1
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Bocanegra EL, Rana A, McCoy AB, Johnson MA. Isomer-Specific, Cryogenic Ion Vibrational Spectroscopy Investigation of D 2- and N 2-Tagged, Protonated Formic Acid Complexes Using Two-Color, IR-IR Photobleaching. J Phys Chem Lett 2024; 15:10944-10949. [PMID: 39451162 DOI: 10.1021/acs.jpclett.4c02685] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2024]
Abstract
Here we analyze cryogenic ion vibrational spectra of tagged protonated formic acid (PFA) with electronic structure and anharmonic vibrational calculations to establish the isomers generated by electrospray ionization (ESI) followed by buffer gas cooling to ∼25 K. Two isomers are identified (the trans form (E,Z) and the cis form (E,E)) and generated in comparable abundance despite the fact that the calculated E,E structure lies 6.40 kJ mol-1 above the E,Z form. A large (∼60 kJ mol-1) barrier separates them such that the E,E form can be kinetically trapped upon cooling in the ion trap. The anticooperativity between the H-bonds of the OH groups is explored by measuring the shift in the D2-bound OH fundamental when a second D2 is attached. Both isomers are observed in the N2-tagged counterparts, displaying the expected red-shifted OH bands. These results indicate that ESI generates both isomers and both must be considered when analyzing cluster spectra based on the PFA core ion.
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Affiliation(s)
- Erica L Bocanegra
- Sterling Chemistry Laboratory, Department of Chemistry, Yale University, New Haven, Connecticut 06511, United States
| | - Abhijit Rana
- Sterling Chemistry Laboratory, Department of Chemistry, Yale University, New Haven, Connecticut 06511, United States
| | - Anne B McCoy
- Department of Chemistry, University of Washington, Seattle, Washington 98195-1700, United States
| | - Mark A Johnson
- Sterling Chemistry Laboratory, Department of Chemistry, Yale University, New Haven, Connecticut 06511, United States
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2
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Lin CK, Kuo JL. Anharmonic IR spectra of solvated ammonium and aminium ions: resemblance between water and bisulfate solvations. Phys Chem Chem Phys 2022; 24:20318-20325. [PMID: 35979887 DOI: 10.1039/d2cp00663d] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
In this work, we analyze the vibrational spectra of ammonium, methylammonium, and dimethylammonium ions solvated by either water molecules or bisulfate anions using anharmonic vibrational algorithms. Rich and complicated spectral features in the 2700-3200 cm-1 region of the experimental spectra of these clusters are attributed to originate from strong Fermi resonance between hydrogen-bonded NH stretching fundamentals and NH bending overtones. Additional weaker bands around 2500-2600 cm-1 in solvated aminium ions are assigned to the combination tones involving the CH-NH (methyl-amino) rocking modes. Furthermore, the qualitative resemblance in band positions and spectral patterns between two-water-solvated and two-bisulfate-solvated cations suggest a common vibrational coupling scheme beneath the two seemingly different micro-solvation environments.
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Affiliation(s)
- Chih-Kai Lin
- Department of Chemistry, National Taiwan University, Taipei, 10617, Taiwan, Republic of China.
| | - Jer-Lai Kuo
- Institute of Atomic and Molecular Sciences, Academia Sinica, Taipei, 10617, Taiwan, Republic of China. .,Department of Chemistry, National Tsing Hua University, Hsinchu 30013, Taiwan, Republic of China.,International Graduate Program of Molecular Science and Technology, National Taiwan University, Taipei, 10617, Taiwan, Republic of China
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3
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Feng YJ, Wang C. Molecular vibrational spectral simulation connects theoretical cluster structure identification and vibrational spectral evidence. Phys Chem Chem Phys 2022; 24:16317-16324. [PMID: 35758847 DOI: 10.1039/d2cp01651f] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Structure identification of molecular clusters has long been a fundamental and challenging issue for cluster science. The traditional theoretical optimization on the potential energy surface heavily depends on the levels of theory and sometimes diverse identifications were reported. A solution to these disputations is to reinspect the theoretical results with the experimental data such as vibrational predissociation spectra with high sensitivity to the molecular cluster structures. Herein, the combination of global low-lying structure search and vibrational predissociation spectral simulation is proposed as an accurate and reliable approach for cluster structure identification, by which the assignments can be validated using experimental measurements. The qualitative agreement between simulated and measured vibrational spectra lends solid experimental evidence to the assignment of the cluster structures. Taking NH4+(H2O)n (n = 2-4) as an example, we have unambiguously identified their structures and directly demonstrated the coexistence of two NH4+(H2O)4 isomers (with 3 and 4 water molecules directly linked to NH4+, respectively), which were debatable in previous studies. The developed methods would pave the way to the structure determination of the molecular clusters.
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Affiliation(s)
- Ya-Juan Feng
- School of Information Science and Technology, University of Science and Technology of China, Hefei, Anhui 230026, China.
| | - Chao Wang
- National Synchrotron Radiation Laboratory, University of Science and Technology of China, Hefei, Anhui 230026, China.
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4
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Xu X, Chen Z, Yang Y. Molecular Dynamics with Constrained Nuclear Electronic Orbital Density Functional Theory: Accurate Vibrational Spectra from Efficient Incorporation of Nuclear Quantum Effects. J Am Chem Soc 2022; 144:4039-4046. [PMID: 35196860 DOI: 10.1021/jacs.1c12932] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Nuclear quantum effects play a crucial role in many chemical and biological systems involving hydrogen atoms yet are difficult to include in practical molecular simulations. In this paper, we combine our recently developed methods of constrained nuclear-electronic orbital density functional theory (cNEO-DFT) and constrained minimized energy surface molecular dynamics (CMES-MD) to create a new method for accurately and efficiently describing nuclear quantum effects in molecular simulations. By use of this new method, dubbed cNEO-MD, the vibrational spectra of a set of small molecules are calculated and compared with those from conventional ab initio molecular dynamics (AIMD) as well as from experiments. With the same formal scaling, cNEO-MD greatly outperforms AIMD in describing the vibrational modes with significant hydrogen motion characters, demonstrating the promise of cNEO-MD for simulating chemical and biological systems with significant nuclear quantum effects.
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Affiliation(s)
- Xi Xu
- Theoretical Chemistry Institute and Department of Chemistry, University of Wisconsin─Madison, 1101 University Avenue, Madison, Wisconsin 53706, United States
| | - Zehua Chen
- Theoretical Chemistry Institute and Department of Chemistry, University of Wisconsin─Madison, 1101 University Avenue, Madison, Wisconsin 53706, United States
| | - Yang Yang
- Theoretical Chemistry Institute and Department of Chemistry, University of Wisconsin─Madison, 1101 University Avenue, Madison, Wisconsin 53706, United States
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5
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Xu X, Yang Y. Molecular vibrational frequencies from analytic Hessian of constrained nuclear-electronic orbital density functional theory. J Chem Phys 2021; 154:244110. [PMID: 34241362 DOI: 10.1063/5.0055506] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
Nuclear quantum effects are important in a variety of chemical and biological processes. The constrained nuclear-electronic orbital density functional theory (cNEO-DFT) has been developed to include nuclear quantum effects in energy surfaces. Herein, we develop the analytic Hessian for cNEO-DFT energy with respect to the change in nuclear (expectation) positions, which can be used to characterize stationary points on energy surfaces and compute molecular vibrational frequencies. This is achieved by constructing and solving the multicomponent cNEO coupled-perturbed Kohn-Sham (cNEO-CPKS) equations, which describe the response of electronic and nuclear orbitals to the displacement of nuclear (expectation) positions. With the analytic Hessian, the vibrational frequencies of a series of small molecules are calculated and compared to those from conventional DFT Hessian calculations as well as those from the vibrational second-order perturbation theory (VPT2). It is found that even with a harmonic treatment, cNEO-DFT significantly outperforms DFT and is comparable to DFT-VPT2 in the description of vibrational frequencies in regular polyatomic molecules. Furthermore, cNEO-DFT can reasonably describe the proton transfer modes in systems with a shared proton, whereas DFT-VPT2 often faces great challenges. Our results suggest the importance of nuclear quantum effects in molecular vibrations, and cNEO-DFT is an accurate and inexpensive method to describe molecular vibrations.
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Affiliation(s)
- Xi Xu
- Theoretical Chemistry Institute and Department of Chemistry, University of Wisconsin-Madison, 1101 University Avenue, Madison, Wisconsin 53706, USA
| | - Yang Yang
- Theoretical Chemistry Institute and Department of Chemistry, University of Wisconsin-Madison, 1101 University Avenue, Madison, Wisconsin 53706, USA
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6
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Wang B, Hou P, Cai Y, Guo Z, Han D, Gao Y, Zhao L. Understanding the Hydrogen-Bonded Clusters of Ammonia (NH 3) n ( n = 3-6): Insights from the Electronic Structure Theory. ACS OMEGA 2020; 5:31724-31729. [PMID: 33344825 PMCID: PMC7745437 DOI: 10.1021/acsomega.0c04274] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/01/2020] [Accepted: 11/20/2020] [Indexed: 05/08/2023]
Abstract
Although it is well known that hydrogen bonds commonly exist in ammonia clusters and play an important role, there are still many challenges in understanding the electronic structure properties of hydrogen bonds. In this paper, the geometric and electronic structure properties of cyclic ammonia clusters are investigated by using first-principles density functional theory (DFT) and the Møller-Plesset perturbation theory (MP2). The calculation results show that the pentamer and hexamer have deviated from the perfect plane, while the trimer and tetramer present planarization that has been confirmed by infrared (IR) spectra. The electronic structure analysis further shows that the covalent properties play a non-negligible role in hydrogen bonding. The results also indicate that the electronic structure facilitates structure planarization. Our work not only provides insight into the role and nature of hydrogen bonds in ammonia clusters but also provides a theoretical basis for frontier science in fields such as atmospheric haze and biomolecular functions.
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Affiliation(s)
- Bo Wang
- College
of Science, Northeast Electric Power University, No. 169 Changchun Road, Jilin City 132012, P. R. China
| | - Pugeng Hou
- College
of Science, Northeast Electric Power University, No. 169 Changchun Road, Jilin City 132012, P. R. China
| | - Yongmao Cai
- College
of Science, Northeast Electric Power University, No. 169 Changchun Road, Jilin City 132012, P. R. China
| | - Zhendong Guo
- College
of Science, Northeast Electric Power University, No. 169 Changchun Road, Jilin City 132012, P. R. China
| | - Dandan Han
- College
of Science, Northeast Electric Power University, No. 169 Changchun Road, Jilin City 132012, P. R. China
| | - Yang Gao
- Institute
of Fundamental and Frontier Sciences, University
of Electronic Science and Technology of China, Chengdu, Sichuan 610054, P. R. China
| | - Lei Zhao
- College
of Science, Northeast Electric Power University, No. 169 Changchun Road, Jilin City 132012, P. R. China
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Bogojeski M, Vogt-Maranto L, Tuckerman ME, Müller KR, Burke K. Quantum chemical accuracy from density functional approximations via machine learning. Nat Commun 2020; 11:5223. [PMID: 33067479 PMCID: PMC7567867 DOI: 10.1038/s41467-020-19093-1] [Citation(s) in RCA: 129] [Impact Index Per Article: 32.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2020] [Accepted: 09/24/2020] [Indexed: 12/21/2022] Open
Abstract
Kohn-Sham density functional theory (DFT) is a standard tool in most branches of chemistry, but accuracies for many molecules are limited to 2-3 kcal ⋅ mol-1 with presently-available functionals. Ab initio methods, such as coupled-cluster, routinely produce much higher accuracy, but computational costs limit their application to small molecules. In this paper, we leverage machine learning to calculate coupled-cluster energies from DFT densities, reaching quantum chemical accuracy (errors below 1 kcal ⋅ mol-1) on test data. Moreover, density-based Δ-learning (learning only the correction to a standard DFT calculation, termed Δ-DFT ) significantly reduces the amount of training data required, particularly when molecular symmetries are included. The robustness of Δ-DFT is highlighted by correcting "on the fly" DFT-based molecular dynamics (MD) simulations of resorcinol (C6H4(OH)2) to obtain MD trajectories with coupled-cluster accuracy. We conclude, therefore, that Δ-DFT facilitates running gas-phase MD simulations with quantum chemical accuracy, even for strained geometries and conformer changes where standard DFT fails.
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Affiliation(s)
- Mihail Bogojeski
- Machine Learning Group, Technische Universität Berlin, Marchstr. 23, 10587, Berlin, Germany
| | | | - Mark E Tuckerman
- Department of Chemistry, New York University, New York, NY, 10003, USA.
- Courant Institute of Mathematical Science, New York University, New York, NY, 10012, USA.
- NYU-ECNU Center for Computational Chemistry at NYU Shanghai, 3663 Zhongshan Road North, Shanghai, 200062, China.
| | - Klaus-Robert Müller
- Machine Learning Group, Technische Universität Berlin, Marchstr. 23, 10587, Berlin, Germany.
- Department of Artificial Intelligence, Korea University, Anam-dong, Seongbuk-gu, Seoul, 02841, Korea.
- Max-Planck-Institut für Informatik, Stuhlsatzenhausweg, 66123, Saarbrücken, Germany.
| | - Kieron Burke
- Department of Physics and Astronomy, University of California, Irvine, CA, 92697, USA.
- Department of Chemistry, University of California, Irvine, CA, 92697, USA.
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8
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Tsybizova A, Paenurk E, Gorbachev V, Chen P. Perturbation of Pyridinium CIVP Spectra by N 2 and H 2 Tags: An Experimental and BOMD Study. J Phys Chem A 2020; 124:8519-8528. [PMID: 32954731 DOI: 10.1021/acs.jpca.0c06752] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
In cryogenic ion vibrational predissociation (CIVP) spectroscopy, the influence of the tag on the spectrum is an important consideration. Whereas for small ions several studies have shown that the tag effects can be significant, these effects are less understood for large ions or for large numbers of tags. Nevertheless, it is commonly assumed that if the investigated molecular ion is large enough, the perturbations arising from the tag are small and can therefore be neglected in the interpretation. In addition, it is generally assumed that the more weakly bound the tag is, the less it perturbs the CIVP spectrum. Under these assumptions, CIVP spectra are claimed to be effectively IR absorption spectra of the free molecular ion. Having observed unexpected splittings in otherwise unproblematic CIVP spectra of some tagged ions, we report Born-Oppenheimer molecular dynamics (BOMD) simulations that strongly indicate that mobility among the more weakly bound tags leads to the surprising splittings. We compared the behavior of two tags commonly used in CIVP spectroscopy (H2 and N2) with a large pyridinium cation. Our experimental results surprisingly show that under the appropriate circumstances, the more weakly bound tag can perturb the CIVP spectra more than the more strongly bound tag by not just shifting but also splitting the observed bands. The more weakly bound tag had significant residence times at several spectroscopically distinct sites on the molecular ion. This indicates that the weakly bound tag is likely to sample several binding sites in the experiment, some of which involve interaction with the reporter chromophore.
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Affiliation(s)
- Alexandra Tsybizova
- Department of Chemistry and Applied Biosciences, ETH Zurich, 8093 Zurich, Switzerland
| | - Eno Paenurk
- Department of Chemistry and Applied Biosciences, ETH Zurich, 8093 Zurich, Switzerland
| | - Vladimir Gorbachev
- Department of Chemistry and Applied Biosciences, ETH Zurich, 8093 Zurich, Switzerland
| | - Peter Chen
- Department of Chemistry and Applied Biosciences, ETH Zurich, 8093 Zurich, Switzerland
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9
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Lin CK, Huang QR, Kuo JL. Anharmonic coupling behind vibrational spectra of solvated ammonium: lighting up overtone states by Fermi resonance through tuning solvation environments. Phys Chem Chem Phys 2020; 22:24059-24069. [DOI: 10.1039/d0cp03519j] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Fascinating Fermi resonance bands emerge from anharmonic couplings between NH stretching fundamentals and bending overtones in ammonium-centered clusters.
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Affiliation(s)
- Chih-Kai Lin
- Institute of Atomic and Molecular Sciences
- Academia Sinica
- Taipei 10617
- Republic of China
| | - Qian-Rui Huang
- Institute of Atomic and Molecular Sciences
- Academia Sinica
- Taipei 10617
- Republic of China
| | - Jer-Lai Kuo
- Institute of Atomic and Molecular Sciences
- Academia Sinica
- Taipei 10617
- Republic of China
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10
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Samala NR, Agmon N. Temperature Dependence of Intramolecular Vibrational Bands in Small Water Clusters. J Phys Chem B 2019; 123:9428-9442. [PMID: 31553613 DOI: 10.1021/acs.jpcb.9b07777] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Cyclic water clusters are pivotal for understanding atmospheric reactions as well as liquid water, yet the temperature (T) dependence of their dynamics and spectroscopy is poorly studied. The development of highly accurate water potentials, such as MB-pol, partly rectifies this. It remains to account for the quantum nuclear effects (NQE), because quantum nuclear dynamics become increasingly inaccurate at low temperatures. From a practical point of view, we find that NQE can be accounted for simply by subtracting a constant from the frequencies obtained from the velocity autocorrelation functions (VACF) of classical nuclear dynamics, resulting in unprecedented agreement with experiment, mostly within 5 cm-1. We have performed classical simulations of (H2O)n clusters (n = 2-5) from 20 K and up to their melting temperature, calculating both all-atom and partial VACF, thus generating the temperature dependence of the vibrational frequencies (IR and Raman bands). Focusing on the hydrogen-bonded (HBed) OH stretch and HOH bend, we find opposing T dependencies. The HBed OH modes blue shift linearly with T, attributed to ring expansion rather than any specific conformational change. The lowest-frequency Raman concerted mode is predicted to show the largest such shift. In contrast, the HOH bend undergoes a red-shift, with the highest frequency concerted band undergoing the largest red-shift. These results can be explained by a coupled-oscillator model for n hydrogen atoms on a ring, constrained to move either tangentially (stretch) or perpendicularly (bend) to the ring. With increasing temperature and weakening of HBs, the intrinsic force constant increases (stretch) or remains constant (bend), while the nearest-neighbor coupling constant decreases, and this results in the interesting behavior revealed herein. T-dependent Raman studies are required for testing some of these predictions.
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Affiliation(s)
- Nagaprasad Reddy Samala
- The Fritz Haber Research Center, Institute of Chemistry , The Hebrew University of Jerusalem , Jerusalem 91904 , Israel
| | - Noam Agmon
- The Fritz Haber Research Center, Institute of Chemistry , The Hebrew University of Jerusalem , Jerusalem 91904 , Israel
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11
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Structural selectivity of supported Pd nanoparticles for catalytic NH3 oxidation resolved using combined operando spectroscopy. Nat Catal 2019. [DOI: 10.1038/s41929-018-0213-3] [Citation(s) in RCA: 48] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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12
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13
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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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14
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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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15
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Yang J, Kong X, Jiang L. On the solvation of hydronium by carbon dioxide: Structural and infrared spectroscopic study of (H3O+)(CO2). Chem Phys 2018. [DOI: 10.1016/j.chemphys.2017.11.015] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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16
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Lawson Daku LM. Spin-state dependence of the structural and vibrational properties of solvated iron(ii) polypyridyl complexes from AIMD simulations: aqueous [Fe(bpy)3]Cl2, a case study. Phys Chem Chem Phys 2018; 20:6236-6253. [DOI: 10.1039/c7cp07862e] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
LS and HS IR spectra of aqueous [Fe(bpy)3]2+ and corresponding HS–LS difference IR spectrum as obtained from state-of-the-art ab initio molecular dynamics simulations applied to the determination of the structural and vibrational properties of the solvated complex.
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17
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Mishra S, Kuo JL, Patwari GN. Hydrogen bond induced enhancement of Fermi resonances in N–H⋯N hydrogen bonded complexes of anilines. Phys Chem Chem Phys 2018; 20:21557-21566. [DOI: 10.1039/c8cp02448k] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Enhancement of Fermi resonance intensities due to the formation of N–H⋯N hydrogen bonding of anilines with alkyl amines is analyzed using a two-state deperturbation model.
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Affiliation(s)
- Saurabh Mishra
- Department of Chemistry
- Indian Institute of Technology Bombay
- Powai
- Mumbai 400 076
- India
| | - Jer-Lai Kuo
- Institute of Atomic and Molecular Sciences
- Academia Sinica
- Taipei 10617
- Taiwan
| | - G. Naresh Patwari
- Department of Chemistry
- Indian Institute of Technology Bombay
- Powai
- Mumbai 400 076
- India
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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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Wang H, Agmon N. Reinvestigation of the Infrared Spectrum of the Gas-Phase Protonated Water Tetramer. J Phys Chem A 2017; 121:3056-3070. [DOI: 10.1021/acs.jpca.7b01856] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Affiliation(s)
- Huan Wang
- The Fritz Haber Research
Center, Institute of Chemistry, The Hebrew University of Jerusalem, Jerusalem 91904, Israel
| | - Noam Agmon
- The Fritz Haber Research
Center, Institute of Chemistry, The Hebrew University of Jerusalem, Jerusalem 91904, Israel
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20
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Agmon N, Bakker HJ, Campen RK, Henchman RH, Pohl P, Roke S, Thämer M, Hassanali A. Protons and Hydroxide Ions in Aqueous Systems. Chem Rev 2016; 116:7642-72. [PMID: 27314430 DOI: 10.1021/acs.chemrev.5b00736] [Citation(s) in RCA: 296] [Impact Index Per Article: 37.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Understanding the structure and dynamics of water's constituent ions, proton and hydroxide, has been a subject of numerous experimental and theoretical studies over the last century. Besides their obvious importance in acid-base chemistry, these ions play an important role in numerous applications ranging from enzyme catalysis to environmental chemistry. Despite a long history of research, many fundamental issues regarding their properties continue to be an active area of research. Here, we provide a review of the experimental and theoretical advances made in the last several decades in understanding the structure, dynamics, and transport of the proton and hydroxide ions in different aqueous environments, ranging from water clusters to the bulk liquid and its interfaces with hydrophobic surfaces. The propensity of these ions to accumulate at hydrophobic surfaces has been a subject of intense debate, and we highlight the open issues and challenges in this area. Biological applications reviewed include proton transport along the hydration layer of various membranes and through channel proteins, problems that are at the core of cellular bioenergetics.
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Affiliation(s)
- Noam Agmon
- The Fritz Haber Research Center, Institute of Chemistry, The Hebrew University of Jerusalem , Jerusalem 91904, Israel
| | - Huib J Bakker
- FOM Institute AMOLF , Science Park 104, 1098 XG Amsterdam, The Netherlands
| | - R Kramer Campen
- Fritz Haber Institute of the Max Planck Society , Faradayweg 4-6, 14195 Berlin, Germany
| | - Richard H Henchman
- Manchester Institute of Biotechnology, School of Chemistry, The University of Manchester , Oxford Road, Manchester M13 9PL, United Kingdom
| | - Peter Pohl
- Johannes Kepler University Linz , Institute of Biophysics, Gruberstrasse 40, 4020 Linz, Austria
| | - Sylvie Roke
- Laboratory for Fundamental BioPhotonics (LBP), Institute of Bioengineering (IBI), and Institute of Material Science (IMX), School of Engineering (STI), and Lausanne Centre for Ultrafast Science (LACUS), École Polytechnique Fédérale de Lausanne (EPFL) , CH-1015, Lausanne, Switzerland
| | - Martin Thämer
- Fritz Haber Institute of the Max Planck Society , Faradayweg 4-6, 14195 Berlin, Germany.,Department of Chemistry, Institute for Biophysical Dynamics, and James Franck Institute, The University of Chicago , Chicago, Illinois 60637, United States
| | - Ali Hassanali
- CMSP Section, The Abdus Salaam International Center for Theoretical Physics , I-34151 Trieste, Italy
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