1
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Wang GX, Shan C, Chen W, Wu B, Zhang P, Wei J, Xi Z, Ye S. Unusual Electronic Structures of an Electron Transfer Series of [Cr(μ-η 1 : η 1 -N 2 )Cr] 0/1+/2. Angew Chem Int Ed Engl 2024; 63:e202315386. [PMID: 38299757 DOI: 10.1002/anie.202315386] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2023] [Revised: 02/01/2024] [Accepted: 02/01/2024] [Indexed: 02/02/2024]
Abstract
In dinitrogen (N2 ) fixation chemistry, bimetallic end-on bridging N2 complexes M(μ-η1 : η1 -N2 )M can split N2 into terminal nitrides and hence attract great attention. To date, only 4d and 5d transition complexes, but none of 3d counterparts, could realize such a transformation. Likewise, complexes {[Cp*Cr(dmpe)]2 (μ-N2 )}0/1+/2+ (1-3) are incapable to cleave N2 , in contrast to their Mo congeners. Remarkably, cross this series the N-N bond length of the N2 ligand and the N-N stretching frequency exhibit unprecedented nonmonotonic variations, and complexes 1 and 2 in both solid and solution states display rare thermally activated ligand-mediated two-center spin transitions, distinct from discrete dinuclear spin crossovers. In-depth analyses using wave function based ab initio calculations reveal that the Cr-N2 -Cr bonding in complexes 1-3 is distinguished by strong multireference character and cannot be described by solely one electron configuration or Lewis structure, and that all intriguing spectroscopic observations originate in their sophisticate multireference electronic structures. More critical is that such multireference bonding of complexes 1-3 is at least a key factor that contributes to their kinetic inertness toward N2 splitting. The mechanistic understanding is then used to rationalize the disparate reactivity of related 3d M(μ-η1 : η1 -N2 )M complexes compared to their 4d and 5d analogs.
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Affiliation(s)
- Gao-Xiang Wang
- Beijing National Laboratory for Molecular Sciences (BNLMS), Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education, College of Chemistry, Peking University, Beijing, 100871, China
| | - Chunxiao Shan
- Beijing National Laboratory for Molecular Sciences (BNLMS), Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education, College of Chemistry, Peking University, Beijing, 100871, China
| | - Wang Chen
- State Key Laboratory of Catalysis, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, 116023, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Botao Wu
- Beijing National Laboratory for Molecular Sciences (BNLMS), Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education, College of Chemistry, Peking University, Beijing, 100871, China
| | - Peng Zhang
- State Key Laboratory of Catalysis, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, 116023, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Junnian Wei
- Beijing National Laboratory for Molecular Sciences (BNLMS), Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education, College of Chemistry, Peking University, Beijing, 100871, China
| | - Zhenfeng Xi
- Beijing National Laboratory for Molecular Sciences (BNLMS), Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education, College of Chemistry, Peking University, Beijing, 100871, China
| | - Shengfa Ye
- State Key Laboratory of Catalysis, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, 116023, China
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2
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Sun Y, Yu X, Liu P, Han W, Xu WW, Su Y, Zhao J. Isomerism effects in relaxation dynamics of Au 24(SR) 16thiolate-protected gold nanoclusters. NANOTECHNOLOGY 2022; 34:105701. [PMID: 36537747 DOI: 10.1088/1361-6528/aca80d] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/05/2022] [Accepted: 12/02/2022] [Indexed: 06/17/2023]
Abstract
Understanding the excited state behavior of isomeric structures of thiolate-protected gold nanoclusters is still a challenging task. In this paper, based on grand unified model and ring model for describing thiolate-protected gold nanoclusters, we have predicted four isomers of Au24(SR)16nanoclusters. Density functional theory calculations show that the total energy of one of the predicted isomers is 0.1 eV lower in energy than previously crystallized isomer. The nonradiative relaxation dynamics simulations of Au24(SH)16isomers are performed to reveal the effects of structural isomerism on relaxation process of the lowest energy states, in which that most of the low-excited states consist of core states. In addition, crystallized isomer possesses the shorter e-h recombination time, whereas the most stable isomer has the longer recombination time, which may be attributed to the synergistic effect of nonadiabatic coupling and decoherence time. Our results could provide practical guidance to predict new gold nanoclusters for future experimental synthesis, and stimulate the exploration of atomic structures of same sized gold nanoclusters for photovoltaic and optoelectronic devices.
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Affiliation(s)
- Yuanze Sun
- Key Laboratory of Materials Modification by Laser, Ion and Electron Beams (Dalian University of Technology), Ministry of Education, Dalian 116024, People's Republic of China
| | - Xueke Yu
- Key Laboratory of Materials Modification by Laser, Ion and Electron Beams (Dalian University of Technology), Ministry of Education, Dalian 116024, People's Republic of China
| | - Pengye Liu
- Department of Physics, School of Physical Science and Technology, Ningbo University, Ningbo 315211, People's Republic of China
| | - Wenhua Han
- Department of Physics, School of Physical Science and Technology, Ningbo University, Ningbo 315211, People's Republic of China
| | - Wen-Wu Xu
- Department of Physics, School of Physical Science and Technology, Ningbo University, Ningbo 315211, People's Republic of China
| | - Yan Su
- Key Laboratory of Materials Modification by Laser, Ion and Electron Beams (Dalian University of Technology), Ministry of Education, Dalian 116024, People's Republic of China
| | - Jijun Zhao
- Key Laboratory of Materials Modification by Laser, Ion and Electron Beams (Dalian University of Technology), Ministry of Education, Dalian 116024, People's Republic of China
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3
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Bac S, Patra A, Kron KJ, Mallikarjun Sharada S. Recent Advances toward Efficient Calculation of Higher Nuclear Derivatives in Quantum Chemistry. J Phys Chem A 2022; 126:7795-7805. [DOI: 10.1021/acs.jpca.2c05459] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Selin Bac
- Mork Family Department of Chemical Engineering and Materials Science, University of Southern California, Los Angeles, California90089, United States
| | - Abhilash Patra
- Mork Family Department of Chemical Engineering and Materials Science, University of Southern California, Los Angeles, California90089, United States
| | - Kareesa J. Kron
- Mork Family Department of Chemical Engineering and Materials Science, University of Southern California, Los Angeles, California90089, United States
| | - Shaama Mallikarjun Sharada
- Mork Family Department of Chemical Engineering and Materials Science, University of Southern California, Los Angeles, California90089, United States
- Department of Chemistry, University of Southern California, Los Angeles, California90089, United States
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4
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Li SC, Lin YC, Li YP. Comparative Analysis of Uncoupled Mode Approximations for Molecular Thermochemistry and Kinetics. J Chem Theory Comput 2022; 18:6866-6877. [PMID: 36269729 DOI: 10.1021/acs.jctc.2c00664] [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 accurate prediction of thermochemistry and kinetic parameters is an important task for reaction modeling. Unfortunately, the commonly used harmonic oscillator model is often not accurate enough due to the absence of anharmonic effects. In this work, we improve the representation of an anharmonic potential energy surface (PES) using uncoupled mode (UM) approximations, which model the full-dimensional PES as a sum of one-dimensional potentials of each mode. We systematically analyze different PES sampling schemes and coordinate systems for constructing the one-dimensional potentials, and benchmark the performance of UM methods on data sets of molecular thermochemistry and kinetic properties. The results show that the accuracy of the UM approach strongly depends on how the one-dimensional potentials are defined. If one-dimensional potentials are constructed by sampling along normal mode directions (UM-N) or along the directions that minimize intermode coupling (E- and E'-optimized), the accuracies of the predicted properties are not significantly improved compared to the harmonic oscillator model. However, significant improvements can be achieved by sampling the torsional modes separately from the vibrational modes (UM-T and UM-VT). In this work, three types of coordinate systems are examined, including redundant internal coordinates (RIC), hybrid internal coordinates (HIC), and translation-rotation-internal coordinates (TRIC). The HIC and TRIC coordinate systems can outperform RIC since transition state species may contain large-amplitude interfragmentary motions that regular internal coordinates can not describe adequately. Among all the methods we examined, the activation energies and pre-exponential factors calculated using UM-VT with either TRIC or HIC best agree with the reference values. Since UM-VT requires only a number of additional single point energy calculations for each independent mode, the scaling of computational costs of UM-VT is the same as that of the standard harmonic oscillator model, making UM-VT an appealing way of calculating the thermochemistry and kinetic properties for large-size systems.
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Affiliation(s)
- Shih-Cheng Li
- Department of Chemical Engineering, National Taiwan University, No. 1, Sec. 4, Roosevelt Road, Taipei 10617, Taiwan
| | - Yen-Chun Lin
- Department of Chemical Engineering, National Taiwan University, No. 1, Sec. 4, Roosevelt Road, Taipei 10617, Taiwan
| | - Yi-Pei Li
- Department of Chemical Engineering, National Taiwan University, No. 1, Sec. 4, Roosevelt Road, Taipei 10617, Taiwan.,Taiwan International Graduate Program on Sustainable Chemical Science and Technology (TIGP-SCST), Academia Sinica, No. 128, Sec. 2, Academia Road, Taipei 11529, Taiwan
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5
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Tian YC, Jiang Y, Lin YH, Zhang P, Wang CC, Ye S, Lee WZ. Hydrogen Atom Transfer Thermodynamics of Homologous Co(III)- and Mn(III)-Superoxo Complexes: The Effect of the Metal Spin State. JACS AU 2022; 2:1899-1909. [PMID: 36032524 PMCID: PMC9400055 DOI: 10.1021/jacsau.2c00268] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/02/2022] [Revised: 07/22/2022] [Accepted: 07/22/2022] [Indexed: 06/15/2023]
Abstract
Systematic investigations on H atom transfer (HAT) thermodynamics of metal O2 adducts is of fundamental importance for the design of transition metal catalysts for substrate oxidation and/or oxygenation directly using O2. Such work should help elucidate underlying electronic-structure features that govern the OO-H bond dissociation free energies (BDFEs) of metal-hydroperoxo species, which can be used to quantitatively appraise the HAT activity of the corresponding metal-superoxo complexes. Herein, the BDFEs of two homologous CoIII- and MnIII-hydroperoxo complexes, 3-Co and 3-Mn, were calculated to be 79.3 and 81.5 kcal/mol, respectively, employing the Bordwell relationship based on experimentally determined pK a values and redox potentials of the one-electron-oxidized forms, 4-Co and 4-Mn. To further verify these values, we tested the HAT capability of their superoxo congeners, 2-Co and 2-Mn, toward three different substrates possessing varying O-H BDFEs. Specifically, both metal-superoxo species are capable of activating the O-H bond of 4-oxo-TEMPOH with an O-H BDFE of 68.9 kcal/mol, only 2-Mn is able to abstract a H atom from 2,4-di-tert-butylphenol with an O-H BDFE of 80.9 kcal/mol, and neither of them can react with 3,5-dimethylphenol with an O-H BDFE of 85.6 kcal/mol. Further computational investigations suggested that it is the high spin state of the MnIII center in 3-Mn that renders its OO-H BDFE higher than that of 3-Co, which features a low-spin CoIII center. The present work underscores the role of the metal spin state being as crucial as the oxidation state in modulating BDFEs.
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Affiliation(s)
- Yao-Cheng Tian
- Department
of Chemistry, National Taiwan Normal University, Taipei 11677, Taiwan
| | - Yang Jiang
- State
Key Laboratory of Catalysis, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China
| | - Yen-Hao Lin
- Department
of Chemistry, National Taiwan Normal University, Taipei 11677, Taiwan
| | - Peng Zhang
- State
Key Laboratory of Catalysis, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China
- University
of Chinese Academy of Sciences, Beijing 100049, China
| | - Chun-Chieh Wang
- Department
of Chemistry, National Taiwan Normal University, Taipei 11677, Taiwan
| | - Shengfa Ye
- State
Key Laboratory of Catalysis, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China
| | - Way-Zen Lee
- Department
of Chemistry, National Taiwan Normal University, Taipei 11677, Taiwan
- Department
of Medicinal and Applied Chemistry, Kaohsiung
Medical University, Kaohsiung 807, Taiwan
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6
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Bajada MA, Sanjosé-Orduna J, Di Liberto G, Tosoni S, Pacchioni G, Noël T, Vilé G. Interfacing single-atom catalysis with continuous-flow organic electrosynthesis. Chem Soc Rev 2022; 51:3898-3925. [PMID: 35481480 DOI: 10.1039/d2cs00100d] [Citation(s) in RCA: 24] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
The global warming crisis has sparked a series of environmentally cautious trends in chemistry, allowing us to rethink the way we conduct our synthesis, and to incorporate more earth-abundant materials in our catalyst design. "Single-atom catalysis" has recently appeared on the catalytic spectrum, and has truly merged the benefits that homogeneous and heterogeneous analogues have to offer. Further still, the possibility to activate these catalysts by means of a suitable electric potential could pave the way for a true integration of diverse synthetic methodologies and renewable electricity. Despite their esteemed benefits, single-atom electrocatalysts are still limited to the energy sector (hydrogen evolution reaction, oxygen reduction, etc.) and numerous examples in the literature still invoke the use of precious metals (Pd, Pt, Ir, etc.). Additionally, batch electroreactors are employed, which limit the intensification of such processes. It is of paramount importance that the field continues to grow in a more sustainable direction, seeking new ventures into the space of organic electrosynthesis and flow electroreactor technologies. In this piece, we discuss some of the progress being made with earth abundant homogeneous and heterogeneous electrocatalysts and flow electrochemistry, within the context of organic electrosynthesis, and highlight the prospects of alternatively utilizing single-atom catalysts for such applications.
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Affiliation(s)
- Mark A Bajada
- Department of Chemistry, Materials, and Chemical Engineering "Giulio Natta", Politecnico di Milano, Piazza Leonardo da Vinci 32, 20133 Milano, Italy.
| | - Jesús Sanjosé-Orduna
- Flow Chemistry Group, van't Hoff Institute for Molecular Sciences, Universiteit van Amsterdam, Science Park 904, 1098 XH Amsterdam, The Netherlands
| | - Giovanni Di Liberto
- Department of Materials Science, Università di Milano Bicocca, via R. Cozzi 55, 20125 Milano, Italy
| | - Sergio Tosoni
- Department of Materials Science, Università di Milano Bicocca, via R. Cozzi 55, 20125 Milano, Italy
| | - Gianfranco Pacchioni
- Department of Materials Science, Università di Milano Bicocca, via R. Cozzi 55, 20125 Milano, Italy
| | - Timothy Noël
- Flow Chemistry Group, van't Hoff Institute for Molecular Sciences, Universiteit van Amsterdam, Science Park 904, 1098 XH Amsterdam, The Netherlands
| | - Gianvito Vilé
- Department of Chemistry, Materials, and Chemical Engineering "Giulio Natta", Politecnico di Milano, Piazza Leonardo da Vinci 32, 20133 Milano, Italy.
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7
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Paenurk E, Chen P. Modeling Gas-Phase Unimolecular Dissociation for Bond Dissociation Energies: Comparison of Statistical Rate Models within RRKM Theory. J Phys Chem A 2021; 125:1927-1940. [PMID: 33635061 DOI: 10.1021/acs.jpca.1c00183] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The Rice-Ramsperger-Kassel-Marcus (RRKM) theory provides a simple yet powerful rate theory for calculating microcanonical rate constants. In particular, it has found widespread use in combination with gas-phase kinetic experiments of unimolecular dissociations to extract experimental bond dissociation energies (BDEs). We have previously found several discrepancies between the computed BDE values and the respective experimental ones, obtained with our empirical rate model, named L-CID. To investigate the reliability of our rate model, we conducted a theoretical analysis and comparison of the performance of conventional rate models and L-CID within the RRKM framework. Using the previously published microcanonical rate data as well as reaction cross-section data, we show that the BDE values obtained with the L-CID model agree with the ones from the other rate models within the expected uncertainty bounds. Based on this agreement, we discuss the possible rationalization of the good performance of the L-CID model.
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Affiliation(s)
- Eno Paenurk
- Department of Chemistry and Applied Biosciences, ETH Zürich, 8093 Zürich, Switzerland
| | - Peter Chen
- Department of Chemistry and Applied Biosciences, ETH Zürich, 8093 Zürich, Switzerland
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8
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Acelas M, Dugarte-Dugarte A, Romero Bohórquez AR, Henao JA, Delgado JM, Díaz de Delgado G. Synthesis, crystal structure, Hirshfeld surface analysis and energy framework calculations of trans-3,7,9,9-tetra-methyl-10-(prop-2-yn-1-yl)-1,2,3,4,4a,9,9a,10-octa-hydro-acridine. Acta Crystallogr E Crystallogr Commun 2021; 77:226-232. [PMID: 33953941 PMCID: PMC8061106 DOI: 10.1107/s2056989021001183] [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: 01/27/2021] [Accepted: 02/02/2021] [Indexed: 11/11/2022]
Abstract
The title heterocyclic compound, C20H27N, has been prepared in good yield (72%) via a BiCl3-catalyzed cationic Povarov reaction between N-propargyl-4-methyl-aniline and (±)-citronellal. The X-ray single-crystal study indicates that the structure consists of mol-ecules connected by C-H⋯π contacts to produce chains, which pack in a sandwich-herringbone fashion along the b-axis direction. Hirshfeld surface analysis indicates that H⋯H inter-actions dominate by contributing 79.1% to the total surface. Energy frameworks and DFT calculations indicate a major contribution of dispersive forces to the total inter-action energy.
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Affiliation(s)
- Mauricio Acelas
- Grupo de Investigación en Compuestos Orgánicos de Interés Medicinal (CODEIM), Parque Tecnológico Guatiguará, Universidad Industrial de Santander, Piedecuesta, Colombia
| | - Analio Dugarte-Dugarte
- Laboratorio de Cristalografía-LNDRX, Departamento de Química, Facultad de Ciencias, Universidad de los Andes, Mérida, Venezuela
| | - Arnold R. Romero Bohórquez
- Grupo de Investigación en Compuestos Orgánicos de Interés Medicinal (CODEIM), Parque Tecnológico Guatiguará, Universidad Industrial de Santander, Piedecuesta, Colombia
| | - José Antonio Henao
- Grupo de Investigación en Química Estructural (GIQUE), Escuela de Química, Facultad de Ciencias, Universidad Industrial de Santander, Bucaramanga, Colombia
| | - José Miguel Delgado
- Laboratorio de Cristalografía-LNDRX, Departamento de Química, Facultad de Ciencias, Universidad de los Andes, Mérida, Venezuela
| | - Graciela Díaz de Delgado
- Laboratorio de Cristalografía-LNDRX, Departamento de Química, Facultad de Ciencias, Universidad de los Andes, Mérida, Venezuela
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9
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Esch BVD, Peters LDM, Sauerland L, Ochsenfeld C. Quantitative Comparison of Experimental and Computed IR-Spectra Extracted from Ab Initio Molecular Dynamics. J Chem Theory Comput 2021; 17:985-995. [PMID: 33512155 DOI: 10.1021/acs.jctc.0c01279] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Experimentally measured infrared spectra are often compared to their computed equivalents. However, the accordance is typically characterized by visual inspection, which is prone to subjective judgment. The primary challenge for a similarity-based analysis is that the artifacts introduced by each approach are very different and, therefore, may require preprocessing steps to determine and correct impeding irregularities. To allow for automated objective assessment, we propose a practical and comprehensive workflow involving scaling factors, a novel baseline correction scheme, and peak smoothing. The resulting spectra can then easily be compared quantitatively using similarity measures, for which we found the Pearson correlation coefficient to be the most suitable. The proposed procedure is then applied to compare the agreement of the experimental infrared spectra from the NIST Chemistry Web book with the calculated spectra using standard harmonic frequency analysis and spectra extracted from ab initio molecular dynamics simulations at different levels of theory. We conclude that the direct, quantitative comparison of calculated and measured IR spectra might become a novel, sophisticated approach to benchmark quantum-chemical methods. In the present benchmark, simulated spectra based on ab initio molecular dynamics show in general better agreement with the experiment than static calculations.
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Affiliation(s)
- Beatriz von der Esch
- Chair of Theoretical Chemistry, Department of Chemistry, University of Munich (LMU), Butenandtstr. 7, D-81377 München, Germany
| | - Laurens D M Peters
- Chair of Theoretical Chemistry, Department of Chemistry, University of Munich (LMU), Butenandtstr. 7, D-81377 München, Germany
| | - Lena Sauerland
- Chair of Theoretical Chemistry, Department of Chemistry, University of Munich (LMU), Butenandtstr. 7, D-81377 München, Germany
| | - Christian Ochsenfeld
- Chair of Theoretical Chemistry, Department of Chemistry, University of Munich (LMU), Butenandtstr. 7, D-81377 München, Germany
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10
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Donati G, Petrone A, Rega N. Multiresolution continuous wavelet transform for studying coupled solute-solvent vibrations via ab initio molecular dynamics. Phys Chem Chem Phys 2020; 22:22645-22661. [PMID: 33015693 DOI: 10.1039/d0cp02495c] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Vibrational analysis in solution and the theoretical determination of infrared and Raman spectra are of key importance in many fields of chemical interest. Vibrational band dynamics of molecules and their sensitivity to the environment can also be captured by these spectroscopies in their time dependent version. However, it is often difficult to provide an interpretation of the experimental data at the molecular scale, such as molecular mechanisms or the processes hidden behind them. In this work, we present a theoretical-computational protocol based on ab initio molecular dynamics simulations and a combination of normal-like (generalized) mode analysis of solute-solvent clusters with a wavelet transform, for the first time. The case study is the vibrational dynamics of N-methyl-acetamide (NMA) in water solution, a well-known model of hydration of peptides and proteins. Amide modes are typical bands of peptide and protein backbone, and their couplings with the environment are very challenging in terms of the accurate prediction of solvent induced intensity and frequency shifts. The contribution of water molecules surrounding NMA to the composition of generalized and time resolved modes is introduced in our vibrational analysis, showing unequivocally its influence on the amide mode spectra. It is also shown that such mode compositions need the inclusion of the first shell solvent molecules to be accurately described. The wavelet analysis is proven to be strongly recommended to follow the time evolution of the spectra, and to capture vibrational band couplings and frequency shifts over time, preserving at the same time a well-balanced time-frequency resolution. This peculiar feature also allows one to perform a combined structural-vibrational analysis, where the different strengths of hydrogen bond interactions can quantitatively affect the amide bands over time at finite temperature. The proposed method allows for the direct connection between vibrational modes and local structural changes, providing a link from the spectroscopic observable to the structure, in this case the peptide backbone, and its hydration layouts.
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Affiliation(s)
- Greta Donati
- Department of Chemical Sciences, University of Napoli Federico II, Complesso Universitario di M. S. Angelo, Via Cintia, I-80126 Napoli, Italy.
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11
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Kröncke S, Herrmann C. Toward a First-Principles Evaluation of Transport Mechanisms in Molecular Wires. J Chem Theory Comput 2020; 16:6267-6279. [PMID: 32886502 DOI: 10.1021/acs.jctc.0c00667] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Understanding charge transport through molecular wires is important for nanoscale electronics and biochemistry. Our goal is to establish a simple first-principles protocol for predicting the charge transport mechanism in such wires, in particular the crossover from coherent tunneling for short wires to incoherent hopping for longer wires. This protocol is based on a combination of density functional theory with a polarizable continuum model introduced by Kaupp et al. for mixed-valence molecules, which we had previously found to work well for length-dependent charge delocalization in such systems. We combine this protocol with a new charge delocalization measure tailored for molecular wires, and we show that it can predict the tunneling-to-hopping transition length with a maximum error of one subunit in five sets of molecular wires studied experimentally in molecular junctions at room temperature. This suggests that the protocol is also well suited for estimating the extent of hopping sites as relevant, for example, for the intermediate tunneling-hopping regime in DNA.
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Affiliation(s)
- Susanne Kröncke
- Department of Chemistry, University of Hamburg, Martin-Luther-King-Platz 6, 20146 Hamburg, Germany
| | - Carmen Herrmann
- Department of Chemistry, University of Hamburg, Martin-Luther-King-Platz 6, 20146 Hamburg, Germany
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12
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Trivedi DJ, Barrow B, Schatz GC. Understanding the chemical contribution to the enhancement mechanism in SERS: Connection with Hammett parameters. J Chem Phys 2020; 153:124706. [DOI: 10.1063/5.0023359] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023] Open
Affiliation(s)
- Dhara J. Trivedi
- Department of Physics, Clarkson University, 8 Clarkson Ave., Potsdam, New York 13699, USA
| | - Brendan Barrow
- Department of Physics, Clarkson University, 8 Clarkson Ave., Potsdam, New York 13699, USA
| | - George C. Schatz
- Department of Chemistry, Northwestern University, 2145 Sheridan Road, Evanston, Illinois 60208, USA
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13
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Acelas M, Camargo HA, Henao JA, Kouznetsov VV, Romero Bohórquez AR, Dugarte-Dugarte A, Delgado JM, Díaz de Delgado G. Synthesis, characterization and crystal structure of two polymorphs of trans N-benzyl-3,9,9-trimethyl-1,2,3,4,4a,9,9a,10-octahydroacridine. J Mol Struct 2020. [DOI: 10.1016/j.molstruc.2020.128222] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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14
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Schnieders D, Tsui BTH, Sung MMH, Bortolus MR, Schrobilgen GJ, Neugebauer J, Morris RH. Metal Hydride Vibrations: The Trans Effect of the Hydride. Inorg Chem 2019; 58:12467-12479. [DOI: 10.1021/acs.inorgchem.9b02302] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Affiliation(s)
- David Schnieders
- Organisch-Chemisches Institut, Westfälische Wilhelms-Universität Münster, Corrensstraße 40, 48149 Münster, Germany
- Center for Multiscale Theory and Computation, Corrensstraße 40, 48149 Münster, Germany
| | - Brian T. H. Tsui
- Department of Chemistry, University of Toronto, 80 St. George Street Toronto, Ontario M5S 3H6, Canada
| | - Molly M. H. Sung
- Department of Chemistry, University of Toronto, 80 St. George Street Toronto, Ontario M5S 3H6, Canada
| | - Mark R. Bortolus
- Department of Chemistry, McMaster University, Hamilton, Ontario L8S 4M1, Canada
| | - Gary J. Schrobilgen
- Department of Chemistry, McMaster University, Hamilton, Ontario L8S 4M1, Canada
| | - Johannes Neugebauer
- Organisch-Chemisches Institut, Westfälische Wilhelms-Universität Münster, Corrensstraße 40, 48149 Münster, Germany
- Center for Multiscale Theory and Computation, Corrensstraße 40, 48149 Münster, Germany
| | - Robert H. Morris
- Department of Chemistry, University of Toronto, 80 St. George Street Toronto, Ontario M5S 3H6, Canada
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15
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Brehm M, Thomas M. Computing Bulk Phase Resonance Raman Spectra from ab Initio Molecular Dynamics and Real-Time TDDFT. J Chem Theory Comput 2019; 15:3901-3905. [PMID: 31246025 DOI: 10.1021/acs.jctc.9b00512] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
We present our novel approach for computing resonance Raman (RR) spectra of periodic bulk phase systems from ab initio molecular dynamics, including solvent influence and some anharmonic effects. Based on real-time time-dependent density functional theory, we obtain the RR spectra for all laser wavelengths in one pass. We compute the RR spectrum of uracil in aqueous solution, which is in good agreement with experiment. This is the first simulation of a bulk phase RR spectrum.
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Affiliation(s)
- Martin Brehm
- Institut für Chemie - Theoretische Chemie , Martin-Luther-Universität Halle-Wittenberg , Von-Danckelmann-Platz 4 , 06120 Halle (Saale) , Germany
| | - Martin Thomas
- Institut für Chemie - Theoretische Chemie , Martin-Luther-Universität Halle-Wittenberg , Von-Danckelmann-Platz 4 , 06120 Halle (Saale) , Germany
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16
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Dreimann JM, Kohls E, Warmeling HFW, Stein M, Guo LF, Garland M, Dinh TN, Vorholt AJ. In Situ Infrared Spectroscopy as a Tool for Monitoring Molecular Catalyst for Hydroformylation in Continuous Processes. ACS Catal 2019. [DOI: 10.1021/acscatal.8b05066] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- J. M. Dreimann
- Laboratory of Industrial Chemistry, Department of Biochemical and Chemical Engineering, TU Dortmund, Emil-Figge-Straße 66, 44227 Dortmund, Germany
| | - E. Kohls
- Molecular Simulations and Design Group, Max Planck Institute for Dynamics of Complex Technical Systems, Sandtorstrasse 1, 39106 Magdeburg, Germany
| | - H. F. W. Warmeling
- Laboratory of Industrial Chemistry, Department of Biochemical and Chemical Engineering, TU Dortmund, Emil-Figge-Straße 66, 44227 Dortmund, Germany
| | - M. Stein
- Molecular Simulations and Design Group, Max Planck Institute for Dynamics of Complex Technical Systems, Sandtorstrasse 1, 39106 Magdeburg, Germany
| | - L. F. Guo
- Institute of Chemical and Engineering Sciences (ICES), 1 Pesek Road, Jurong Island 627833, Singapore
| | - M. Garland
- Institute of Chemical and Engineering Sciences (ICES), 1 Pesek Road, Jurong Island 627833, Singapore
| | - T. N. Dinh
- Institute of Chemical and Engineering Sciences (ICES), 1 Pesek Road, Jurong Island 627833, Singapore
| | - A. J. Vorholt
- Max-Planck-Institute for Chemical Energy Conversion, Stiftstraße 34-36, 45740 Mülheim, Germany
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17
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Sprague-Klein EA, Negru B, Madison LR, Coste SC, Rugg BK, Felts AM, McAnally MO, Banik M, Apkarian VA, Wasielewski MR, Ratner MA, Seideman T, Schatz GC, Van Duyne RP. Photoinduced Plasmon-Driven Chemistry in trans-1,2-Bis(4-pyridyl)ethylene Gold Nanosphere Oligomers. J Am Chem Soc 2018; 140:10583-10592. [DOI: 10.1021/jacs.8b06347] [Citation(s) in RCA: 34] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Affiliation(s)
| | | | | | | | | | - Alanna M. Felts
- Department of Chemistry, University of California, Irvine, California 92697, United States
| | | | - Mayukh Banik
- Department of Chemistry, University of California, Irvine, California 92697, United States
| | - Vartkess A. Apkarian
- Department of Chemistry, University of California, Irvine, California 92697, United States
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18
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Proppe J, Husch T, Simm GN, Reiher M. Uncertainty quantification for quantum chemical models of complex reaction networks. Faraday Discuss 2018; 195:497-520. [PMID: 27730243 DOI: 10.1039/c6fd00144k] [Citation(s) in RCA: 47] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
For the quantitative understanding of complex chemical reaction mechanisms, it is, in general, necessary to accurately determine the corresponding free energy surface and to solve the resulting continuous-time reaction rate equations for a continuous state space. For a general (complex) reaction network, it is computationally hard to fulfill these two requirements. However, it is possible to approximately address these challenges in a physically consistent way. On the one hand, it may be sufficient to consider approximate free energies if a reliable uncertainty measure can be provided. On the other hand, a highly resolved time evolution may not be necessary to still determine quantitative fluxes in a reaction network if one is interested in specific time scales. In this paper, we present discrete-time kinetic simulations in discrete state space taking free energy uncertainties into account. The method builds upon thermo-chemical data obtained from electronic structure calculations in a condensed-phase model. Our kinetic approach supports the analysis of general reaction networks spanning multiple time scales, which is here demonstrated for the example of the formose reaction. An important application of our approach is the detection of regions in a reaction network which require further investigation, given the uncertainties introduced by both approximate electronic structure methods and kinetic models. Such cases can then be studied in greater detail with more sophisticated first-principles calculations and kinetic simulations.
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Affiliation(s)
- Jonny Proppe
- Laboratory of Physical Chemistry, ETH Zürich, Zürich, Switzerland.
| | - Tamara Husch
- Laboratory of Physical Chemistry, ETH Zürich, Zürich, Switzerland.
| | - Gregor N Simm
- Laboratory of Physical Chemistry, ETH Zürich, Zürich, Switzerland.
| | - Markus Reiher
- Laboratory of Physical Chemistry, ETH Zürich, Zürich, Switzerland.
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19
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Abstract
Statistical estimation of the prediction uncertainty of physical models is typically hindered by the inadequacy of these models due to various approximations they are built upon. The prediction errors caused by model inadequacy can be handled either by correcting the model's results or by adapting the model's parameter uncertainty to generate prediction uncertainties representative, in a way to be defined, of model inadequacy errors. The main advantage of the latter approach (thereafter called PUI, for Parameter Uncertainty Inflation) is its transferability to the prediction of other quantities of interest based on the same parameters. A critical review of implementations of PUI in several areas of computational chemistry shows that it is biased, in the sense that it does not produce prediction uncertainty bands conforming to model inadequacy errors.
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Affiliation(s)
- Pascal Pernot
- Laboratoire de Chimie Physique, UMR 8000, CNRS/Université Paris-Sud, F-91405 Orsay, France
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20
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Fritsche L, Bach A, Miloglyadova L, Tsybizova A, Chen P. A 4 K FT-ICR cell for infrared ion spectroscopy. THE REVIEW OF SCIENTIFIC INSTRUMENTS 2018; 89:063119. [PMID: 29960550 DOI: 10.1063/1.5026973] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
We present the design of the newly constructed cryogenic Fourier-transform ion cyclotron resonance (FT-ICR) ion trap for infrared ion spectroscopy. Trapped ions are collisionally cooled by the pulsed introduction of buffer gas into the cell. Using different buffer gases and cell temperatures, we record action spectra of weakly bound neutral gas-analyte complexes with an IR laser source. We show for the first time that ion-He complexes can be observed in an ICR cell at temperatures around 4 K. We compare the experimental vibrational spectra of Ag(PPh3)2+ obtained by tagging with different neutral gases: He, Ne, Ar, H2, and N2 to computed vibrational spectra. Furthermore, the conditions necessary for the formation of neutral tags within an ICR ion trap are studied.
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Affiliation(s)
- Lukas Fritsche
- Laboratorium für Organische Chemie, ETH Zurich, Vladimir-Prelog-Weg 2, CH-8093 Zürich, Switzerland
| | - Andreas Bach
- Laboratorium für Organische Chemie, ETH Zurich, Vladimir-Prelog-Weg 2, CH-8093 Zürich, Switzerland
| | - Larisa Miloglyadova
- Laboratorium für Organische Chemie, ETH Zurich, Vladimir-Prelog-Weg 2, CH-8093 Zürich, Switzerland
| | - Alexandra Tsybizova
- Laboratorium für Organische Chemie, ETH Zurich, Vladimir-Prelog-Weg 2, CH-8093 Zürich, Switzerland
| | - Peter Chen
- Laboratorium für Organische Chemie, ETH Zurich, Vladimir-Prelog-Weg 2, CH-8093 Zürich, Switzerland
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21
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Husch T, Freitag L, Reiher M. Calculation of Ligand Dissociation Energies in Large Transition-Metal Complexes. J Chem Theory Comput 2018; 14:2456-2468. [PMID: 29595973 DOI: 10.1021/acs.jctc.8b00061] [Citation(s) in RCA: 52] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
The accurate calculation of ligand dissociation (or equivalently, ligand binding) energies is crucial for computational coordination chemistry. Despite its importance, obtaining accurate ab initio reference data is difficult, and density-functional methods of uncertain reliability are chosen for feasibility reasons. Here, we consider advanced coupled-cluster and multiconfigurational approaches to reinvestigate our WCCR10 set of 10 gas-phase ligand dissociation energies [ J. Chem. Theory Comput. 2014, 10, 3092]. We assess the potential multiconfigurational character of all molecules involved in these reactions with a multireference diagnostic [ Mol. Phys. 2017, 115, 2110] in order to determine where single-reference coupled-cluster approaches can be applied. For some reactions of the WCCR10 set, large deviations of density-functional results including semiclassical dispersion corrections from experimental reference data had been observed. This puzzling observation deserves special attention here, and we tackle the issue (i) by comparing to ab initio data that comprise dispersion effects on a rigorous first-principles footing and (ii) by a comparison of density-functional approaches that model dispersion interactions in various ways. For two reactions, species exhibiting nonnegligible static electron correlation were identified. These two reactions represent hard problems for electronic structure methods and also for multireference perturbation theories. However, most of the ligand dissociation reactions in WCCR10 do not exhibit static electron correlation effects, and hence, we may choose standard single-reference coupled-cluster approaches to compare with density-functional methods. For WCCR10, the Minnesota M06-L functional yielded the smallest mean absolute deviation of 13.2 kJ mol-1 out of all density functionals considered (PBE, BP86, BLYP, TPSS, M06-L, PBE0, B3LYP, TPSSh, and M06-2X) without additional dispersion corrections in comparison to the coupled-cluster results, and the PBE0-D3 functional produced the overall smallest mean absolute deviation of 4.3 kJ mol-1. The agreement of density-functional results with coupled-cluster data increases significantly upon inclusion of any type of dispersion correction. It is important to emphasize that different density-functional schemes available for this purpose perform equally well. The coupled-cluster dissociation energies, however, deviate from experimental results on average by 30.3 kJ mol-1. Possible reasons for these deviations are discussed.
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Affiliation(s)
- Tamara Husch
- Laboratorium für Physikalische Chemie , ETH Zürich , Vladimir-Prelog-Weg 2 , 8093 Zürich , Switzerland
| | - Leon Freitag
- Laboratorium für Physikalische Chemie , ETH Zürich , Vladimir-Prelog-Weg 2 , 8093 Zürich , Switzerland
| | - Markus Reiher
- Laboratorium für Physikalische Chemie , ETH Zürich , Vladimir-Prelog-Weg 2 , 8093 Zürich , Switzerland
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22
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Schneider AG, Schomborg L, Rüscher CH, Bredow T. Identification of Intermediates during the Hydration of Na 8[AlSiO 4] 6(BH 4) 2: A Combined Theoretical and Experimental Approach. J Phys Chem A 2018. [DOI: 10.1021/acs.jpca.8b00898] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Alexander G. Schneider
- Mulliken Center for Theoretical Chemistry, Institut für Physikalische und Theoretische Chemie, Rheinische Friedrich-Wilhelms-Universität Bonn, Beringstrasse 4-6, D-53115 Bonn, Germany
| | - Lars Schomborg
- Institut für Mineralogie, Leibniz Universität Hannover, Callinstrasse 3, D-30167 Hannover, Germany
| | - Claus H. Rüscher
- Institut für Mineralogie, Leibniz Universität Hannover, Callinstrasse 3, D-30167 Hannover, Germany
| | - Thomas Bredow
- Mulliken Center for Theoretical Chemistry, Institut für Physikalische und Theoretische Chemie, Rheinische Friedrich-Wilhelms-Universität Bonn, Beringstrasse 4-6, D-53115 Bonn, Germany
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23
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Straub S, Brünker P, Lindner J, Vöhringer P. An Iron Complex with a Bent, O-Coordinated CO2
Ligand Discovered by Femtosecond Mid-Infrared Spectroscopy. Angew Chem Int Ed Engl 2018. [DOI: 10.1002/ange.201800672] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- Steffen Straub
- Institut für Physikalische und Theoretische Chemie; Rheinische Friedrich-Wilhelms-Universität; Wegelerstraße 12 53117 Bonn Germany
| | - Paul Brünker
- Institut für Physikalische und Theoretische Chemie; Rheinische Friedrich-Wilhelms-Universität; Wegelerstraße 12 53117 Bonn Germany
| | - Jörg Lindner
- Institut für Physikalische und Theoretische Chemie; Rheinische Friedrich-Wilhelms-Universität; Wegelerstraße 12 53117 Bonn Germany
| | - Peter Vöhringer
- Institut für Physikalische und Theoretische Chemie; Rheinische Friedrich-Wilhelms-Universität; Wegelerstraße 12 53117 Bonn Germany
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24
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Straub S, Brünker P, Lindner J, Vöhringer P. An Iron Complex with a Bent, O-Coordinated CO2
Ligand Discovered by Femtosecond Mid-Infrared Spectroscopy. Angew Chem Int Ed Engl 2018; 57:5000-5005. [DOI: 10.1002/anie.201800672] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2018] [Revised: 02/14/2018] [Indexed: 11/06/2022]
Affiliation(s)
- Steffen Straub
- Institut für Physikalische und Theoretische Chemie; Rheinische Friedrich-Wilhelms-Universität; Wegelerstraße 12 53117 Bonn Germany
| | - Paul Brünker
- Institut für Physikalische und Theoretische Chemie; Rheinische Friedrich-Wilhelms-Universität; Wegelerstraße 12 53117 Bonn Germany
| | - Jörg Lindner
- Institut für Physikalische und Theoretische Chemie; Rheinische Friedrich-Wilhelms-Universität; Wegelerstraße 12 53117 Bonn Germany
| | - Peter Vöhringer
- Institut für Physikalische und Theoretische Chemie; Rheinische Friedrich-Wilhelms-Universität; Wegelerstraße 12 53117 Bonn Germany
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25
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Cornaton Y, Ringholm M, Ruud K. Complete analytic anharmonic hyper-Raman scattering spectra. Phys Chem Chem Phys 2018; 18:22331-42. [PMID: 27459194 DOI: 10.1039/c6cp03463b] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
We present the first computational treatment of the complete second-order vibrational perturbation theory applied to hyper-Raman scattering spectroscopy. The required molecular properties are calculated in a fully analytic manner using a recently developed program [Ringholm, Jonsson and Ruud, J. Comp. Chem., 2014, 35, 622] that utilizes recursive routines. For some of the properties, these calculations are the first analytic calculations of their kind at their respective levels of theory. We apply this approach to the calculation of the hyper-Raman spectra of methane, ethane and ethylene and compare these to available experimental data. We show that the anharmonic corrections have a larger effect on the vibrational frequencies than on the spectral intensities, but that the inclusion of combination and overtone bands in the anharmonic treatment can improve the agreement with the experimental data, although the quality of available experimental data limits a detailed comparison.
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Affiliation(s)
- Yann Cornaton
- Centre for Theoretical and Computational Chemistry, Department of Chemistry, University of Tromsø-The Arctic University of Norway, N-9037 Tromsø, Norway.
| | - Magnus Ringholm
- Centre for Theoretical and Computational Chemistry, Department of Chemistry, University of Tromsø-The Arctic University of Norway, N-9037 Tromsø, Norway.
| | - Kenneth Ruud
- Centre for Theoretical and Computational Chemistry, Department of Chemistry, University of Tromsø-The Arctic University of Norway, N-9037 Tromsø, Norway.
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26
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Krasnoshchekov SV, Craig NC, Koroleva LA, Stepanov NF. Anharmonic vibrational analysis of s-trans and s-cis conformers of acryloyl fluoride using numerical-analytic Van Vleck operator perturbation theory. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2018; 189:66-79. [PMID: 28800431 DOI: 10.1016/j.saa.2017.07.062] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/28/2017] [Revised: 07/22/2017] [Accepted: 07/30/2017] [Indexed: 06/07/2023]
Abstract
A new gas-phase infrared (IR) spectrum of acryloyl fluoride (ACRF, CH2CHCFO) with a resolution of 0.1cm-1 in the range 4000-450cm-1 was measured. Theoretical ab initio molecular structures, full quartic potential energy surfaces (PES), and cubic surfaces of dipole moments and polarizability tensor components (electro-optical properties, EOP) of the s-trans and s-cis conformers of the ACRF were calculated by the second-order Møller-Plesset electronic perturbation theory with a correlation consistent Dunning triple-ζ basis set. The numerical-analytic implementation of the second-order operator canonical Van Vleck perturbation theory was employed for predicting anharmonic IR and Raman scattering (RS) spectra of ACRF. To improve the anharmonic predictions, harmonic frequencies were replaced by their counterparts evaluated with the higher-level CCSD(T)/cc-pVTZ model, to form a "hybrid" PES. The original operator representation of the Hamiltonian is analytically reduced to a quasi-diagonal form, integrated in the harmonic oscillator basis and diagonalized to account for strong resonance couplings. Double canonical transformations of EOP expansions enabled prediction of integral intensities of both fundamental and multi-quanta transitions in IR/RS spectra. Enhanced band shape analysis reinforced the assignments. A thorough interpretation of the new IR experimental spectra and existing matrix-isolation literature data for the mixture of two conformers of ACRF was accomplished, and a number of assignments clarified.
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Affiliation(s)
- Sergey V Krasnoshchekov
- Department of Chemistry, Lomonosov Moscow State University, Leninskiye Gory 1-3, 119991 Moscow, Russian Federation.
| | - Norman C Craig
- Department of Chemistry and Biochemistry, Oberlin College, Oberlin, Ohio 44074, USA
| | - Lidiya A Koroleva
- Department of Chemistry, Lomonosov Moscow State University, Leninskiye Gory 1-3, 119991 Moscow, Russian Federation
| | - Nikolay F Stepanov
- Department of Chemistry, Lomonosov Moscow State University, Leninskiye Gory 1-3, 119991 Moscow, Russian Federation
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27
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Wang J, Xie W, Wang J, Gao Y, Lei J, Zhang RQ, Wang Z. Actinide embedded nearly planar gold superatoms: structural properties and applications in surface-enhanced Raman scattering (SERS). Phys Chem Chem Phys 2018; 20:27523-27527. [DOI: 10.1039/c8cp05350b] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Actinide embedded in a gold ring and applications in surface-enhanced Raman scattering (SERS).
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Affiliation(s)
- Jianpeng Wang
- Institute of Atomic and Molecular Physics, Jilin University
- Changchun 130012
- China
- Jilin Provincial Key Laboratory of Applied Atomic and Molecular Spectroscopy, Jilin University
- Changchun 130012
| | - Weiyu Xie
- Institute of Atomic and Molecular Physics, Jilin University
- Changchun 130012
- China
- Jilin Provincial Key Laboratory of Applied Atomic and Molecular Spectroscopy, Jilin University
- Changchun 130012
| | - Jia Wang
- Institute of Atomic and Molecular Physics, Jilin University
- Changchun 130012
- China
- Jilin Provincial Key Laboratory of Applied Atomic and Molecular Spectroscopy, Jilin University
- Changchun 130012
| | - Yang Gao
- Institute of Atomic and Molecular Physics, Jilin University
- Changchun 130012
- China
- Jilin Provincial Key Laboratory of Applied Atomic and Molecular Spectroscopy, Jilin University
- Changchun 130012
| | - Jiehong Lei
- Physics and Space Science College, China West Normal University
- Nanchong 637009
- China
| | - Rui-Qin Zhang
- Department of Physics, City University of Hong Kong
- Hong Kong SAR
- P. R. China
- Beijing Computational Science Research Center
- Beijing 100193
| | - Zhigang Wang
- Institute of Atomic and Molecular Physics, Jilin University
- Changchun 130012
- China
- Jilin Provincial Key Laboratory of Applied Atomic and Molecular Spectroscopy, Jilin University
- Changchun 130012
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28
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Straub S, Brünker P, Lindner J, Vöhringer P. Femtosecond infrared spectroscopy reveals the primary events of the ferrioxalate actinometer. Phys Chem Chem Phys 2018; 20:21390-21403. [DOI: 10.1039/c8cp03824d] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Ultrafast vibrational spectroscopy unravels the primary processes of Hatchard and Parker's ferrioxalate actinometer – a widely used tool in the photochemistry community.
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Affiliation(s)
- Steffen Straub
- Institut für Physikalische und Theoretische Chemie
- Rheinische Friedrich-Wilhelms-Universität
- 53115 Bonn
- Germany
| | - Paul Brünker
- Institut für Physikalische und Theoretische Chemie
- Rheinische Friedrich-Wilhelms-Universität
- 53115 Bonn
- Germany
| | - Jörg Lindner
- Institut für Physikalische und Theoretische Chemie
- Rheinische Friedrich-Wilhelms-Universität
- 53115 Bonn
- Germany
| | - Peter Vöhringer
- Institut für Physikalische und Theoretische Chemie
- Rheinische Friedrich-Wilhelms-Universität
- 53115 Bonn
- Germany
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29
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Chiang N, Jiang N, Madison LR, Pozzi EA, Wasielewski MR, Ratner MA, Hersam MC, Seideman T, Schatz GC, Van Duyne RP. Probing Intermolecular Vibrational Symmetry Breaking in Self-Assembled Monolayers with Ultrahigh Vacuum Tip-Enhanced Raman Spectroscopy. J Am Chem Soc 2017; 139:18664-18669. [PMID: 29198112 DOI: 10.1021/jacs.7b10645] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Ultrahigh vacuum tip-enhanced Raman spectroscopy (UHV-TERS) combines the atomic-scale imaging capability of scanning probe microscopy with the single-molecule chemical sensitivity and structural specificity of surface-enhanced Raman spectroscopy. Here, we use these techniques in combination with theory to reveal insights into the influence of intermolecular interactions on the vibrational spectra of a N-N'-bis(2,6-diisopropylphenyl)-perylene-3,4:9,10-bis(dicarboximide) (PDI) self-assembled monolayer adsorbed on single-crystal Ag substrates at room temperature. In particular, we have revealed the lifting of a vibrational degeneracy of a mode of PDI on Ag(111) and Ag(100) surfaces, with the most strongly perturbed mode being that associated with the largest vibrational amplitude on the periphery of the molecule. This work demonstrates that UHV-TERS enables direct measurement of molecule-molecule interaction at nanoscale. We anticipate that this information will advance the fundamental understanding of the most important effect of intermolecular interactions on the vibrational modes of surface-bound molecules.
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Affiliation(s)
| | - Nan Jiang
- Department of Chemistry, University of Illinois at Chicago , Chicago, Illinois 60607, United States
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30
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Li Q, Chen M. SERRS and absorption spectra of pyridine on Au m Ag n (m + n = 6) bimetallic nanoclusters: substrate composition and applied electric field effects. NANOTECHNOLOGY 2017; 28:475201. [PMID: 28885195 DOI: 10.1088/1361-6528/aa8b58] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
Surface-enhanced Raman scattering (SERS) and absorption spectra of the pyridine molecule adsorbed on Au m Ag n (m + n = 6) bimetallic clusters are theoretically investigated by time-dependent density functional theory. The contributions of static chemical enhancement to the ground-state system are analyzed, and the static Raman intensity of Py-Au m Ag n complexes are enhanced by an order of 10. A method of visualization on charge transfer is used to distinguish the contributions of charge-transfer enhancement and electromagnetic enhancement. The intensity of surface-enhanced resonance Raman scattering (SERRS) spectroscopy of Py-Au m Ag n is strongly enhanced by an order of 103-105, compared to the static Raman intensity of pyridine. The influence of the static external electric field on SERS is investigated by calculating the optical properties of the Py-Au3Ag3 complex. The intensity of SERRS spectra and normal Raman spectra can be significantly enhanced by the positive electric fields, and the intensities of specific Raman vibrational modes could be selectively enhanced or weakened by tuning the direction and strength of the static electric field applied on Py-Au3Ag3.
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Affiliation(s)
- Quanjiang Li
- Key Laboratory of Materials Modification by Laser, Electron, and Ion Beams (Ministry of Education), School of Physics and Optoelectronic Technology, Dalian University of Technology, Dalian 116024, People's Republic of China
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31
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Peters LDM, Kussmann J, Ochsenfeld C. Efficient and Accurate Born-Oppenheimer Molecular Dynamics for Large Molecular Systems. J Chem Theory Comput 2017; 13:5479-5485. [PMID: 29068678 DOI: 10.1021/acs.jctc.7b00937] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
An efficient scheme for the calculation of Born-Oppenheimer molecular dynamics (BOMD) simulations is introduced. It combines the corrected small basis set Hartree-Fock (HF-3c) method by Sure and Grimme [J. Comput. Chem. 2013, 43, 1672], extended Lagrangian BOMD (XL-BOMD) by Niklasson et al. [J. Chem. Phys. 2009, 130, 214109], and the calculation of the two electron integrals on graphics processing units (GPUs) [J. Chem. Phys. 2013, 138, 134114; J. Chem. Theory Comput. 2015, 11, 918]. To explore the parallel performance of our strong scaling implementation of the method, we present timings and extract, as its validation and first illustrative application, high-quality vibrational spectra from simulated trajectories of β-carotene, paclitaxel, and liquid water (up to 500 atoms). We conclude that the presented BOMD scheme may be used as a cost-efficient and reliable tool for computing vibrational spectra and thermodynamics of large molecular systems including explicit solvent molecules containing 500 atoms and more. Simulating 50 ps of maitotoxin (nearly 500 atoms) employing time steps of 0.5 fs requires ∼3 weeks on 12 CPUs (Intel Xeon E5 2620 v3) with 24 GPUs (AMD FirePro 3D W8100).
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Affiliation(s)
- Laurens D M Peters
- Chair of Theoretical Chemistry, Department of Chemistry, University of Munich (LMU) , Butenandtstr. 7, D-81377 München, Germany.,Center for Integrated Protein Science (CIPSM) at the Department of Chemistry, University of Munich (LMU) , Butenandtstr. 5-13, D-81377 München, Germany
| | - Jörg Kussmann
- Chair of Theoretical Chemistry, Department of Chemistry, University of Munich (LMU) , Butenandtstr. 7, D-81377 München, Germany.,Center for Integrated Protein Science (CIPSM) at the Department of Chemistry, University of Munich (LMU) , Butenandtstr. 5-13, D-81377 München, Germany
| | - Christian Ochsenfeld
- Chair of Theoretical Chemistry, Department of Chemistry, University of Munich (LMU) , Butenandtstr. 7, D-81377 München, Germany.,Center for Integrated Protein Science (CIPSM) at the Department of Chemistry, University of Munich (LMU) , Butenandtstr. 5-13, D-81377 München, Germany
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32
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Couzijn EPA, Lai YY, Limacher A, Chen P. Intuitive Quantifiers of Charge Flows in Coordinate Bonding. Organometallics 2017. [DOI: 10.1021/acs.organomet.7b00365] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Erik P. A. Couzijn
- Laboratorium für Organische
Chemie, ETH Zürich, Vladimir-Prelog-Weg 2, CH-8093 Zürich, Switzerland
| | - Yu-Ying Lai
- Laboratorium für Organische
Chemie, ETH Zürich, Vladimir-Prelog-Weg 2, CH-8093 Zürich, Switzerland
| | - Armin Limacher
- Laboratorium für Organische
Chemie, ETH Zürich, Vladimir-Prelog-Weg 2, CH-8093 Zürich, Switzerland
| | - Peter Chen
- Laboratorium für Organische
Chemie, ETH Zürich, Vladimir-Prelog-Weg 2, CH-8093 Zürich, Switzerland
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33
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Brehm M, Thomas M. Computing Bulk Phase Raman Optical Activity Spectra from ab initio Molecular Dynamics Simulations. J Phys Chem Lett 2017; 8:3409-3414. [PMID: 28685571 DOI: 10.1021/acs.jpclett.7b01616] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
We present our novel methodology for computing Raman optical activity (ROA) spectra of liquid systems from ab initio molecular dynamics (AIMD) simulations. The method is built upon the recent developments to obtain magnetic dipole moments from AIMD and to integrate molecular properties by using radical Voronoi tessellation. These techniques are used to calculate optical activity tensors for large and complex periodic bulk phase systems. Only AIMD simulations are required as input, and no time-consuming perturbation theory is involved. The approach relies only on the total electron density in each time step and can readily be combined with a wide range of electronic structure methods. To the best of our knowledge, these are the first computed ROA spectra for a periodic bulk phase system. As an example, the experimental ROA spectrum of liquid (R)-propylene oxide is reproduced very well.
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Affiliation(s)
- Martin Brehm
- Institut für Chemie - Theoretische Chemie, Martin-Luther-Universität Halle-Wittenberg , Von-Danckelmann-Platz 4, 06120 Halle (Saale), Germany
| | - Martin Thomas
- Institut für Chemie - Theoretische Chemie, Martin-Luther-Universität Halle-Wittenberg , Von-Danckelmann-Platz 4, 06120 Halle (Saale), Germany
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34
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Proppe J, Reiher M. Reliable Estimation of Prediction Uncertainty for Physicochemical Property Models. J Chem Theory Comput 2017; 13:3297-3317. [PMID: 28581746 DOI: 10.1021/acs.jctc.7b00235] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
One of the major challenges in computational science is to determine the uncertainty of a virtual measurement, that is the prediction of an observable based on calculations. As highly accurate first-principles calculations are in general unfeasible for most physical systems, one usually resorts to parameteric property models of observables, which require calibration by incorporating reference data. The resulting predictions and their uncertainties are sensitive to systematic errors such as inconsistent reference data, parametric model assumptions, or inadequate computational methods. Here, we discuss the calibration of property models in the light of bootstrapping, a sampling method that can be employed for identifying systematic errors and for reliable estimation of the prediction uncertainty. We apply bootstrapping to assess a linear property model linking the 57Fe Mössbauer isomer shift to the contact electron density at the iron nucleus for a diverse set of 44 molecular iron compounds. The contact electron density is calculated with 12 density functionals across Jacob's ladder (PWLDA, BP86, BLYP, PW91, PBE, M06-L, TPSS, B3LYP, B3PW91, PBE0, M06, TPSSh). We provide systematic-error diagnostics and reliable, locally resolved uncertainties for isomer-shift predictions. Pure and hybrid density functionals yield average prediction uncertainties of 0.06-0.08 mm s-1 and 0.04-0.05 mm s-1, respectively, the latter being close to the average experimental uncertainty of 0.02 mm s-1. Furthermore, we show that both model parameters and prediction uncertainty depend significantly on the composition and number of reference data points. Accordingly, we suggest that rankings of density functionals based on performance measures (e.g., the squared coefficient of correlation, r2, or the root-mean-square error, RMSE) should not be inferred from a single data set. This study presents the first statistically rigorous calibration analysis for theoretical Mössbauer spectroscopy, which is of general applicability for physicochemical property models and not restricted to isomer-shift predictions. We provide the statistically meaningful reference data set MIS39 and a new calibration of the isomer shift based on the PBE0 functional.
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Affiliation(s)
- Jonny Proppe
- Laboratorium für Physikalische Chemie, ETH Zürich , Vladimir-Prelog-Weg 2, 8093 Zürich, Switzerland
| | - Markus Reiher
- Laboratorium für Physikalische Chemie, ETH Zürich , Vladimir-Prelog-Weg 2, 8093 Zürich, Switzerland
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35
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Computational study of Th(4+) and Np(4+) hydration and hydrolysis of Th(4+) from first principles. J Mol Model 2017; 23:69. [PMID: 28197840 DOI: 10.1007/s00894-017-3252-9] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2016] [Accepted: 01/23/2017] [Indexed: 10/20/2022]
Abstract
The aqueous solvation of Th and Np in the IV oxidation state was examined using cluster models generated by Monte Carlo simulations and density functional theory embedded within the COSMO continuum model to approximate the effect of bulk water. Our results suggest that the coordination number (CN) for both Th(IV) and NP(IV) should be 9, in accordance to some experimental and theoretical results from the literature. The structural values for average oxygen-metal distances are within 0.01 Å compared to experimental data, and also within the experimental error. The calculated ΔG Sol0 are in very good agreement with experimental reported values, with deviations at CN = 9 lower than 1% for both Th(IV) and Np(IV). The hydrolysis constants are also in very good agreement with experimental values. Finally, this [corrected] methodology has the advantage of using a GGA functional (BP86) that not only makes the calculations more affordable computationally than hybrid functional or ab initio molecular dynamics simulations (Car-Parrinello) calculations, but also opens the perspective to use resolution of identity (RI) calculations for more extended systems.
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36
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Panek PT, Jacob CR. On the benefits of localized modes in anharmonic vibrational calculations for small molecules. J Chem Phys 2017; 144:164111. [PMID: 27131535 DOI: 10.1063/1.4947213] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
Anharmonic vibrational calculations can already be computationally demanding for relatively small molecules. The main bottlenecks lie in the construction of the potential energy surface and in the size of the excitation space in the vibrational configuration interaction (VCI) calculations. To address these challenges, we use localized-mode coordinates to construct potential energy surfaces and perform vibrational self-consistent field and L-VCI calculations [P. T. Panek and C. R. Jacob, ChemPhysChem 15, 3365 (2014)] for all vibrational modes of two prototypical test cases, the ethene and furan molecules. We find that the mutual coupling between modes is reduced when switching from normal-mode coordinates to localized-mode coordinates. When using such localized-mode coordinates, we observe a faster convergence of the n-mode expansion of the potential energy surface. This makes it possible to neglect higher-order contributions in the n-mode expansion of the potential energy surface or to approximate higher-order contributions in hybrid potential energy surfaces, which reduced the computational effort for the construction of the anharmonic potential energy surface significantly. Moreover, we find that when using localized-mode coordinates, the convergence with respect to the VCI excitation space proceeds more smoothly and that the error at low orders is reduced significantly. This makes it possible to devise low-cost models for obtaining a first approximation of anharmonic corrections. This demonstrates that the use of localized-mode coordinates can be beneficial already in anharmonic vibrational calculations of small molecules and provides a possible avenue for enabling such accurate calculations also for larger molecules.
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Affiliation(s)
- Paweł T Panek
- TU Braunschweig, Institute of Physical and Theoretical Chemistry, Hans-Sommer-Str. 10, 38106 Braunschweig, Germany
| | - Christoph R Jacob
- TU Braunschweig, Institute of Physical and Theoretical Chemistry, Hans-Sommer-Str. 10, 38106 Braunschweig, Germany
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37
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Liang L, Hu W, Zhang Z, Shen JW. Theoretic Study on Dispersion Mechanism of Boron Nitride Nanotubes by Polynucleotides. Sci Rep 2016; 6:39747. [PMID: 28004832 PMCID: PMC5177943 DOI: 10.1038/srep39747] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2016] [Accepted: 11/28/2016] [Indexed: 01/01/2023] Open
Abstract
Due to the unique electrical and mechanical properties of boron nitride nanotubes (BNNT), BNNT has been a promising material for many potential applications, especially in biomedical field. Understanding the dispersion of BNNT in aqueous solution by biomolecules is essential for its use in biomedical applications. In this study, BNNT wrapped by polynucleotides in aqueous solution was investigated by molecular dynamics (MD) simulations. Our results demonstrated that the BNNT wrapped by polynucleotides could greatly hinder the aggregation of BNNTs and improve the dispersion of BNNTs in aqueous solution. Dispersion of BNNTs with the assistance of polynucleotides is greatly affected by the wrapping manner of polynucleotides on BNNT, which mainly depends on two factors: the type of polynucleotides and the radius of BNNT. The interaction between polynucleotides and BNNT(9, 9) is larger than that between polynucleotides and BNNT(5, 5), which leads to the fact that dispersion of BNNT(9, 9) is better than that of BNNT(5, 5) with the assistance of polynucleotides in aqueous solution. Our study revealed the molecular-level dispersion mechanism of BNNT with the assistance of polynucleotides in aqueous solution. It shades a light on the understanding of dispersion of single wall nanotubes by biomolecules.
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Affiliation(s)
- Lijun Liang
- College of Life Information Science and Instrument Engineering, Hangzhou Dianzi University, Hangzhou, People’s Republic of China
| | - Wei Hu
- Division of Theoretical Chemistry and Biology, School of Biotechnology, KTH Royal Institute of Technology, SE-10691 Stockholm, Sweden
| | - Zhisen Zhang
- Research Institute for Biomimetic and Soft Matter, Fujian Provincial Key Laboratory of Soft Functional Materials, Department of Physics, Xiamen University, Xiamen, 361005, People’s Republic of China
| | - Jia-Wei Shen
- School of Medicine, Hangzhou Normal University, Hangzhou 310016, People’s Republic of China
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38
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Sharma B, Bugga P, Madison LR, Henry AI, Blaber MG, Greeneltch NG, Chiang N, Mrksich M, Schatz GC, Van Duyne RP. Bisboronic Acids for Selective, Physiologically Relevant Direct Glucose Sensing with Surface-Enhanced Raman Spectroscopy. J Am Chem Soc 2016; 138:13952-13959. [PMID: 27668444 DOI: 10.1021/jacs.6b07331] [Citation(s) in RCA: 72] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
This paper demonstrates the direct sensing of glucose at physiologically relevant concentrations with surface-enhanced Raman spectroscopy (SERS) on gold film-over-nanosphere (AuFON) substrates functionalized with bisboronic acid receptors. The combination of selectivity in the bisboronic acid receptor and spectral resolution in the SERS data allow the sensors to resolve glucose in high backgrounds of fructose and, in combination with multivariate statistical analysis, detect glucose accurately in the 1-10 mM range. Computational modeling supports assignments of the normal modes and vibrational frequencies for the monoboronic acid base of our bisboronic acids, glucose and fructose. These results are promising for the use of bisboronic acids as receptors in SERS-based in vivo glucose monitoring sensors.
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Affiliation(s)
- Bhavya Sharma
- Department of Chemistry, Northwestern University , 2145 Sheridan Rd., Evanston, Illinois 60208, United States.,Department of Chemistry, University of Tennessee , 1420 Circle Dr., Knoxville, Tennessee 37931, United States
| | - Pradeep Bugga
- Department of Chemistry, Northwestern University , 2145 Sheridan Rd., Evanston, Illinois 60208, United States
| | - Lindsey R Madison
- Department of Chemistry, Northwestern University , 2145 Sheridan Rd., Evanston, Illinois 60208, United States
| | - Anne-Isabelle Henry
- Department of Chemistry, Northwestern University , 2145 Sheridan Rd., Evanston, Illinois 60208, United States
| | - Martin G Blaber
- Department of Chemistry, Northwestern University , 2145 Sheridan Rd., Evanston, Illinois 60208, United States
| | - Nathan G Greeneltch
- Department of Chemistry, Northwestern University , 2145 Sheridan Rd., Evanston, Illinois 60208, United States
| | - Naihao Chiang
- Department of Chemistry, Northwestern University , 2145 Sheridan Rd., Evanston, Illinois 60208, United States
| | - Milan Mrksich
- Department of Chemistry, Northwestern University , 2145 Sheridan Rd., Evanston, Illinois 60208, United States
| | - George C Schatz
- Department of Chemistry, Northwestern University , 2145 Sheridan Rd., Evanston, Illinois 60208, United States
| | - Richard P Van Duyne
- Department of Chemistry, Northwestern University , 2145 Sheridan Rd., Evanston, Illinois 60208, United States
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39
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Molina A, Smereka P, Zimmerman PM. Exploring the relationship between vibrational mode locality and coupling using constrained optimization. J Chem Phys 2016; 144:124111. [PMID: 27036431 DOI: 10.1063/1.4944743] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
The use of alternate coordinate systems as a means to improve the efficiency and accuracy of anharmonic vibrational structure analysis has seen renewed interest in recent years. While normal modes (which diagonalize the mass-weighted Hessian matrix) are a typical choice, the delocalized nature of this basis makes it less optimal when anharmonicity is in play. When a set of modes is not designed to treat anharmonicity, anharmonic effects will contribute to inter-mode coupling in an uncontrolled fashion. These effects can be mitigated by introducing locality, but this comes at its own cost of potentially large second-order coupling terms. Herein, a method is described which partially localizes vibrations to connect the fully delocalized and fully localized limits. This allows a balance between the treatment of harmonic and anharmonic coupling, which minimizes the error that arises from neglected coupling terms. Partially localized modes are investigated for a range of model systems including a tetramer of hydrogen fluoride, water dimer, ethene, diphenylethane, and stilbene. Generally, partial localization reaches ∼75% of maximal locality while introducing less than ∼30% of the harmonic coupling of the fully localized system. Furthermore, partial localization produces mode pairs that are spatially separated and thus weakly coupled to one another. It is likely that this property can be exploited in the creation of model Hamiltonians that omit the coupling parameters of the distant (and therefore uncoupled) pairs.
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Affiliation(s)
- Andrew Molina
- Department of Chemistry, University of Michigan, 930 N. University Ave., Ann Arbor, Michigan 48109, USA
| | - Peter Smereka
- Department of Applied Mathematics, University of Michigan, Ann Arbor, Michigan 48109, USA
| | - Paul M Zimmerman
- Department of Chemistry, University of Michigan, 930 N. University Ave., Ann Arbor, Michigan 48109, USA
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40
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Schwörer M, Wichmann C, Tavan P. A polarizable QM/MM approach to the molecular dynamics of amide groups solvated in water. J Chem Phys 2016; 144:114504. [PMID: 27004884 DOI: 10.1063/1.4943972] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
The infrared (IR) spectra of polypeptides are dominated by the so-called amide bands. Because they originate from the strongly polar and polarizable amide groups (AGs) making up the backbone, their spectral positions sensitively depend on the local electric fields. Aiming at accurate computations of these IR spectra by molecular dynamics (MD) simulations, which derive atomic forces from a hybrid quantum and molecular mechanics (QM/MM) Hamiltonian, here we consider the effects of solvation in bulk liquid water on the amide bands of the AG model compound N-methyl-acetamide (NMA). As QM approach to NMA we choose grid-based density functional theory (DFT). For the surrounding MM water, we develop, largely based on computations, a polarizable molecular mechanics (PMM) model potential called GP6P, which features six Gaussian electrostatic sources (one induced dipole, five static partial charge distributions) and, therefore, avoids spurious distortions of the DFT electron density in hybrid DFT/PMM simulations. Bulk liquid GP6P is shown to have favorable properties at the thermodynamic conditions of the parameterization and beyond. Lennard-Jones (LJ) parameters of the DFT fragment NMA are optimized by comparing radial distribution functions in the surrounding GP6P liquid with reference data obtained from a "first-principles" DFT-MD simulation. Finally, IR spectra of NMA in GP6P water are calculated from extended DFT/PMM-MD trajectories, in which the NMA is treated by three different DFT functionals (BP, BLYP, B3LYP). Method-specific frequency scaling factors are derived from DFT-MD simulations of isolated NMA. The DFT/PMM-MD simulations with GP6P and with the optimized LJ parameters then excellently predict the effects of aqueous solvation and deuteration observed in the IR spectra of NMA. As a result, the methods required to accurately compute such spectra by DFT/PMM-MD also for larger peptides in aqueous solution are now at hand.
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Affiliation(s)
- Magnus Schwörer
- Lehrstuhl für BioMolekulare Optik, Ludwig-Maximilians Universität München, Oettingenstr. 67, 80538 München, Germany
| | - Christoph Wichmann
- Lehrstuhl für BioMolekulare Optik, Ludwig-Maximilians Universität München, Oettingenstr. 67, 80538 München, Germany
| | - Paul Tavan
- Lehrstuhl für BioMolekulare Optik, Ludwig-Maximilians Universität München, Oettingenstr. 67, 80538 München, Germany
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41
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Schilter D, Camara JM, Huynh MT, Hammes-Schiffer S, Rauchfuss TB. Hydrogenase Enzymes and Their Synthetic Models: The Role of Metal Hydrides. Chem Rev 2016; 116:8693-749. [PMID: 27353631 PMCID: PMC5026416 DOI: 10.1021/acs.chemrev.6b00180] [Citation(s) in RCA: 397] [Impact Index Per Article: 49.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Hydrogenase enzymes efficiently process H2 and protons at organometallic FeFe, NiFe, or Fe active sites. Synthetic modeling of the many H2ase states has provided insight into H2ase structure and mechanism, as well as afforded catalysts for the H2 energy vector. Particularly important are hydride-bearing states, with synthetic hydride analogues now known for each hydrogenase class. These hydrides are typically prepared by protonation of low-valent cores. Examples of FeFe and NiFe hydrides derived from H2 have also been prepared. Such chemistry is more developed than mimicry of the redox-inactive monoFe enzyme, although functional models of the latter are now emerging. Advances in physical and theoretical characterization of H2ase enzymes and synthetic models have proven key to the study of hydrides in particular, and will guide modeling efforts toward more robust and active species optimized for practical applications.
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Affiliation(s)
- David Schilter
- Center for Multidimensional Carbon Materials, Institute for Basic Science (IBS), Ulsan 44919, Republic of Korea
- Department of Chemistry, Ulsan National Institute of Science and Technology (UNIST), Ulsan 44919, Republic of Korea
| | - James M. Camara
- Department of Chemistry, Yeshiva University, 500 West 185th Street, New York, New York 10033, United States
| | - Mioy T. Huynh
- Department of Chemistry, University of Illinois at Urbana–Champaign, 600 South Mathews Avenue, Urbana, Illinois 61801, United States
| | - Sharon Hammes-Schiffer
- Department of Chemistry, University of Illinois at Urbana–Champaign, 600 South Mathews Avenue, Urbana, Illinois 61801, United States
| | - Thomas B. Rauchfuss
- Department of Chemistry, University of Illinois at Urbana–Champaign, 600 South Mathews Avenue, Urbana, Illinois 61801, United States
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42
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Greene SM, Shan X, Clary DC. Rate constants of chemical reactions from semiclassical transition state theory in full and one dimension. J Chem Phys 2016; 144:244116. [DOI: 10.1063/1.4954840] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- Samuel M. Greene
- Physical and Theoretical Chemistry Laboratory, Department of Chemistry, University of Oxford, South Parks Road, Oxford OX1 3QZ, United Kingdom
| | - Xiao Shan
- Physical and Theoretical Chemistry Laboratory, Department of Chemistry, University of Oxford, South Parks Road, Oxford OX1 3QZ, United Kingdom
| | - David C. Clary
- Physical and Theoretical Chemistry Laboratory, Department of Chemistry, University of Oxford, South Parks Road, Oxford OX1 3QZ, United Kingdom
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43
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Jiang N, Chiang N, Madison LR, Pozzi EA, Wasielewski MR, Seideman T, Ratner MA, Hersam MC, Schatz GC, Van Duyne RP. Nanoscale Chemical Imaging of a Dynamic Molecular Phase Boundary with Ultrahigh Vacuum Tip-Enhanced Raman Spectroscopy. NANO LETTERS 2016; 16:3898-904. [PMID: 27183322 DOI: 10.1021/acs.nanolett.6b01405] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/19/2023]
Abstract
Nanoscale chemical imaging of a dynamic molecular phase boundary has broad implications for a range of problems in catalysis, surface science, and molecular electronics. While scanning probe microscopy (SPM) is commonly used to study molecular phase boundaries, its information content can be severely compromised by surface diffusion, irregular packing, or three-dimensional adsorbate geometry. Here, we demonstrate the simultaneous chemical and structural analysis of N-N'-bis(2,6-diisopropylphenyl)-1,7-(4'-t-butylphenoxy)perylene-3,4:9,10-bis(dicarboximide) (PPDI) molecules by UHV tip-enhanced Raman spectroscopy. Both condensed and diffusing domains of PPDI coexist on Ag(100) at room temperature. Through comparison with time-dependent density functional theory simulations, we unravel the orientation of PPDI molecules at the dynamic molecular domain boundary with unprecedented ∼4 nm spatial resolution.
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Affiliation(s)
- Nan Jiang
- Department of Chemistry, University of Illinois at Chicago , Chicago, Illinois 60607, United States
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44
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Li YP, Bell AT, Head-Gordon M. Thermodynamics of Anharmonic Systems: Uncoupled Mode Approximations for Molecules. J Chem Theory Comput 2016; 12:2861-70. [DOI: 10.1021/acs.jctc.5b01177] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Yi-Pei Li
- Department
of Chemical and Biomolecular Engineering, University of California, Berkeley, California 94720-1462, United States
| | - Alexis T. Bell
- Department
of Chemical and Biomolecular Engineering, University of California, Berkeley, California 94720-1462, United States
- Chemical
Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
| | - Martin Head-Gordon
- Department
of Chemistry, University of California, Berkeley, California 94720-1462, United States
- Chemical
Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
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45
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Mohammadpour M, Jamshidi Z. Comparative assessment of density functional methods for evaluating essential parameters to simulate SERS spectra within the excited state energy gradient approximation. J Chem Phys 2016; 144:194302. [DOI: 10.1063/1.4948813] [Citation(s) in RCA: 10] [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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46
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Knaanie R, Šebek J, Tsuge M, Myllys N, Khriachtchev L, Räsänen M, Albee B, Potma EO, Gerber RB. Infrared Spectrum of Toluene: Comparison of Anharmonic Isolated-Molecule Calculations and Experiments in Liquid Phase and in a Ne Matrix. J Phys Chem A 2016; 120:3380-9. [DOI: 10.1021/acs.jpca.6b01604] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Roie Knaanie
- Institute
of Chemistry and The Fritz Haber Research Center, The Hebrew University, Jerusalem 91904, Israel
| | - Jiří Šebek
- Institute
of Chemistry and The Fritz Haber Research Center, The Hebrew University, Jerusalem 91904, Israel
- Department
of Physical Chemistry, University of Chemistry and Technology, Prague 16628, Czech Republic
| | - Masashi Tsuge
- Department
of Chemistry, University of Helsinki, P.O. Box 55, FI-00014 Helsinki, Finland
| | - Nanna Myllys
- Department
of Chemistry, University of Helsinki, P.O. Box 55, FI-00014 Helsinki, Finland
| | - Leonid Khriachtchev
- Department
of Chemistry, University of Helsinki, P.O. Box 55, FI-00014 Helsinki, Finland
| | - Markku Räsänen
- Department
of Chemistry, University of Helsinki, P.O. Box 55, FI-00014 Helsinki, Finland
| | - Brian Albee
- Department
of Chemistry, University of California, Irvine, California 92697, United States
| | - Eric O. Potma
- Department
of Chemistry, University of California, Irvine, California 92697, United States
| | - R. Benny Gerber
- Institute
of Chemistry and The Fritz Haber Research Center, The Hebrew University, Jerusalem 91904, Israel
- Department
of Chemistry, University of Helsinki, P.O. Box 55, FI-00014 Helsinki, Finland
- Department
of Chemistry, University of California, Irvine, California 92697, United States
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47
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Ye S, Bill E, Neese F. Electronic Structures of the [Fe(N2)(SiPiPr3)]+1/0/–1 Electron Transfer Series: A Counterintuitive Correlation between Isomer Shifts and Oxidation States. Inorg Chem 2016; 55:3468-74. [DOI: 10.1021/acs.inorgchem.5b02908] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Shengfa Ye
- Max-Planck Institute for Chemical Energy Conversion, Stiftstrasse 34-36, D-45470 Mülheim an der Ruhr, Germany
| | - Eckhard Bill
- Max-Planck Institute for Chemical Energy Conversion, Stiftstrasse 34-36, D-45470 Mülheim an der Ruhr, Germany
| | - Frank Neese
- Max-Planck Institute for Chemical Energy Conversion, Stiftstrasse 34-36, D-45470 Mülheim an der Ruhr, Germany
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48
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Zimmerman PM, Smereka P. Optimizing Vibrational Coordinates To Modulate Intermode Coupling. J Chem Theory Comput 2016; 12:1883-91. [PMID: 26914536 DOI: 10.1021/acs.jctc.5b01168] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The choice of coordinate system strongly affects the convergence properties of vibrational structure computations. Two methods for efficient generation of improved vibrational coordinates are presented and justified by analysis of a model anharmonic two-mode Hessian and numerical computations on polyatomic molecules. To produce optimal coordinates, metrics which quantify off-diagonal couplings over a grid of Hessian matrices are minimized through unitary rotations of the vibrational basis. The first proposed metric minimizes the total squared off-diagonal coupling, and the second minimizes the total squared change in off-diagonal coupling. In this procedure certain anharmonic modes tend to localize, for example X-H stretches. The proposed methods do not rely on prior fitting of the potential energy, vibrational structure computations, or localization metrics, so they are unique from previous vibrational coordinate generation algorithms and are generally applicable to polyatomic molecules. Fitting the potential to the approximate n-mode representation in the optimized bases for all-trans polyenes shows that off-diagonal anharmonic couplings are substantially reduced by the new choices of coordinate system. Convergence of vibrational energies is examined in detail for ethylene, and it is shown that coupling-optimized modes converge in vibrational configuration interaction computations to within 1 cm(-1) using only 3-mode couplings, where normal modes require 4-mode couplings for convergence. Comparison of the vibrational configuration interaction convergence with respect to excitation level for the two proposed metrics shows that minimization of the total off-diagonal coupling is most effective for low-cost vibrational structure computations.
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Affiliation(s)
- Paul M Zimmerman
- Department of Chemistry and ‡Department of Mathematics, University of Michigan , Ann Arbor, Michigan 48109, United States
| | - Peter Smereka
- Department of Chemistry and ‡Department of Mathematics, University of Michigan , Ann Arbor, Michigan 48109, United States
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Greene SM, Shan X, Clary DC. An investigation of one- versus two-dimensional semiclassical transition state theory for H atom abstraction and exchange reactions. J Chem Phys 2016; 144:084113. [DOI: 10.1063/1.4942161] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Affiliation(s)
- Samuel M. Greene
- Physical and Theoretical Chemistry Laboratory, Department of Chemistry, University of Oxford, South Parks Road, Oxford OX1 3QZ, United Kingdom
| | - Xiao Shan
- Physical and Theoretical Chemistry Laboratory, Department of Chemistry, University of Oxford, South Parks Road, Oxford OX1 3QZ, United Kingdom
| | - David C. Clary
- Physical and Theoretical Chemistry Laboratory, Department of Chemistry, University of Oxford, South Parks Road, Oxford OX1 3QZ, United Kingdom
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Chen L, Gao Y, Cheng Y, Li H, Wang Z, Li Z, Zhang RQ. Nonresonant chemical mechanism in surface-enhanced Raman scattering of pyridine on M@Au12 clusters. NANOSCALE 2016; 8:4086-4093. [PMID: 26822548 DOI: 10.1039/c5nr07246h] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
By employing density functional theory (DFT), this study presents a detailed analysis of nonresonant surface-enhanced Raman scattering (SERS) of pyridine on M@Au12 (M = V(-), Nb(-), Ta(-), Cr, Mo, W, Mn(+), Tc(+), and Re(+))-the stable 13-atom neutral and charged gold buckyball clusters. Changing the core atom in M@Au12 enabled us to modulate the direct chemical interactions between pyridine and the metal cluster. The results of our calculations indicate that the ground-state chemical enhancement does not increase as the binding interaction strengthens or the transfer charge increases between pyridine and the cluster. Instead, the magnitude of the chemical enhancement is governed, to a large extent, by the charged properties of the metal clusters. Pyridine on M@Au12 anion clusters exhibits strong chemical enhancement of a factor of about 10(2), but the equivalent increase for pyridine adsorbed on M@Au12 neutral and cation clusters is no more than 10. Polarizability and deformation density analyses clearly show that compared with the neutral and cation clusters, the anion clusters have more delocalized electrons and occupy higher energy levels in the pyridine-metal complex. Accordingly, they produce larger polarizability, leading to a stronger nonresonant enhancement effect.
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Affiliation(s)
- Lei Chen
- Key Laboratory for Molecular Enzymology and Engineering of Ministry of Education, College of Life Sciences, Jilin University, Changchun, 130012, China and Institute of Atomic and Molecular Physics, Jilin University, Changchun, 130012, China
| | - Yang Gao
- Institute of Atomic and Molecular Physics, Jilin University, Changchun, 130012, China
| | - Yingkun Cheng
- Key Laboratory for Molecular Enzymology and Engineering of Ministry of Education, College of Life Sciences, Jilin University, Changchun, 130012, China
| | - Haichao Li
- Key Laboratory for Molecular Enzymology and Engineering of Ministry of Education, College of Life Sciences, Jilin University, Changchun, 130012, China
| | - Zhigang Wang
- Institute of Atomic and Molecular Physics, Jilin University, Changchun, 130012, China and Institute of Theoretical Chemistry, Jilin University, Changchun 130023, China
| | - Zhengqiang Li
- Key Laboratory for Molecular Enzymology and Engineering of Ministry of Education, College of Life Sciences, Jilin University, Changchun, 130012, China
| | - Rui-Qin Zhang
- Department of Physics and Materials Science and Centre for Functional Photonics (CFP), City University of Hong Kong, Hong Kong SAR, P. R. China and Beijing Computational Science Research Center, Beijing 100084, P. R. China.
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