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Limmer DT, Götz AW, Bertram TH, Nathanson GM. Molecular Insights into Chemical Reactions at Aqueous Aerosol Interfaces. Annu Rev Phys Chem 2024; 75:111-135. [PMID: 38360527 DOI: 10.1146/annurev-physchem-083122-121620] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/17/2024]
Abstract
Atmospheric aerosols facilitate reactions between ambient gases and dissolved species. Here, we review our efforts to interrogate the uptake of these gases and the mechanisms of their reactions both theoretically and experimentally. We highlight the fascinating behavior of N2O5 in solutions ranging from pure water to complex mixtures, chosen because its aerosol-mediated reactions significantly impact global ozone, hydroxyl, and methane concentrations. As a hydrophobic, weakly soluble, and highly reactive species, N2O5 is a sensitive probe of the chemical and physical properties of aerosol interfaces. We employ contemporary theory to disentangle the fate of N2O5 as it approaches pure and salty water, starting with adsorption and ending with hydrolysis to HNO3, chlorination to ClNO2, or evaporation. Flow reactor and gas-liquid scattering experiments probe even greater complexity as added ions, organic molecules, and surfactants alter the interfacial composition and reaction rates. Together, we reveal a new perspective on multiphase chemistry in the atmosphere.
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Affiliation(s)
- David T Limmer
- Department of Chemistry, University of California, Berkeley, California, USA;
- Materials Science Division, Lawrence Berkeley National Laboratory, Berkeley, California, USA
- Kavli Energy NanoScience Institute, Berkeley, California, USA
- Chemical Science Division, Lawrence Berkeley National Laboratory, Berkeley, California, USA
| | - Andreas W Götz
- San Diego Supercomputer Center, University of California San Diego, La Jolla, California, USA;
| | - Timothy H Bertram
- Department of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin, USA; ,
| | - Gilbert M Nathanson
- Department of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin, USA; ,
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2
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Das A, Musharaf Ali S. Structure and dynamics of dissociated and undissociated forms of nitric acid and their implications in interfacial mass transfer: insights from molecular dynamics simulations. Phys Chem Chem Phys 2024; 26:6916-6938. [PMID: 38334446 DOI: 10.1039/d3cp05622h] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/10/2024]
Abstract
Nitric acid (HNO3) is widely used in various chemical and nuclear industries. Therefore, it is important to develop an understanding of the different forms of nitric acid for its practical applications. Molecular dynamics (MD) simulation is one of the best tools to investigate the behavior of concentrated nitric acid in aqueous solution with various forms together with pure nitric acid to identify a suitable model of nitric acid for use in simulations of biphasic systems for interfacial mass transfer. The Mulliken partial charge embedded OPLS-AA force field was used to model the neutral nitric acid, hydronium ion and nitrate ion, and it was found that the Mulliken partial charge embedded force field works quite well. The computed density of the dissociated and mixed-form acid was in good agreement with the experimental values. In water, the HNO3 molecule was seen to be coordinated with three water molecules in the first sphere of coordination. The distribution of water surrounding the HNO3 molecule and nitrate ion was corroborated by the DFT-optimized hydrated cluster. The calculated diffusivity values of the neutral acid and ions were significantly higher in the mixed form of nitric acid, which is an important dynamic quantity controlling the kinetics of the liquid-liquid interfacial extraction. The structural analysis revealed that the local aggregation is minimized when both forms of acid are present together in the solution. The water-ion and water-neutral acid interactions were predicted to be enhanced, as confirmed by H-bond studies. The shear viscosity of the mixed acid exhibited excellent agreement with the experimental values, which again confirms the consideration of the mixed form of nitric acid. The simulated value of surface tension for the mixed form of acid also appeared to be quite accurate based on the surface tension of water. The mixed form of nitric acid comprising both forms of acid is the best representation for nitric acid to be considered for MD simulations of biphasic systems. The mixed form of nitric acid established that the concentrated nitric acid may not be present either in the fully dissociated form or fully undissociated form in the solution.
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Affiliation(s)
- Arya Das
- Nuclear Recycle Board, Bhabha Atomic Research Centre, Mumbai, 400094, India
- Homi Bhabha National Institute, Mumbai, 400094, India.
| | - Sk Musharaf Ali
- Chemical Engineering Division, Bhabha Atomic Research Centre, Mumbai, 400085, India
- Homi Bhabha National Institute, Mumbai, 400094, India.
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3
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de la Puente M, David R, Gomez A, Laage D. Acids at the Edge: Why Nitric and Formic Acid Dissociations at Air-Water Interfaces Depend on Depth and on Interface Specific Area. J Am Chem Soc 2022; 144:10524-10529. [PMID: 35658415 DOI: 10.1021/jacs.2c03099] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Whether the air-water interface decreases or increases the acidity of simple organic and inorganic acids compared to the bulk is critically important in a broad range of environmental and biochemical processes. However, a consensus has not yet been achieved on this key question. Here we use machine learning-based reactive molecular dynamics simulations to study the dissociation of paradigmatic nitric and formic acids at the air-water interface. We show that the local acidity profile across the interface is determined by changes in acid and conjugate base solvation and that the acidity decreases abruptly over a transition region of a few molecular layers. At the interface, both acids are weaker than in the bulk due to desolvation. In contrast, acidities below the interface reach a plateau and are all the stronger compared to those in the bulk as the surface to volume ratio of the aqueous phase is large, due to the growing impact of the stabilization of the released proton at the surface of the water. These results imply that the measured degree of dissociation sensitively depends on the experimental probing length and system size and suggest a molecular explanation for the contrasting experimental results. The aerosol size dependence of acidity has important consequences for atmospheric chemistry.
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Affiliation(s)
- Miguel de la Puente
- PASTEUR, Department of Chemistry, École Normale Supérieure-PSL, Sorbonne Université, CNRS, Paris 75005, France
| | - Rolf David
- PASTEUR, Department of Chemistry, École Normale Supérieure-PSL, Sorbonne Université, CNRS, Paris 75005, France
| | - Axel Gomez
- PASTEUR, Department of Chemistry, École Normale Supérieure-PSL, Sorbonne Université, CNRS, Paris 75005, France
| | - Damien Laage
- PASTEUR, Department of Chemistry, École Normale Supérieure-PSL, Sorbonne Université, CNRS, Paris 75005, France
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Abstract
We use molecular dynamics simulations to study the thermodynamics and kinetics of alanine dipeptide isomerization at the air-water interface. Thermodynamically, we find an affinity of the dipeptide to the interface. This affinity arises from stabilizing intramolecular interactions that become unshielded as the dipeptide is desolvated. Kinetically, we consider the rate of transitions between the αL and β conformations of alanine dipeptide and evaluate it as a continuous function of the distance from the interface using a recent extension of transition path sampling, TPS+U. The rate of isomerization at the Gibbs dividing surface is suppressed relative to the bulk by a factor of 3. Examination of the ensemble of transition states elucidates the role of solvent degrees of freedom in mediating favorable intramolecular interactions along the reaction pathway of isomerization. Near the air-water interface, water is less effective at mediating these intramolecular interactions.
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Affiliation(s)
- Aditya N Singh
- Department of Chemistry, University of California, Berkeley, California 94720, United States
- Chemical Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
| | - David T Limmer
- Department of Chemistry, University of California, Berkeley, California 94720, United States
- Chemical Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
- Materials Science Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
- Kavli Energy Nanoscience Institute at Berkeley, Berkeley, California 94720, United States
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5
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Ab initio metadynamics calculations reveal complex interfacial effects in acetic acid deprotonation dynamics. J Mol Liq 2021. [DOI: 10.1016/j.molliq.2021.115624] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
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6
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Mitra S, Yang N, McCaslin LM, Gerber RB, Johnson MA. Size-Dependent Onset of Nitric Acid Dissociation in Cs +·(HNO 3)(H 2O) n=0-11 Clusters at 20 K. J Phys Chem Lett 2021; 12:3335-3342. [PMID: 33779169 DOI: 10.1021/acs.jpclett.1c00235] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
We report the water-mediated charge separation of nitric acid upon incorporation into size-selected Cs+·(HNO3)(H2O)n=0-11 clusters at 20 K. Dramatic spectral changes are observed in the n = 7-9 range that are traced to the formation of many isomeric structures associated with intermediate transfer of the acidic proton to the water network. This transfer is complete by n = 10, which exhibits much simpler vibrational band patterns consistent with those expected for a tricoordinated hydronium ion (the Eigen motif) along with the NO stretching bands predicted for a hydrated NO3- anion that is directly complexed to the Cs+ cation. Theoretical analysis of the n = 10 spectrum indicates that the dissociated ions adopt a solvent-separated ion-pair configuration such that the Cs+ and H3O+ cations flank the NO3- anion in a microhydrated salt bridge. This charge separation motif is evidently assisted by the electrostatic stabilization of the product NO3-/H3O+ ion pair by the proximal metal ion.
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Affiliation(s)
- Sayoni Mitra
- Sterling Chemistry Laboratory, Yale University, New Haven, Connecticut 06511, United States
| | - Nan Yang
- Sterling Chemistry Laboratory, Yale University, New Haven, Connecticut 06511, United States
| | - Laura M McCaslin
- Combustion Research Facility, Sandia National Laboratories, Livermore, California 94550, United States
| | - R Benny Gerber
- Institute of Chemistry and the Fritz-Haber Center for Molecular Dynamics, The Hebrew University, Jerusalem, Israel
- Department of Chemistry, University of California Irvine, Irvine, California 92697, United States
| | - Mark A Johnson
- Sterling Chemistry Laboratory, Yale University, New Haven, Connecticut 06511, United States
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7
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Anglada JM, Martins-Costa MTC, Francisco JS, Ruiz-López MF. Reactivity of Undissociated Molecular Nitric Acid at the Air-Water Interface. J Am Chem Soc 2020; 143:453-462. [PMID: 33355444 DOI: 10.1021/jacs.0c11841] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Recent experiments and theoretical calculations have shown that HNO3 may exist in molecular form in aqueous environments, where in principle one would expect this strong acid to be completely dissociated. Much effort has been devoted to understanding this fact, which has huge environmental relevance since nitric acid is a component of acid rain and also contributes to renoxification processes in the atmosphere. Although the importance of heterogeneous processes such as oxidation and photolysis have been evidenced by experiments, most theoretical studies on hydrated molecular HNO3 have focused on the acid dissociation mechanism. In the present work, we carry out calculations at various levels of theory to obtain insight into the properties of molecular nitric acid at the surface of liquid water (the air-water interface). Through multi-nanosecond combined quantum-classical molecular dynamics simulations, we analyze the interface affinity of nitric acid and provide an order of magnitude for its lifetime with regard to acid dissociation, which is close to the value deduced using thermodynamic data in the literature (∼0.3 ns). Moreover, we study the electronic absorption spectrum and calculate the rate constant for the photolytic process HNO3 + hν → NO2 + OH, leading to 2 × 10-6 s-1, about twice the value in the gas phase. Finally, we describe the reaction HNO3 + OH → NO3 + H2O using a cluster model containing 21 water molecules with the help of high-level ab initio calculations. A large number of reaction paths are explored, and our study leads to the conclusion that the most favorable mechanism involves the formation of a pre-reactive complex (HNO3)(OH) from which product are obtained through a coupled proton-electron transfer mechanism that has a free-energy barrier of 6.65 kcal·mol-1. Kinetic calculations predict a rate constant increase by ∼4 orders of magnitude relative to the gas phase, and we conclude that at the air-water interface, a lower limit for the rate constant is k = 1.2 × 10-9 cm3·molecule-1·s-1. The atmospheric significance of all these results is discussed.
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Affiliation(s)
- Josep M Anglada
- Departament de Química Biològica, Institut de Química Avançada de Catalunya (IQAC - CSIC), c/Jordi Girona 18, E-08034 Barcelona, Spain
| | - Marilia T C Martins-Costa
- Laboratoire de Physique et Chimie Théoriques, UMR CNRS 7019, University of Lorraine, BP 70239, 54506 Vandoeuvre-lès-Nancy, France
| | - Joseph S Francisco
- Department of Earth and Environmental Science and Department of Chemistry, University of Pennsylvania, Philadelphia, Pennsylvania 19104-6316, United States
| | - Manuel F Ruiz-López
- Laboratoire de Physique et Chimie Théoriques, UMR CNRS 7019, University of Lorraine, BP 70239, 54506 Vandoeuvre-lès-Nancy, France
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8
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Martins‐Costa MTC, Ruiz‐López MF. Isoprene Reactivity on Water Surfaces from ab initio QM/MM Molecular Dynamics Simulations. Chemphyschem 2020; 21:2263-2271. [DOI: 10.1002/cphc.202000652] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2020] [Revised: 08/17/2020] [Indexed: 11/07/2022]
Affiliation(s)
- Marilia T. C. Martins‐Costa
- Laboratoire de Physique et Chimie Théoriques UMR CNRS 7019 University of Lorraine CNRS BP 70239 54506 Vandoeuvre-lès-Nancy France
| | - Manuel F. Ruiz‐López
- Laboratoire de Physique et Chimie Théoriques UMR CNRS 7019 University of Lorraine CNRS BP 70239 54506 Vandoeuvre-lès-Nancy France
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9
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Ruiz-Lopez MF, Francisco JS, Martins-Costa MTC, Anglada JM. Molecular reactions at aqueous interfaces. Nat Rev Chem 2020; 4:459-475. [PMID: 37127962 DOI: 10.1038/s41570-020-0203-2] [Citation(s) in RCA: 120] [Impact Index Per Article: 30.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/02/2020] [Indexed: 12/16/2022]
Abstract
This Review aims to critically analyse the emerging field of chemical reactivity at aqueous interfaces. The subject has evolved rapidly since the discovery of the so-called 'on-water catalysis', alluding to the dramatic acceleration of reactions at the surface of water or at its interface with hydrophobic media. We review critical experimental studies in the fields of atmospheric and synthetic organic chemistry, as well as related research exploring the origins of life, to showcase the importance of this phenomenon. The physico-chemical aspects of these processes, such as the structure, dynamics and thermodynamics of adsorption and solvation processes at aqueous interfaces, are also discussed. We also present the basic theories intended to explain interface catalysis, followed by the results of advanced ab initio molecular-dynamics simulations. Although some topics addressed here have already been the focus of previous reviews, we aim at highlighting their interconnection across diverse disciplines, providing a common perspective that would help us to identify the most fundamental issues still incompletely understood in this fast-moving field.
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10
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Mitra S, Duong CH, McCaslin LM, Gerber RB, Johnson MA. Isomer-specific cryogenic ion vibrational spectroscopy of the D 2 tagged Cs +(HNO 3)(H 2O) n=0-2 complexes: ion-driven enhancement of the acidic H-bond to water. Phys Chem Chem Phys 2020; 22:4501-4507. [PMID: 32068217 DOI: 10.1039/c9cp06689f] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
We report how the binary HNO3(H2O) interaction is modified upon complexation with a nearby Cs+ ion. Isomer-selective IR photodissociation spectra of the D2-tagged, ternary Cs+(HNO3)H2O cation confirms that two structural isomers are generated in the cryogenic ion source. In one of these, both HNO3 and H2O are directly coordinated to the ion, while in the other, the water molecule is attached to the OH group of the acid, which in turn binds to Cs+ with its -NO2 group. The acidic OH stretching fundamental in the latter isomer displays a ∼300 cm-1 red-shift relative to that in the neutral H-bonded van der Waals complex, HNO3(H2O). This behavior is analyzed with the aid of electronic structure calculations and discussed in the context of the increased effective acidity of HNO3 in the presence of the cation.
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Affiliation(s)
- Sayoni Mitra
- Sterling Chemistry Laboratory, Yale University, New Haven, CT, USA.
| | - Chinh H Duong
- Sterling Chemistry Laboratory, Yale University, New Haven, CT, USA.
| | - Laura M McCaslin
- Department of Chemistry, University of California Irvine, Irvine, CA, USA. and Institute of Chemistry and the Fritz-Haber Center for Molecular Dynamics, The Hebrew University, Jerusalem, Israel
| | - R Benny Gerber
- Department of Chemistry, University of California Irvine, Irvine, CA, USA. and Institute of Chemistry and the Fritz-Haber Center for Molecular Dynamics, The Hebrew University, Jerusalem, Israel
| | - Mark A Johnson
- Sterling Chemistry Laboratory, Yale University, New Haven, CT, USA.
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11
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Cordeiro RM, Yusupov M, Razzokov J, Bogaerts A. Parametrization and Molecular Dynamics Simulations of Nitrogen Oxyanions and Oxyacids for Applications in Atmospheric and Biomolecular Sciences. J Phys Chem B 2020; 124:1082-1089. [DOI: 10.1021/acs.jpcb.9b08172] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Rodrigo M. Cordeiro
- Centro de Ciências Naturais e Humanas, Universidade Federal do ABC, Avenida dos Estados 5001, CEP 09210-580 Santo André (SP), Brazil
| | - Maksudbek Yusupov
- Research Group PLASMANT, Department of Chemistry, University of Antwerp, Universiteitsplein 1, B-2610 Antwerp, Belgium
| | - Jamoliddin Razzokov
- Research Group PLASMANT, Department of Chemistry, University of Antwerp, Universiteitsplein 1, B-2610 Antwerp, Belgium
| | - Annemie Bogaerts
- Research Group PLASMANT, Department of Chemistry, University of Antwerp, Universiteitsplein 1, B-2610 Antwerp, Belgium
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12
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Balamurugan K, Prakash M, Subramanian V. Theoretical Insights into the Role of Water Molecules in the Guanidinium-Based Protein Denaturation Process in Specific to Aromatic Amino Acids. J Phys Chem B 2019; 123:2191-2202. [PMID: 30672268 DOI: 10.1021/acs.jpcb.8b08968] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Noncovalent interactions between the guanidinium cation (Gdm+) and aromatic amino acids (AAs) in the water molecules have been studied using quantum chemical calculation and molecular dynamics (MD) simulations. Our studies show that there are two different modes of interactions between Gdm+ and AAs with and without water molecules. It is observed that nonhydrated Gdm+ interacts with AAs through N-H···π interactions, whereas hydrated clusters of Gdm+ are stabilized by stacking interactions with the help of the water-mediated hydrogen bond. Thus, different hydration patterns have significant effects on the predominant cation···π interactions in AAs-Gdm+ complexes. Findings from MD simulation elicit that the interaction pattern of Gdm+ with AAs varies as Phe < Tyr < Trp. Both the QM and MD calculations show a similar trend in the interaction of AAs with Gdm+. Moreover, the interaction of AAs with Gdm+ depends on the spatial orientation of AAs in the protein and the concomitant local structure, that is, the AAs present in the unstructured region of protein such as coils and bends exhibit higher binding for Gdm+ when compared to the AAs present in the structured region of the protein such as the α-helix and the β-sheet. Our study clearly reveals that H-bonded water molecules and the hydration pattern of Gdm+ as well as the positional presence of these AAs in the protein structure context play determining roles in the denaturation of protein by the Gdm+ cation.
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Affiliation(s)
- Kanagasabai Balamurugan
- Chemical Laboratory , CSIR-Central Leather Research Institute , Adyar, Chennai 600 020 , India
| | - Muthuramalingam Prakash
- Chemical Laboratory , CSIR-Central Leather Research Institute , Adyar, Chennai 600 020 , India
| | - Venkatesan Subramanian
- Chemical Laboratory , CSIR-Central Leather Research Institute , Adyar, Chennai 600 020 , India.,Academy of Scientific and Innovative Research (AcSIR) , CSIR-CLRI Campus , Chennai 600 020 , India
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13
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Qiu J, Ishizuka S, Tonokura K, Enami S. Reactions of Criegee Intermediates with Benzoic Acid at the Gas/Liquid Interface. J Phys Chem A 2018; 122:6303-6310. [DOI: 10.1021/acs.jpca.8b04995] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Junting Qiu
- Graduate School of Frontier Sciences, The University of Tokyo, 5-1-5 Kashiwanoha, Kashiwa 277-8563, Japan
| | - Shinnosuke Ishizuka
- National Institute for Environmental Studies, 16-2 Onogawa, Tsukuba 305-8506, Japan
| | - Kenichi Tonokura
- Graduate School of Frontier Sciences, The University of Tokyo, 5-1-5 Kashiwanoha, Kashiwa 277-8563, Japan
| | - Shinichi Enami
- National Institute for Environmental Studies, 16-2 Onogawa, Tsukuba 305-8506, Japan
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14
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Parashar S, Lesnicki D, Sulpizi M. Increased Acid Dissociation at the Quartz/Water Interface. J Phys Chem Lett 2018; 9:2186-2189. [PMID: 29634900 DOI: 10.1021/acs.jpclett.8b00686] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
As shown by a quite significant amount of literature, acids at the water surface tend to be "less" acid, meaning that their associated form is favored over the conjugated base. What happens at the solid/liquid interface? In the case of the silica/water interface, we show how the acidity of adsorbed molecules can instead increase. Using a free energy perturbation approach in combination with electronic structure-based molecular dynamics simulations, we show how the acidity of pyruvic acid at the quartz/water interface is increased by almost two units. Such increased acidity is the result of the specific microsolvation at the interface and, in particular, of the stabilization of the deprotonated form by the silanols on the quartz surface and the special interfacial water layer.
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Affiliation(s)
- Shivam Parashar
- Department of Chemical Engineering , Indian Institute of Technology Roorkee , Roorkee , Uttarakhand 247667 , India
| | - Dominika Lesnicki
- Institute of Physics , Johannes Gutenberg University Mainz , Staudingerweg 7 , 55099 Mainz , Germany
| | - Marialore Sulpizi
- Institute of Physics , Johannes Gutenberg University Mainz , Staudingerweg 7 , 55099 Mainz , Germany
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15
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Prakash M, Subramanian V. Ab initio and density functional theory (DFT) studies on triflic acid with water and protonated water clusters. J Mol Model 2016; 22:293. [PMID: 27888404 DOI: 10.1007/s00894-016-3158-y] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2016] [Accepted: 11/08/2016] [Indexed: 02/04/2023]
Abstract
The structure, stability and infrared spectral signatures of triflic acid (TA) with water clusters (Wn) and protonated water clusters (TAH+Wn, n = 1 - 6) were computed using DFT and MP2 methods. Our calculations show that a minimum of three water molecules are necessary to stabilize the dissociated zwitterionic form of TA. It can be seen from the results that there is no significant movement of protons in smaller (n = 1 and 2) and linear (n = 1 - 6) types of water clusters. Further, the geometries of TAWn clusters first form a neutral pair (NP) to contact ion pair (CIP), then form a solvent separated ion pair (SSIP) in a water hexamer. These findings reveal that proton transfer may take place through NP to CIP and then CIP to SSIP. The calculated binding energies (BEs) of ion pair clusters is always higher than that of NP clusters (i.e., more stable than the NP). Existing excess proton linear chain clusters transfer a proton to adjacent water molecules via a Grotthuss mechanism, whereas the same isomers in the branched motifs do not conduct protons. Examination of geometrical parameters and infrared frequencies reveals hydronium ion (H3O+ also called Eigen cation) formation in both TAWn and protonated TAWn clusters. The stability of Eigen water clusters is three times higher than that of other non-Eigen water clusters. Our study shows clearly that formation of ion pairs in TAWn and TAH+Wn clusters greatly favors proton transfer to neighboring water molecules and also enhances the stability of these complexes.
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Affiliation(s)
- M Prakash
- Department of Chemistry and Research Institute, SRM University, Kattankulathur, 603203, Tamil Nadu, India
- Chemical Laboratory, CSIR-Central Leather Research Institute, Adyar, Chennai, 600 020, India
| | - V Subramanian
- Chemical Laboratory, CSIR-Central Leather Research Institute, Adyar, Chennai, 600 020, India.
- Academy of Scientific and Innovative Research (AcSIR), CSIR-CLRI Campus, Chennai, 600 020, India.
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16
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Agmon N, Bakker HJ, Campen RK, Henchman RH, Pohl P, Roke S, Thämer M, Hassanali A. Protons and Hydroxide Ions in Aqueous Systems. Chem Rev 2016; 116:7642-72. [PMID: 27314430 DOI: 10.1021/acs.chemrev.5b00736] [Citation(s) in RCA: 287] [Impact Index Per Article: 35.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Understanding the structure and dynamics of water's constituent ions, proton and hydroxide, has been a subject of numerous experimental and theoretical studies over the last century. Besides their obvious importance in acid-base chemistry, these ions play an important role in numerous applications ranging from enzyme catalysis to environmental chemistry. Despite a long history of research, many fundamental issues regarding their properties continue to be an active area of research. Here, we provide a review of the experimental and theoretical advances made in the last several decades in understanding the structure, dynamics, and transport of the proton and hydroxide ions in different aqueous environments, ranging from water clusters to the bulk liquid and its interfaces with hydrophobic surfaces. The propensity of these ions to accumulate at hydrophobic surfaces has been a subject of intense debate, and we highlight the open issues and challenges in this area. Biological applications reviewed include proton transport along the hydration layer of various membranes and through channel proteins, problems that are at the core of cellular bioenergetics.
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Affiliation(s)
- Noam Agmon
- The Fritz Haber Research Center, Institute of Chemistry, The Hebrew University of Jerusalem , Jerusalem 91904, Israel
| | - Huib J Bakker
- FOM Institute AMOLF , Science Park 104, 1098 XG Amsterdam, The Netherlands
| | - R Kramer Campen
- Fritz Haber Institute of the Max Planck Society , Faradayweg 4-6, 14195 Berlin, Germany
| | - Richard H Henchman
- Manchester Institute of Biotechnology, School of Chemistry, The University of Manchester , Oxford Road, Manchester M13 9PL, United Kingdom
| | - Peter Pohl
- Johannes Kepler University Linz , Institute of Biophysics, Gruberstrasse 40, 4020 Linz, Austria
| | - Sylvie Roke
- Laboratory for Fundamental BioPhotonics (LBP), Institute of Bioengineering (IBI), and Institute of Material Science (IMX), School of Engineering (STI), and Lausanne Centre for Ultrafast Science (LACUS), École Polytechnique Fédérale de Lausanne (EPFL) , CH-1015, Lausanne, Switzerland
| | - Martin Thämer
- Fritz Haber Institute of the Max Planck Society , Faradayweg 4-6, 14195 Berlin, Germany.,Department of Chemistry, Institute for Biophysical Dynamics, and James Franck Institute, The University of Chicago , Chicago, Illinois 60637, United States
| | - Ali Hassanali
- CMSP Section, The Abdus Salaam International Center for Theoretical Physics , I-34151 Trieste, Italy
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17
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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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18
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Murdachaew G, Nathanson GM, Benny Gerber R, Halonen L. Deprotonation of formic acid in collisions with a liquid water surface studied by molecular dynamics and metadynamics simulations. Phys Chem Chem Phys 2016; 18:29756-29770. [DOI: 10.1039/c6cp06071d] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Formic acid has a lower barrier to deprotonation at the air–water interface than in bulk liquid water.
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Affiliation(s)
- Garold Murdachaew
- Laboratory of Physical Chemistry
- Department of Chemistry
- FI-00014 University of Helsinki
- Finland
| | | | - R. Benny Gerber
- Laboratory of Physical Chemistry
- Department of Chemistry
- FI-00014 University of Helsinki
- Finland
- Institute of Chemistry and the Fritz Haber Research Center
| | - Lauri Halonen
- Laboratory of Physical Chemistry
- Department of Chemistry
- FI-00014 University of Helsinki
- Finland
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19
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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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20
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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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21
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Baer MD, Kuo IFW, Tobias DJ, Mundy CJ. Toward a unified picture of the water self-ions at the air-water interface: a density functional theory perspective. J Phys Chem B 2014; 118:8364-72. [PMID: 24762096 DOI: 10.1021/jp501854h] [Citation(s) in RCA: 82] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
The propensities of the water self-ions, H3O(+) and OH(-), for the air-water interface have implications for interfacial acid-base chemistry. Despite numerous experimental and computational studies, no consensus has been reached on the question of whether or not H3O(+) and/or OH(-) prefer to be at the water surface or in the bulk. Here we report a molecular dynamics simulation study of the bulk vs interfacial behavior of H3O(+) and OH(-) that employs forces derived from density functional theory with a generalized gradient approximation exchange-correlation functional (specifically, BLYP) and empirical dispersion corrections. We computed the potential of mean force (PMF) for H3O(+) as a function of the position of the ion in the vicinity of an air-water interface. The PMF suggests that H3O(+) has equal propensity for the interface and the bulk. We compare the PMF for H3O(+) to our previously computed PMF for OH(-) adsorption, which contains a shallow minimum at the interface, and we explore how differences in solvation of each ion at the interface vs in the bulk are connected with interfacial propensity. We find that the solvation shell of H3O(+) is only slightly dependent on its position in the water slab, while OH(-) partially desolvates as it approaches the interface, and we examine how this difference in solvation behavior is manifested in the electronic structure and chemistry of the two ions.
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Affiliation(s)
- Marcel D Baer
- Physical Science Division, Pacific Northwest National Laboratory , Richland, Washington 99352, United States
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22
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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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23
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Varner ME, Finlayson-Pitts BJ, Benny Gerber R. Reaction of a charge-separated ONONO2 species with water in the formation of HONO: an MP2 Molecular Dynamics study. Phys Chem Chem Phys 2014; 16:4483-7. [DOI: 10.1039/c3cp55024a] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
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24
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Wick CD. HCl Accommodation, Dissociation, and Propensity for the Surface of Water. J Phys Chem A 2013; 117:12459-67. [DOI: 10.1021/jp4084212] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Collin D. Wick
- Louisiana Tech University, P.O. Box 10348, Ruston, Louisiana 71270, United States
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25
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Bianco R, Hay PJ, Hynes JT. Theoretical Study of Water Oxidation by the Ruthenium Blue Dimer. II. Proton Relay Chain Mechanism for the Step [bpy2(HOO)RuIVORuIV(OH)bpy2]4+ → [bpy2(O2–)RuIVORuIII(OH2)bpy2]4+. J Phys Chem B 2013; 117:15761-73. [DOI: 10.1021/jp406504h] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Affiliation(s)
- Roberto Bianco
- Department
of Chemistry and Biochemistry, University of Colorado, Boulder, Colorado 80309-0215, United States
| | - P. Jeffrey Hay
- 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, Ecole Normale Supérieure, UMR ENS-CNRS-UPMC 8640, 24 rue Lhomond, 75005 Paris, France
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26
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Riikonen S, Parkkinen P, Halonen L, Gerber RB. Ionization of Nitric Acid on Crystalline Ice: The Role of Defects and Collective Proton Movement. J Phys Chem Lett 2013; 4:1850-1855. [PMID: 26283120 DOI: 10.1021/jz400531q] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
Ionization of nitric acid (HNO3) on a model ice surface is studied using ab initio molecular dynamics at temperatures of 200 and 40 K with a surface slab model that consists of the ideal ice basal plane with locally optimized and annealed defects. Pico- and subpicosecond ionization of nitric acid can be achieved in the defect sites. Key features of the rapid ionization are (a) the efficient solvation of the polyatomic nitrate anion, by stealing hydrogen bonds from the weakened hydrogen bonds at defect sites, (b) formation of contact ion pairs to stable "presolvated" molecular species that are present at the defects,
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Affiliation(s)
- S Riikonen
- †Laboratory of Physical Chemistry, Department of Chemistry, University of Helsinki, P.O. Box 55, FI-00014, Helsinki, Finland
| | - P Parkkinen
- †Laboratory of Physical Chemistry, Department of Chemistry, University of Helsinki, P.O. Box 55, FI-00014, Helsinki, Finland
| | - L Halonen
- †Laboratory of Physical Chemistry, Department of Chemistry, University of Helsinki, P.O. Box 55, FI-00014, Helsinki, Finland
| | - R B Gerber
- †Laboratory of Physical Chemistry, Department of Chemistry, University of Helsinki, P.O. Box 55, FI-00014, Helsinki, Finland
- ‡Institute of Chemistry and the Fritz Haber Research Center, The Hebrew University, Jerusalem 91904 Israel
- §Department of Chemistry, University of California Irvine, Irvine, California 92697, United States
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27
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Tobias DJ, Stern AC, Baer MD, Levin Y, Mundy CJ. Simulation and Theory of Ions at Atmospherically Relevant Aqueous Liquid-Air Interfaces. Annu Rev Phys Chem 2013; 64:339-59. [DOI: 10.1146/annurev-physchem-040412-110049] [Citation(s) in RCA: 133] [Impact Index Per Article: 12.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Douglas J. Tobias
- Department of Chemistry, University of California, Irvine, California 92697-2025; ,
| | - Abraham C. Stern
- Department of Chemistry, University of California, Irvine, California 92697-2025; ,
| | - Marcel D. Baer
- Chemical and Materials Science Division, Pacific Northwest National Laboratory, Richland, Washington 99352; ,
| | - Yan Levin
- Insituto de Física, Universidade Federal do Rio Grande do Sul, CEP 91501-970 Porto Alegre, RS, Brazil;
| | - Christopher J. Mundy
- Chemical and Materials Science Division, Pacific Northwest National Laboratory, Richland, Washington 99352; ,
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28
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Moussa SG, Stern AC, Raff JD, Dilbeck CW, Tobias DJ, Finlayson-Pitts BJ. Experimental and theoretical studies of the interaction of gas phase nitric acid and water with a self-assembled monolayer. Phys Chem Chem Phys 2013; 15:448-58. [DOI: 10.1039/c2cp42405c] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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29
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Hlushak S, Simonin JP, De Sio S, Bernard O, Ruas A, Pochon P, Jan S, Moisy P. Speciation in aqueous solutions of nitric acid. Dalton Trans 2013; 42:2853-60. [DOI: 10.1039/c2dt32256k] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
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30
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Marchand P, Marcotte G, Ayotte P. Spectroscopic Study of HNO3 Dissociation on Ice. J Phys Chem A 2012; 116:12112-22. [DOI: 10.1021/jp309533f] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Affiliation(s)
- Patrick Marchand
- Département de Chimie, Université de Sherbrooke, 2500, boulevard université, Sherbrooke,
Québec J1K 2R1, Canada
| | - Guillaume Marcotte
- Département de Chimie, Université de Sherbrooke, 2500, boulevard université, Sherbrooke,
Québec J1K 2R1, Canada
| | - Patrick Ayotte
- Département de Chimie, Université de Sherbrooke, 2500, boulevard université, Sherbrooke,
Québec J1K 2R1, Canada
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31
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Richards NK, Finlayson-Pitts BJ. Production of gas phase NO₂ and halogens from the photochemical oxidation of aqueous mixtures of sea salt and nitrate ions at room temperature. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2012; 46:10447-10454. [PMID: 22506935 DOI: 10.1021/es300607c] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
Nitrate and halide ions coexist in a number of environmental systems, including sea salt particles, the Arctic snowpack, and alkaline dry lakes. However, little is known about potential synergisms between halide and nitrate ions. The effect of sea salt on NO(3)(-) photochemistry at 311 nm was investigated at 298 K using thin films of deliquesced NaNO(3)-synthetic sea salt mixtures. Gas phase NO(2), NO, and halogen products were measured as a function of photolysis time using NO(y) chemiluminescence and atmospheric pressure ionization mass spectrometry (API-MS). The production of NO(2) increases with the halide-to-nitrate ratio, and is similar to that for mixtures of NaCl with NaNO(3). Gas phase halogen production also increased with the halide-to-nitrate ratio, consistent with NO(3)(-) photolysis yielding OH which oxidizes halide ions in the film. Yields of gas phase halogens and NO were strongly dependent on the acidity of the solution, while that of NO(2) was not. An additional halogen formation mechanism in the dark involving molecular HNO(3) is proposed that may be important in other systems such as reactions on surfaces. These studies show that the yield of Br(2) relative to NO(2) during photolysis of halide-nitrate mixtures could be as high as 35% under some atmospheric conditions.
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Affiliation(s)
- Nicole K Richards
- Department of Chemistry, University of California, Irvine, California 92697-2025, United States
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32
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Anions dramatically enhance proton transfer through aqueous interfaces. Proc Natl Acad Sci U S A 2012; 109:10228-32. [PMID: 22689964 DOI: 10.1073/pnas.1200949109] [Citation(s) in RCA: 53] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Proton transfer (PT) through and across aqueous interfaces is a fundamental process in chemistry and biology. Notwithstanding its importance, it is not generally realized that interfacial PT is quite different from conventional PT in bulk water. Here we show that, in contrast with the behavior of strong nitric acid in aqueous solution, gas-phase HNO(3) does not dissociate upon collision with the surface of water unless a few ions (> 1 per 10(6) H(2)O) are present. By applying online electrospray ionization mass spectrometry to monitor in situ the surface of aqueous jets exposed to HNO(3(g)) beams we found that NO(3)(-) production increases dramatically on > 30-μM inert electrolyte solutions. We also performed quantum mechanical calculations confirming that the sizable barrier hindering HNO(3) dissociation on the surface of small water clusters is drastically lowered in the presence of anions. Anions electrostatically assist in drawing the proton away from NO(3)(-) lingering outside the cluster, whose incorporation is hampered by the energetic cost of opening a cavity therein. Present results provide both direct experimental evidence and mechanistic insights on the counterintuitive slowness of PT at water-hydrophobe boundaries and its remarkable sensitivity to electrostatic effects.
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33
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Hammerich AD, Buch V. Ab Initio Molecular Dynamics Simulations of the Liquid/Vapor Interface of Sulfuric Acid Solutions. J Phys Chem A 2012; 116:5637-52. [DOI: 10.1021/jp2126398] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Affiliation(s)
- Audrey Dell Hammerich
- Department of Chemistry, University of Illinois at Chicago, Chicago, Illinois
60607, United States
| | - Victoria Buch
- The Fritz
Haber Institute for Molecular Dynamics, The Hebrew University, Jerusalem 91904, Israel
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34
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Wren SN, Donaldson D. Glancing-angle Raman study of nitrate and nitric acid at the air–aqueous interface. Chem Phys Lett 2012. [DOI: 10.1016/j.cplett.2011.10.019] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/16/2022]
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35
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Sugawara S, Yoshikawa T, Takayanagi T, Shiga M, Tachikawa M. Quantum proton transfer in hydrated sulfuric acid clusters: a perspective from semiempirical path integral simulations. J Phys Chem A 2011; 115:11486-94. [PMID: 21910433 DOI: 10.1021/jp202380h] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
We have carried out path-integral molecular dynamics simulations for hydrated sulfuric acid clusters to understand acid-dissociation and hydrogen-bonded structural rearrangement processes in these clusters from a quantum mechanical viewpoint. The simulations were performed using the PM6 semiempirical electronic structure level whose parameters were modified on the basis of the specific reaction parameters strategy so that relative energies of optimized structures, as well as water binding energies reproduce ab initio and density-functional theory calculations. We have found that the acid dissociation processes, first and second deprotonation, effectively occur in a hydrated cluster with a specific cluster size. The mechanisms of the proton-transfer processes were analyzed in detail and it was found that the distance between O in sulfuric acid and O in the proton-accepting water is playing an important role. We also found that the water coordination number of the poton-accepting water is important in the proton-transfer processes.
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Affiliation(s)
- Shuichi Sugawara
- Department of Chemistry, Saitama University, Sakura-ku, Saitama City, Saitama, Japan
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36
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Bhargava BL, Yasaka Y, Klein ML. Hydrogen Evolution from Formic Acid in an Ionic Liquid Solvent: A Mechanistic Study by ab Initio Molecular Dynamics. J Phys Chem B 2011; 115:14136-40. [DOI: 10.1021/jp204007w] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- B. L. Bhargava
- Institute for Computational Molecular Science, Temple University, 1900 N. 12th Street, Philadelphia, Pennsylvania 19122, United States
- Laboratory for Research on the Structure of Matter, University of Pennsylvania, 3231 Walnut Street, Philadelphia, Pennsylvania 19104-6202, United States
| | - Yoshiro Yasaka
- Institute for Computational Molecular Science, Temple University, 1900 N. 12th Street, Philadelphia, Pennsylvania 19122, United States
| | - Michael L. Klein
- Institute for Computational Molecular Science, Temple University, 1900 N. 12th Street, Philadelphia, Pennsylvania 19122, United States
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37
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Affiliation(s)
- Veronica Vaida
- Department of Chemistry and Biochemistry, CIRES, University of Colorado, Boulder, Colorado 80309-0215, USA
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38
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Lewis T, Winter B, Stern AC, Baer MD, Mundy CJ, Tobias DJ, Hemminger JC. Dissociation of Strong Acid Revisited: X-ray Photoelectron Spectroscopy and Molecular Dynamics Simulations of HNO3 in Water. J Phys Chem B 2011; 115:9445-51. [DOI: 10.1021/jp205510q] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Affiliation(s)
- Tanza Lewis
- Department of Chemistry, University of California, Irvine, Irvine, California 92697, United States
| | - Bernd Winter
- Helmholtz-Zentrum Berlin für Materialien und Energie, and BESSY D-12489 Berlin, Germany
| | - Abraham C. Stern
- Department of Chemistry, University of California, Irvine, Irvine, California 92697, United States
| | - Marcel D. Baer
- Chemical and Materials Sciences Division, Pacific Northwest National Laboratory, Richland, Washington 99352, United States
| | - Christopher J. Mundy
- Chemical and Materials Sciences Division, Pacific Northwest National Laboratory, Richland, Washington 99352, United States
| | - Douglas J. Tobias
- Department of Chemistry, University of California, Irvine, Irvine, California 92697, United States
| | - John C. Hemminger
- Department of Chemistry, University of California, Irvine, Irvine, California 92697, United States
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39
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Laage D, Stirnemann G, Sterpone F, Rey R, Hynes JT. Reorientation and Allied Dynamics in Water and Aqueous Solutions. Annu Rev Phys Chem 2011; 62:395-416. [DOI: 10.1146/annurev.physchem.012809.103503] [Citation(s) in RCA: 271] [Impact Index Per Article: 20.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Damien Laage
- Department of Chemistry, Ecole Normale Supérieure, UMR ENS-CNRS-UPMC 8640, 75005 Paris, France;
| | - Guillaume Stirnemann
- Department of Chemistry, Ecole Normale Supérieure, UMR ENS-CNRS-UPMC 8640, 75005 Paris, France;
| | - Fabio Sterpone
- Department of Chemistry, Ecole Normale Supérieure, UMR ENS-CNRS-UPMC 8640, 75005 Paris, France;
| | - Rossend Rey
- Departament de Física i Enginyeria Nuclear, Universitat Politècnica de Catalunya, Barcelona 08034, Spain;
| | - James T. Hynes
- Department of Chemistry, Ecole Normale Supérieure, UMR ENS-CNRS-UPMC 8640, 75005 Paris, France;
- Department of Chemistry and Biochemistry, University of Colorado, Boulder, Colorado 80309-0215;
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40
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García VP. Acid epimerization of 20-keto pregnane glycosides is determined by 2D-NMR spectroscopy. JOURNAL OF BIOMOLECULAR NMR 2011; 50:91-7. [PMID: 21431831 PMCID: PMC3085064 DOI: 10.1007/s10858-011-9499-z] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/27/2010] [Accepted: 02/22/2011] [Indexed: 05/03/2023]
Abstract
Carbohydrates influence many essential biological events such as apoptosis, differentiation, tumor metastasis, cancer, neurobiology, immunology, development, host-pathogen interactions, diabetes, signal transduction, protein folding, and many other contexts. We now report on the structure determination of pregnane glycosides isolated from the aerial parts of Ceropegia fusca Bolle (Asclepiadaceae). The observation of cicatrizant, vulnerary and cytostatic activities in some humans and animals of Ceropegia fusca Bolle, a species endemic to the Canary Islands, encouraged us to begin a pharmacological study to determine their exact therapeutic properties. High resolution (1)H-NMR spectra of pregnane glycosides very often display well-resolved signals that can be used as starting points in several selective NMR experiments to study scalar (J coupling), and dipolar (NOE) interactions. ROESY is especially suited for molecules such that ωτ(c) ~ 1, where τ(c) are the motional correlation times and ω is the angular frequency. In these cases the NOE is nearly zero, while the rotating-frame Overhauser effect spectroscopy (ROESY) is always positive and increases monotonically for increasing values of τ(c). The ROESY shows dipolar interactions cross peaks even in medium-sized molecules which are helpful in unambiguous assignment of all the interglycosidic linkages. Selective excitation was carried out using a double pulsed-field gradient spin-echo sequence (DPFGSE) in which 180° Gaussian pulses are sandwiched between sine shaped z-gradients. Scalar interactions were studied by homonuclear DPFGSE-COSY and DPFGSE-TOCSY experiments, while DPFGSE-ROESY was used to monitor the spatial environment of the selectively excited proton. Dipolar interactions between nuclei close in space can be detected by the 1D GROESY experiment, which is a one-dimensional counterpart of the 2D ROESY method. The C-12 and C-17 configurations were determined by ROESY experiments.
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Affiliation(s)
- Víctor P García
- Departamento de Química de Productos Naturales y Biotecnología, Instituto de Productos Naturales de Canarias, La Laguna, Tenerife, Canary Islands.
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41
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42
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Wick CD, Dang LX. The behavior of NaOH at the air-water interface: A computational study. J Chem Phys 2010; 133:024705. [DOI: 10.1063/1.3455332] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
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43
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Wang S, Bianco R, Hynes JT. Dissociation of nitric acid at an aqueous surface: Large amplitude motions in the contact ion pair to solvent-separated ion pair conversion. Phys Chem Chem Phys 2010; 12:8241-9. [DOI: 10.1039/c002299n] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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44
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Ramesh SG, Re S, Boisson J, Hynes JT. Vibrational Symmetry Breaking of NO3− in Aqueous Solution: NO Asymmetric Stretch Frequency Distribution and Mean Splitting. J Phys Chem A 2009; 114:1255-69. [DOI: 10.1021/jp903626t] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Sai G. Ramesh
- Chemistry Department, École Normale Supérieure, and Centre National de la Recherche Scientifique, Unité Mixte de Recherche 8640, 24 rue Lhomond, 75005 Paris, France, and Department of Chemistry and Biochemistry, University of Colorado, Boulder, Colorado 80309-0215
| | - Suyong Re
- Chemistry Department, École Normale Supérieure, and Centre National de la Recherche Scientifique, Unité Mixte de Recherche 8640, 24 rue Lhomond, 75005 Paris, France, and Department of Chemistry and Biochemistry, University of Colorado, Boulder, Colorado 80309-0215
| | - Jean Boisson
- Chemistry Department, École Normale Supérieure, and Centre National de la Recherche Scientifique, Unité Mixte de Recherche 8640, 24 rue Lhomond, 75005 Paris, France, and Department of Chemistry and Biochemistry, University of Colorado, Boulder, Colorado 80309-0215
| | - James T. Hynes
- Chemistry Department, École Normale Supérieure, and Centre National de la Recherche Scientifique, Unité Mixte de Recherche 8640, 24 rue Lhomond, 75005 Paris, France, and Department of Chemistry and Biochemistry, University of Colorado, Boulder, Colorado 80309-0215
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Wang S, Bianco R, Hynes JT. Nitric Acid Dissociation at an Aqueous Surface: Occurrence and Mechanism. Isr J Chem 2009. [DOI: 10.1560/ijc.49.2.251] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
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Gerber RB, Sebek J. Dynamics simulations of atmospherically relevant molecular reactions. INT REV PHYS CHEM 2009. [DOI: 10.1080/01442350903016684] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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