1
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Dundas KHM, Beerepoot MTP, Ringholm M, Reine S, Bast R, List NH, Kongsted J, Ruud K, Olsen JMH. Harmonic Infrared and Raman Spectra in Molecular Environments Using the Polarizable Embedding Model. J Chem Theory Comput 2021; 17:3599-3617. [PMID: 34009969 PMCID: PMC8278393 DOI: 10.1021/acs.jctc.0c01323] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2020] [Indexed: 12/14/2022]
Abstract
We present a fully analytic approach to calculate infrared (IR) and Raman spectra of molecules embedded in complex molecular environments modeled using the fragment-based polarizable embedding (PE) model. We provide the theory for the calculation of analytic second-order geometric derivatives of molecular energies and first-order geometric derivatives of electric dipole moments and dipole-dipole polarizabilities within the PE model. The derivatives are implemented using a general open-ended response theory framework, thus allowing for an extension to higher-order derivatives. The embedding-potential parameters used to describe the environment in the PE model are derived through first-principles calculations, thus allowing a wide variety of systems to be modeled, including solvents, proteins, and other large and complex molecular environments. Here, we present proof-of-principle calculations of IR and Raman spectra of acetone in different solvents. This work is an important step toward calculating accurate vibrational spectra of molecules embedded in realistic environments.
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Affiliation(s)
- Karen
Oda Hjorth Minde Dundas
- Hylleraas
Centre for Quantum Molecular Sciences, Department of Chemistry, UiT The Arctic University of Norway, N-9037 Tromsø, Norway
| | - Maarten T. P. Beerepoot
- Hylleraas
Centre for Quantum Molecular Sciences, Department of Chemistry, UiT The Arctic University of Norway, N-9037 Tromsø, Norway
| | - Magnus Ringholm
- Hylleraas
Centre for Quantum Molecular Sciences, Department of Chemistry, UiT The Arctic University of Norway, N-9037 Tromsø, Norway
| | - Simen Reine
- Hylleraas
Centre for Quantum Molecular Sciences, Department of Chemistry, University of Oslo, N-0315 Oslo, Norway
| | - Radovan Bast
- Department
of Information Technology, UiT The Arctic
University of Norway, N-9037 Tromsø, Norway
| | - Nanna Holmgaard List
- Department
of Chemistry and the PULSE Institute, Stanford
University, 94305 Stanford, California, United States
- SLAC
National Accelerator Laboratory, 94025 Menlo Park, California, United States
| | - Jacob Kongsted
- Department
of Physics, Chemistry and Pharmacy, University
of Southern Denmark, DK-5230 Odense M, Denmark
| | - Kenneth Ruud
- Hylleraas
Centre for Quantum Molecular Sciences, Department of Chemistry, UiT The Arctic University of Norway, N-9037 Tromsø, Norway
| | - Jógvan Magnus Haugaard Olsen
- Hylleraas
Centre for Quantum Molecular Sciences, Department of Chemistry, UiT The Arctic University of Norway, N-9037 Tromsø, Norway
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2
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Pracht P, Grant DF, Grimme S. Comprehensive Assessment of GFN Tight-Binding and Composite Density Functional Theory Methods for Calculating Gas-Phase Infrared Spectra. J Chem Theory Comput 2020; 16:7044-7060. [PMID: 33054183 DOI: 10.1021/acs.jctc.0c00877] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
Vibrational spectroscopy is a valuable and widely used analytical tool for the characterization of chemical substances. We investigate the performance of semiempirical quantum mechanical GFN tight-binding and force-field methods for the calculation of gas-phase infrared spectra in comparison to experiment and low-cost (B3LYP-3c) density functional theory. A data set of 7247 experimental references was used to evaluate method performance based on automatic spectra comparison. Various quantitative spectral similarity measures were employed for the comparison between theory and experiment and for determining empirical scaling factors. It is shown that the scaling of atomic masses provides an accurate yet simple alternative to standard global frequency scaling in density functional theory (DFT) and semiempirical calculations. Furthermore, the method performance for 58 exemplary transition metal complexes was investigated. The efficient DFT composite method B3LYP-3c, that was introduced in the course of this work, was found to be excellently suited for general IR spectra calculations. The GFN1- and GFN2-xTB tight-binding methods clearly outperformed the PMx competitors. Conformational changes were investigated for a subset of the data and are found to have a mediocre strong influence on the simulated spectra suggesting that the corresponding elaborate sampling steps may be neglected in automated compound identification workflows.
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Affiliation(s)
- Philipp Pracht
- Mulliken Center for Theoretical Chemistry, Institute for Physical and Theoretical Chemistry, University of Bonn, Beringstrasse 4, 53115 Bonn, Germany
| | - David F Grant
- Department of Pharmaceutical Sciences, University of Connecticut, Storrs, Connecticut 06268, United States
| | - Stefan Grimme
- Mulliken Center for Theoretical Chemistry, Institute for Physical and Theoretical Chemistry, University of Bonn, Beringstrasse 4, 53115 Bonn, Germany
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3
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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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4
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Teodoro TQ, Koenis MAJ, Galembeck SE, Nicu VP, Buma WJ, Visscher L. Frequency Range Selection Method for Vibrational Spectra. J Phys Chem Lett 2018; 9:6878-6882. [PMID: 30449106 PMCID: PMC6287222 DOI: 10.1021/acs.jpclett.8b02963] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2018] [Accepted: 11/18/2018] [Indexed: 06/09/2023]
Abstract
Theoretical calculations of vibrational properties are widely used to explain and predict experimental spectra. However, with standard quantum chemical methods all molecular motions are considered, which is rather time-consuming for large molecules. Because typically only a specific spectral region is of experimental interest, we propose here an efficient method that allows calculation of only a selected frequency interval. After a computationally cheap low-level estimate of the molecular motions, the computational time is proportional to the number of normal modes needed to describe this frequency range. Results for a medium-sized molecule show a reduction in computational time of up to 1 order of magnitude with negligible loss in accuracy. We also show that still larger computational savings are possible by using an additional intensity-selection procedure.
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Affiliation(s)
- T. Q. Teodoro
- Amsterdam
Center for Multiscale Modeling, Faculty of Science, Vrije Universiteit Amsterdam, de Boelelaan 1083, 1081 HV Amsterdam, The Netherlands
- Departamento
de Química, FFCLRP, Universidade
de São Paulo, Av. Bandeirantes 3900, Ribeirão Preto, 14040-901 São Paulo, Brazil
| | - M. A. J. Koenis
- Van’t
Hoff Institute for Molecular Sciences, University
of Amsterdam, Science Park 904, 1098 XH Amsterdam, The Netherlands
| | - S. E. Galembeck
- Departamento
de Química, FFCLRP, Universidade
de São Paulo, Av. Bandeirantes 3900, Ribeirão Preto, 14040-901 São Paulo, Brazil
| | - V. P. Nicu
- Department
of Environmental Science, Physics, Physical Education and Sport, Lucian Blaga University of Sibiu, loan Ratiu Street, Nr. 7-9, 550012 Sibiu, Romania
| | - W. J. Buma
- Van’t
Hoff Institute for Molecular Sciences, University
of Amsterdam, Science Park 904, 1098 XH Amsterdam, The Netherlands
| | - L. Visscher
- Amsterdam
Center for Multiscale Modeling, Faculty of Science, Vrije Universiteit Amsterdam, de Boelelaan 1083, 1081 HV Amsterdam, The Netherlands
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5
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Zhang X. Large-scaleab initiocalculations of Raman scattering spectra within time-dependent density functional perturbation theory. J Chem Phys 2018; 148:244103. [DOI: 10.1063/1.5038112] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- Xu Zhang
- Department of Physics and Astronomy, California State University Northridge, Northridge, California 91330, USA
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6
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Costa GJ, Borin AC, Custodio R, Vidal LN. Fully Anharmonic Vibrational Resonance Raman Spectrum of Diatomic Systems. J Chem Theory Comput 2018; 14:843-855. [DOI: 10.1021/acs.jctc.7b01034] [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)
- Gustavo J. Costa
- Departamento Acadêmico de Química e Biologia, Universidade Tecnológica Federal do Paraná, Av. Dep. Heitor de Alencar Furtado, 5000, Curitiba/PR 81280-340, Brazil
| | - Antonio C. Borin
- Department of Fundamental Chemistry, Institute of Chemistry, University of São Paulo, NAP-Photo Tech the USP Consortium of Photochemical Technology, Av. Prof. Lineu Prestes, 748, São Paulo/SP 05508-000, Brazil
| | - Rogério Custodio
- Instituto de Química, Universidade Estadual de Campinas, R. Josué de Castro, 126, Campinas/SP 13083-970, Brazil
| | - Luciano N. Vidal
- Departamento Acadêmico de Química e Biologia, Universidade Tecnológica Federal do Paraná, Av. Dep. Heitor de Alencar Furtado, 5000, Curitiba/PR 81280-340, Brazil
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7
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Ma Y, Knecht S, Reiher M. Multiconfigurational Effects in Theoretical Resonance Raman Spectra. Chemphyschem 2017; 18:384-393. [PMID: 27933695 PMCID: PMC5324552 DOI: 10.1002/cphc.201601072] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2016] [Revised: 12/06/2016] [Indexed: 01/26/2023]
Abstract
We analyze resonance Raman spectra of the nucleobase uracil in the short‐time approximation calculated with multiconfigurational methods. We discuss the importance of static electron correlation by means of density‐matrix renormalization group self‐consistent field (DMRG‐SCF) calculations. Our DMRG‐SCF results reveal that a minimal active orbital space that leads to a qualitatively correct description of the resonance Raman spectrum of uracil should encompass parts of the σ/σ* bonding/anti‐bonding orbitals of the pyrimidine ring. We trace these findings back to the considerable entanglement between the σ/σ* bonding/anti‐bonding as well as valence π/π* orbitals in the excited‐state electronic structure of uracil, which indicates non‐negligible non‐dynamical correlation effects that are less pronounced in the electronic ground state.
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Affiliation(s)
- Yingjin Ma
- ETH Zürich, Laboratorium für Physikalische Chemie, Vladimir-Prelog-Weg 2, 8093, Zürich, Switzerland
| | - Stefan Knecht
- ETH Zürich, Laboratorium für Physikalische Chemie, Vladimir-Prelog-Weg 2, 8093, Zürich, Switzerland
| | - Markus Reiher
- ETH Zürich, Laboratorium für Physikalische Chemie, Vladimir-Prelog-Weg 2, 8093, Zürich, Switzerland
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8
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Abstract
Because of the size of polypeptides and proteins, the quantum-chemical prediction of their vibrational spectra presents an exceptionally challenging task. Here, we address one of these challenges, namely, the inclusion of anharmonicities. By performing the expansion of the potential energy surface in localized-mode coordinates instead of the normal-mode coordinates, it becomes possible to calculate anharmonic vibrational spectra of polypeptides efficiently and reliably. We apply this approach to calculate the infrared, Raman, and Raman optical activity spectra of helical alanine polypeptides consisting of up to 20 amino acids. We find that while anharmonicities do not alter the band shapes, simple scaling procedures cannot account for the different shifts found for the individual bands. This closes an important gap in theoretical vibrational spectroscopy by making it possible to quantify the anharmonic contributions and opens the door to a first-principles calculation of multidimensional vibrational spectra.
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Affiliation(s)
- Paweł T Panek
- Institute of Physical and Theoretical Chemistry, TU Braunschweig , Hans-Sommer-Str. 10, 38106 Braunschweig, Germany
| | - Christoph R Jacob
- Institute of Physical and Theoretical Chemistry, TU Braunschweig , Hans-Sommer-Str. 10, 38106 Braunschweig, Germany
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9
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Louant O, Champagne B, Liégeois V. Numerical differentiation method to calculate molecular properties at ground and excited states – Application to Julolidinemalononitrile. Chem Phys Lett 2015. [DOI: 10.1016/j.cplett.2015.06.014] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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10
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Barton D, König C, Neugebauer J. Vibronic-structure tracking: a shortcut for vibrationally resolved UV/Vis-spectra calculations. J Chem Phys 2015; 141:164115. [PMID: 25362280 DOI: 10.1063/1.4898665] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
The vibrational coarse structure and the band shapes of electronic absorption spectra are often dominated by just a few molecular vibrations. By contrast, the simulation of the vibronic structure even in the simplest theoretical models usually requires the calculation of the entire set of normal modes of vibration. Here, we exploit the idea of the mode-tracking protocol [M. Reiher and J. Neugebauer, J. Chem. Phys. 118, 1634 (2003)] in order to directly target and selectively calculate those normal modes which have the largest effect on the vibronic band shape for a certain electronic excitation. This is achieved by defining a criterion for the importance of a normal mode to the vibrational progressions in the absorption band within the so-called "independent mode, displaced harmonic oscillator" (IMDHO) model. We use this approach for a vibronic-structure investigation for several small test molecules as well as for a comparison of the vibronic absorption spectra of a truncated chlorophyll a model and the full chlorophyll a molecule. We show that the method allows to go beyond the often-used strategy to simulate absorption spectra based on broadened vertical excitation peaks with just a minimum of computational effort, which in case of chlorophyll a corresponds to about 10% of the cost for a full simulation within the IMDHO approach.
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Affiliation(s)
- Dennis Barton
- Theoretische Organische Chemie, Organisch-Chemisches Institut and Center for Multiscale Theory and Computation, Westfälische Wilhelms-Universität Münster, Corrensstraße 40, 48149 Münster, Germany
| | - Carolin König
- Theoretische Organische Chemie, Organisch-Chemisches Institut and Center for Multiscale Theory and Computation, Westfälische Wilhelms-Universität Münster, Corrensstraße 40, 48149 Münster, Germany
| | - Johannes Neugebauer
- Theoretische Organische Chemie, Organisch-Chemisches Institut and Center for Multiscale Theory and Computation, Westfälische Wilhelms-Universität Münster, Corrensstraße 40, 48149 Münster, Germany
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11
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Panek PT, Jacob CR. Efficient calculation of anharmonic vibrational spectra of large molecules with localized modes. Chemphyschem 2014; 15:3365-77. [PMID: 25080397 DOI: 10.1002/cphc.201402251] [Citation(s) in RCA: 57] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2014] [Indexed: 11/11/2022]
Abstract
The analysis and interpretation of the vibrational spectra of complex (bio)molecular systems, such as polypeptides and proteins, requires support from quantum-chemical calculations. Such calculations are currently restricted to the harmonic approximation. Here, we show how one of the main bottlenecks in such calculations, the evaluation of the potential energy surface, can be overcome by using localized modes instead of the commonly employed normal modes. We apply such local vibrational self-consistent field (L-VSCF) and vibrational configuration interaction (L-VCI) calculations to a cyclic water tetramer and a helical hexa-alanine peptide. The results show that the use of localized modes is equivalent to the commonly used normal modes, but offers several advantages. First, a faster convergence with respect to the excitation level is observed in L-VCI calculations. Second, the localized modes provide a reduced representation of the couplings between modes that show a regular coupling pattern. This can be used to disregard a significant number of small two-mode potentials a priori. Several such reduced coupling approximations are explored, and we show that the number of single-point calculations required to evaluate the potential energy surface can be significantly reduced without introducing noticeable errors in the resulting vibrational spectra.
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Affiliation(s)
- Paweł T Panek
- Karlsruhe Institute of Technology (KIT), Center for Functional Nanostructures and Institute of Physical Chemistry, Wolfgang-Gaede-Str. 1a, 76131 Karlsruhe (Germany) http://www.christophjacob.eu
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12
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Avila Ferrer FJ, Barone V, Cappelli C, Santoro F. Duschinsky, Herzberg–Teller, and Multiple Electronic Resonance Interferential Effects in Resonance Raman Spectra and Excitation Profiles. The Case of Pyrene. J Chem Theory Comput 2013; 9:3597-611. [DOI: 10.1021/ct400197y] [Citation(s) in RCA: 52] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Francisco J. Avila Ferrer
- Consiglio Nazionale delle Ricerche
− CNR, Istituto di Chimica dei Composti Organo Metallici (ICCOM-CNR), UOS di Pisa, Area della Ricerca, Via G. Moruzzi 1,
I-56124 Pisa, Italy
- Physical Chemistry, Faculty
of Science, University of Málaga, Málaga 29071, Spain
| | - Vincenzo Barone
- Scuola Normale Superiore di Pisa, Piazza dei Cavalieri 7, I-56126 Pisa,
Italy
| | - Chiara Cappelli
- Scuola Normale Superiore di Pisa, Piazza dei Cavalieri 7, I-56126 Pisa,
Italy
- Dipartimento di Chimica
e Chimica
Industriale dell’Università di Pisa, Via Risorgimento 35, I-56126 Pisa, Italy
| | - Fabrizio Santoro
- Consiglio Nazionale delle Ricerche
− CNR, Istituto di Chimica dei Composti Organo Metallici (ICCOM-CNR), UOS di Pisa, Area della Ricerca, Via G. Moruzzi 1,
I-56124 Pisa, Italy
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13
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dos Santos MVP, Aguiar EC, da Silva JBP, Longo RL. PICVib: an accurate, fast, and simple procedure to investigate selected vibrational modes at high theoretical levels. J Comput Chem 2013; 34:611-21. [PMID: 23175235 DOI: 10.1002/jcc.23166] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2012] [Revised: 08/22/2012] [Accepted: 09/30/2012] [Indexed: 11/09/2022]
Abstract
A new approach Procedure for Investigating Categories of Vibrations (PICVib) for estimating vibrational frequencies of selected modes using only the structure and energy calculations at a more demanding computational level is presented and explored. The PICVib has an excellent performance at only a small fraction of the computational demand required for a complete analytical calculation. The errors are smaller than ca. 0.5% when DFT functionals are combined with high level ab initio methods. The approach is general because it can use any quantum chemical program and electronic structure method. It is very robust because it was validated for a wide range of frequency values (ca. 20-4800 cm(-1)) and systems: XH(3) (D(3h) ) with X = B, Al, Ga, N, P, As, O, S, and Se, YH(4) (D(4h) ) with Y = C, Si, and Ge, conformers of RDX, S(N) 2 and E2 reactions, [W(dppe)(2)(NNC(5)H(10))] complex, carbon nanotubes, and hydrogen-bonded complexes including guanine-cytosine pair.
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Affiliation(s)
- Marcus V P dos Santos
- Centro de Ciências Exatas e da Natureza, Universidade Federal de Pernambuco, Cidade Universitária, Recife-PE, Brazil
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14
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Huh J, Berger R. Coherent state-based generating function approach for Franck–Condon transitions and beyond. ACTA ACUST UNITED AC 2012. [DOI: 10.1088/1742-6596/380/1/012019] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
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15
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Weymuth T, Haag MP, Kiewisch K, Luber S, Schenk S, Jacob CR, Herrmann C, Neugebauer J, Reiher M. MOVIPAC: Vibrational spectroscopy with a robust meta-program for massively parallel standard and inverse calculations. J Comput Chem 2012; 33:2186-98. [DOI: 10.1002/jcc.23036] [Citation(s) in RCA: 53] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2012] [Revised: 05/16/2012] [Accepted: 05/19/2012] [Indexed: 11/08/2022]
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16
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Champagne B, Plaquet A, Pozzo JL, Rodriguez V, Castet F. Nonlinear Optical Molecular Switches as Selective Cation Sensors. J Am Chem Soc 2012; 134:8101-3. [DOI: 10.1021/ja302395f] [Citation(s) in RCA: 234] [Impact Index Per Article: 19.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Affiliation(s)
- Benoît Champagne
- Laboratoire de Chimie Théorique,
UCPTS, Facultés Universitaires Notre-Dame de la Paix (FUNDP),
rue de Bruxelles 61, B-5000 Namur, Belgium
| | - Aurélie Plaquet
- Laboratoire de Chimie Théorique,
UCPTS, Facultés Universitaires Notre-Dame de la Paix (FUNDP),
rue de Bruxelles 61, B-5000 Namur, Belgium
| | - Jean-Luc Pozzo
- Université de Bordeaux,
Institut des Sciences Moléculaires (ISM), UMR 5255 CNRS, Cours
de la Libération, 351, F-33405 Talence CEDEX, France
| | - Vincent Rodriguez
- Université de Bordeaux,
Institut des Sciences Moléculaires (ISM), UMR 5255 CNRS, Cours
de la Libération, 351, F-33405 Talence CEDEX, France
| | - Frédéric Castet
- Université de Bordeaux,
Institut des Sciences Moléculaires (ISM), UMR 5255 CNRS, Cours
de la Libération, 351, F-33405 Talence CEDEX, France
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17
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Rokob TA, Srnec M, Rulíšek L. Theoretical calculations of physico-chemical and spectroscopic properties of bioinorganic systems: current limits and perspectives. Dalton Trans 2012; 41:5754-68. [DOI: 10.1039/c2dt12423h] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
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18
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Bieler NS, Haag MP, Jacob CR, Reiher M. Analysis of the Cartesian Tensor Transfer Method for Calculating Vibrational Spectra of Polypeptides. J Chem Theory Comput 2011; 7:1867-81. [DOI: 10.1021/ct2001478] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Noah S. Bieler
- ETH Zurich, Laboratorium für Physikalische Chemie, Wolfgang-Pauli-Strasse 10, 8093 Zurich, Switzerland
| | - Moritz P. Haag
- ETH Zurich, Laboratorium für Physikalische Chemie, Wolfgang-Pauli-Strasse 10, 8093 Zurich, Switzerland
| | - Christoph R. Jacob
- Karlsruhe Institute of Technology (KIT), Center for Functional Nanostructures, Wolfgang-Gaede-Str. 1a, 76131 Karlsruhe, Germany
| | - Markus Reiher
- ETH Zurich, Laboratorium für Physikalische Chemie, Wolfgang-Pauli-Strasse 10, 8093 Zurich, Switzerland
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19
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Santoro F, Cappelli C, Barone V. Effective Time-Independent Calculations of Vibrational Resonance Raman Spectra of Isolated and Solvated Molecules Including Duschinsky and Herzberg–Teller Effects. J Chem Theory Comput 2011; 7:1824-39. [DOI: 10.1021/ct200054w] [Citation(s) in RCA: 71] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Fabrizio Santoro
- CNR−Consiglio Nazionale delle Ricerche, Istituto di Chimica dei Composti Organo Metallici (ICCOM-CNR), UOS di Pisa, Area della Ricerca, via G. Moruzzi 1, I-56124 Pisa, Italy
| | - Chiara Cappelli
- CNR−Consiglio Nazionale delle Ricerche, Istituto di Chimica dei Composti Organo Metallici (ICCOM-CNR), UOS di Pisa, Area della Ricerca, via G. Moruzzi 1, I-56124 Pisa, Italy
- Dipartimento di Chimica e Chimica Industriale, Università di Pisa, via Risorgimento, 35 I-56126 Pisa, Italy
| | - Vincenzo Barone
- CNR−Consiglio Nazionale delle Ricerche, Istituto di Chimica dei Composti Organo Metallici (ICCOM-CNR), UOS di Pisa, Area della Ricerca, via G. Moruzzi 1, I-56124 Pisa, Italy
- Scuola Normale Superiore, Piazza dei Cavalieri, 7 I-56126 Pisa, Italy
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20
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Luber S, Neugebauer J, Reiher M. Enhancement and de-enhancement effects in vibrational resonance Raman optical activity. J Chem Phys 2010; 132:044113. [DOI: 10.1063/1.3300069] [Citation(s) in RCA: 52] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
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21
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Botek E, d'Antuono P, Jacques A, Carion R, Champagne B, Maton L, Taziaux D, Habib-Jiwan JL. Theoretical and experimental investigation of the structural and spectroscopic properties of coumarin 343 fluoroionophores. Phys Chem Chem Phys 2010; 12:14172-87. [DOI: 10.1039/c003514a] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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22
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Neugebauer J. Subsystem-Based Theoretical Spectroscopy of Biomolecules and Biomolecular Assemblies. Chemphyschem 2009; 10:3148-73. [DOI: 10.1002/cphc.200900538] [Citation(s) in RCA: 83] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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23
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Guthmuller J, Champagne B, Moucheron C, Kirsch - De Mesmaeker A. Investigation of the Resonance Raman Spectra and Excitation Profiles of a Monometallic Ruthenium(II) [Ru(bpy)2(HAT)]2+ Complex by Time-Dependent Density Functional Theory. J Phys Chem B 2009; 114:511-20. [DOI: 10.1021/jp908154q] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Julien Guthmuller
- Laboratoire de Chimie Théorique, Facultés Universitaires Notre-Dame de la Paix (FUNDP), Rue de Bruxelles 61, B-5000 Namur, Belgium, and Service de Chimie Organique et Photochimie, Université Libre de Bruxelles, Avenue F. D. Roosevelt 50, CP 160/08, B-1050 Bruxelles, Belgium
| | - Benoît Champagne
- Laboratoire de Chimie Théorique, Facultés Universitaires Notre-Dame de la Paix (FUNDP), Rue de Bruxelles 61, B-5000 Namur, Belgium, and Service de Chimie Organique et Photochimie, Université Libre de Bruxelles, Avenue F. D. Roosevelt 50, CP 160/08, B-1050 Bruxelles, Belgium
| | - Cécile Moucheron
- Laboratoire de Chimie Théorique, Facultés Universitaires Notre-Dame de la Paix (FUNDP), Rue de Bruxelles 61, B-5000 Namur, Belgium, and Service de Chimie Organique et Photochimie, Université Libre de Bruxelles, Avenue F. D. Roosevelt 50, CP 160/08, B-1050 Bruxelles, Belgium
| | - Andrée Kirsch - De Mesmaeker
- Laboratoire de Chimie Théorique, Facultés Universitaires Notre-Dame de la Paix (FUNDP), Rue de Bruxelles 61, B-5000 Namur, Belgium, and Service de Chimie Organique et Photochimie, Université Libre de Bruxelles, Avenue F. D. Roosevelt 50, CP 160/08, B-1050 Bruxelles, Belgium
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Luber S, Reiher M. Intensity-Carrying Modes in Raman and Raman Optical Activity Spectroscopy. Chemphyschem 2009; 10:2049-57. [DOI: 10.1002/cphc.200900255] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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25
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Guthmuller J, Cecchet F, Lis D, Caudano Y, Mani AA, Thiry PA, Peremans A, Champagne B. Theoretical Simulation of Vibrational Sum-Frequency Generation Spectra from Density Functional Theory: Application top-Nitrothiophenol and 2,4-Dinitroaniline. Chemphyschem 2009; 10:2132-42. [DOI: 10.1002/cphc.200900184] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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26
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Witlicki EH, Hansen SW, Christensen M, Hansen TS, Nygaard SD, Jeppesen JO, Wong EW, Jensen L, Flood AH. Determination of Binding Strengths of a Host−Guest Complex Using Resonance Raman Scattering. J Phys Chem A 2009; 113:9450-7. [DOI: 10.1021/jp905202x] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Affiliation(s)
- Edward H. Witlicki
- Chemistry Department, Indiana University, 800 East Kirkwood Avenue, Bloomington, Indiana 47405, Department of Physics and Chemistry, University of Southern Denmark, Odense University, Campusvej 55, 5230 Odense M, Denmark, Atomate Corporation, 2665-D Park Center Drive, Simi Valley, California 93065, and Department of Chemistry, The Pennsylvania State University, 104 Chemistry Building, University Park, Pennsylvania 16802
| | - Stinne W. Hansen
- Chemistry Department, Indiana University, 800 East Kirkwood Avenue, Bloomington, Indiana 47405, Department of Physics and Chemistry, University of Southern Denmark, Odense University, Campusvej 55, 5230 Odense M, Denmark, Atomate Corporation, 2665-D Park Center Drive, Simi Valley, California 93065, and Department of Chemistry, The Pennsylvania State University, 104 Chemistry Building, University Park, Pennsylvania 16802
| | - Martin Christensen
- Chemistry Department, Indiana University, 800 East Kirkwood Avenue, Bloomington, Indiana 47405, Department of Physics and Chemistry, University of Southern Denmark, Odense University, Campusvej 55, 5230 Odense M, Denmark, Atomate Corporation, 2665-D Park Center Drive, Simi Valley, California 93065, and Department of Chemistry, The Pennsylvania State University, 104 Chemistry Building, University Park, Pennsylvania 16802
| | - Thomas S. Hansen
- Chemistry Department, Indiana University, 800 East Kirkwood Avenue, Bloomington, Indiana 47405, Department of Physics and Chemistry, University of Southern Denmark, Odense University, Campusvej 55, 5230 Odense M, Denmark, Atomate Corporation, 2665-D Park Center Drive, Simi Valley, California 93065, and Department of Chemistry, The Pennsylvania State University, 104 Chemistry Building, University Park, Pennsylvania 16802
| | - Sune D. Nygaard
- Chemistry Department, Indiana University, 800 East Kirkwood Avenue, Bloomington, Indiana 47405, Department of Physics and Chemistry, University of Southern Denmark, Odense University, Campusvej 55, 5230 Odense M, Denmark, Atomate Corporation, 2665-D Park Center Drive, Simi Valley, California 93065, and Department of Chemistry, The Pennsylvania State University, 104 Chemistry Building, University Park, Pennsylvania 16802
| | - Jan O. Jeppesen
- Chemistry Department, Indiana University, 800 East Kirkwood Avenue, Bloomington, Indiana 47405, Department of Physics and Chemistry, University of Southern Denmark, Odense University, Campusvej 55, 5230 Odense M, Denmark, Atomate Corporation, 2665-D Park Center Drive, Simi Valley, California 93065, and Department of Chemistry, The Pennsylvania State University, 104 Chemistry Building, University Park, Pennsylvania 16802
| | - Eric W. Wong
- Chemistry Department, Indiana University, 800 East Kirkwood Avenue, Bloomington, Indiana 47405, Department of Physics and Chemistry, University of Southern Denmark, Odense University, Campusvej 55, 5230 Odense M, Denmark, Atomate Corporation, 2665-D Park Center Drive, Simi Valley, California 93065, and Department of Chemistry, The Pennsylvania State University, 104 Chemistry Building, University Park, Pennsylvania 16802
| | - Lasse Jensen
- Chemistry Department, Indiana University, 800 East Kirkwood Avenue, Bloomington, Indiana 47405, Department of Physics and Chemistry, University of Southern Denmark, Odense University, Campusvej 55, 5230 Odense M, Denmark, Atomate Corporation, 2665-D Park Center Drive, Simi Valley, California 93065, and Department of Chemistry, The Pennsylvania State University, 104 Chemistry Building, University Park, Pennsylvania 16802
| | - Amar H. Flood
- Chemistry Department, Indiana University, 800 East Kirkwood Avenue, Bloomington, Indiana 47405, Department of Physics and Chemistry, University of Southern Denmark, Odense University, Campusvej 55, 5230 Odense M, Denmark, Atomate Corporation, 2665-D Park Center Drive, Simi Valley, California 93065, and Department of Chemistry, The Pennsylvania State University, 104 Chemistry Building, University Park, Pennsylvania 16802
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27
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Jacob CR, Luber S, Reiher M. Analysis of Secondary Structure Effects on the IR and Raman Spectra of Polypeptides in Terms of Localized Vibrations. J Phys Chem B 2009; 113:6558-73. [DOI: 10.1021/jp900354g] [Citation(s) in RCA: 68] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Christoph R. Jacob
- ETH Zurich, Laboratorium für Physikalische Chemie, Wolfgang-Pauli-Strasse 10, 8093 Zurich, Switzerland
| | - Sandra Luber
- ETH Zurich, Laboratorium für Physikalische Chemie, Wolfgang-Pauli-Strasse 10, 8093 Zurich, Switzerland
| | - Markus Reiher
- ETH Zurich, Laboratorium für Physikalische Chemie, Wolfgang-Pauli-Strasse 10, 8093 Zurich, Switzerland
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28
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29
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Luber S, Neugebauer J, Reiher M. Intensity tracking for theoretical infrared spectroscopy of large molecules. J Chem Phys 2009; 130:064105. [DOI: 10.1063/1.3069834] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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