1
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Wheaton AM, Chipman JA, Roy MD, Berry JF. Metal-Metal Bond Umpolung in Heterometallic Extended Metal Atom Chains. Inorg Chem 2022; 61:15058-15069. [PMID: 36094078 PMCID: PMC9632685 DOI: 10.1021/acs.inorgchem.2c02118] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
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Understanding the fundamental properties governing metal–metal
interactions is crucial to understanding the electronic structure
and thereby applications of multimetallic systems in catalysis, material
science, and magnetism. One such property that is relatively underexplored
within multimetallic systems is metal–metal bond polarity,
parameterized by the electronegativities (χ) of the metal atoms
involved in the bond. In heterobimetallic systems, metal–metal
bond polarity is a function of the donor–acceptor (Δχ)
interactions of the two bonded metal atoms, with electropositive early
transition metals acting as electron acceptors and electronegative
late transition metals acting as electron donors. We show in this
work, through the preparation and systematic study of a series of
Mo2M(dpa)4(OTf)2 (M = Cr, Mn, Fe,
Co, and Ni; dpa = 2,2′-dipyridylamide; OTf = trifluoromethanesulfonate)
heterometallic extended metal atom chain (HEMAC) complexes that this
expected trend in χ can be reversed. Physical characterization
via single-crystal X-ray diffraction, magnetometry, and spectroscopic
methods as well as electronic structure calculations supports the
presence of a σ symmetry 3c/3e– bond that
is delocalized across the entire metal-atom chain and forms the basis
of the heterometallic Mo2–M interaction. The delocalized
3c/3e– interaction is discussed within the context
of the analogous 3c/3e– π bonding in the vinoxy
radical, CH2CHO. The vinoxy comparison establishes three
predictions for the σ symmetry 3c/3e– bond
in HEMACS: (1) an umpolung effect that causes the
Mo–M interactions to become more covalent as Δχ
increases, (2) distortion of the σ bonding and non-bonding orbitals
to emphasize Mo–M bonding and de-emphasize Mo–Mo bonding,
and (3) an increase in Mo spin population with increasing Mo–M
covalency. In agreement with these predictions, we find that the Mo2···M covalency increases with increasing Δχ
of the Mo and M atoms (ΔχMo–M increases
as M = Cr < Mn < Fe < Co < Ni), an umpolung of the trend predicted in the absence of σ delocalization.
We attribute the observed trend in covalency to the decreased energic
differential (ΔE) between the heterometal orbital and the σ bonding molecular
orbital of the Mo2 quadruple bond, which serves as an energetically
stable, “ligand”-like electron-pair donor to the heterometal
ion acceptor. As M is changed from Cr to Ni, the σ bonding and
nonbonding orbitals do indeed distort as anticipated, and the spin
population of the outer Mo group is increased by at least a factor
of 2. These findings provide a predictive framework for multimetallic
compounds and advance the current understanding of the electronic
structures of molecular heteromultimetallic systems, which can be
extrapolated to applications in the context of mixed-metal surface
catalysis and multimetallic proteins. This
work describes how use of a metal−metal quadruply
bonded metalloligand can reverse expected trends in metal−metal
bond polarity through the preparation and systematic study of a novel
series of Mo2M(dpa)4(OTf)2 (M = Cr,
Mn, Fe, Co, and Ni) heterotrimetallic extended metal atom chain (HEMAC)
complexes. These complexes feature a 3c/3e− metal−metal
bond that is delocalized across the entire metal atom chain and is
compared to the 3c/3e− π bonding in the vinoxyl
radical.
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Affiliation(s)
- Amelia M Wheaton
- Department of Chemistry, University of Wisconsin-Madison, 1101 University Avenue, Madison, Wisconsin 53706, United States
| | - Jill A Chipman
- Department of Chemistry, University of Wisconsin-Madison, 1101 University Avenue, Madison, Wisconsin 53706, United States
| | - Michael D Roy
- Department of Chemistry, University of Wisconsin-Madison, 1101 University Avenue, Madison, Wisconsin 53706, United States
| | - John F Berry
- Department of Chemistry, University of Wisconsin-Madison, 1101 University Avenue, Madison, Wisconsin 53706, United States
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2
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Warburton RE, Soudackov AV, Hammes-Schiffer S. Theoretical Modeling of Electrochemical Proton-Coupled Electron Transfer. Chem Rev 2022; 122:10599-10650. [PMID: 35230812 DOI: 10.1021/acs.chemrev.1c00929] [Citation(s) in RCA: 42] [Impact Index Per Article: 21.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Proton-coupled electron transfer (PCET) plays an essential role in a wide range of electrocatalytic processes. A vast array of theoretical and computational methods have been developed to study electrochemical PCET. These methods can be used to calculate redox potentials and pKa values for molecular electrocatalysts, proton-coupled redox potentials and bond dissociation free energies for PCET at metal and semiconductor interfaces, and reorganization energies associated with electrochemical PCET. Periodic density functional theory can also be used to compute PCET activation energies and perform molecular dynamics simulations of electrochemical interfaces. Various approaches for maintaining a constant electrode potential in electronic structure calculations and modeling complex interactions in the electric double layer (EDL) have been developed. Theoretical formulations for both homogeneous and heterogeneous electrochemical PCET spanning the adiabatic, nonadiabatic, and solvent-controlled regimes have been developed and provide analytical expressions for the rate constants and current densities as functions of applied potential. The quantum mechanical treatment of the proton and inclusion of excited vibronic states have been shown to be critical for describing experimental data, such as Tafel slopes and potential-dependent kinetic isotope effects. The calculated rate constants can be used as input to microkinetic models and voltammogram simulations to elucidate complex electrocatalytic processes.
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Affiliation(s)
- Robert E Warburton
- Department of Chemistry, Yale University, 225 Prospect Street, New Haven, Connecticut 06520, United States
| | - Alexander V Soudackov
- Department of Chemistry, Yale University, 225 Prospect Street, New Haven, Connecticut 06520, United States
| | - Sharon Hammes-Schiffer
- Department of Chemistry, Yale University, 225 Prospect Street, New Haven, Connecticut 06520, United States
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3
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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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4
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Gámez F, Avilés-Moreno JR, Berden G, Oomens J, Martínez-Haya B. Proton in the ring: spectroscopy and dynamics of proton bonding in macrocycle cavities. Phys Chem Chem Phys 2021; 23:21532-21543. [PMID: 34549205 DOI: 10.1039/d1cp03033g] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The proton bond is a paradigmatic quantum molecular interaction and a major driving force of supramolecular chemistry. The ring cavities of crown ethers provide an intriguing environment, promoting competitive proton sharing with multiple coordination anchors. This study shows that protons confined in crown ether cavities form dynamic bonds that migrate to varying pairs of coordinating atoms when allowed by the flexibility of the macrocycle backbone. Prototypic native crown ethers (12-crown-4, 15-crown-5 and 18-crown-6) and aza-crown ethers (cyclen, 1-aza-18-crown-6 and hexacyclen) are investigated. For each system, Infrared action spectroscopy experiments and ab initio Molecular Dynamics computations are employed to elucidate the structural effects associated with proton diffusion and its entanglement with the conformational and vibrational dynamics of the protonated host.
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Affiliation(s)
- Francisco Gámez
- Department of Physical Chemistry, Universidad de Granada, Avenida de la Fuente Nueva s/n, 18071, Granada, Spain
| | - Juan R Avilés-Moreno
- Department of Applied Physical Chemistry, Universidad Autónoma de Madrid, 28049, Madrid, Spain
| | - Giel Berden
- FELIX Laboratory, Institute for Molecules and Materials, Radboud University, Toernooiveld 7, 6525ED Nijmegen, The Netherlands
| | - Jos Oomens
- FELIX Laboratory, Institute for Molecules and Materials, Radboud University, Toernooiveld 7, 6525ED Nijmegen, The Netherlands
| | - Bruno Martínez-Haya
- Department of Physical, Chemical and Natural Systems, Universidad Pablo de Olavide, Ctra. de Utrera, km. 1, 41013 Seville, Spain.
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5
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Leier J, Michenfelder NC, Unterreiner AN, Olzmann M. Indications for an intermolecular photo-induced excited-state proton transfer of p-nitrophenol in water. Mol Phys 2021. [DOI: 10.1080/00268976.2021.1975051] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Affiliation(s)
- Julia Leier
- Institut für Physikalische Chemie, Karlsruher Institut für Technologie (KIT), Karlsruhe, Germany
| | - Nadine C. Michenfelder
- Institut für Physikalische Chemie, Karlsruher Institut für Technologie (KIT), Karlsruhe, Germany
| | - Andreas-Neil Unterreiner
- Institut für Physikalische Chemie, Karlsruher Institut für Technologie (KIT), Karlsruhe, Germany
| | - Matthias Olzmann
- Institut für Physikalische Chemie, Karlsruher Institut für Technologie (KIT), Karlsruhe, Germany
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6
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Liu ZY, Wei YC, Chou PT. Correlation between Kinetics and Thermodynamics for Excited-State Intramolecular Proton Transfer Reactions. J Phys Chem A 2021; 125:6611-6620. [PMID: 34308634 DOI: 10.1021/acs.jpca.1c04192] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Finding the relation between thermodynamics and kinetics for a reaction is of fundamental importance. Here, the thermodynamics and kinetics correlation of excited-state intramolecular proton transfer (ESIPT) was investigated by the TD-DFT calculation under the CAM-B3LYP/6-311+G** level. We choose the family 2-(2'-aminophyenyl)benzothiazole and its amino derivatives as paradigms, which all possess the NH-type intramolecular hydrogen bond (H-bond), and investigate the corresponding ESIPT reaction. The H-bond strength can be systematically tuned, so both activation energy ΔG‡ and free energy difference between proton transfer tautomer (T*, product) and normal species (N*, reactant) ΔGT*-N* can be varied. To minimize the environmental interference such as solvent external H-bond and polarity perturbation, a nonpolar solvent such as cyclohexane is chosen as a bath with a polarizable continuum solvation model for the calculation. As a result, the comprehensive computational approach reveals a linear relationship between ΔGT*-N* and ΔG‡, which can be expressed as ΔG‡ = ΔG0 + αΔGT*-N*. The fundamental insight is reminiscent of the Bell-Evans-Polanyi (BEP) principle where α represents the character of the position of the transition state along the proton motion coordinate. In other words, the more exergonic the ESIPT reaction is, the faster the proton transfer rate can be observed. To verify that such a correlation is not a sporadic event, another ESIPT family with an -OH proton, 1-hydroxy-11H-benzo[b]fluoren-11-one and its derivatives, was also investigated and proved to follow the BEP principle as well. Unlike the quantum mechanics description of proton transfer where either proton tunneling is dominant or solute/solvent is coupled in ESIPT, this work demonstrates that reaction kinetics and thermodynamics are strongly correlated within the same class of ESIPT molecules with an intrinsic barrier free from solvent perturbation, being faster with the more exergonic reaction.
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Affiliation(s)
- Zong-Ying Liu
- Department of Chemistry, National Taiwan University, Taipei, 10617 Taiwan, R.O.C
| | - Yu-Chen Wei
- Department of Chemistry, National Taiwan University, Taipei, 10617 Taiwan, R.O.C
| | - Pi-Tai Chou
- Department of Chemistry, National Taiwan University, Taipei, 10617 Taiwan, R.O.C
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7
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Dreier C, Prädel L, Ehrhard AA, Wagner M, Hunger J. Association Equilibria of Organo-Phosphoric Acids with Imines from a Combined Dielectric and Nuclear Magnetic Resonance Spectroscopy Approach. Anal Chem 2021; 93:3914-3921. [PMID: 33600142 PMCID: PMC7931174 DOI: 10.1021/acs.analchem.0c04669] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2020] [Accepted: 02/08/2021] [Indexed: 11/29/2022]
Abstract
Aggregates formed between organo-phosphoric acids and imine bases in aprotic solvents are the reactive intermediates in Brønsted acid organo-catalysis. Due to the strong hydrogen-bonding interaction of the acids in solution, multiple homo- and heteroaggregates are formed with profound effects on catalytic activity. Yet, due to the similar binding motifs-hydrogen-bonds-it is challenging to experimentally quantify the abundance of these aggregates in solution. Here we demonstrate that a combination of nuclear magnetic resonance (NMR) and dielectric relaxation spectroscopy (DRS) allows for accurate speciation of these aggregates in solution. We show that only by using the observables of both experiments heteroaggregates can be discriminated with simultaneously taking homoaggregation into account. Comparison of the association of diphenyl phosphoric acid and quinaldine or phenylquinaline in chloroform, dichloromethane, or tetrahydrofuran suggests that the basicity of the base largely determines the association of one acid and one base molecule to form an ion-pair. We find the ion-pair formation constants to be highest in chloroform, slightly lower in dichloromethane and lowest in tetrahydrofuran, which indicates that the hydrogen-bonding ability of the solvent also alters ion-pairing equilibria. We find evidence for the formation of multimers, consisting of one imine base and multiple diphenyl phosphoric acid molecules for both bases in all three solvents. This subsequent association of an acid to an ion-pair is however little affected by the nature of the base or the solvent. As such our findings provide routes to enhance the overall fraction of these multimers in solution, which have been reported to open new catalytic pathways.
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Affiliation(s)
- Christian Dreier
- Max
Planck Institute for Polymer Research, Department for Molecular Spectroscopy, Ackermannweg 10, 55128 Mainz, Germany
| | - Leon Prädel
- Max
Planck Institute for Polymer Research, Department for Molecular Spectroscopy, Ackermannweg 10, 55128 Mainz, Germany
| | - Amelie A. Ehrhard
- Max
Planck Institute for Polymer Research, Department for Molecular Spectroscopy, Ackermannweg 10, 55128 Mainz, Germany
| | - Manfred Wagner
- Max
Planck Institute for Polymer Research, Department for Molecular Spectroscopy, Ackermannweg 10, 55128 Mainz, Germany
| | - Johannes Hunger
- Max
Planck Institute for Polymer Research, Department for Molecular Spectroscopy, Ackermannweg 10, 55128 Mainz, Germany
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8
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Brown SE, Shakib FA. Recent progress in approximate quantum dynamics methods for the study of proton-coupled electron transfer reactions. Phys Chem Chem Phys 2021; 23:2535-2556. [PMID: 33367437 DOI: 10.1039/d0cp05166g] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
Proton-coupled electron transfer (PCET) reactions are ubiquitous natural processes at the heart of energy conversion reactions in photosynthesis and respiration, DNA repair, and diverse enzymatic reactions. Theoretical formulation and computational method developments have eyed modeling of thermal and photoinduced PCET for the last three decades. The accumulation of these studies, collected in dozens of reviews, accounts, and perspectives, has firmly established the influence of quantum effects, including non-adiabatic electronic transitions, vibrational relaxation, zero-point energy, and proton tunneling, on the rate and mechanism of PCET reactions. Here, we focus on some recently-developed methods, spanning the last eight years, that can quantitatively capture these effects in the PCET context and provide efficient means for their qualitative description in complex systems. The theoretical background of each method and their accuracy with respect to exact results are discussed and the results of relevant PCET simulations based on each method are presented.
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Affiliation(s)
- Sandra E Brown
- Department of Chemistry and Biochemistry, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Farnaz A Shakib
- Department of Chemistry and Environmental Science, New Jersey Institute of Technology, Newark, NJ 07102, USA.
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9
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Rey R, Hynes JT. Solvation Dynamics in Water. 4. On the Initial Regime of Solvation Relaxation. J Phys Chem B 2020; 124:7668-7681. [PMID: 32790403 DOI: 10.1021/acs.jpcb.0c05706] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
It is shown, by means of numerical and analytic work, that initial molecular momenta play little significant role in the initial fast solvation relaxation that follows electronic excitation of, and charge creation for, a standard model system of a solute in water. Instead, the nonequilibrium dynamics are predominantly described by noninertial "steering" by the torques directly generated by the newly created charge distribution. It is this process that largely overcomes inertia and drives the relaxation dynamics on a time scale of a few tens of femtoseconds in the key initial regime of the dynamics. These results are discussed in the context of commonly employed descriptions such as inertial, Gaussian, and underdamped dynamical behavior.
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Affiliation(s)
- Rossend Rey
- Departament de Fı́sica, Universitat Politècnica de Catalunya, Campus Nord B4-B5, Barcelona 08034, Spain
| | - James T Hynes
- PASTEUR, Department of Chemistry, École Normale Supérieure, PSL University, Sorbonne Université, CNRS, 75005 Paris, France.,Department of Chemistry, University of Colorado, Boulder, Colorado 80309, United States
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10
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Maffucci I, Laage D, Sterpone F, Stirnemann G. Thermal Adaptation of Enzymes: Impacts of Conformational Shifts on Catalytic Activation Energy and Optimum Temperature. Chemistry 2020; 26:10045-10056. [DOI: 10.1002/chem.202001973] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2020] [Revised: 06/02/2020] [Indexed: 12/25/2022]
Affiliation(s)
- Irene Maffucci
- PASTEUR, Département de chimie École Normale Supérieure, PSL University Sorbonne Université, CNRS 24 rue Lhomond 75005 Paris France
- CNRS Laboratoire de Biochimie Théorique Institut de Biologie Physico-Chimique PSL University, Université de Paris 13 rue Pierre et Marie Curie 75005 Paris France
- Present address: Centre de recherche Royallieu Université de Technologie de Compiègne, UPJV CNRS, Enzyme and Cell Engineering CS 60319-60203 Compiègne Cedex France
| | - Damien Laage
- PASTEUR, Département de chimie École Normale Supérieure, PSL University Sorbonne Université, CNRS 24 rue Lhomond 75005 Paris France
| | - Fabio Sterpone
- CNRS Laboratoire de Biochimie Théorique Institut de Biologie Physico-Chimique PSL University, Université de Paris 13 rue Pierre et Marie Curie 75005 Paris France
| | - Guillaume Stirnemann
- CNRS Laboratoire de Biochimie Théorique Institut de Biologie Physico-Chimique PSL University, Université de Paris 13 rue Pierre et Marie Curie 75005 Paris France
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11
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Hridya VM, Hynes JT, Mukherjee A. Dynamical Recrossing in the Intercalation Process of the Anticancer Agent Proflavine into DNA. J Phys Chem B 2019; 123:10904-10914. [PMID: 31671261 DOI: 10.1021/acs.jpcb.9b08470] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Intercalation into DNA is the interaction mode of some anthracycline antibiotics. Recently, the molecular mechanism of this process was explored using the static free energy landscape. Here we explore the dynamical effects in the intercalation of proflavine into DNA by calculating the transmission coefficient κ-providing a measure of the departure from transition state theory for the reaction rate constant-by examination of the recrossing events at the transition state. For that purpose, we first found the accurate transition state of this complex system-as judged by a committor analysis-using a set of all-atom simulations of total length 6.3 ms. In a subsequent calculation of the transmission coefficient κ in another extensive set of simulations the small value κ = 0.1 was found, indicating a significant departure from TST. Comparison of this result with Grote-Hynes and Kramers theories shows that neither theory is able to capture this complex system's recrossing events; the source of this striking failure is discussed, as are related aspects of the mechanism. This study suggests that, for biomolecular processes similar to this, dynamical effects essential for the process are complex in nature and require novel approaches for their elucidation.
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Affiliation(s)
- V M Hridya
- Department of Chemistry , Indian Institute of Science Education and Research , Pune 411008 , India
| | - 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
| | - Arnab Mukherjee
- Department of Chemistry , Indian Institute of Science Education and Research , Pune 411008 , India
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12
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Garcia-Meseguer R, Carpenter BK. Re-Evaluating the Transition State for Reactions in Solution. European J Org Chem 2018. [DOI: 10.1002/ejoc.201800841] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
| | - Barry K. Carpenter
- School of Chemistry; Cardiff University; CF10 3AT Cardiff United Kingdom
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13
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Theoretical study on excited-state multiple proton-transfer process of 7-azaindole with ammonia and mixed water-ammonia: Stepwise or concerted? J Photochem Photobiol A Chem 2018. [DOI: 10.1016/j.jphotochem.2018.06.040] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
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14
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Schramm VL, Schwartz SD. Promoting Vibrations and the Function of Enzymes. Emerging Theoretical and Experimental Convergence. Biochemistry 2018; 57:3299-3308. [PMID: 29608286 DOI: 10.1021/acs.biochem.8b00201] [Citation(s) in RCA: 46] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
A complete understanding of enzyme catalysis requires knowledge of both transition state features and the detailed motions of atoms that cause reactant molecules to form and traverse the transition state. The seeming intractability of the problem arises from the femtosecond lifetime of chemical transition states, preventing most experimental access. Computational chemistry is admirably suited to short time scale analysis but can be misled by inappropriate starting points or by biased assumptions. Kinetic isotope effects provide an experimental approach to transition state structure and a method for obtaining transition state analogues but, alone, do not inform how that transition state is reached. Enzyme structures with transition state analogues provide computational starting points near the transition state geometry. These well-conditioned starting points, combined with the unbiased computational method of transition path sampling, provide realistic atomistic motions involved in transition state formation and passage. In many, but not all, enzymatic systems, femtosecond local protein motions near the catalytic site are linked to transition state formation. These motions are not inherently revealed by most approaches of transition state theory, because transition state theory replaces dynamics with the statistics of the transition state. Experimental and theoretical convergence of the link between local catalytic site vibrational modes and catalysis comes from heavy atom ("Born-Oppenheimer") enzymes. Fully labeled and catalytic site local heavy atom labels perturb the probability of finding enzymatic transition states in ways that can be analyzed and predicted by transition path sampling. Recent applications of these experimental and computational approaches reveal how subpicosecond local catalytic site protein modes play important roles in creating the transition state.
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Affiliation(s)
- Vern L Schramm
- Department of Biochemistry , Albert Einstein College of Medicine , Bronx , New York 10461 , United States
| | - Steven D Schwartz
- Department of Chemistry and Biochemistry , University of Arizona , Tucson , Arizona 85721 , United States
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15
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Oostenrijk B, Walsh N, Laksman J, Månsson EP, Grunewald C, Sorensen SL, Gisselbrecht M. The role of charge and proton transfer in fragmentation of hydrogen-bonded nanosystems: the breakup of ammonia clusters upon single photon multi-ionization. Phys Chem Chem Phys 2018; 20:932-940. [PMID: 29230456 DOI: 10.1039/c7cp06688k] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The charge and proton dynamics in hydrogen-bonded networks are investigated using ammonia as a model system. The fragmentation dynamics of medium-sized clusters (1-2 nm) upon single photon multi-ionization is studied, by analyzing the momenta of small ionic fragments. The observed fragmentation pattern of the doubly- and triply-charged clusters reveals a spatial anisotropy of emission between fragments (back-to-back). Protonated fragments exhibit a distinct kinematic correlation, indicating a delay between ionization and fragmentation (fission). The different kinematics observed for channels containing protonated and unprotonated species provides possible insights into the prime mechanisms of charge and proton transfer, as well as proton hopping, in such a nanoscale system.
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Affiliation(s)
- Bart Oostenrijk
- Division of Synchrotron Radiation Research, Department of Physics, Lund University, Box 118, 22100 Lund, Sweden.
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16
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Chen C, Liu W, Baranov MS, Baleeva NS, Yampolsky IV, Zhu L, Wang Y, Shamir A, Solntsev KM, Fang C. Unveiling Structural Motions of a Highly Fluorescent Superphotoacid by Locking and Fluorinating the GFP Chromophore in Solution. J Phys Chem Lett 2017; 8:5921-5928. [PMID: 29148819 DOI: 10.1021/acs.jpclett.7b02661] [Citation(s) in RCA: 36] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/27/2023]
Abstract
Superphotoacidity involves ultrafast proton motions implicated in numerous chemical and biological processes. We used conformational locking and strategic addition of electron-withdrawing substituents to synthesize a new GFP chromophore analogue: p-HO-3,5-diF-BDI:BF2 (diF). It is highly fluorescent and exhibits excited-state proton transfer (ESPT) in various solvents, placing it among the strongest photoacids. Tunable femtosecond stimulated Raman spectroscopy with unique resonance conditions and transient absorption are complementarily employed to elucidate the structural basis for superphotoacidity. We reveal a multistep ESPT reaction from diF to methanol with an initial proton dissociation on the ∼600 fs time scale that forms a charge-separated state, stabilized by solvation, and followed by a diffusion-controlled proton transfer on the ∼350 ps time scale. A ∼1580 cm-1 phenolic ring motion is uncovered to accompany ESPT before 1 ps. This study provides a vivid movie of the photoinduced proton dissociation of a superphotoacid with bright fluorescence, effectively bridging fundamental mechanistic insights to precise control of macroscopic functions.
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Affiliation(s)
- Cheng Chen
- Department of Chemistry, Oregon State University , 153 Gilbert Hall, Corvallis, Oregon 97331, United States
| | - Weimin Liu
- Department of Chemistry, Oregon State University , 153 Gilbert Hall, Corvallis, Oregon 97331, United States
| | - Mikhail S Baranov
- Institute of Bioorganic Chemistry, Russian Academy of Sciences , Miklukho-Maklaya 16/10, 117997 Moscow, Russia
| | - Nadezhda S Baleeva
- Institute of Bioorganic Chemistry, Russian Academy of Sciences , Miklukho-Maklaya 16/10, 117997 Moscow, Russia
| | - Ilia V Yampolsky
- Institute of Bioorganic Chemistry, Russian Academy of Sciences , Miklukho-Maklaya 16/10, 117997 Moscow, Russia
- Pirogov Russian National Research Medical University , Ostrovitianov 1, Moscow 117997, Russia
| | - Liangdong Zhu
- Department of Chemistry, Oregon State University , 153 Gilbert Hall, Corvallis, Oregon 97331, United States
| | - Yanli Wang
- Department of Chemistry, Oregon State University , 153 Gilbert Hall, Corvallis, Oregon 97331, United States
| | - Alexandra Shamir
- School of Chemistry and Biochemistry, Georgia Institute of Technology , 901 Atlantic Drive, Atlanta, Georgia 30332, United States
| | - Kyril M Solntsev
- School of Chemistry and Biochemistry, Georgia Institute of Technology , 901 Atlantic Drive, Atlanta, Georgia 30332, United States
| | - Chong Fang
- Department of Chemistry, Oregon State University , 153 Gilbert Hall, Corvallis, Oregon 97331, United States
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17
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Bircher MP, Liberatore E, Browning NJ, Brickel S, Hofmann C, Patoz A, Unke OT, Zimmermann T, Chergui M, Hamm P, Keller U, Meuwly M, Woerner HJ, Vaníček J, Rothlisberger U. Nonadiabatic effects in electronic and nuclear dynamics. STRUCTURAL DYNAMICS (MELVILLE, N.Y.) 2017; 4:061510. [PMID: 29376108 PMCID: PMC5760266 DOI: 10.1063/1.4996816] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/19/2017] [Accepted: 10/19/2017] [Indexed: 05/25/2023]
Abstract
Due to their very nature, ultrafast phenomena are often accompanied by the occurrence of nonadiabatic effects. From a theoretical perspective, the treatment of nonadiabatic processes makes it necessary to go beyond the (quasi) static picture provided by the time-independent Schrödinger equation within the Born-Oppenheimer approximation and to find ways to tackle instead the full time-dependent electronic and nuclear quantum problem. In this review, we give an overview of different nonadiabatic processes that manifest themselves in electronic and nuclear dynamics ranging from the nonadiabatic phenomena taking place during tunnel ionization of atoms in strong laser fields to the radiationless relaxation through conical intersections and the nonadiabatic coupling of vibrational modes and discuss the computational approaches that have been developed to describe such phenomena. These methods range from the full solution of the combined nuclear-electronic quantum problem to a hierarchy of semiclassical approaches and even purely classical frameworks. The power of these simulation tools is illustrated by representative applications and the direct confrontation with experimental measurements performed in the National Centre of Competence for Molecular Ultrafast Science and Technology.
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Affiliation(s)
- Martin P Bircher
- Laboratory of Computational Chemistry and Biochemistry, Institut des Sciences et Ingénierie Chimiques, Ecole Polytechnique Fédérale de Lausanne (EPFL), CH-1015 Lausanne, Switzerland
| | - Elisa Liberatore
- Laboratory of Computational Chemistry and Biochemistry, Institut des Sciences et Ingénierie Chimiques, Ecole Polytechnique Fédérale de Lausanne (EPFL), CH-1015 Lausanne, Switzerland
| | - Nicholas J Browning
- Laboratory of Computational Chemistry and Biochemistry, Institut des Sciences et Ingénierie Chimiques, Ecole Polytechnique Fédérale de Lausanne (EPFL), CH-1015 Lausanne, Switzerland
| | - Sebastian Brickel
- Department of Chemistry, University of Basel, Klingelbergstrasse 80, CH-4056 Basel, Switzerland
| | | | - Aurélien Patoz
- Laboratory of Theoretical Physical Chemistry, Institut des Sciences et Ingénierie Chimiques, Ecole Polytechnique Fédérale de Lausanne (EPFL), CH-1015 Lausanne, Switzerland
| | - Oliver T Unke
- Department of Chemistry, University of Basel, Klingelbergstrasse 80, CH-4056 Basel, Switzerland
| | - Tomáš Zimmermann
- Laboratory of Theoretical Physical Chemistry, Institut des Sciences et Ingénierie Chimiques, Ecole Polytechnique Fédérale de Lausanne (EPFL), CH-1015 Lausanne, Switzerland
| | - Majed Chergui
- Laboratoire de Spectroscopie Ultrarapide (LSU) and Lausanne Centre for Ultrafast Science (LACUS), Institut des Sciences et Ingénierie Chimiques, Ecole Polytechnique Fédérale de Lausanne (EPFL), CH-1015 Lausanne, Switzerland
| | - Peter Hamm
- Department of Chemistry, University of Zurich, Zürich, Switzerland
| | - Ursula Keller
- Physics Department, ETH Zurich, CH-8093 Zurich, Switzerland
| | - Markus Meuwly
- Department of Chemistry, University of Basel, Klingelbergstrasse 80, CH-4056 Basel, Switzerland
| | - Hans-Jakob Woerner
- Laboratorium für Physikalische Chemie, ETH Zürich, CH-8093 Zürich, Switzerland
| | - Jiří Vaníček
- Laboratory of Theoretical Physical Chemistry, Institut des Sciences et Ingénierie Chimiques, Ecole Polytechnique Fédérale de Lausanne (EPFL), CH-1015 Lausanne, Switzerland
| | - Ursula Rothlisberger
- Laboratory of Computational Chemistry and Biochemistry, Institut des Sciences et Ingénierie Chimiques, Ecole Polytechnique Fédérale de Lausanne (EPFL), CH-1015 Lausanne, Switzerland
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18
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Malm C, Kim H, Wagner M, Hunger J. Complexity in Acid-Base Titrations: Multimer Formation Between Phosphoric Acids and Imines. Chemistry 2017; 23:10853-10860. [PMID: 28597513 PMCID: PMC5582606 DOI: 10.1002/chem.201701576] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2017] [Indexed: 11/08/2022]
Abstract
Solutions of Brønsted acids with bases in aprotic solvents are not only common model systems to study the fundamentals of proton transfer pathways but are also highly relevant to Brønsted acid catalysis. Despite their importance the light nature of the proton makes characterization of acid-base aggregates challenging. Here, we track such acid-base interactions over a broad range of relative compositions between diphenyl phosphoric acid and the base quinaldine in dichloromethane, by using a combination of dielectric relaxation and NMR spectroscopy. In contrast to what one would expect for an acid-base titration, we find strong deviations from quantitative proton transfer from the acid to the base. Even for an excess of the base, multimers consisting of one base and at least two acid molecules are formed, in addition to the occurrence of proton transfer from the acid to the base and simultaneous formation of ion pairs. For equimolar mixtures such multimers constitute about one third of all intermolecular aggregates. Quantitative analysis of our results shows that the acid-base association constant is only around six times larger than that for the acid binding to an acid-base dimer, that is, to an already protonated base. Our findings have implications for the interpretation of previous studies of reactive intermediates in organocatalysis and provide a rationale for previously observed nonlinear effects in phosphoric acid catalysis.
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Affiliation(s)
- Christian Malm
- Department of Molecular SpectroscopyMax Planck Institute for Polymer ResearchAckermannweg 1055128MainzGermany
| | - Heejae Kim
- Department of Molecular SpectroscopyMax Planck Institute for Polymer ResearchAckermannweg 1055128MainzGermany
| | - Manfred Wagner
- Department of Molecular SpectroscopyMax Planck Institute for Polymer ResearchAckermannweg 1055128MainzGermany
| | - Johannes Hunger
- Department of Molecular SpectroscopyMax Planck Institute for Polymer ResearchAckermannweg 1055128MainzGermany
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19
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Geneste G, Hermet J, Dezanneau G. Reply to the 'Comment on "Proton transport in barium stannate: classical, semi-classical and quantum regime"'. Phys Chem Chem Phys 2017; 19:21191-21209. [PMID: 28758646 DOI: 10.1039/c7cp02385e] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
We respond to the erroneous criticisms about our modeling of proton transport in barium stannate [G. Geneste et al., Phys. Chem. Chem. Phys., 2015, 17, 19104]. In this previous work, we described, on the basis of density-functional calculations, proton transport in the classical and semi-classical regimes, and provided arguments in favor of an adiabatic picture for proton transfer at low temperature. We re-explain here our article (with more detail and precision), the content of which has been distorted in the Comment, and reiterate our arguments in this reply. We refute all criticisms. They are completely wrong in the context of our article. Even though a few of them are based on considerations probably true in some metals, they make no sense here since they do not correspond to the content of our work. It has not been understood in the Comment that two competitive configurations, associated with radically different transfer mechanisms, have been studied in our work. It has also not been understood in the Comment that the adiabatic regime described for transfer occurs in the protonic ground state, in a very-low barrier configuration with the protonic ground state energy larger than the barrier. Serious confusion has been made in the Comment with the case of H in metals like Nb or Ta, leading to the introduction of the notion of (protonic) "excited-state proton transfer", relevant for H in some metals, but (i) that does not correspond to the (ground state) adiabatic transfers here described, and (ii) that does not correspond to what is commonly described as the "adiabatic limit for proton transfer" in the scientific literature. We emphasize, accordingly, the large differences between proton transfer in the present oxide and hydrogen jumps in metals like Nb or Ta, and the similarities between proton transfer in the present oxide and in acid-base solutions. We finally describe a scenario for proton transfer in the present oxide regardless of the temperature regime.
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20
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Zakai I, Varner ME, Gerber RB. Concerted transfer of multiple protons in acid-water clusters: [(HCl)(H 2O)] 2 and [(HF)(H 2O)] 4. Phys Chem Chem Phys 2017; 19:20641-20646. [PMID: 28737803 DOI: 10.1039/c7cp04006g] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Molecular dynamics simulations using directly ab initio potentials are carried out for the ionically bonded clusters [(Cl-)(H3O+)]2 and [(F-)(H3O+)]4 to explore their transitions to the hydrogen-bonded [(HCl)(H2O)]2 and [(HF)(H2O)]4 structures during the first picosecond of simulation. Both the ionic and the H-bonded structures that are formed are highly symmetric. It is found that proton transfers are concerted in all trajectories for [(Cl-)(H3O+)]2. For [(F-)(H3O+)]4, the fully concerted mechanism is dominant but partially concerted transfers of two or three protons at the same time also occur. The concerted mechanism also holds for the reverse process of ionization of neutral acid molecules. It is suggested that the high symmetry of the ionic and the H-bonded structures plays a role in the preference for concerted transfers. Possible implications of the results for proton transfers in other systems are discussed.
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Affiliation(s)
- I Zakai
- Institute of Chemistry and The Fritz Haber Research Center, The Hebrew University, Jerusalem 91904, Israel
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21
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Liu W, Wang Y, Tang L, Oscar BG, Zhu L, Fang C. Panoramic portrait of primary molecular events preceding excited state proton transfer in water. Chem Sci 2016; 7:5484-5494. [PMID: 30034688 PMCID: PMC6021748 DOI: 10.1039/c6sc00672h] [Citation(s) in RCA: 76] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2016] [Accepted: 05/11/2016] [Indexed: 12/31/2022] Open
Abstract
Primary events that power ultrafast excited state proton transfer in water are revealed to involve coupled intermolecular and intramolecular motions.
Photochemistry powers numerous processes from luminescence and human vision, to light harvesting. However, the elucidation of multidimensional photochemical reaction coordinates on molecular timescales remains challenging. We developed wavelength-tunable femtosecond stimulated Raman spectroscopy to simultaneously achieve pre-resonance enhancement for transient reactant and product species of the widely used photoacid pyranine undergoing excited-state proton transfer (ESPT) reaction in solution. In the low-frequency region, the 280 cm–1 ring deformation mode following 400 nm photoexcitation exhibits pronounced intensity oscillations on the sub-picosecond timescale due to anharmonic vibrational coupling to the 180 cm–1 hydrogen-bond stretching mode only in ESPT-capable solvents, indicating a primary event of functional relevance. This leads to the contact ion pair formation on the 3 ps timescale before diffusion-controlled separation. The intermolecular 180 cm–1 mode also reveals vibrational cooling time constants, ∼500 fs and 45 ps in both H2O and D2O, which differ from ESPT time constants of ∼3/8 and 90/250 ps in H2O/D2O, respectively. Spectral results using H218O further substantiate the functional role of the intermolecular 180 cm–1 mode in modulating the distance between proton donor and acceptor and forming the transient ion pair. The direct observation of molecular structural evolution across a wide spectral region during photochemical reactions enriches our fundamental understanding of potential energy surface and holds the key to advancing energy and biological sciences with exceptional atomic and temporal precision.
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Affiliation(s)
- Weimin Liu
- Oregon State University , Department of Chemistry , 263 Linus Pauling Science Centre (lab) , 153 Gilbert Hall (office) , Corvallis , OR 97331 , USA . ; ; Tel: +1 541 737 6704
| | - Yanli Wang
- Oregon State University , Department of Chemistry , 263 Linus Pauling Science Centre (lab) , 153 Gilbert Hall (office) , Corvallis , OR 97331 , USA . ; ; Tel: +1 541 737 6704
| | - Longteng Tang
- Oregon State University , Department of Chemistry , 263 Linus Pauling Science Centre (lab) , 153 Gilbert Hall (office) , Corvallis , OR 97331 , USA . ; ; Tel: +1 541 737 6704
| | - Breland G Oscar
- Oregon State University , Department of Chemistry , 263 Linus Pauling Science Centre (lab) , 153 Gilbert Hall (office) , Corvallis , OR 97331 , USA . ; ; Tel: +1 541 737 6704
| | - Liangdong Zhu
- Oregon State University , Department of Chemistry , 263 Linus Pauling Science Centre (lab) , 153 Gilbert Hall (office) , Corvallis , OR 97331 , USA . ; ; Tel: +1 541 737 6704
| | - Chong Fang
- Oregon State University , Department of Chemistry , 263 Linus Pauling Science Centre (lab) , 153 Gilbert Hall (office) , Corvallis , OR 97331 , USA . ; ; Tel: +1 541 737 6704
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22
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Hamm P, Stock G. Nonadiabatic vibrational dynamics in the HCO2−⋅H2O complex. J Chem Phys 2015; 143:134308. [DOI: 10.1063/1.4932189] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- Peter Hamm
- Department of Chemistry, University of Zurich, Zurich, Switzerland
| | - Gerhard Stock
- Biomolecular Dynamics, Institute of Physics, Albert Ludwigs University, 79104 Freiburg, Germany
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23
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Chen W, Gerasimov JY, Zhao P, Liu K, Herrmann A. High-Density Noncovalent Functionalization of DNA by Electrostatic Interactions. J Am Chem Soc 2015; 137:12884-9. [DOI: 10.1021/jacs.5b05432] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Wei Chen
- Zernike Institute for Advanced
Materials, Department of Polymer Chemistry, University of Groningen, Nijenborgh 4, 9747 AG Groningen, Netherlands
| | - Jennifer Y. Gerasimov
- Zernike Institute for Advanced
Materials, Department of Polymer Chemistry, University of Groningen, Nijenborgh 4, 9747 AG Groningen, Netherlands
| | - Pei Zhao
- Zernike Institute for Advanced
Materials, Department of Polymer Chemistry, University of Groningen, Nijenborgh 4, 9747 AG Groningen, Netherlands
| | - Kai Liu
- Zernike Institute for Advanced
Materials, Department of Polymer Chemistry, University of Groningen, Nijenborgh 4, 9747 AG Groningen, Netherlands
| | - Andreas Herrmann
- Zernike Institute for Advanced
Materials, Department of Polymer Chemistry, University of Groningen, Nijenborgh 4, 9747 AG Groningen, Netherlands
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24
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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: 29] [Impact Index Per Article: 3.2] [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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25
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Sifain AE, Wang L, Prezhdo OV. Mixed quantum-classical equilibrium in global flux surface hopping. J Chem Phys 2015; 142:224102. [DOI: 10.1063/1.4922162] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- Andrew E. Sifain
- Department of Physics and Astronomy, University of Southern California, Los Angeles, California 90089-0485, USA
| | - Linjun Wang
- Department of Chemistry, University of Southern California, Los Angeles, California 90089-1062, USA
| | - Oleg V. Prezhdo
- Department of Chemistry, University of Southern California, Los Angeles, California 90089-1062, USA
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26
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Pylaeva S, Allolio C, Koeppe B, Denisov GS, Limbach HH, Sebastiani D, Tolstoy PM. Proton transfer in a short hydrogen bond caused by solvation shell fluctuations: an ab initio MD and NMR/UV study of an (OHO)(-) bonded system. Phys Chem Chem Phys 2015; 17:4634-44. [PMID: 25586486 DOI: 10.1039/c4cp04727c] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
We present a joint experimental and quantum chemical study on the influence of solvent dynamics on the protonation equilibrium in a strongly hydrogen bonded phenol-acetate complex in CD2Cl2. Particular attention is given to the correlation of the proton position distribution with the internal conformation of the complex itself and with fluctuations of the aprotic solvent. Specifically, we have focused on a complex formed by 4-nitrophenol and tetraalkylammonium-acetate in CD2Cl2. Experimentally we have used combined low-temperature (1)H and (13)C NMR and UV-vis spectroscopy and showed that a very strong OHO hydrogen bond is formed with proton tautomerism (PhOH···(-)OAc and PhO(-)···HOAc forms, both strongly hydrogen bonded). Computationally, we have employed ab initio molecular dynamics (70 and 71 solvent molecules, with and without the presence of a counter-cation, respectively). We demonstrate that the relative motion of the counter-cation and the "free" carbonyl group of the acid plays the major role in the OHO bond geometry and causes proton "jumps", i.e. interconversion of PhOH···(-)OAc and PhO(-)···HOAc tautomers. Weak H-bonds between CH(CD) groups of the solvent and the oxygen atom of carbonyl stabilize the PhOH···(-)OAc type of structures. Breaking of CH···O bonds shifts the equilibrium towards PhO(-)···HOAc form.
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Affiliation(s)
- Svetlana Pylaeva
- Department of Physics, St. Petersburg State University, Ulianovskaya st. 3, 198504 St. Petersburg, Russia.
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27
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Kojima H, Yamada A, Okazaki S. A molecular dynamics study of intramolecular proton transfer reaction of malonaldehyde in solution based upon a mixed quantum–classical approximation. II. Proton transfer reaction in non-polar solvent. J Chem Phys 2015; 142:174502. [DOI: 10.1063/1.4919635] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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28
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Spies C, Shomer S, Finkler B, Pines D, Pines E, Jung G, Huppert D. Solvent dependence of excited-state proton transfer from pyranine-derived photoacids. Phys Chem Chem Phys 2015; 16:9104-14. [PMID: 24700348 DOI: 10.1039/c3cp55292f] [Citation(s) in RCA: 57] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Steady-state and time-resolved techniques were employed to study the excited-state proton-transfer (ESPT) rate of two newly synthesized 8-hydroxy-1,3,6-pyrenetrisulfonate (pyranine, HPTS) derived photoacids in three protic solvents, water, methanol and ethanol. The ESPT rate constant k(PT) of tris(1,1,1,3,3,3-hexafluoropropan-2-yl)-8-hydroxypyrene-1,3,6-trisulfonate, 1a, whose pK(a)* ~ -4, in water, methanol and ethanol is 3 × 10(11) s(-1), 8 × 10(9) s(-1) and 5 × 10(9) s(-1) respectively. (8-Hydroxy-N1,N3,N6-tris(2-hydroxyethyl)-N1,N3,N6-trimethylpyrene-1,3,6 trisulfonamide, 1b) is a weaker acid than 1a but still a strong photoacid with pK(a)* ~ -1 and the ESPT rate in water, methanol and ethanol is 7 × 10(10) s(-1), 4 × 10(8) s(-1) and 2 × 10(8) s(-1). We qualitatively explain our kinetic results by a Marcus-like free-energy correlation which was found to have a general form suitable for describing proton transfer reactions in both the proton-adiabatic and the proton-non-adiabatic limits.
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Affiliation(s)
- Christian Spies
- Biophysical Chemistry, Saarland University, Campus, Building B2 2, D-66123 Saarbrücken, Germany.
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29
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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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30
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Yamada A, Kojima H, Okazaki S. A molecular dynamics study of intramolecular proton transfer reaction of malonaldehyde in solutions based upon mixed quantum-classical approximation. I. Proton transfer reaction in water. J Chem Phys 2014; 141:084509. [DOI: 10.1063/1.4893933] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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31
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Xie W, Xu Y, Zhu L, Shi Q. Mixed quantum classical calculation of proton transfer reaction rates: From deep tunneling to over the barrier regimes. J Chem Phys 2014; 140:174105. [DOI: 10.1063/1.4873135] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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32
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Migliore A, Polizzi NF, Therien M, Beratan DN. Biochemistry and theory of proton-coupled electron transfer. Chem Rev 2014; 114:3381-465. [PMID: 24684625 PMCID: PMC4317057 DOI: 10.1021/cr4006654] [Citation(s) in RCA: 345] [Impact Index Per Article: 34.5] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2013] [Indexed: 02/01/2023]
Affiliation(s)
- Agostino Migliore
- Department
of Chemistry, Department of Biochemistry, and Department of Physics, Duke University, Durham, North Carolina 27708, United States
| | - Nicholas F. Polizzi
- Department
of Chemistry, Department of Biochemistry, and Department of Physics, Duke University, Durham, North Carolina 27708, United States
| | - Michael
J. Therien
- Department
of Chemistry, Department of Biochemistry, and Department of Physics, Duke University, Durham, North Carolina 27708, United States
| | - David N. Beratan
- Department
of Chemistry, Department of Biochemistry, and Department of Physics, Duke University, Durham, North Carolina 27708, United States
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Affiliation(s)
- Joshua P. Layfield
- Department of Chemistry, 600 South Mathews Avenue, University of Illinois at Urbana-Champaign, Urbana, IL 61801
| | - Sharon Hammes-Schiffer
- Department of Chemistry, 600 South Mathews Avenue, University of Illinois at Urbana-Champaign, Urbana, IL 61801
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34
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Roberts ST, Mandal A, Tokmakoff A. Local and collective reaction coordinates in the transport of the aqueous hydroxide ion. J Phys Chem B 2014; 118:8062-9. [PMID: 24666116 DOI: 10.1021/jp501145p] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
We investigate local and collective reaction coordinates for the structural diffusion of the hydroxide ion in dilute aqueous NaOH solution using a multistate empirical valence bond (MS-EVB) simulation. We characterize a 15 fs time scale associated with shifting of the equally shared proton within a Zundel-like H3O2(-) ion to form a water molecule, a 550 fs relaxation from this transition state largely guided by electrostatic fluctuations of the surrounding environment, and a 9.6 ps time scale that corresponds to the solvation of the water molecule formed by the proton transfer event. When individual proton transfer events are examined, we are unable to identify a unique transition state solely on the basis of a decrease in the hydroxide ion's coordination number. Instead, we find that the collective electric field along the proton transfer direction is better suited to describe the creation and relaxation of Zundel-like transition states that allow structural diffusion of the hydroxide ion.
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Affiliation(s)
- Sean T Roberts
- Department of Chemistry, Massachusetts Institute of Technology , Cambridge, Massachusetts 02139, United States
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35
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Clare LA, Pham AT, Magdaleno F, Acosta J, Woods JE, Cooksy AL, Smith DK. Electrochemical evidence for intermolecular proton-coupled electron transfer through a hydrogen bond complex in a p-phenylenediamine-based urea. Introduction of the "wedge scheme" as a useful means to describe reactions of this type. J Am Chem Soc 2013; 135:18930-41. [PMID: 24283378 DOI: 10.1021/ja410061x] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Abstract
The electrochemistry of several p-phenylenediamine derivatives, in which one of the amino groups is part of an urea functional group, has been investigated in methylene chloride and acetonitrile. The ureas are abbreviated U(R)R', where R' indicates the substituent on the N that is part of the phenylenediamine redox couple and R indicates the substituent on the other urea N. Cyclic voltammetry and UV-vis spectroelectrochemical studies indicate that U(Me)H and U(H)H undergo an apparent 1e(-) oxidation that actually corresponds to 2e(-) oxidation of half the ureas to a quinoidal-diimine cation, U(R)(+). This is accompanied by proton transfer to the other half of the ureas to make the electroinactive cation HU(R)H(+). This explains the observed irreversibility of the oxidation of U(Me)H in both solvents and U(H)H in acetonitrile. However, the oxidation of U(H)H in methylene chloride is reversible at higher concentrations and slower scan rates. Several lines of evidence suggest that the most likely reason for this is the accessibility of a H-bond complex between U(H)(+) and HU(H)H(+) in methylene chloride. Reduction of the H-bond complex occurs at a less negative potential than that of U(H)(+), leading to reversible behavior. This conclusion is strongly supported by the appearance of a more negative reduction peak at lower concentrations and faster scan rates, conditions in which the H-bond complex is less favored. The overall reaction mechanism is conveniently described by a "wedge scheme", which is a more general version of the square scheme typically used to describe redox processes in which proton transfer accompanies electron transfer.
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Affiliation(s)
- Laurie A Clare
- Department of Chemistry and Biochemistry, San Diego State University , San Diego, California 92182-1030, United States
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Nibbering ET, Chudoba C, Elsaesser T. Hydrogen-Bond Dynamics and Solvation of Electronically Excited States as Determined by Femtosecond Vibrational Spectroscopy. Isr J Chem 2013. [DOI: 10.1002/ijch.199900040] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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37
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Decornez H, Hammes-Schiffer S. Effects of Model Protein Environments on the Dynamics of Proton Wires. Isr J Chem 2013. [DOI: 10.1002/ijch.199900045] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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38
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Tomkins J, Hanna G. Signatures of nanoconfinement on the linear and nonlinear vibrational spectroscopy of a model hydrogen-bonded complex dissolved in a polar solvent. J Phys Chem B 2013; 117:13619-30. [PMID: 24079369 DOI: 10.1021/jp407469f] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The one-dimensional IR (1D-IR) absorption and IR pump-probe spectra of a hydrogen stretch in a model hydrogen-bonded complex dissolved in a polar solvent confined in spherical hydrophobic cavities of different sizes were simulated using ground-state mixed quantum-classical dynamics. Due to a thorough analysis of key properties of the complex and solvent from equilibrium trajectory data, we were able to gain insight into the microscopic details underlying the spectra. Both the 1D-IR and IR pump-probe spectra manifested the effects of confinement on the relative stabilities of the covalent and ionic forms of the complex through pronounced changes in their peak intensities and numbers. However, in contrast to the 1D-IR spectra, the time-resolved pump-probe spectra were found to be uniquely sensitive to the changes in the molecular dynamics as the cavity size is varied. In particular, it was found that the variations in the time evolutions of the peak intensities in the pump-probe spectra reflect the differences in the solvation dynamics associated with the various forms of the complex in different locations within the cavities. The ability to detect these differences underscores the advantage of using pump-probe spectroscopy for studying nanoconfined systems.
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Affiliation(s)
- Joseph Tomkins
- Department of Chemistry, University of Alberta , Edmonton, Alberta, Canada T6G 2G2
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Sow CS, Tomkins J, Hanna G. Computational study of the one- and two-dimensional infrared spectra of a proton-transfer mode in a hydrogen-bonded complex dissolved in a polar nanocluster. Chemphyschem 2013; 14:3309-18. [PMID: 23946271 DOI: 10.1002/cphc.201300610] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2013] [Indexed: 11/07/2022]
Abstract
The signatures of nanosolvation on the one- and two-dimensional (1D and 2D) IR spectra of a proton-transfer mode in a hydrogen-bonded complex dissolved in polar solvent molecule nanoclusters of varying size are elucidated by using mixed quantum-classical molecular dynamics simulations. For this particular system, increasing the number of solvent molecules successively from N=7 to N=9 initiates the transition of the system from a cluster state to a bulk-like state. Both the 1D and 2D IR spectra reflect this transition through pronounced changes in their peak intensities and numbers, but the time-resolved 2D IR spectra also manifest spectral features that uniquely identify the onset of the cluster-to-bulk transition. In particular, it is observed that in the 1D IR spectra, the relative intensities of the peaks change such that the number of peaks decreases from three to two as the size of the cluster increases from N=7 to N=9. In the 2D IR spectra, off-diagonal peaks are observed in the N=7 and N=8 cases at zero waiting time, but not in the N=9 case. It is known that there are no off-diagonal peaks in the 2D IR spectrum of the bulk version of this system at zero waiting time, so the disappearance of these peaks is a unique signature of the onset of bulk-like behavior. Through an examination of the trajectories of various properties of the complex and solvent, it is possible to relate the emergence of these off-diagonal peaks to an interplay between the vibrations of the complex and the solvent polarization dynamics.
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Affiliation(s)
- Chia Shen Sow
- Department of Chemistry, University of Alberta, Edmonton, AB T6G 2G2 (Canada)
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Blaser S, Ottiger P, Frey HM, Leutwyler S. NH3 as a Strong H-Bond Donor in Singly- and Doubly-Bridged Ammonia Solvent Clusters: 2-Pyridone·(NH3)n, n = 1–3. J Phys Chem A 2013; 117:7523-34. [DOI: 10.1021/jp401786f] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Susan Blaser
- Departement für Chemie und Biochemie, Universität Bern, Freiestrasse
3, CH-3012 Bern, Switzerland
| | - Philipp Ottiger
- Departement für Chemie und Biochemie, Universität Bern, Freiestrasse
3, CH-3012 Bern, Switzerland
| | - Hans-Martin Frey
- Departement für Chemie und Biochemie, Universität Bern, Freiestrasse
3, CH-3012 Bern, Switzerland
| | - Samuel Leutwyler
- Departement für Chemie und Biochemie, Universität Bern, Freiestrasse
3, CH-3012 Bern, Switzerland
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41
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Kretchmer JS, Miller TF. Direct simulation of proton-coupled electron transfer across multiple regimes. J Chem Phys 2013; 138:134109. [DOI: 10.1063/1.4797462] [Citation(s) in RCA: 70] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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Abstract
Visible light excitation of the ligand-bridged assembly [(bpy)(2)Ru(a)(II)(L)Ru(b)(II)(bpy)(OH(2))(4+)] (bpy is 2,2'-bipyridine; L is the bridging ligand, 4-phen-tpy) results in emission from the lowest energy, bridge-based metal-to-ligand charge transfer excited state (L(-•))Ru(b)(III)-OH(2) with an excited-state lifetime of 13 ± 1 ns. Near-diffusion-controlled quenching of the emission occurs with added HPO(4)(2-) and partial quenching by added acetate anion (OAc(-)) in buffered solutions with pH control. A Stern-Volmer analysis of quenching by OAc(-) gave a quenching rate constant of k(q) = 4.1 × 10(8) M(-1) • s(-1) and an estimated pK(a)* value of ~5 ± 1 for the [(bpy)(2)Ru(a)(II)(L(•-))Ru(b)(III)(bpy)(OH(2))(4+)]* excited state. Following proton loss and rapid excited-state decay to give [(bpy)(2)Ru(a)(II)(L)Ru(b)(II)(bpy)(OH)(3+)] in a H(2)PO(4)(-)/HPO(4)(2-) buffer, back proton transfer occurs from H(2)PO(4)(-) to give [(bpy)(2)Ru(a)(II)(L)Ru(b)(bpy)(OH(2))(4+)] with k(PT,2) = 4.4 × 10(8) M(-1) • s(-1). From the intercept of a plot of k(obs) vs. [H(2)PO(4)(-)], k = 2.1 × 10(6) s(-1) for reprotonation by water providing a dramatic illustration of kinetically limiting, slow proton transfer for acids and bases with pK(a) values intermediate between pK(a)(H(3)O(+)) = -1.74 and pK(a)(H(2)O) = 15.7.
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Abstract
This brief review analyzes the underlying physical principles of enzyme catalysis, with an emphasis on the role of equilibrium enzyme motions and conformational sampling. The concepts are developed in the context of three representative systems, namely, dihydrofolate reductase, ketosteroid isomerase, and soybean lipoxygenase. All of these reactions involve hydrogen transfer, but many of the concepts discussed are more generally applicable. The factors that are analyzed in this review include hydrogen tunneling, proton donor-acceptor motion, hydrogen bonding, pKa shifting, electrostatics, preorganization, reorganization, and conformational motions. The rate constant for the chemical step is determined primarily by the free energy barrier, which is related to the probability of sampling configurations conducive to the chemical reaction. According to this perspective, stochastic thermal motions lead to equilibrium conformational changes in the enzyme and ligands that result in configurations favorable for the breaking and forming of chemical bonds. For proton, hydride, and proton-coupled electron transfer reactions, typically the donor and acceptor become closer to facilitate the transfer. The impact of mutations on the catalytic rate constants can be explained in terms of the factors enumerated above. In particular, distal mutations can alter the conformational motions of the enzyme and therefore the probability of sampling configurations conducive to the chemical reaction. Methods such as vibrational Stark spectroscopy, in which environmentally sensitive probes are introduced site-specifically into the enzyme, provide further insight into these aspects of enzyme catalysis through a combination of experiments and theoretical calculations.
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Affiliation(s)
- Sharon Hammes-Schiffer
- Department of Chemistry, 600 South Mathews Avenue, University of Illinois at Urbana-Champaign , Urbana, Illinois 61801, United States
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Hamm P, Stock G. Vibrational conical intersections as a mechanism of ultrafast vibrational relaxation. PHYSICAL REVIEW LETTERS 2012; 109:173201. [PMID: 23215183 DOI: 10.1103/physrevlett.109.173201] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/09/2012] [Indexed: 06/01/2023]
Abstract
Presenting true crossings of adiabatic potential energy surfaces, conical intersections are a paradigm of ultrafast and efficient electronic relaxation dynamics. The same mechanism is shown to apply also for vibrational conical intersections, which may occur when two high-frequency modes (such as OH stretch vibrations) are coupled to low-frequency modes (such as hydrogen bonding modes). By derivation of a model Hamiltonian and its parametrization for a concrete example, malonaldehyde, the conditions that such conical intersections occur are identified and the consequences for the vibrational dynamics and spectra are demonstrated.
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Affiliation(s)
- Peter Hamm
- Physikalisch-Chemisches Institut, Universität Zürich, Winterthurerstrasse 190, CH-8057 Zürich, Switzerland
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Thomas V, Rivard U, Maurer P, Bruhács A, Siwick BJ, Iftimie R. Concerted and Sequential Proton Transfer Mechanisms in Water-Separated Acid-Base Encounter Pairs. J Phys Chem Lett 2012; 3:2633-2637. [PMID: 26295883 DOI: 10.1021/jz3012639] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
The proton transfer mechanisms involved inside aqueous, solvent-separated encounter complexes between phenol and carboxyl moieties are studied using ab initio molecular dynamics and computational time-resolved vibrational spectroscopy. This model framework can be viewed as a ground-state analog of the excited-state proton transfer reactions that have been actively investigated using ultrafast spectroscopy. Three qualitatively distinct proton transfer pathways are observed in the simulations. These can be described as direct concerted, direct sequential, and through bulk transfers. The primary difference between the sequential and concerted mechanism is the involvement of a reaction intermediate in which the proton fluctuates for several picoseconds through the hydrogen bonds connecting donor and acceptor but resides primarily on an intervening water molecule in the encounter complex. These results contribute to our molecular level understanding of the diverse processes involved in proton transfer within water-separated encounter complexes.
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Affiliation(s)
- Vibin Thomas
- †Département de Chimie, Université de Montréal,CP 6128, succursale Centre-Ville, Montréal H3C3J7, Canada
| | - Ugo Rivard
- †Département de Chimie, Université de Montréal,CP 6128, succursale Centre-Ville, Montréal H3C3J7, Canada
| | - Patrick Maurer
- †Département de Chimie, Université de Montréal,CP 6128, succursale Centre-Ville, Montréal H3C3J7, Canada
| | - Andrew Bruhács
- ‡Departments of Chemistry and Physics, Center for the Physics of Materials, McGill University, 801 Sherbrooke Street West, Montréal, Canada
| | - Bradley J Siwick
- ‡Departments of Chemistry and Physics, Center for the Physics of Materials, McGill University, 801 Sherbrooke Street West, Montréal, Canada
| | - Radu Iftimie
- †Département de Chimie, Université de Montréal,CP 6128, succursale Centre-Ville, Montréal H3C3J7, Canada
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Aono S, Yamamoto T, Kato S. Solution reaction space Hamiltonian based on an electrostatic potential representation of solvent dynamics. J Chem Phys 2011; 134:144108. [DOI: 10.1063/1.3572057] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
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Cohen B, Martin Álvarez C, Alarcos Carmona N, Organero JA, Douhal A. Proton-Transfer Reaction Dynamics within the Human Serum Albumin Protein. J Phys Chem B 2011; 115:7637-47. [DOI: 10.1021/jp200294q] [Citation(s) in RCA: 67] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Boiko Cohen
- Departamento de Química Física, Facultad de Ciencias Ambientales y Bioquímica, and INAMOL, Universidad de Castilla-La Mancha, Avenida Carlos III, S/N, 45071 Toledo, Spain
| | - Cristina Martin Álvarez
- Departamento de Química Física, Facultad de Ciencias Ambientales y Bioquímica, and INAMOL, Universidad de Castilla-La Mancha, Avenida Carlos III, S/N, 45071 Toledo, Spain
| | - Noemí Alarcos Carmona
- Departamento de Química Física, Facultad de Ciencias Ambientales y Bioquímica, and INAMOL, Universidad de Castilla-La Mancha, Avenida Carlos III, S/N, 45071 Toledo, Spain
| | - Juan Angel Organero
- Departamento de Química Física, Facultad de Ciencias Ambientales y Bioquímica, and INAMOL, Universidad de Castilla-La Mancha, Avenida Carlos III, S/N, 45071 Toledo, Spain
| | - Abderrazzak Douhal
- Departamento de Química Física, Facultad de Ciencias Ambientales y Bioquímica, and INAMOL, Universidad de Castilla-La Mancha, Avenida Carlos III, S/N, 45071 Toledo, Spain
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Churakov AV, Prikhodchenko PV, Lev O, Medvedev AG, Tripol'skaya TA, Vener MV. A model proton-transfer system in the condensed phase: NH4(+)OOH(-), a crystal with short intermolecular H-bonds. J Chem Phys 2011; 133:164506. [PMID: 21033804 DOI: 10.1063/1.3493688] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023] Open
Abstract
The crystal structure of NH(4)(+)OOH(-) is determined from single-crystal x-ray data obtained at 150 K. The crystal belongs to the space group P2(1)/c and has four molecules in a unit cell. The structure consists of discrete NH(4)(+) and OOH(-) ions. The OOH(-) ions are linked by short hydrogen bonds (2.533 Å) to form parallel infinite chains. The ammonium ions form links between these chains (the N⋯O distances vary from 2.714 to 2.855 Å) giving a three-dimensional network. The harmonic IR spectrum and H-bond energies are computed at the Perdew-Burke-Ernzerhof (PBE)/6-31G(∗∗) level with periodic boundary conditions. A detailed analysis of the shared (bridging) protons' dynamics is obtained from the CPMD simulations at different temperatures. PBE functional with plane-wave basis set (110 Ry) is used. At 10 K the shared proton sits near the oxygen atom, only a few proton jumps along the chain are detected at 70 K while at 270 K numerous proton jumps exist in the trajectory. The local-minimum structure of the space group Cc is localized. It appears as a result of proton transfer along a chain. This process is endothermic (∼2 kJ/mol) and is described as P2(1)/c↔2Cc. The computed IR spectrum at 10 K is close to the harmonic one, the numerous bands appear at 70 K while at 270 K it shows a very broad absorption band that covers frequencies from about 1000 to 3000 cm(-1). The advantages of the NH(4)(+)OOH(-) crystal as a promising model for the experimental and DFT based molecular dynamics simulation studies of proton transfer along the chain are discussed.
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Affiliation(s)
- Andrei V Churakov
- Kurnakov Institute of General and Inorganic Chemistry, Russian Academy of Sciences, Leninskii prosp. 31, Moscow 119991, Russia
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Joutsuka T, Ando K. Dynamics of Proton Transfer and Vibrational Relaxation in Dilute Hydrofluoric Acid. J Phys Chem A 2011; 115:678-84. [DOI: 10.1021/jp108413p] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Tatsuya Joutsuka
- Department of Chemistry, Kyoto University, Sakyo-ku, Kyoto 606-8502, Japan
| | - Koji Ando
- Department of Chemistry, Kyoto University, Sakyo-ku, Kyoto 606-8502, Japan
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50
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Lankau T, Yu CH. A quantum description of the proton movement in an idealized NHN+ bridge. Phys Chem Chem Phys 2011; 13:12758-69. [DOI: 10.1039/c0cp02172e] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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