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Ma Z, Chen L, Xu C, Fournier JA. Two-Dimensional Infrared Spectroscopy of Isolated Molecular Ions. J Phys Chem Lett 2023; 14:9683-9689. [PMID: 37871134 DOI: 10.1021/acs.jpclett.3c02661] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2023]
Abstract
Two-dimensional infrared (2D IR) spectroscopy of mass-selected, cryogenically cooled molecular ions is presented. Nonlinear response pathways, encoded in the time-domain photodissociation action response of weakly bound N2 messenger tags, were isolated using pulse shaping techniques following excitation with four collinear ultrafast IR pulses. 2D IR spectra of Re(CO)3(CH3CN)3+ ions capture off-diagonal cross-peak bleach signals between the asymmetric and symmetric carbonyl stretching transitions. These cross peaks display intensity variations as a function of pump-probe delay time due to coherent coupling between the vibrational modes. Well-resolved 2D IR features in the congested fingerprint region of protonated caffeine (C8H10N4O2H+) are also reported. Importantly, intense cross-peak signals were observed at 3 ps waiting time, indicating that tag-loss dynamics are not competing with the measured nonlinear signals. These demonstrations pave the way for more precise studies of molecular interactions and dynamics that are not easily obtainable with current condensed-phase methodologies.
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Affiliation(s)
- Zifan Ma
- Department of Chemistry, Washington University in St. Louis, St. Louis, Missouri 63130, United States
| | - Liangyi Chen
- Department of Chemistry, Washington University in St. Louis, St. Louis, Missouri 63130, United States
| | - Chuzhi Xu
- Department of Chemistry, Washington University in St. Louis, St. Louis, Missouri 63130, United States
| | - Joseph A Fournier
- Department of Chemistry, Washington University in St. Louis, St. Louis, Missouri 63130, United States
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2
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Boutwell D, Pierre-Jacques D, Cochran O, Dyke J, Salazar D, Tyler C, Kaledin M. Intramolecular Proton Transfer in the Hydrogen Oxalate Anion and the Cooperativity Effects of the Low-Frequency Vibrations: A Driven Molecular Dynamics Study. J Phys Chem A 2022; 126:583-592. [PMID: 35049313 DOI: 10.1021/acs.jpca.1c09686] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
We report first-principles molecular dynamics (MD) and dipole-driven molecular dynamics (μ-DMD) simulations of the hydrogen oxalate anion at the MP2/aug-cc-pVDZ level of theory. We examine the role of vibrational coupling between the OH stretching bands, that is, the fundamental and a few combination bands spanning the 2900-3100 cm-1 range, and several of the low-frequency bending and stretching fundamental modes. The low-frequency modes between 300 and 825 cm-1 play a crucial role in the proton-transfer motion. Strong involvement of CO2 and CCO bending and the CC stretching vibrations indicate that these large amplitude motions cause the shortening of the O···O distance and thus promote H+ transfer to the other oxygen by bringing it over the 3.4 kcal/mol barrier. Analysis of resonant μ-DMD trajectories shows that the complex spectral feature near 825 cm-1, closely corresponding to both an overtone of two quanta of 425 cm-1 and a combination band of low-frequency CO2 rocking (300 cm-1) and CCO bending (575 cm-1) modes, is involved in the proton transfer. μ-DMD shows that exciting the system at these mode combinations leads to faster barrier activation than exciting at the OH fundamental mode.
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Affiliation(s)
- Dalton Boutwell
- Department of Chemistry & Biochemistry, Kennesaw State University, 370 Paulding Ave NW, Box # 1203, Kennesaw, Georgia 30144, United States
| | - Dominick Pierre-Jacques
- Department of Chemistry & Biochemistry, Kennesaw State University, 370 Paulding Ave NW, Box # 1203, Kennesaw, Georgia 30144, United States
| | - Olivia Cochran
- Department of Chemistry & Biochemistry, Kennesaw State University, 370 Paulding Ave NW, Box # 1203, Kennesaw, Georgia 30144, United States
| | - Jason Dyke
- Department of Chemistry & Biochemistry, Kennesaw State University, 370 Paulding Ave NW, Box # 1203, Kennesaw, Georgia 30144, United States
| | - Dayana Salazar
- Department of Chemistry & Biochemistry, Kennesaw State University, 370 Paulding Ave NW, Box # 1203, Kennesaw, Georgia 30144, United States
| | - Ciara Tyler
- Department of Chemistry & Biochemistry, Kennesaw State University, 370 Paulding Ave NW, Box # 1203, Kennesaw, Georgia 30144, United States
| | - Martina Kaledin
- Department of Chemistry & Biochemistry, Kennesaw State University, 370 Paulding Ave NW, Box # 1203, Kennesaw, Georgia 30144, United States
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3
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On-the-Fly Ring-Polymer Molecular Dynamics Calculations of the Dissociative Photodetachment Process of the Oxalate Anion. Molecules 2021; 26:molecules26237250. [PMID: 34885831 PMCID: PMC8658898 DOI: 10.3390/molecules26237250] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2021] [Revised: 11/22/2021] [Accepted: 11/26/2021] [Indexed: 11/16/2022] Open
Abstract
The dissociative photodetachment dynamics of the oxalate anion, C2O4H- + hν → CO2 + HOCO + e-, were theoretically studied using the on-the-fly path-integral and ring-polymer molecular dynamics methods, which can account for nuclear quantum effects at the density-functional theory level in order to compare with the recent experimental study using photoelectron-photofragment coincidence spectroscopy. To reduce computational time, the force acting on each bead of ring-polymer was approximately calculated from the first and second derivatives of the potential energy at the centroid position of the nuclei beads. We find that the calculated photoelectron spectrum qualitatively reproduces the experimental spectrum and that nuclear quantum effects are playing a role in determining spectral widths. The calculated coincidence spectrum is found to reasonably reproduce the experimental spectrum, indicating that a relatively large energy is partitioned into the relative kinetic energy between the CO2 and HOCO fragments. This is because photodetachment of the parent anion leads to Franck-Condon transition to the repulsive region of the neutral potential energy surface. We also find that the dissociation dynamics are slightly different between the two isomers of the C2O4H- anion with closed- and open-form structures.
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4
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Kwasigroch B, Khuu T, Perez EH, Denton JK, Schneider EK, Straßner A, Theisen M, Kruppa SV, Weis P, Kappes MM, Riehn C, Johnson MA, Niedner-Schatteburg G. On the Hydrogen Oxalate Binding Motifs onto Dinuclear Cu and Ag Metal Phosphine Complexes. Chemistry 2021; 27:15136-15146. [PMID: 34632659 PMCID: PMC8597048 DOI: 10.1002/chem.202102768] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2021] [Indexed: 11/23/2022]
Abstract
We report the binding geometries of the isomers that are formed when the hydrogen oxalate ((CO2)2H=HOx) anion attaches to dinuclear coinage metal phosphine complexes of the form [M1M2dcpm2(HOx)]+ with M=Cu, Ag and dcpm=bis(dicyclohexylphosphino)methane, abbreviated [MM]+. These structures are established by comparison of isomer‐selective experimental vibrational band patterns displayed by the cryogenically cooled and N2‐tagged cations with DFT calculations of the predicted spectra for various local minima. Two isomeric classes are identified that feature either attachment of the carboxylate oxygen atoms to the two metal centers (end‐on docking) or attachment of oxygen atoms on different carbon atoms asymmetrically to the metal ions (side‐on docking). Within each class, there are additional isomeric variations according to the orientation of the OH group. This behavior indicates that HOx undergoes strong and directional coordination to [CuCu]+ but adopts a more flexible coordination to [AgAg]+. Infrared spectra of the bare ions, fragmentation thresholds and ion mobility measurements are reported to explore the behaviors of the complexes at ambient temperature.
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Affiliation(s)
- Björn Kwasigroch
- Department of Chemistry, Technische Universität Kaiserslautern (TUK), Erwin-Schrödinger-Str. 52, 67663, Kaiserslautern, Germany
| | - Thien Khuu
- Sterling Chemistry Laboratory, Yale University, 225 Prospect Str., New Haven, Connecticut, 06520, USA
| | - Evan H Perez
- Sterling Chemistry Laboratory, Yale University, 225 Prospect Str., New Haven, Connecticut, 06520, USA
| | - Joanna K Denton
- Sterling Chemistry Laboratory, Yale University, 225 Prospect Str., New Haven, Connecticut, 06520, USA
| | - Erik K Schneider
- Institute of Physical Chemistry, Karlsruhe Institute of Technology (KIT), Fritz-Haber Weg 2, 76131, Karlsruhe, Germany
| | - Annika Straßner
- Department of Chemistry, Technische Universität Kaiserslautern (TUK), Erwin-Schrödinger-Str. 52, 67663, Kaiserslautern, Germany
| | - Marvin Theisen
- Department of Chemistry, Technische Universität Kaiserslautern (TUK), Erwin-Schrödinger-Str. 52, 67663, Kaiserslautern, Germany
| | - Sebastian V Kruppa
- Department of Chemistry, Technische Universität Kaiserslautern (TUK), Erwin-Schrödinger-Str. 52, 67663, Kaiserslautern, Germany
| | - Patrick Weis
- Institute of Physical Chemistry, Karlsruhe Institute of Technology (KIT), Fritz-Haber Weg 2, 76131, Karlsruhe, Germany
| | - Manfred M Kappes
- Institute of Physical Chemistry, Karlsruhe Institute of Technology (KIT), Fritz-Haber Weg 2, 76131, Karlsruhe, Germany.,Institute for Nanotechnology, Karlsruhe Institute of Technology (KIT), Hermann-von-Helmholtz-Platz 1, 76344, Eggenstein-Leopoldshafen, Germany
| | - Christoph Riehn
- Department of Chemistry, Technische Universität Kaiserslautern (TUK), Erwin-Schrödinger-Str. 52, 67663, Kaiserslautern, Germany.,Research Center OPTIMAS, Erwin-Schrödinger Str. 46, 67663, Kaiserslautern, Germany
| | - Mark A Johnson
- Sterling Chemistry Laboratory, Yale University, 225 Prospect Str., New Haven, Connecticut, 06520, USA
| | - Gereon Niedner-Schatteburg
- Department of Chemistry, Technische Universität Kaiserslautern (TUK), Erwin-Schrödinger-Str. 52, 67663, Kaiserslautern, Germany.,Research Center OPTIMAS, Erwin-Schrödinger Str. 46, 67663, Kaiserslautern, Germany
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5
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Thomas DA, Taccone M, Ober K, Mucha E, Meijer G, von Helden G. Helium Nanodroplet Infrared Action Spectroscopy of the Proton-Bound Dimer of Hydrogen Sulfate and Formate: Examining Nuclear Quantum Effects. J Phys Chem A 2021; 125:9279-9287. [PMID: 34652165 PMCID: PMC8558860 DOI: 10.1021/acs.jpca.1c05705] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Abstract
The proton-bound dimer of hydrogen sulfate and formate is an archetypal structure for ionic hydrogen-bonding complexes that contribute to biogenic aerosol nucleation. Of central importance for the structure and properties of this complex is the location of the bridging proton connecting the two conjugate base moieties. The potential energy surface for bridging proton translocation features two local minima, with the proton localized at either the formate or hydrogen sulfate moiety. However, electronic structure methods reveal a shallow potential energy surface governing proton translocation, with a barrier on the order of the zero-point energy. This shallow potential complicates structural assignment and necessitates a consideration of nuclear quantum effects. In this work, we probe the structure of this complex and its isotopologues, utilizing infrared (IR) action spectroscopy of ions captured in helium nanodroplets. The IR spectra indicate a structure in which a proton is shared between the hydrogen sulfate and formate moieties, HSO4-···H+···-OOCH. However, because of the nuclear quantum effects and vibrational anharmonicities associated with the shallow potential for proton translocation, the extent of proton displacement from the formate moiety remains unclear, requiring further experiments or more advanced theoretical treatments for additional insight.
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Affiliation(s)
- Daniel A Thomas
- Fritz-Haber-Institut der Max-Planck-Gesellschaft, Faradayweg 4-6, 14195 Berlin, Germany
| | - Martín Taccone
- Fritz-Haber-Institut der Max-Planck-Gesellschaft, Faradayweg 4-6, 14195 Berlin, Germany
| | - Katja Ober
- Fritz-Haber-Institut der Max-Planck-Gesellschaft, Faradayweg 4-6, 14195 Berlin, Germany
| | - Eike Mucha
- Fritz-Haber-Institut der Max-Planck-Gesellschaft, Faradayweg 4-6, 14195 Berlin, Germany
| | - Gerard Meijer
- Fritz-Haber-Institut der Max-Planck-Gesellschaft, Faradayweg 4-6, 14195 Berlin, Germany
| | - Gert von Helden
- Fritz-Haber-Institut der Max-Planck-Gesellschaft, Faradayweg 4-6, 14195 Berlin, Germany
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6
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Chen L, Fournier JA. Probing Hydrogen-Bonding Interactions within Phenol-Benzimidazole Proton-Coupled Electron Transfer Model Complexes with Cryogenic Ion Vibrational Spectroscopy. J Phys Chem A 2021; 125:9288-9297. [PMID: 34652915 DOI: 10.1021/acs.jpca.1c05879] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Hydrogen-bonding interactions within a series of phenol-benzimidazole model proton-coupled electron transfer (PCET) dyad complexes are characterized using cryogenic ion vibrational spectroscopy. A highly red-shifted and surprisingly broad (>1000 cm-1) transition is observed in one of the models and assigned to the phenolic OH stretch strongly H-bonded to the N(3) benzimidazole atom. The breadth is attributed to a combination of anharmonic Fermi-resonance coupling between the OH stretch and background doorway states involving OH bending modes and strong coupling of the OH stretch frequency to structural deformations along the proton-transfer coordinate accessible at the vibrational zero-point level. The other models show unexpected protonation of the benzimidazole group upon electrospray ionization instead of at more basic remote amine/amide groups. This leads to the formation of HO-+HN(3) H-bond motifs that are much weaker than the OH-N(3) H-bond arrangement. H-bonding between the N(1)H+ benzimidazole group and the carbonyl on the tyrosine backbone is the stronger and preferred interaction in these complexes. The results show that conjugation effects, secondary H-bond interactions, and H-bond soft modes strongly influence the OH-N(3) interaction and highlight the importance of the direct monitoring of proton stretch transitions in characterizing the proton-transfer reaction coordinate in PCET systems.
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Affiliation(s)
- Liangyi Chen
- Department of Chemistry, Washington University in St. Louis, St. Louis, Missouri 63130, United States
| | - Joseph A Fournier
- Department of Chemistry, Washington University in St. Louis, St. Louis, Missouri 63130, United States
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7
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Jestilä JS, Denton JK, Perez EH, Khuu T, Aprà E, Xantheas SS, Johnson MA, Uggerud E. Characterization of the alkali metal oxalates (MC 2O 4-) and their formation by CO 2 reduction via the alkali metal carbonites (MCO 2-). Phys Chem Chem Phys 2020; 22:7460-7473. [PMID: 32219243 DOI: 10.1039/d0cp00547a] [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
The reduction of carbon dioxide to oxalate has been studied by experimental Collisionally Induced Dissociation (CID) and vibrational characterization of the alkali metal oxalates, supplemented by theoretical electronic structure calculations. The critical step in the reductive process is the coordination of CO2 to an alkali metal anion, forming a metal carbonite MCO2- able to subsequently receive a second CO2 molecule. While the energetic demand for these reactions is generally low, we find that the degree of activation of CO2 in terms of charge transfer and transition state energies is the highest for lithium and systematically decreases down the group (M = Li-Cs). This is correlated to the strength of the binding interaction between the alkali metal and CO2, which can be related to the structure of the oxalate moiety within the product metal complexes evolving from a planar to a staggered conformer with increasing atomic number of the interacting metal. Similar structural changes are observed for crystalline alkali metal oxalates, although the C2O42- moiety is in general more planar in these, a fact that is attributed to the increased number of interacting alkali metal cations compared to the gas-phase ions.
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Affiliation(s)
- Joakim S Jestilä
- Department of Chemistry and Hylleraas Centre for Quantum Molecular Sciences, University of Oslo, P.O. Box 1033, Blindern, Oslo N-0135, Norway.
| | - Joanna K Denton
- Sterling Chemistry Laboratory, Yale University, New Haven, Connecticut 06520, USA
| | - Evan H Perez
- Sterling Chemistry Laboratory, Yale University, New Haven, Connecticut 06520, USA
| | - Thien Khuu
- Sterling Chemistry Laboratory, Yale University, New Haven, Connecticut 06520, USA
| | - Edoardo Aprà
- Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, P.O. Box 999, Richland, Washington 99352, USA
| | - Sotiris S Xantheas
- Advanced Computing, Mathematics and Data Division, Pacific Northwest National Laboratory, 902 Battelle Boulevard, P.O. Box 999, MS K1-83, Richland, Washington, USA and Department of Chemistry, University of Washington, Seattle, Washington 98195, USA
| | - Mark A Johnson
- Sterling Chemistry Laboratory, Yale University, New Haven, Connecticut 06520, USA
| | - Einar Uggerud
- Department of Chemistry and Hylleraas Centre for Quantum Molecular Sciences, University of Oslo, P.O. Box 1033, Blindern, Oslo N-0135, Norway.
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8
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Multistate Reactive Molecular Dynamics Simulations of Proton Diffusion in Water Clusters and in the Bulk. J Phys Chem B 2019; 123:9846-9861. [PMID: 31647873 DOI: 10.1021/acs.jpcb.9b03258] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
The molecular mechanics with proton transfer (MMPT) force field is combined with multistate adiabatic reactive molecular dynamics (MS-ARMD) to describe proton transport in the condensed phase. Parametrization for small protonated water clusters based on electronic structure calculations at the MP2/6-311+G(2d,2p) level of theory and refinement by comparing with infrared spectra for a protonated water tetramer yields a force field which faithfully describes the minimum energy structures of small protonated water clusters. In protonated water clusters up to (H2O)100H+, the proton hopping rate is around 100 hops/ns. This rate converges for 21 ≤ n ≤ 31, and no further speedup in bulk water is found. This indicates that bulklike behavior requires the solvation of a Zundel motif by ∼25 water molecules, which corresponds to the second solvation sphere. For smaller cluster sizes, the number of available states (i.e., the number of proton acceptors) is too small and slows down proton-transfer rates. The cluster simulations confirm that the excess proton is typically located on the surface. The free-energy surface as a function of the weights of the two lowest states and a configurational parameter suggests that the "special pair" plays a central role in rapid proton transport. The barriers between this minimum-energy structure and the Zundel and Eigen minima are sufficiently low (∼1 kcal/mol, consistent with recent experiments and commensurate with a hopping rate of ∼100/ns or 1 every 10 ps), leading to a highly dynamic environment. These findings are also consistent with recent experiments which find that Zundel-type hydration geometries are prevalent in bulk water.
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9
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Thaunay F, Calvo F, Nicol E, Ohanessian G, Clavaguéra C. Infrared Spectra of Deprotonated Dicarboxylic Acids: IRMPD Spectroscopy and Empirical Valence‐Bond Modeling. Chemphyschem 2019; 20:803-814. [PMID: 30695125 DOI: 10.1002/cphc.201800947] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2018] [Revised: 01/28/2019] [Indexed: 01/08/2023]
Abstract
Experimental infrared multiple-photon dissociation (IRMPD) spectra recorded for a series of deprotonated dicarboxylic acids, HO2 (CH2 )n CO 2 - (n=2-4), are interpreted using a variety of computational methods. The broad bands centered near 1600 cm-1 can be reproduced neither by static vibrational calculations based on quantum chemistry nor by a dynamical description of individual structures using the many-body polarizable AMOEBA force field, strongly suggesting that these molecules experience dynamical proton sharing between the two carboxylic ends. To confirm this assumption, AMOEBA was combined with a two-state empirical valence-bond (EVB) model to allow for proton transfer in classical molecular dynamics simulations. Upon suitable parametrization based on ab initio reference data, the EVB-AMOEBA model satisfactorily reproduces the experimental infrared spectra, and the finite temperature dynamics reveals a significant amount of proton sharing in such systems.
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Affiliation(s)
| | - Florent Calvo
- LIPhyUniversité Grenoble Alpes, CNRS, LiPhy 38000 Grenoble France
| | - Edith Nicol
- LCM, CNRSEcole Polytechnique 91128 Palaiseau Cedex France
| | | | - Carine Clavaguéra
- Laboratoire de Chimie PhysiqueCNRS – Université Paris Sud, Université Paris-Saclay 15 avenue Jean Perrin 91405 Orsay Cedex France
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10
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Thomas DA, Marianski M, Mucha E, Meijer G, Johnson MA, von Helden G. Ground‐State Structure of the Proton‐Bound Formate Dimer by Cold‐Ion Infrared Action Spectroscopy. Angew Chem Int Ed Engl 2018. [DOI: 10.1002/ange.201805436] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Daniel A. Thomas
- Fritz-Haber-Institut der Max-Planck-Gesellschaft Faradayweg 4–6 14195 Berlin Germany
| | - Mateusz Marianski
- Fritz-Haber-Institut der Max-Planck-Gesellschaft Faradayweg 4–6 14195 Berlin Germany
| | - Eike Mucha
- Fritz-Haber-Institut der Max-Planck-Gesellschaft Faradayweg 4–6 14195 Berlin Germany
| | - Gerard Meijer
- Fritz-Haber-Institut der Max-Planck-Gesellschaft Faradayweg 4–6 14195 Berlin Germany
| | - Mark A. Johnson
- Sterling Chemistry Laboratory Yale University 225 Prospect Street New Haven CT 06520 USA
| | - Gert von Helden
- Fritz-Haber-Institut der Max-Planck-Gesellschaft Faradayweg 4–6 14195 Berlin Germany
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11
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Thomas DA, Marianski M, Mucha E, Meijer G, Johnson MA, von Helden G. Ground‐State Structure of the Proton‐Bound Formate Dimer by Cold‐Ion Infrared Action Spectroscopy. Angew Chem Int Ed Engl 2018; 57:10615-10619. [DOI: 10.1002/anie.201805436] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2018] [Indexed: 11/11/2022]
Affiliation(s)
- Daniel A. Thomas
- Fritz-Haber-Institut der Max-Planck-Gesellschaft Faradayweg 4–6 14195 Berlin Germany
| | - Mateusz Marianski
- Fritz-Haber-Institut der Max-Planck-Gesellschaft Faradayweg 4–6 14195 Berlin Germany
| | - Eike Mucha
- Fritz-Haber-Institut der Max-Planck-Gesellschaft Faradayweg 4–6 14195 Berlin Germany
| | - Gerard Meijer
- Fritz-Haber-Institut der Max-Planck-Gesellschaft Faradayweg 4–6 14195 Berlin Germany
| | - Mark A. Johnson
- Sterling Chemistry Laboratory Yale University 225 Prospect Street New Haven CT 06520 USA
| | - Gert von Helden
- Fritz-Haber-Institut der Max-Planck-Gesellschaft Faradayweg 4–6 14195 Berlin Germany
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12
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Wagner JP, McDonald DC, Duncan MA. Spectroscopy of Proton Coordination with Ethylenediamine. J Phys Chem A 2018; 122:5168-5176. [PMID: 29771517 DOI: 10.1021/acs.jpca.8b03592] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Protonated ethylenediamine monomer, dimer, and trimer were produced in the gas phase by an electrical discharge/supersonic expansion of argon seeded with ethylenediamine (C2H8N2, en) vapor. Infrared spectra of these ions were measured in the region from 1000 to 4000 cm-1 using laser photodissociation and argon tagging. Computations at the CBS-QB3 level were performed to explore possible isomers and understand the infrared spectra. The protonated monomer exhibits a gauche conformation and an intramolecular hydrogen bond. Its parallel shared proton vibration occurs as a broad band around 2785 cm-1, despite the formally equivalent proton affinities of the two amino groups involved, which usually leads to low frequency bands. The barrier to intramolecular proton transfer is 2.2 kcal mol-1 and does not vanish upon addition of the zero-point energy, unlike the related protonated ammonia dimer. The structure of the dimer is formed by chelation of the monomer's NH3+ group, thereby localizing the excess proton and increasing the frequency of the intramolecular shared proton vibration to 3157 cm-1. Other highly fluxional dimer structures with facile intermolecular proton transfer and concomitant structural reorganization were computed to lie within 2 kcal mol-1 of the experimentally observed structure. The spectrum of the trimer is rather diffuse, and a clear assignment is not possible. However, an isomer with an intramolecular proton transfer like that of the monomer is most consistent with the experimental spectrum.
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Affiliation(s)
- J Philipp Wagner
- Department of Chemistry , University of Georgia , 140 Cedar Street , Athens , Georgia 30602 , United States
| | - David C McDonald
- Department of Chemistry , University of Georgia , 140 Cedar Street , Athens , Georgia 30602 , United States
| | - Michael A Duncan
- Department of Chemistry , University of Georgia , 140 Cedar Street , Athens , Georgia 30602 , United States
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13
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Dodson LG, Thompson MC, Weber JM. Characterization of Intermediate Oxidation States in CO2Activation. Annu Rev Phys Chem 2018; 69:231-252. [DOI: 10.1146/annurev-physchem-050317-021122] [Citation(s) in RCA: 44] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Leah G. Dodson
- JILA and NIST, University of Colorado, Boulder, Colorado 80309-0440, USA
| | - Michael C. Thompson
- JILA and Department of Chemistry and Biochemistry, University of Colorado, Boulder, Colorado 80309-0440, USA;,
| | - J. Mathias Weber
- JILA and Department of Chemistry and Biochemistry, University of Colorado, Boulder, Colorado 80309-0440, USA;,
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14
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Van Hoozen BL, Petersen PB. Vibrational tug-of-war: The pKAdependence of the broad vibrational features of strongly hydrogen-bonded carboxylic acids. J Chem Phys 2018; 148:134309. [PMID: 29626887 DOI: 10.1063/1.5026675] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- Brian L. Van Hoozen
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, New York 14853, USA
| | - Poul B. Petersen
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, New York 14853, USA
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15
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Avilés-Moreno JR, Berden G, Oomens J, Martínez-Haya B. Intra-cavity proton bonding and anharmonicity in the anionophore cyclen. Phys Chem Chem Phys 2018; 20:8968-8975. [PMID: 29557457 DOI: 10.1039/c8cp00660a] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Abstract
Proton bonding drives the supramolecular chemistry of a broad range of materials with polar moieties. Proton delocalization and electronic charge redistribution have a profound impact on the structure of proton-bound molecular frameworks, and pose fundamental challenges to quantum chemical modelling. This study provides insights into the structural and spectral signatures of the intramolecular proton bond formed in a benchmark polyazamacrocycle anionophore (cyclen, 1,4,7,10-tetraazacyclododecane). Infrared action spectroscopy is employed to characterize the macrocycle, isolated in protonated form. In its most stable configuration, protonated cyclen adopts an open arrangement of Cs symmetry with a particularly strong NHδ+N bond across the cavity. The quantum chemical analysis of the infrared spectrum reveals intrinsic difficulties for the accurate description of the vibrational modes of the system. The reconciliation of the computational predictions with experiment demands a careful anharmonic treatment of the proton motion, which exposes the limitations of current methods. Best results are obtained with the incorporation of anharmonicity only to the fundamental modes directly related to motions of the proton. However, the full anharmonic treatment of the system fails to describe correctly the vibrations related to the macrocycle backbone. The results should serve as motivation for new developments in the modelling of proton bonded systems.
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Affiliation(s)
- Juan Ramón Avilés-Moreno
- Department of Physical, Chemical and Natural Systems, Universidad Pablo de Olavide, E-41013 Seville, Spain.
| | - Giel Berden
- Radboud University, Institute for Molecules and Materials, FELIX Laboratory, Toernooiveld 7c, 6525ED Nijmegen, The Netherlands
| | - Jos Oomens
- Radboud University, Institute for Molecules and Materials, FELIX Laboratory, Toernooiveld 7c, 6525ED Nijmegen, The Netherlands
| | - Bruno Martínez-Haya
- Department of Physical, Chemical and Natural Systems, Universidad Pablo de Olavide, E-41013 Seville, Spain.
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16
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Karandashev K, Xu ZH, Meuwly M, Vaníček J, Richardson JO. Kinetic isotope effects and how to describe them. STRUCTURAL DYNAMICS (MELVILLE, N.Y.) 2017; 4:061501. [PMID: 29282447 PMCID: PMC5729036 DOI: 10.1063/1.4996339] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/16/2017] [Accepted: 08/23/2017] [Indexed: 06/01/2023]
Abstract
We review several methods for computing kinetic isotope effects in chemical reactions including semiclassical and quantum instanton theory. These methods describe both the quantization of vibrational modes as well as tunneling and are applied to the ⋅H + H2 and ⋅H + CH4 reactions. The absolute rate constants computed with the semiclassical instanton method both using on-the-fly electronic structure calculations and fitted potential-energy surfaces are also compared directly with exact quantum dynamics results. The error inherent in the instanton approximation is found to be relatively small and similar in magnitude to that introduced by using fitted surfaces. The kinetic isotope effect computed by the quantum instanton is even more accurate, and although it is computationally more expensive, the efficiency can be improved by path-integral acceleration techniques. We also test a simple approach for designing potential-energy surfaces for the example of proton transfer in malonaldehyde. The tunneling splittings are computed, and although they are found to deviate from experimental results, the ratio of the splitting to that of an isotopically substituted form is in much better agreement. We discuss the strengths and limitations of the potential-energy surface and based on our findings suggest ways in which it can be improved.
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Affiliation(s)
- Konstantin Karandashev
- Laboratory of Theoretical Physical Chemistry, Institut des Sciences et Ingénierie Chimiques, Ecole Polytechnique Fédérale de Lausanne (EPFL), CH-1015 Lausanne, Switzerland
| | - Zhen-Hao Xu
- Department of Chemistry, University of Basel, Klingelbergstrasse 80, CH-4056 Basel, Switzerland
| | - Markus Meuwly
- Department of Chemistry, University of Basel, Klingelbergstrasse 80, CH-4056 Basel, Switzerland
| | - Jiří Vaníček
- Laboratory of Theoretical Physical Chemistry, Institut des Sciences et Ingénierie Chimiques, Ecole Polytechnique Fédérale de Lausanne (EPFL), CH-1015 Lausanne, Switzerland
| | - Jeremy O Richardson
- Laboratory of Physical Chemistry, Department of Chemistry and Applied Biosciences, Eidgenössische Technische Hochschule Zürich (ETHZ), CH-8093 Zürich, Switzerland
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17
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Antipov SV, Bhattacharyya S, El Hage K, Xu ZH, Meuwly M, Rothlisberger U, Vaníček J. Ultrafast dynamics induced by the interaction of molecules with electromagnetic fields: Several quantum, semiclassical, and classical approaches. STRUCTURAL DYNAMICS (MELVILLE, N.Y.) 2017; 4:061509. [PMID: 29376107 PMCID: PMC5758379 DOI: 10.1063/1.4996559] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/17/2017] [Accepted: 10/11/2017] [Indexed: 06/07/2023]
Abstract
Several strategies for simulating the ultrafast dynamics of molecules induced by interactions with electromagnetic fields are presented. After a brief overview of the theory of molecule-field interaction, we present several representative examples of quantum, semiclassical, and classical approaches to describe the ultrafast molecular dynamics, including the multiconfiguration time-dependent Hartree method, Bohmian dynamics, local control theory, semiclassical thawed Gaussian approximation, phase averaging, dephasing representation, molecular mechanics with proton transfer, and multipolar force fields. In addition to the general overview, some focus is given to the description of nuclear quantum effects and to the direct dynamics, in which the ab initio energies and forces acting on the nuclei are evaluated on the fly. Several practical applications, performed within the framework of the Swiss National Center of Competence in Research "Molecular Ultrafast Science and Technology," are presented: These include Bohmian dynamics description of the collision of H with H2, local control theory applied to the photoinduced ultrafast intramolecular proton transfer, semiclassical evaluation of vibrationally resolved electronic absorption, emission, photoelectron, and time-resolved stimulated emission spectra, infrared spectroscopy of H-bonding systems, and multipolar force fields applications in the condensed phase.
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Affiliation(s)
- Sergey V Antipov
- Laboratory of Theoretical Physical Chemistry, Institut des Sciences et Ingénierie Chimiques, École Polytechnique Fédérale de Lausanne (EPFL), CH-1015 Lausanne, Switzerland
| | - Swarnendu Bhattacharyya
- Laboratory of Computational Chemistry and Biochemistry, École Polytechnique Fédérale de Lausanne (EPFL), CH-1015 Lausanne, Switzerland
| | - Krystel El Hage
- Department of Chemistry, University of Basel, Klingelbergstrasse 80, CH-4056 Basel, Switzerland
| | - Zhen-Hao Xu
- Department of Chemistry, University of Basel, Klingelbergstrasse 80, CH-4056 Basel, Switzerland
| | - Markus Meuwly
- Department of Chemistry, University of Basel, Klingelbergstrasse 80, CH-4056 Basel, Switzerland
| | - Ursula Rothlisberger
- Laboratory of Computational Chemistry and Biochemistry, École Polytechnique Fédérale de Lausanne (EPFL), CH-1015 Lausanne, Switzerland
| | - Jiří Vaníček
- Laboratory of Theoretical Physical Chemistry, Institut des Sciences et Ingénierie Chimiques, École Polytechnique Fédérale de Lausanne (EPFL), CH-1015 Lausanne, Switzerland
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18
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Xu ZH, Meuwly M. Vibrational Spectroscopy and Proton Transfer Dynamics in Protonated Oxalate. J Phys Chem A 2017; 121:5389-5398. [PMID: 28597659 DOI: 10.1021/acs.jpca.7b02234] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The dynamics and infrared spectroscopic signatures of proton transfer in protonated oxalate (p-Oxa) are studied using classical and quantum dynamics. The intermolecular interactions are described by a force field suitable to follow proton transfer. This allows to carry out multiple extended classical molecular dynamics (MD) and ring polymer MD simulations from which the infrared spectrum is determined. Simulations at 600 K sample the quantum mechanical ground state probability distribution and best reproduce the experimentally observed maximum absorption wavelength and part of the line shape. Comparison with the experimentally measured spectrum provides an estimate for the barrier height for proton transfer which can not be determined directly from experiment. A barrier of 4.2 kcal/mol is found to best reproduce the position and width of the infrared absorption of the transferring proton in p-Oxa and also leads to an infrared (IR) spectrum in good agreement with experiment for the deuterated species d-Oxa. A novel means to capture the two resonance forms of oxalate depending on the localization of the excess proton on either CO moiety is found to yield improved results for the spectroscopy in the framework region between 1000 and 2000 cm-1.
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Affiliation(s)
- Zhen-Hao Xu
- Department of Chemistry, University of Basel , Klingelbergstrasse 80, CH-4056 Basel, Switzerland
| | - Markus Meuwly
- Department of Chemistry, University of Basel , Klingelbergstrasse 80, CH-4056 Basel, Switzerland
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19
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Hidden role of intermolecular proton transfer in the anomalously diffuse vibrational spectrum of a trapped hydronium ion. Proc Natl Acad Sci U S A 2017; 114:E4706-E4713. [PMID: 28566495 DOI: 10.1073/pnas.1705089114] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023] Open
Abstract
We report the vibrational spectra of the hydronium and methyl-ammonium ions captured in the C3v binding pocket of the 18-crown-6 ether ionophore. Although the NH stretching bands of the CH3NH3+ ion are consistent with harmonic expectations, the OH stretching bands of H3O+ are surprisingly broad, appearing as a diffuse background absorption with little intensity modulation over 800 cm-1 with an onset ∼400 cm-1 below the harmonic prediction. This structure persists even when only a single OH group is present in the HD2O+ isotopologue, while the OD stretching region displays a regular progression involving a soft mode at about 85 cm-1 These results are rationalized in a vibrationally adiabatic (VA) model in which the motion of the H3O+ ion in the crown pocket is strongly coupled with its OH stretches. In this picture, H3O+ resides in the center of the crown in the vibrational zero-point level, while the minima in the VA potentials associated with the excited OH vibrational states are shifted away from the symmetrical configuration displayed by the ground state. Infrared excitation between these strongly H/D isotope-dependent VA potentials then accounts for most of the broadening in the OH stretching manifold. Specifically, low-frequency motions involving concerted motions of the crown scaffold and the H3O+ ion are driven by a Franck-Condon-like mechanism. In essence, vibrational spectroscopy of these systems can be viewed from the perspective of photochemical interconversion between transient, isomeric forms of the complexes corresponding to the initial stage of intermolecular proton transfer.
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20
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DeBlase AF, Harrilal CP, Lawler JT, Burke NL, McLuckey SA, Zwier TS. Conformation-Specific Infrared and Ultraviolet Spectroscopy of Cold [YAPAA+H]+ and [YGPAA+H]+ Ions: A Stereochemical “Twist” on the β-Hairpin Turn. J Am Chem Soc 2017; 139:5481-5493. [PMID: 28353347 DOI: 10.1021/jacs.7b01315] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Andrew F. DeBlase
- Department of Chemistry, Purdue University, West Lafayette, Indiana 47907-2084, United States
| | - Christopher P. Harrilal
- Department of Chemistry, Purdue University, West Lafayette, Indiana 47907-2084, United States
| | - John T. Lawler
- Department of Chemistry, Purdue University, West Lafayette, Indiana 47907-2084, United States
| | - Nicole L. Burke
- Department of Chemistry, Purdue University, West Lafayette, Indiana 47907-2084, United States
| | - Scott A. McLuckey
- Department of Chemistry, Purdue University, West Lafayette, Indiana 47907-2084, United States
| | - Timothy S. Zwier
- Department of Chemistry, Purdue University, West Lafayette, Indiana 47907-2084, United States
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21
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Fagiani MR, Song X, Debnath S, Gewinner S, Schöllkopf W, Asmis KR, Bischoff FA, Müller F, Sauer J. Dissociative Water Adsorption by Al 3O 4+ in the Gas Phase. J Phys Chem Lett 2017; 8:1272-1277. [PMID: 28262025 DOI: 10.1021/acs.jpclett.7b00273] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
We use cryogenic ion trap vibrational spectroscopy in combination with density functional theory (DFT) to study the adsorption of up to four water molecules on Al3O4+. The infrared photodissociation spectra of [Al3O4(D2O)1-4]+ are measured in the O-D stretching (3000-2000 cm-1) as well as the fingerprint spectral region (1300-400 cm-1) and are assigned based on a comparison with simulated harmonic infrared spectra for global minimum-energy structures obtained with DFT. We find that dissociative water adsorption is favored in all cases. The unambiguous assignment of the vibrational spectra of these gas phase model systems allows identifying characteristic spectral regions for O-D and O-H stretching modes of terminal (μ1) and bridging (μ2) hydroxyl groups in aluminum oxide/water systems, which sheds new light on controversial assignments for solid Al2O3 phases.
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Affiliation(s)
- Matias R Fagiani
- Wilhelm-Ostwald-Institut für Physikalische und Theoretische Chemie, Universität Leipzig , Linnéstrasse 2, D-04103 Leipzig, Germany
- Fritz-Haber-Institut der Max-Planck-Gesellschaft, Faradayweg 4-6, D-14195 Berlin, Germany
| | - Xiaowei Song
- Wilhelm-Ostwald-Institut für Physikalische und Theoretische Chemie, Universität Leipzig , Linnéstrasse 2, D-04103 Leipzig, Germany
- Fritz-Haber-Institut der Max-Planck-Gesellschaft, Faradayweg 4-6, D-14195 Berlin, Germany
| | - Sreekanta Debnath
- Wilhelm-Ostwald-Institut für Physikalische und Theoretische Chemie, Universität Leipzig , Linnéstrasse 2, D-04103 Leipzig, Germany
- Fritz-Haber-Institut der Max-Planck-Gesellschaft, Faradayweg 4-6, D-14195 Berlin, Germany
| | - Sandy Gewinner
- Fritz-Haber-Institut der Max-Planck-Gesellschaft, Faradayweg 4-6, D-14195 Berlin, Germany
| | - Wieland Schöllkopf
- Fritz-Haber-Institut der Max-Planck-Gesellschaft, Faradayweg 4-6, D-14195 Berlin, Germany
| | - Knut R Asmis
- Wilhelm-Ostwald-Institut für Physikalische und Theoretische Chemie, Universität Leipzig , Linnéstrasse 2, D-04103 Leipzig, Germany
| | - Florian A Bischoff
- Institut für Chemie, Humboldt-Universität zu Berlin , Unter den Linden 6, D-10099 Berlin, Germany
| | - Fabian Müller
- Institut für Chemie, Humboldt-Universität zu Berlin , Unter den Linden 6, D-10099 Berlin, Germany
| | - Joachim Sauer
- Institut für Chemie, Humboldt-Universität zu Berlin , Unter den Linden 6, D-10099 Berlin, Germany
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22
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Mackeprang K, Xu ZH, Maroun Z, Meuwly M, Kjaergaard HG. Spectroscopy and dynamics of double proton transfer in formic acid dimer. Phys Chem Chem Phys 2016; 18:24654-62. [PMID: 27545453 DOI: 10.1039/c6cp03462d] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
We present the isolated gas phase infrared spectra of formic acid dimer, (HCOOH)2, and its deuterated counterpart formic-d acid, (DCOOH)2, at room temperature. The formic acid dimer spectrum was obtained by spectral subtraction of a spectrum of formic acid vapor recorded at low pressure from that recorded at a higher pressure. The spectra of formic acid vapor contain features from both formic acid monomer and formic acid dimer, but at low and high pressures of formic acid, the equilibrium is pushed towards the monomer and dimer, respectively. A similar approach was used for the formic-d acid dimer. Building on the previous development of the Molecular Mechanics with Proton Transfer (MMPT) force field for simulating proton transfer reactions, molecular dynamics (MD) simulations were carried out to interpret the experimental spectra in the OH-stretching region. Within the framework of MMPT, a combination of symmetric single and double minimum potential energy surfaces (PESs) provides a good description of the double proton transfer PES. In a next step, potential morphing together with electronic structure calculations at the B3LYP and MP2 level of theory was used to align the computed and experimentally observed spectral features in the OH-stretching region. From this analysis, a barrier for double proton transfer between 5 and 7 kcal mol(-1) was derived, which compares with a CCSD(T)/aug-cc-pVTZ calculated barrier of 7.9 kcal mol(-1). Such a combination of experimental and computational techniques for estimating barriers for proton transfer in gas phase systems is generic and holds promise for further improved PESs and energetics of these important systems. Additional MD simulations at the semi-empirical DFTB level of theory agree quite well for the center band position but underestimate the width of the OH-stretching band.
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Affiliation(s)
- Kasper Mackeprang
- Department of Chemistry, University of Copenhagen, Universitetsparken 5, DK-2100 Copenhagen Ø, Denmark.
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