1
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Niemeyer N, Caricato M, Neugebauer J. Origin invariant electronic circular dichroism in the length dipole gauge without London atomic orbitals. J Chem Phys 2022; 156:154114. [PMID: 35459317 DOI: 10.1063/5.0088922] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
We present a method for obtaining origin-independent electronic circular dichroism (ECD) in the length-gauge representation LG(OI) without the usage of London atomic orbitals. This approach builds upon the work by Caricato [J. Chem. Phys. 153, 151101 (2020)] and is applied to rotatory strengths and ECD spectra from damped response theory. Numerical results are presented for time-dependent Hartree-Fock and density-functional theory, the second-order algebraic diagrammatic construction method, and linear-response coupled-cluster theory with singles and approximate doubles. We can support the finding that the common choice of placing the gauge origin in the center of mass of a molecule in conventional length-gauge calculations involving chiroptical properties might not be optimal and show that LG(OI) is a valuable alternative for the origin-independent calculation of ECD spectra. We show that, for a limited test set, the convergence of the rotatory strengths calculated with the LG(OI) approach toward the basis-set limit tends to be faster than for the established velocity gauge representation. Relationships between the sum-over-states expression of the optical rotation in the LG(OI) framework and its representation in terms of response functions are analyzed.
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Affiliation(s)
- Niklas Niemeyer
- Theoretische Organische Chemie, Organisch-Chemisches Institut and Center for Multiscale Theory and Computation, Westfälische Wilhelms-Universität Münster, Corrensstraße 40, 48149 Münster, Germany
| | - Marco Caricato
- Department of Chemistry, University of Kansas, Lawrence, Kansas 66045, USA
| | - 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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2
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Ozcelik A, Pereira R, Peña-Gallego Á, Alonso Gómez JL. A Tetracyanobutadiene Spirobifluorene: Synthesis, Enantiomeric Resolution and Chiroptical Properties. European J Org Chem 2022. [DOI: 10.1002/ejoc.202101333] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Affiliation(s)
- Ani Ozcelik
- University of Vigo - Lagoas Marcosende Campus: Universidade de Vigo Organic Chemistry SPAIN
| | - Raquel Pereira
- University of Vigo - Lagoas Marcosende Campus: Universidade de Vigo Organic Chemistry SPAIN
| | - Ángeles Peña-Gallego
- University of Vigo - Lagoas Marcosende Campus: Universidade de Vigo Physical Chemistry SPAIN
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3
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Scott M, Rehn DR, Coriani S, Norman P, Dreuw A. Electronic circular dichroism spectra using the algebraic diagrammatic construction schemes of the polarization propagator up to third order. J Chem Phys 2021; 154:064107. [DOI: 10.1063/5.0038315] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023] Open
Affiliation(s)
- Mikael Scott
- Interdisciplinary Center for Scientific Computing, Ruprecht-Karls University, Im Neuenheimer Feld 205, 69120 Heidelberg, Germany
| | - Dirk R. Rehn
- Interdisciplinary Center for Scientific Computing, Ruprecht-Karls University, Im Neuenheimer Feld 205, 69120 Heidelberg, Germany
| | - Sonia Coriani
- DTU Chemistry, Technical University of Denmark, Kemitorvet Bldg. 207, DK-2800 Kongens Lyngby, Denmark
| | - Patrick Norman
- Department of Theoretical Chemistry and Biology, School of Engineering Sciences in Chemistry, Biotechnology and Health, KTH Royal Institute of Technology, SE-106 91 Stockholm, Sweden
| | - Andreas Dreuw
- Interdisciplinary Center for Scientific Computing, Ruprecht-Karls University, Im Neuenheimer Feld 205, 69120 Heidelberg, Germany
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4
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Uudsemaa M, Trummal A, de Reguardati S, Callis PR, Rebane A. TD-DFT calculations of one- and two-photon absorption in Coumarin C153 and Prodan: attuning theory to experiment. Phys Chem Chem Phys 2018; 19:28824-28833. [PMID: 29052672 DOI: 10.1039/c7cp04735e] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
We use TD-DFT to calculate the one-photon absorption (1PA) and two-photon absorption (2PA) properties of C153 and Prodan in toluene and DMSO, and benchmark different methods relative to accurate experimental data available from the literature on these particular systems. As the first step, we modify the range-separated TD-DFT to provide the best prediction for the peak 1PA wavelength, and then apply the optimized functionals to achieve quantitative predictions of the corresponding two-photon absorption cross section, σ2PA, with an accuracy ∼10-20% in C153 and ∼20-30% in Prodan. To elucidate the origin of residual discrepancies between the theory and experimental observations, we invoked the two essential states model for σ2PA, which allows us to verify not only the transition wavelength and the σ2PA value, but also to quantitatively benchmark the calculation of key molecular parameters such as the transition dipole moment and the change of the permanent dipole moment. Such comprehensive cross-checking indicates that a larger discrepancy in Prodan is most likely caused by a noted failure of DFT to predict the relative intensity and relative ordering of closely lying excited states with different degrees of intramolecular charge transfer, which we further support by analyzing the predictions obtained by high-level coupled-cluster calculations in the gas phase. Our results highlight the utility of benchmarking the calculations not only relative to other theoretical methods, but also in comparison to the experimental measurements, wherever such data are available.
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Affiliation(s)
- Merle Uudsemaa
- Laboratory of Chemical Physics, National Institute of Chemical Physics and Biophysics, 23 Akadeemia tee, Tallinn 12618, Estonia
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5
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Komjáti B, Urai Á, Hosztafi S, Kökösi J, Kováts B, Nagy J, Horváth P. Systematic study on the TD-DFT calculated electronic circular dichroism spectra of chiral aromatic nitro compounds: A comparison of B3LYP and CAM-B3LYP. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2016; 155:95-102. [PMID: 26583523 DOI: 10.1016/j.saa.2015.11.002] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/22/2015] [Revised: 10/05/2015] [Accepted: 11/01/2015] [Indexed: 06/05/2023]
Abstract
B3LYP is one of the most widely used functional for the prediction of electronic circular dichroism spectra, however if the studied molecule contains aromatic nitro group computations may fail to produce reliable results. A test set of molecules of known stereochemistry were synthesized to study this phenomenon in detail. Spectra were computed by B3LYP and CAM-B3LYP functionals with 6-311++G(2d,2p) basis set. It was found that the range separated CAM-B3LYP gives better predictions than B3LYP for all test molecules. Fragment population analysis revealed that the nitro groups form highly localized molecule orbitals but the exact composition depends on the functional. CAM-B3LYP allows sufficient spatial overlap between the nitro group and distant parts of the molecule, which is necessary for the accurate description of excited states especially for charge transfer states. This phenomenon and the synthesized test molecules can be used to benchmark theoretical methods as well as to help the development of new functionals intended for spectroscopical studies.
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Affiliation(s)
- Balázs Komjáti
- Department of Organic Chemistry and Technology, Budapest University of Technology and Economics, Szent Gellért tér 4, Budapest 1111, Hungary.
| | - Ákos Urai
- Department of Pharmaceutical Chemistry, Semmelweis University, Hőgyes Endre utca 7, Budapest 1092, Hungary
| | - Sándor Hosztafi
- Department of Pharmaceutical Chemistry, Semmelweis University, Hőgyes Endre utca 7, Budapest 1092, Hungary
| | - József Kökösi
- Department of Pharmaceutical Chemistry, Semmelweis University, Hőgyes Endre utca 7, Budapest 1092, Hungary
| | - Benjámin Kováts
- Department of Organic Chemistry and Technology, Budapest University of Technology and Economics, Szent Gellért tér 4, Budapest 1111, Hungary
| | - József Nagy
- Department of Organic Chemistry and Technology, Budapest University of Technology and Economics, Szent Gellért tér 4, Budapest 1111, Hungary
| | - Péter Horváth
- Department of Pharmaceutical Chemistry, Semmelweis University, Hőgyes Endre utca 7, Budapest 1092, Hungary
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6
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Haghdani S, Åstrand PO, Koch H. Optical Rotation from Coupled Cluster and Density Functional Theory: The Role of Basis Set Convergence. J Chem Theory Comput 2016; 12:535-48. [DOI: 10.1021/acs.jctc.5b00721] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Shokouh Haghdani
- Department
of Chemistry, Norwegian University of Science and Technology (NTNU), N-7491 Trondheim, Norway
| | - Per-Olof Åstrand
- Department
of Chemistry, Norwegian University of Science and Technology (NTNU), N-7491 Trondheim, Norway
| | - Henrik Koch
- Department
of Chemistry, Norwegian University of Science and Technology (NTNU), N-7491 Trondheim, Norway
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7
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Møller KH, Hansen AS, Kjaergaard HG. Gas Phase Detection of the NH-P Hydrogen Bond and Importance of Secondary Interactions. J Phys Chem A 2015; 119:10988-98. [PMID: 26451467 DOI: 10.1021/acs.jpca.5b08358] [Citation(s) in RCA: 49] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
We have observed the NH···P hydrogen bond in a gas phase complex. The bond is identified in the dimethylamine-trimethylphosphine complex by a red shift of the fundamental NH-stretching frequency observed using Fourier transform infrared spectroscopy (FT-IR). On the basis of the measured NH-stretching frequency red shifts, we find that P is a hydrogen bond acceptor atom similar in strength to S. Both are stronger acceptors than O and significantly weaker acceptors than N. The hydrogen bond angle, ∠NHP, is found to be very sensitive to the functional employed in density functional theory (DFT) optimizations of the complex and is a possible parameter to assess the quality of DFT functionals. Natural bonding orbital (NBO) energies and results from the topological methods atoms in molecules (AIM) and noncovalent interactions (NCI) indicate that the sensitivity is caused by the weakness of the hydrogen bond compared to secondary interactions. We find that B3LYP favors the hydrogen bond and M06-2X favors the secondary interactions leading to under- and overestimation, respectively, of the hydrogen bond angle relative to a DF-LCCSD(T)-F12a calculated angle. The remaining functionals tested, B3LYP-D3, B3LYP-D3BJ, CAM-B3LYP, and ωB97X-D, as well as MP2, show comparable contributions from the hydrogen bond and the secondary interactions and are close to DF-LCCSD(T)-F12a results.
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Affiliation(s)
- Kristian H Møller
- Department of Chemistry, University of Copenhagen , Universitetsparken 5, DK-2100 Copenhagen Ø, Denmark
| | - Anne S Hansen
- Department of Chemistry, University of Copenhagen , Universitetsparken 5, DK-2100 Copenhagen Ø, Denmark
| | - Henrik G Kjaergaard
- Department of Chemistry, University of Copenhagen , Universitetsparken 5, DK-2100 Copenhagen Ø, Denmark
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8
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Berardozzi R, Guido CA, Capozzi MAM, Cardellicchio C, Di Bari L, Pescitelli G. Circular Dichroism and TDDFT Investigation of Chiral Fluorinated Aryl Benzyl Sulfoxides. European J Org Chem 2015. [DOI: 10.1002/ejoc.201500648] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
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9
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Pikulska A, Steindal AH, Beerepoot MTP, Pecul M. Electronic Circular Dichroism of Fluorescent Proteins: A Computational Study. J Phys Chem B 2015; 119:3377-86. [DOI: 10.1021/jp511199g] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Affiliation(s)
- Anna Pikulska
- Faculty
of Chemistry, University of Warsaw, Pasteura 1, 02-093 Warszawa, Poland
| | - Arnfinn Hykkerud Steindal
- Centre
for Theoretical and Computational Chemistry, Department of Chemistry, University of Tromsø−The Arctic University of Norway, N-9037 Tromsø, Norway
| | - Maarten T. P. Beerepoot
- Centre
for Theoretical and Computational Chemistry, Department of Chemistry, University of Tromsø−The Arctic University of Norway, N-9037 Tromsø, Norway
| | - Magdalena Pecul
- Faculty
of Chemistry, University of Warsaw, Pasteura 1, 02-093 Warszawa, Poland
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10
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Jorge FE, Jorge SS, Suave RN. Electronic circular dichroism of chiral alkenes: B3LYP and CAM-B3LYP calculations. Chirality 2014; 27:23-31. [PMID: 25283773 DOI: 10.1002/chir.22384] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2014] [Accepted: 08/02/2014] [Indexed: 11/07/2022]
Abstract
Time-dependent density functional theory (TDDFT) calculations of electronic circular dichroism (ECD) are widely used to determine absolute configurations (ACs) of chiral molecules. Two very popular DFT exchange-correlation functionals, one hybrid (B3LYP) and one long-range corrected (CAM-B3LYP), along with a hierarchical sequence of basis sets were investigated, and the ECD spectra predicted for eight alkenes and compared to gas-phase experimental spectra. Little variation in predicted ECD spectra was found with the basis set size enlargement, but the sensitivity to the functional is greater. Good agreement was obtained only with the CAM-B3LYP functional, leading to the conclusion that TDDFT calculations of ECD spectra can routinely provide reliable ACs if and only if an appropriate functional is used. For camphene, twistene, syn-(E)-bisfenchylidene, and phyllocladene, solvent effects were estimated.
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Affiliation(s)
- Francisco E Jorge
- Departamento de Física, Universidade Federal do Espírito Santo, Vitória, Brazil
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11
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Alam MM, Chattopadhyaya M, Chakrabarti S, Rizzo A. On the origin of the very strong two-photon activity of squaraine dyes – a standard/damped response theory study. Phys Chem Chem Phys 2014; 16:8030-5. [DOI: 10.1039/c3cp55485f] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
In the present work, we report the mechanism of a very large increase in the two-photon (TP) activity of squaraine based molecules upon changing the substituents.
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Affiliation(s)
- Md. Mehboob Alam
- Department of Chemistry
- University of Calcutta
- Kolkata-700 009, India
| | | | | | - Antonio Rizzo
- Istituto per i Processi Chimico-Fisici del Consiglio Nazionale delle Ricerche (IPCF-CNR)
- Area della Ricerca
- I-56124 Pisa, Italy
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12
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Zanna N, Monari A, Assfeld X. Theoretical Study of the Absorption Spectrum of a Photoisomerizable Iron Complex. J Phys Chem A 2012; 116:11905-12. [DOI: 10.1021/jp310171r] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Affiliation(s)
- Nicola Zanna
- Dipartimento di Chimica Organica
A. Mangini, Università di Bologna, Viale Risorgimento 4, 40136 Bologna, Italy
| | - Antonio Monari
- Université de Lorraine Nancy, Théorie Modélisation
Simulations, Photosens Laboratoire SRSMC, Boulevard des Aiguillettes,
54506 Vandoeuvre-lès-Nancy, France
- CNRS, Théorie Modélisation
Simulations, Photosens Laboratoire
SRSMC, Boulevard des Aiguillettes, 54506 Vandoeuvre-lès-Nancy,
France
| | - Xavier Assfeld
- Université de Lorraine Nancy, Théorie Modélisation
Simulations, Photosens Laboratoire SRSMC, Boulevard des Aiguillettes,
54506 Vandoeuvre-lès-Nancy, France
- CNRS, Théorie Modélisation
Simulations, Photosens Laboratoire
SRSMC, Boulevard des Aiguillettes, 54506 Vandoeuvre-lès-Nancy,
France
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13
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Lachaud F, Jeandon C, Beley M, Ruppert R, Gros PC, Monari A, Assfeld X. Ground and Excited State Properties of New Porphyrin Based Dyads: A Combined Theoretical and Experimental Study. J Phys Chem A 2012; 116:10736-44. [DOI: 10.1021/jp307452d] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Affiliation(s)
| | - Christophe Jeandon
- Laboratoire CLAC, UMR 7177 du
CNRS, Université de Strasbourg,
1 rue Blaise Pascal, BP 296 R8, 67008 Strasbourg Cedex, France
| | | | - Romain Ruppert
- Laboratoire CLAC, UMR 7177 du
CNRS, Université de Strasbourg,
1 rue Blaise Pascal, BP 296 R8, 67008 Strasbourg Cedex, France
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14
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Padula D, Di Bari L, Santoro F, Gerlach H, Rizzo A. Analysis of the Electronic Circular Dichroism Spectrum of (−)-[9](2,5)Pyridinophane. Chirality 2012; 24:994-1004. [DOI: 10.1002/chir.22087] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2012] [Accepted: 05/30/2012] [Indexed: 12/28/2022]
Affiliation(s)
- Daniele Padula
- Dipartimento di Chimica e Chimica Industriale; Università di Pisa; Pisa Italy
| | - Lorenzo Di Bari
- Dipartimento di Chimica e Chimica Industriale; Università di Pisa; Pisa Italy
| | - Fabrizio Santoro
- Consiglio Nazionale delle Ricerche - CNR; Istituto di Chimica dei Composti Organo Metallici (ICCOM-CNR), UOS di Pisa, Area della Ricerca; Pisa Italy
| | - Hans Gerlach
- Department of Chemistry; University of Bayreuth; Bayreuth Germany
| | - Antonio Rizzo
- Consiglio Nazionale delle Ricerche - CNR; Istituto per i Processi Chimico-Fisici (IPCF-CNR); Pisa Italy
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15
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Elm J, Lykkebo J, Sørensen TJ, Laursen BW, Mikkelsen KV. Obtaining Enhanced Circular Dichroism in [4]Heterohelicenium Analogues. J Phys Chem A 2012; 116:8744-52. [DOI: 10.1021/jp304997b] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Affiliation(s)
- Jonas Elm
- Department
of Chemistry and ‡Nano Science Center, H. C. Ørsted Institute, University of Copenhagen, Universitetsparken 5, DK-2100
Copenhagen, Denmark
| | - Jacob Lykkebo
- Department
of Chemistry and ‡Nano Science Center, H. C. Ørsted Institute, University of Copenhagen, Universitetsparken 5, DK-2100
Copenhagen, Denmark
| | - Thomas J. Sørensen
- Department
of Chemistry and ‡Nano Science Center, H. C. Ørsted Institute, University of Copenhagen, Universitetsparken 5, DK-2100
Copenhagen, Denmark
| | - Bo W. Laursen
- Department
of Chemistry and ‡Nano Science Center, H. C. Ørsted Institute, University of Copenhagen, Universitetsparken 5, DK-2100
Copenhagen, Denmark
| | - Kurt V. Mikkelsen
- Department
of Chemistry and ‡Nano Science Center, H. C. Ørsted Institute, University of Copenhagen, Universitetsparken 5, DK-2100
Copenhagen, Denmark
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16
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Arulmozhiraja S, Coote ML. 1La and 1Lb States of Indole and Azaindole: Is Density Functional Theory Inadequate? J Chem Theory Comput 2012; 8:575-84. [DOI: 10.1021/ct200768b] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Sundaram Arulmozhiraja
- ARC Centre of Excellence for Free- Radical Chemistry and Biotechnology, Research School of Chemistry, Australian National University, Canberra, 0200 ACT, Australia
| | - Michelle L. Coote
- ARC Centre of Excellence for Free- Radical Chemistry and Biotechnology, Research School of Chemistry, Australian National University, Canberra, 0200 ACT, Australia
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17
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Hopmann KH, Šebestík J, Novotná J, Stensen W, Urbanová M, Svenson J, Svendsen JS, Bouř P, Ruud K. Determining the Absolute Configuration of Two Marine Compounds Using Vibrational Chiroptical Spectroscopy. J Org Chem 2012; 77:858-69. [DOI: 10.1021/jo201598x] [Citation(s) in RCA: 63] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
| | - Jaroslav Šebestík
- Institute of Organic Chemistry
and Biochemistry, Academy of Sciences, Flemingovo nám. 2, 166
10 Prague, Czech Republic
| | | | - Wenche Stensen
- Lytix Biopharma AS, Tromsø Research
Park, N-9294 Tromsø, Norway
| | | | | | | | - Petr Bouř
- Institute of Organic Chemistry
and Biochemistry, Academy of Sciences, Flemingovo nám. 2, 166
10 Prague, Czech Republic
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18
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Srebro M, Autschbach J. Tuned Range-Separated Time-Dependent Density Functional Theory Applied to Optical Rotation. J Chem Theory Comput 2011; 8:245-56. [DOI: 10.1021/ct200764g] [Citation(s) in RCA: 96] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Monika Srebro
- Department of Chemistry, University at Buffalo, State University of New York, Buffalo, New York 14260-3000, United States
- Department of Theoretical Chemistry, Faculty of Chemistry, Jagiellonian University, R. Ingardena 3, 30-060 Krakow, Poland
| | - Jochen Autschbach
- Department of Chemistry, University at Buffalo, State University of New York, Buffalo, New York 14260-3000, United States
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19
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Rudolph M, Autschbach J. Performance of Conventional and Range-Separated Hybrid Density Functionals in Calculations of Electronic Circular Dichroism Spectra of Transition Metal Complexes. J Phys Chem A 2011; 115:14677-86. [DOI: 10.1021/jp2093725] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Affiliation(s)
- Mark Rudolph
- Department of Chemistry, University at Buffalo, State University of New York, Buffalo, New York 14260, United States
| | - Jochen Autschbach
- Department of Chemistry, University at Buffalo, State University of New York, Buffalo, New York 14260, United States
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20
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Lin N, Luo Y, Ruud K, Zhao X, Santoro F, Rizzo A. Differences in Two-Photon and One-Photon Absorption Profiles Induced by Vibronic Coupling: The Case of Dioxaborine Heterocyclic Dye. Chemphyschem 2011; 12:3392-403. [DOI: 10.1002/cphc.201100500] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2011] [Indexed: 11/08/2022]
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21
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Srebro M, Govind N, de Jong WA, Autschbach J. Optical Rotation Calculated with Time-Dependent Density Functional Theory: The OR45 Benchmark. J Phys Chem A 2011; 115:10930-49. [DOI: 10.1021/jp2055409] [Citation(s) in RCA: 100] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Monika Srebro
- Department of Chemistry, State University of New York at Buffalo, Buffalo, New York 14260−3000, United States
- Department of Theoretical Chemistry, Faculty of Chemistry, Jagiellonian University, R. Ingardena 3, 30-060 Krakow, Poland
| | - Niranjan Govind
- William R. Wiley Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, P. O. Box 999, Richland, Washington 99352, United States
| | - Wibe A. de Jong
- William R. Wiley Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, P. O. Box 999, Richland, Washington 99352, United States
| | - Jochen Autschbach
- Department of Chemistry, State University of New York at Buffalo, Buffalo, New York 14260−3000, United States
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22
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Murphy VL, Kahr B. Planar Hydrocarbons More Optically Active Than Their Isomeric Helicenes. J Am Chem Soc 2011; 133:12918-21. [DOI: 10.1021/ja203509s] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Veronica L. Murphy
- Department of Chemistry, New York University, 100 Washington Square East, New York, New York 10003, United States
| | - Bart Kahr
- Department of Chemistry, New York University, 100 Washington Square East, New York, New York 10003, United States
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23
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Pomogaev V, Pomogaeva A, Avramov P, Jalkanen KJ, Kachin S. Thermo-dynamical contours of electronic-vibrational spectra simulated using the statistical quantum–mechanical methods. Theor Chem Acc 2011. [DOI: 10.1007/s00214-011-0936-6] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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24
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Guillaume M, Ruud K, Rizzo A, Monti S, Lin Z, Xu X. Computational Study of the One- and Two-Photon Absorption and Circular Dichroism of (l)-Tryptophan. J Phys Chem B 2010; 114:6500-12. [DOI: 10.1021/jp1004659] [Citation(s) in RCA: 44] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
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25
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Julínek O, Krupička M, Lindner W, Urbanová M. Enantioselective interaction of carbamoylated quinine and (S)-3,5-dinitrobenzoyl alanine: theoretical and experimental circular dichroism study. Phys Chem Chem Phys 2010; 12:11487-97. [DOI: 10.1039/c000046a] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
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Autschbach J, Nitsch-Velasquez L, Rudolph M. Time-dependent density functional response theory for electronic chiroptical properties of chiral molecules. Top Curr Chem (Cham) 2010; 298:1-98. [PMID: 21321799 DOI: 10.1007/128_2010_72] [Citation(s) in RCA: 74] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/02/2022]
Abstract
Methodology to calculate electronic chiroptical properties from time-dependent density functional theory (TDDFT) is outlined. Applications of TDDFT to computations of electronic circular dichroism, optical rotation, and optical rotatory dispersion are reviewed. Emphasis is put on publications from 2005 to 2010, but much of the older literature is also cited and discussed. The determination of the absolute configuration of chiral molecules by combined measurements and computations is an important application of TDDFT chiroptical methods and discussed in some detail. Raman optical activity (ROA) spectra are obtained from normal-mode derivatives of the optical rotation tensor and other linear response tensors. A few selected (ROA) benchmarks are reviewed.
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Affiliation(s)
- Jochen Autschbach
- Department of Chemistry, University at Buffalo State University of New York, New York, NY, USA.
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Julínek O, Setnička V, Miklášová N, Putala M, Ruud K, Urbanová M. Determination of Molecular Structure of Bisphenylene Homologues of BINOL-Based Phosphoramidites by Chiroptical Methods. J Phys Chem A 2009; 113:10717-25. [DOI: 10.1021/jp906724f] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Ondřej Julínek
- Department of Analytical Chemistry and Department of Physics and Measurements, Institute of Chemical Technology, Prague, Technická 5, 166 28 Prague 6, Czech Republic, Department of Organic Chemistry, Faculty of Natural Sciences, Comenius University in Bratislava, Mlynská dolina, 842 15 Bratislava, Slovak Republic, and Centre for Theoretical and Computational Chemistry, Department of Chemistry, University of Tromsø, N-9037 Tromsø, Norway
| | - Vladimír Setnička
- Department of Analytical Chemistry and Department of Physics and Measurements, Institute of Chemical Technology, Prague, Technická 5, 166 28 Prague 6, Czech Republic, Department of Organic Chemistry, Faculty of Natural Sciences, Comenius University in Bratislava, Mlynská dolina, 842 15 Bratislava, Slovak Republic, and Centre for Theoretical and Computational Chemistry, Department of Chemistry, University of Tromsø, N-9037 Tromsø, Norway
| | - Natalia Miklášová
- Department of Analytical Chemistry and Department of Physics and Measurements, Institute of Chemical Technology, Prague, Technická 5, 166 28 Prague 6, Czech Republic, Department of Organic Chemistry, Faculty of Natural Sciences, Comenius University in Bratislava, Mlynská dolina, 842 15 Bratislava, Slovak Republic, and Centre for Theoretical and Computational Chemistry, Department of Chemistry, University of Tromsø, N-9037 Tromsø, Norway
| | - Martin Putala
- Department of Analytical Chemistry and Department of Physics and Measurements, Institute of Chemical Technology, Prague, Technická 5, 166 28 Prague 6, Czech Republic, Department of Organic Chemistry, Faculty of Natural Sciences, Comenius University in Bratislava, Mlynská dolina, 842 15 Bratislava, Slovak Republic, and Centre for Theoretical and Computational Chemistry, Department of Chemistry, University of Tromsø, N-9037 Tromsø, Norway
| | - Kenneth Ruud
- Department of Analytical Chemistry and Department of Physics and Measurements, Institute of Chemical Technology, Prague, Technická 5, 166 28 Prague 6, Czech Republic, Department of Organic Chemistry, Faculty of Natural Sciences, Comenius University in Bratislava, Mlynská dolina, 842 15 Bratislava, Slovak Republic, and Centre for Theoretical and Computational Chemistry, Department of Chemistry, University of Tromsø, N-9037 Tromsø, Norway
| | - Marie Urbanová
- Department of Analytical Chemistry and Department of Physics and Measurements, Institute of Chemical Technology, Prague, Technická 5, 166 28 Prague 6, Czech Republic, Department of Organic Chemistry, Faculty of Natural Sciences, Comenius University in Bratislava, Mlynská dolina, 842 15 Bratislava, Slovak Republic, and Centre for Theoretical and Computational Chemistry, Department of Chemistry, University of Tromsø, N-9037 Tromsø, Norway
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Yan W, Xie D, Zeng J. The 559-to-600 nm shift observed in red fluorescent protein eqFP611 is attributed to cis-trans isomerization of the chromophore in an anionic protein pocket. Phys Chem Chem Phys 2009; 11:6042-50. [PMID: 19606312 DOI: 10.1039/b903544c] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2023]
Abstract
Fluorescent proteins are commonly used as molecular labels, noninvasive markers of gene expression, and reporters of environmental conditions in live cells. We investigate the structural and spectroscopic properties of the chromophore of a far-red fluorescent protein eqFP611. Both the cis and trans isomers of the chromophore are examined within the protein for which both anionic and neutral states of protonation are considered. Spectroscopic properties are examined using time-dependent density functional theory (TDDFT), employing the B3LYP, PBE and B3PW91 density functionals. Intermolecular and long-range contributions to the structure and spectroscopy were treated using the own n-layered integrated molecular orbital and molecular mechanics (ONIOM) approach. The results indicated that the chromophore before excitation is in an anionic, protonated state, with the long-range contributions inducing a blue shift in the absorption and fluorescence maxima of the chromophore. Moreover, the calculated changes of the lowest pi-pi* excitation energy upon isomerization match the observed shift from 559 to 600 nm in the absorption maximum of the system following prolonged irradiation. Furthermore, decomposition analysis of the electrostatic contributions from individual residues indicated that the interactions from four residues Arg92, Lys67, Glu145, and His197 to the chromophore play a key role in the absorption and fluorescence spectra of eqFP611, suggesting that mutations at these sites should provide very useful mechanistic information.
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Affiliation(s)
- Weizhong Yan
- Institute of Theoretical and Computational Chemistry, Key Laboratory of Mesoscopic Chemistry of MOE, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210093, China
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Chakrabarti S, Ruud K. Large two-photon absorption cross section: molecular tweezer as a new promising class of compounds for nonlinear optics. Phys Chem Chem Phys 2009; 11:2592-6. [DOI: 10.1039/b822395e] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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Lin N, Santoro F, Zhao X, Rizzo A, Barone V. Vibronically Resolved Electronic Circular Dichroism Spectra of (R)-(+)-3-Methylcyclopentanone: A Theoretical Study. J Phys Chem A 2008; 112:12401-11. [DOI: 10.1021/jp8064695] [Citation(s) in RCA: 72] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Affiliation(s)
- Na Lin
- Department of Theoretical Chemistry, School of Biotechnology, Royal Institute of Technology, SE-10691 Stockholm, Sweden, Institute of Crystal Materials, Shandong University, 250100 Jinan, Shandong, People’s Republic of China, and Area della Ricerca, Istituto per i Processi Chimico-Fisici del Consiglio Nazionale delle Ricerche (IPCF-CNR), Via G. Moruzzi 1, I-56124 Pisa, Italy
| | - Fabrizio Santoro
- Department of Theoretical Chemistry, School of Biotechnology, Royal Institute of Technology, SE-10691 Stockholm, Sweden, Institute of Crystal Materials, Shandong University, 250100 Jinan, Shandong, People’s Republic of China, and Area della Ricerca, Istituto per i Processi Chimico-Fisici del Consiglio Nazionale delle Ricerche (IPCF-CNR), Via G. Moruzzi 1, I-56124 Pisa, Italy
| | - Xian Zhao
- Department of Theoretical Chemistry, School of Biotechnology, Royal Institute of Technology, SE-10691 Stockholm, Sweden, Institute of Crystal Materials, Shandong University, 250100 Jinan, Shandong, People’s Republic of China, and Area della Ricerca, Istituto per i Processi Chimico-Fisici del Consiglio Nazionale delle Ricerche (IPCF-CNR), Via G. Moruzzi 1, I-56124 Pisa, Italy
| | - Antonio Rizzo
- Department of Theoretical Chemistry, School of Biotechnology, Royal Institute of Technology, SE-10691 Stockholm, Sweden, Institute of Crystal Materials, Shandong University, 250100 Jinan, Shandong, People’s Republic of China, and Area della Ricerca, Istituto per i Processi Chimico-Fisici del Consiglio Nazionale delle Ricerche (IPCF-CNR), Via G. Moruzzi 1, I-56124 Pisa, Italy
| | - Vincenzo Barone
- Department of Theoretical Chemistry, School of Biotechnology, Royal Institute of Technology, SE-10691 Stockholm, Sweden, Institute of Crystal Materials, Shandong University, 250100 Jinan, Shandong, People’s Republic of China, and Area della Ricerca, Istituto per i Processi Chimico-Fisici del Consiglio Nazionale delle Ricerche (IPCF-CNR), Via G. Moruzzi 1, I-56124 Pisa, Italy
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