrierless and very rapid, on an ∼100 fs time scale, with the proton transfer (PT) event itself being very sudden (<10 fs). This transfer is preceded by the acid-base H-bond's compression, while the water solvent changes little until the actual PT occurrence; this results from the very strong driving force for the reaction, as indicated by the very favorable acid-protonated base ΔpKa difference. Further solvent rearrangement follows immediately the sudden PT's production of an incipient contact ion pair, stabilizing it by establishment of equilibrium solvation. The solvent water's short time scale ∼120 fs response to the incipient ion pair formation is primarily associated with librational modes and H-bond compression of water molecules around the carboxylate anion and the protonated base. This is consistent with this stabilization involving significant increase in H-bonding of hydration shell waters to the negatively charged carboxylate group oxygens' (especially the former H2CO3 donor oxygen) and the nitrogen of the positively charged protonated base's NH3(+).
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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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37
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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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Dongare P, Maji S, Hammarström L. Direct Evidence of a Tryptophan Analogue Radical Formed in a Concerted Electron−Proton Transfer Reaction in Water. J Am Chem Soc 2016; 138:2194-9. [DOI: 10.1021/jacs.5b08294] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Prateek Dongare
- Department of Chemistry,
Ångström Laboratory, Uppsala University, Box 523, Uppsala SE-751 20, Sweden
| | - Somnath Maji
- Department of Chemistry,
Ångström Laboratory, Uppsala University, Box 523, Uppsala SE-751 20, Sweden
| | - Leif Hammarström
- Department of Chemistry,
Ångström Laboratory, Uppsala University, Box 523, Uppsala SE-751 20, Sweden
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39
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Ditkovich J, Pines D, Pines E. Controlling reactivity by remote protonation of a basic side group in a bifunctional photoacid. Phys Chem Chem Phys 2016; 18:16106-15. [DOI: 10.1039/c5cp07672b] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Ultrafast reactivity-switch is achieved by remote-protonation caused by protons diffusing from acidic to basic side-groups of bifunctional photoacids.
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Affiliation(s)
- Julia Ditkovich
- Department of Chemistry
- Ben-Gurion University of the Negev
- Beer-Sheva 84105
- Israel
| | - Dina Pines
- Department of Chemistry
- Ben-Gurion University of the Negev
- Beer-Sheva 84105
- Israel
| | - Ehud Pines
- Department of Chemistry
- Ben-Gurion University of the Negev
- Beer-Sheva 84105
- Israel
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40
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Partanen L, Murdachaew G, Gerber RB, Halonen L. Temperature and collision energy effects on dissociation of hydrochloric acid on water surfaces. Phys Chem Chem Phys 2016; 18:13432-42. [DOI: 10.1039/c6cp00597g] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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41
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Biswas R, Tse YLS, Tokmakoff A, Voth GA. Role of Presolvation and Anharmonicity in Aqueous Phase Hydrated Proton Solvation and Transport. J Phys Chem B 2015; 120:1793-804. [PMID: 26575795 DOI: 10.1021/acs.jpcb.5b09466] [Citation(s) in RCA: 58] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Results from condensed phase ab initio molecular dynamics (AIMD) simulations suggest a proton transfer reaction is facilitated by "presolvation" in which the hydronium is transiently solvated by four water molecules, similar to the typical solvation structure of water, by accepting a weak hydrogen bond from the fourth water molecule. A new version 3.2 multistate empirical valence bond (MS-EVB 3.2) model for the hydrated excess proton incorporating this presolvation behavior is therefore developed. The classical MS-EVB simulations show similar structural properties as those of the previous model but with significantly improved diffusive behavior. The inclusion of nuclear quantum effects in the MS-EVB also provides an even better description of the proton diffusion rate. To quantify the influence of anharmonicity, a second model (aMS-EVB 3.2) is developed using the anharmonic aSPC/Fw water model, which provides similar structural properties but improved spectroscopic responses at high frequencies.
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Affiliation(s)
- Rajib Biswas
- Department of Chemistry, James Franck Institute, and Institute for Biophysical Dynamics, The University of Chicago , Chicago, Illinois 60637, United States
| | - Ying-Lung Steve Tse
- Department of Chemistry, James Franck Institute, and Institute for Biophysical Dynamics, The University of Chicago , Chicago, Illinois 60637, United States
| | - Andrei Tokmakoff
- Department of Chemistry, James Franck Institute, and Institute for Biophysical Dynamics, The University of Chicago , Chicago, Illinois 60637, United States
| | - Gregory A Voth
- Department of Chemistry, James Franck Institute, and Institute for Biophysical Dynamics, The University of Chicago , Chicago, Illinois 60637, United States
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Thämer M, De Marco L, Ramasesha K, Mandal A, Tokmakoff A. Ultrafast 2D IR spectroscopy of the excess proton in liquid water. Science 2015; 350:78-82. [DOI: 10.1126/science.aab3908] [Citation(s) in RCA: 218] [Impact Index Per Article: 24.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Despite decades of study, the structures adopted to accommodate an excess proton in water and the mechanism by which they interconvert remain elusive. We used ultrafast two-dimensional infrared (2D IR) spectroscopy to investigate protons in aqueous hydrochloric acid solutions. By exciting O–H stretching vibrations and detecting the spectral response throughout the mid-IR region, we observed the interaction between the stretching and bending vibrations characteristic of the flanking waters of the Zundel complex, [H(H2O)2]+, at 3200 and 1760 cm−1, respectively. From time-dependent shifts of the stretch-bend cross peak, we determined a lower limit on the lifetime of this complex of 480 femtoseconds. These results suggest a key role for the Zundel complex in aqueous proton transfer.
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43
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Mesele OO, Vartia AA, Laage D, Thompson WH. Reorientation of Isomeric Butanols: The Multiple Effects of Steric Bulk Arrangement on Hydrogen-Bond Dynamics. J Phys Chem B 2015; 120:1546-59. [DOI: 10.1021/acs.jpcb.5b07692] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Oluwaseun O. Mesele
- Department
of Chemistry, University of Kansas, Lawrence, Kansas 66045, United States
| | - Anthony A. Vartia
- Department
of Chemistry, University of Kansas, Lawrence, Kansas 66045, United States
| | - Damien Laage
- Department
of Chemistry, Ecole Normale Supérieure, UMR ENS-CNRS-UPMC 8640, 24 rue Lhmond, 75005 Paris, France
| | - Ward H. Thompson
- Department
of Chemistry, University of Kansas, Lawrence, Kansas 66045, United States
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44
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Tuñón I, Laage D, Hynes JT. Are there dynamical effects in enzyme catalysis? Some thoughts concerning the enzymatic chemical step. Arch Biochem Biophys 2015; 582:42-55. [PMID: 26087289 PMCID: PMC4560206 DOI: 10.1016/j.abb.2015.06.004] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2015] [Revised: 06/05/2015] [Accepted: 06/06/2015] [Indexed: 11/21/2022]
Abstract
We offer some thoughts on the much debated issue of dynamical effects in enzyme catalysis, and more specifically on their potential role in the acceleration of the chemical step. Since the term 'dynamics' has been used with different meanings, we find it useful to first return to the Transition State Theory rate constant, its assumptions and the choices it involves, and detail the various sources of deviations from it due to dynamics (or not). We suggest that much can be learned about the key current questions for enzyme catalysis from prior extensive studies of dynamical and other effects in the case of reactions in solution. We analyze dynamical effects both in the neighborhood of the transition state and far from it, together with the situation when quantum nuclear motion is central to the reaction, and we illustrate our discussion with various examples of enzymatic reactions.
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Affiliation(s)
- Iñaki Tuñón
- Departamento de Química Física, Universidad de Valencia, Spain.
| | - Damien Laage
- Ecole Normale Supérieure-PSL Research University, Chemistry Department, Sorbonne Universités-UPMC University Paris 06, CNRS UMR 8640 Pasteur, 24 rue Lhomond, 75005 Paris, France.
| | - James T Hynes
- Ecole Normale Supérieure-PSL Research University, Chemistry Department, Sorbonne Universités-UPMC University Paris 06, CNRS UMR 8640 Pasteur, 24 rue Lhomond, 75005 Paris, France; Department of Chemistry and Biochemistry, University of Colorado, Boulder, CO 80309-0215, USA.
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45
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Lespes N, Filhol JS. Using Implicit Solvent in Ab Initio Electrochemical Modeling: Investigating Li+/Li Electrochemistry at a Li/Solvent Interface. J Chem Theory Comput 2015; 11:3375-82. [DOI: 10.1021/acs.jctc.5b00170] [Citation(s) in RCA: 48] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Nicolas Lespes
- Institut Charles
Gerhardt−CNRS 5253 and Université de Montpellier, Place Eugène Bataillon, 34 095 Montpellier Cédex 5, France
- Réseau
sur le Stockage Electrochimique de l’Energie (RS2E), CNRS FR3459, 80039 Amiens Cedex, France
| | - Jean-Sébastien Filhol
- Institut Charles
Gerhardt−CNRS 5253 and Université de Montpellier, Place Eugène Bataillon, 34 095 Montpellier Cédex 5, France
- Réseau
sur le Stockage Electrochimique de l’Energie (RS2E), CNRS FR3459, 80039 Amiens Cedex, France
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46
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Szabla R, Sponer JE, Sponer J, Sobolewski AL, Góra RW. Solvent effects on the photochemistry of 4-aminoimidazole-5-carbonitrile, a prebiotically plausible precursor of purines. Phys Chem Chem Phys 2015; 16:17617-26. [PMID: 25026912 DOI: 10.1039/c4cp02074j] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
4-Aminoimidazole-5-carbonitrile (AICN) was suggested as a prebiotically plausible precursor of purine nucleobases and nucleotides. Although it can be formed in a sequence of photoreactions, AICN is immune to further irradiation with UV-light. We present state-of-the-art multi-reference quantum-chemical calculations of potential energy surface cuts and conical intersection optimizations to explain the molecular mechanisms underlying the photostability of this compound. We have identified the N-H bond stretching and ring-puckering mechanisms that should be responsible for the photochemistry of AICN in the gas phase. We have further considered the photochemistry of AICN-water clusters, while including up to six explicit water molecules. The calculations reveal charge transfer to solvent followed by formation of an H3O(+) cation, both of which occur on the (1)πσ* hypersurface. Interestingly, a second proton transfer to an adjacent water molecule leads to a (1)πσ*/S0 conical intersection. We suggest that this electron-driven proton relay might be characteristic of low-lying (1)πσ* states in chromophore-water clusters. Owing to its nature, this mechanism might also be responsible for the photostability of analogous organic molecules in bulk water.
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Affiliation(s)
- Rafał Szabla
- Institute of Biophysics, Academy of Sciences of the Czech Republic, Královopolská 135, 61265, Brno, Czech Republic.
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47
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Hynes JT. Molecules in Motion: Chemical Reaction and Allied Dynamics in Solution and Elsewhere. Annu Rev Phys Chem 2015; 66:1-20. [DOI: 10.1146/annurev-physchem-040214-121833] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- James T. Hynes
- Department of Chemistry and Biochemistry, University of Colorado, Boulder, Colorado 80309;
- Department of Chemistry, UMR ENS-CNRS-UPMC-8640, Ecole Normale Supérieure, Paris, France 75005
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48
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Geneste G, Ottochian A, Hermet J, Dezanneau G. Proton transport in barium stannate: classical, semi-classical and quantum regimes. Phys Chem Chem Phys 2015; 17:19104-18. [PMID: 26126772 DOI: 10.1039/c5cp01216c] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
Density-functional theory calculations are performed to investigate proton transport in BaSnO3.
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Affiliation(s)
| | - Alistar Ottochian
- Laboratoire Structures
- Propriétés et Modélisation des Solides
- UMR CNRS 8580
- 92295 Châtenay-Malabry Cedex
- France
| | | | - Guilhem Dezanneau
- Laboratoire Structures
- Propriétés et Modélisation des Solides
- UMR CNRS 8580
- 92295 Châtenay-Malabry Cedex
- France
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49
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Pines D, Keinan S, Kiefer PM, Hynes JT, Pines E. Effect of Solvent Dielectric Constant and Acidity on the OH Vibration Frequency in Hydrogen-Bonded Complexes of Fluorinated Ethanols. J Phys Chem B 2014; 119:9278-86. [DOI: 10.1021/jp509914w] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Dina Pines
- Department
of Chemistry, Ben-Gurion University of the Negev, P.O. Box 653, Beer-Sheva, 84105, Israel
| | - Sharon Keinan
- 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
| | - James T. Hynes
- Department
of Chemistry and Biochemistry, University of Colorado, Boulder, Colorado 80309-0215, United States
- Chemistry
Department, École Normale Supérieure, UMR ENS-CNRS-UPMC 8640, 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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50
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Xie Y, Luk HL, Yang X, Glusac KD. Excited-State Hydroxide Ion Transfer from a Model Xanthenol Photobase. J Phys Chem B 2014; 119:2498-506. [DOI: 10.1021/jp5080169] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Yun Xie
- Department of Chemistry and
Center for Photochemical Sciences, Bowling Green State University, Bowling
Green, Ohio 43403, United States
| | - Hoi Ling Luk
- Department of Chemistry and
Center for Photochemical Sciences, Bowling Green State University, Bowling
Green, Ohio 43403, United States
| | - Xin Yang
- Department of Chemistry and
Center for Photochemical Sciences, Bowling Green State University, Bowling
Green, Ohio 43403, United States
| | - Ksenija D. Glusac
- Department of Chemistry and
Center for Photochemical Sciences, Bowling Green State University, Bowling
Green, Ohio 43403, United States
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