1
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Loos PF, Jacquemin D. A Mountaineering Strategy to Excited States: Highly Accurate Energies and Benchmarks for Bicyclic Systems. J Phys Chem A 2021; 125:10174-10188. [PMID: 34792354 DOI: 10.1021/acs.jpca.1c08524] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
Pursuing our efforts to define highly accurate estimates of the relative energies of excited states in organic molecules, we investigate, with coupled-cluster methods including iterative triples (CC3 and CCSDT), the vertical excitation energies of 10 bicyclic molecules (azulene, benzoxadiazole, benzothiadiazole, diketopyrrolopyrrole, furofuran, phthalazine, pyrrolopyrrole, quinoxaline, tetrathiafulvalene, and thienothiophene). In total, we provide aug-cc-pVTZ reference vertical excitation energies for 91 excited states of these relatively large systems. We use these reference values to benchmark various wave function methods, i.e., CIS(D), EOM-MP2, CC2, CCSD, STEOM-CCSD, CCSD(T)(a)*, CCSDR(3), CCSDT-3, ADC(2), ADC(2.5), and ADC(3), as well as some spin-scaled variants of both CC2 and ADC(2). These results are compared to those obtained previously on smaller molecules. It turns out that while the accuracy of some methods is almost unaffected by system size, e.g., CIS(D) and CC3, the performance of others can significantly deteriorate as the systems grow, e.g., EOM-MP2 and CCSD, whereas others, e.g., ADC(2) and CC2, become more accurate for larger derivatives.
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Affiliation(s)
- Pierre-François Loos
- Laboratoire de Chimie et Physique Quantiques, Université de Toulouse, CNRS, UPS, F-31062, Toulouse, France
| | - Denis Jacquemin
- Université de Nantes, CNRS, CEISAM UMR 6230, F-44000 Nantes, France
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2
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Yang Q, Fusè M, Bloino J. Theoretical Investigation of the Circularly Polarized Luminescence of a Chiral Boron Dipyrromethene (BODIPY) Dye. Front Chem 2020; 8:801. [PMID: 33102435 PMCID: PMC7522172 DOI: 10.3389/fchem.2020.00801] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2020] [Accepted: 07/30/2020] [Indexed: 01/11/2023] Open
Abstract
Over the last decade, molecules capable of emitting circularly polarized light have attracted growing attention for potential technological and biological applications. The efficiency of such devices depend on multiple parameters, in particular the magnitude and wavelength of the peak of emitted light, and also on the dissymmetry factor for chiral applications. In light of these considerations, molecular systems with tunable optical properties, preferably in the visible spectral region, are particularly appealing. This is the case of boron dipyrromethene (BODIPY) dyes, which exhibit large molecular absorption coefficients, have high fluorescence yields, are very stable, both thermally and photochemically, and can be easily functionalized. The latter property has been extensively exploited in the literature to produce chromophores with a wide range of optical properties. Nevertheless, only a few chiral BODIPYs have been synthetized and investigated so far. Using a recently reported axially chiral BODIPY derivative where an axially chiral BINOL unit has been attached to the chromophore unit, we present a comprehensive computational protocol to predict and interpret the one-photon absorption and emission spectra, together with their chiroptical counterparts. From the physico-chemical properties of this molecule, it will be possible to understand the origin of the circularly polarized luminescence better, thus helping to fine-tune the properties of interest. The sensitivity of such processes require accurate results, which can be achieved through a proper account of the vibrational structure in optical spectra. Methodologies to compute vibrationally-resolved electronic spectra can now be applied on relatively large chromophores, such as BODIPYs, but require more extensive computational protocols. For this reason, particular attention is paid in the description of the different steps of the protocol, and the potential pitfalls. Finally, we show how, by means of appropriate tools and approaches, data from intermediate steps of the simulation of the final spectra can be used to obtain further insights into the properties of the molecular system under investigation and the origin of the visible bands.
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Affiliation(s)
- Qin Yang
- Scuola Normale Superiore, Pisa, Italy
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3
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Fusè M, Egidi F, Bloino J. Vibrational circular dichroism under the quantum magnifying glass: from the electronic flow to the spectroscopic observable. Phys Chem Chem Phys 2019; 21:4224-4239. [DOI: 10.1039/c8cp06514d] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
A chemically intuitive method to analyse and interpret vibrational circular dichroism spectra based on the vibrational transition current density.
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Affiliation(s)
- Marco Fusè
- Scuola Normale Superiore
- Piazza dei Cavalieri 7
- Pisa
- Italy
| | - Franco Egidi
- Scuola Normale Superiore
- Piazza dei Cavalieri 7
- Pisa
- Italy
| | - Julien Bloino
- Scuola Normale Superiore
- Piazza dei Cavalieri 7
- Pisa
- Italy
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4
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Saielli G. Computational Spectroscopy of Ionic Liquids for Bulk Structure Elucidation. ADVANCED THEORY AND SIMULATIONS 2018. [DOI: 10.1002/adts.201800084] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Affiliation(s)
- Giacomo Saielli
- CNR Institute on Membrane Technology; Unit of Padova; Via Marzolo 1-35131 Padova Italy
- Department of Chemical Sciences; University of Padova; Via Marzolo 1-35131 Padova Italy
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5
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Egidi F, Fusè M, Baiardi A, Bloino J, Li X, Barone V. Computational simulation of vibrationally resolved spectra for spin-forbidden transitions. Chirality 2018; 30:850-865. [PMID: 29727500 DOI: 10.1002/chir.22864] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2017] [Revised: 03/22/2018] [Accepted: 03/23/2018] [Indexed: 12/25/2022]
Abstract
In this computational study, we illustrate a method for computing phosphorescence and circularly polarized phosphorescence spectra of molecular systems, which takes into account vibronic effects including both Franck-Condon and Herzberg-Teller contributions. The singlet and triplet states involved in the phosphorescent emission are described within the harmonic approximation, and the method fully takes mode-mixing effects into account when evaluating Franck-Condon integrals. Spin-orbit couplings, which are responsible for these otherwise forbidden phenomena, are accounted for by means of a relativistic two-component time-dependent density functional theory method. The model is applied to two types of chiral systems: camphorquinone, a rigid organic system that allows for an extensive benchmark, and some members of a class of iridium complexes. The merits and shortcomings of the methods are discussed, and some perspectives for future developments are offered.
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Affiliation(s)
| | | | | | - Julien Bloino
- Institute of Chemistry of Organometallic Compounds, National Research Council of Italy, Pisa, Italy
| | - Xiaosong Li
- Department of Chemistry, University of Washington, Seattle, Washington, USA
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6
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Egidi F, Williams-Young DB, Baiardi A, Bloino J, Scalmani G, Frisch MJ, Li X, Barone V. Effective Inclusion of Mechanical and Electrical Anharmonicity in Excited Electronic States: VPT2-TDDFT Route. J Chem Theory Comput 2017; 13:2789-2803. [PMID: 28453287 DOI: 10.1021/acs.jctc.7b00218] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
We present a reliable and cost-effective procedure for the inclusion of anharmonic effects in excited-state energies and spectroscopic intensities by means of second-order vibrational perturbation theory. This development is made possible thanks to a recent efficient implementation of excited-state analytic Hessians and properties within the time-dependent density functional theory framework. As illustrated in this work, by taking advantage of such algorithmic developments, it is possible to perform calculations of excited-state infrared spectra of medium-large isolated molecular systems, with anharmonicity effects included in both the energy and property surfaces. We also explore the use of this procedure for the inclusion of anharmonic effects in the simulation of vibronic bandshapes of electronic spectra and compare the results with previous, more approximate models.
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Affiliation(s)
- Franco Egidi
- Scuola Normale Superiore , Piazza dei Cavalieri 7, 56126 Pisa, Italy
| | - David B Williams-Young
- Department of Chemistry, University of Washington , Seattle, Washington 98195, United States
| | - Alberto Baiardi
- Scuola Normale Superiore , Piazza dei Cavalieri 7, 56126 Pisa, Italy
| | - Julien Bloino
- Consiglio Nazionale delle Ricerche, Istituto di Chimica dei Composti OrganoMetallici (ICCOM-CNR) , UOS di Pisa, Area della Ricerca CNR, Via G. Moruzzi 1, Pisa 56124, Italy
| | - Giovanni Scalmani
- Gaussian, Inc. , 340 Quinnipiac St., Bldg. 40, Wallingford, Connecticut 06492, United States
| | - Michael J Frisch
- Gaussian, Inc. , 340 Quinnipiac St., Bldg. 40, Wallingford, Connecticut 06492, United States
| | - Xiaosong Li
- Department of Chemistry, University of Washington , Seattle, Washington 98195, United States
| | - Vincenzo Barone
- Scuola Normale Superiore , Piazza dei Cavalieri 7, 56126 Pisa, Italy
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7
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Burgueño-Tapia E, Joseph-Nathan P. Vibrational Circular Dichroism: Recent Advances for the Assignment of the Absolute Configuration of Natural Products. Nat Prod Commun 2017. [DOI: 10.1177/1934578x1701200501] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
Vibrational circular dichroism (VCD) emerged during the last decade as a reliable tool for the absolute configuration (AC) determination of organic compounds. The principles, instrumentation, and methodology applied prior to early 2013 were recently reviewed by us. Since VCD is a very dynamic field, the aim of this review is to update VCD advances for the AC assignment of terpenoids, aromatic compounds, alkaloids, and other natural products for the 2013–2014 period, when VCD was applied to the AC assignment of some 70 natural products. In addition, although discovered in 2012, a brief introduction to the VCD exciton coupling approach and its applications in natural products AC assignment is presented.
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Affiliation(s)
- Eleuterio Burgueño-Tapia
- Departamento de Química Orgánica, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, Prolongación de Carpio y Plan de Ayala, Col. Santo Tomás, México D.F., 11340 Mexico
| | - Pedro Joseph-Nathan
- Departamento de Química, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional, Apartado 14–740, México D.F., 07000 Mexico
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8
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Giovannini T, Olszòwka M, Cappelli C. Effective Fully Polarizable QM/MM Approach To Model Vibrational Circular Dichroism Spectra of Systems in Aqueous Solution. J Chem Theory Comput 2016; 12:5483-5492. [PMID: 27704812 DOI: 10.1021/acs.jctc.6b00768] [Citation(s) in RCA: 44] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
We propose a methodology, based on the combination of classical Molecular Dynamics (MD) simulations with a fully polarizable Quantum Mechanical (QM)/Molecular Mechanics (MM)/Polarizable Continuum Model (PCM) Hamiltonian, to calculate Vibrational Circular Dichroism (VCD) spectra of chiral systems in aqueous solution. Polarization effects are included in the MM force field by exploiting an approach based on Fluctuating Charges (FQ). By performing the MD, the description of the solvating environment is enriched by taking into account the dynamical aspects of the solute-solvent interactions. On the other hand, the QM/FQ/PCM calculation of the VCD spectrum ensures an accurate description of the electronic density of the solute and a proper account for the specific interactions in solution. The application of our approach to (R)-methyloxirane and (l)-alanine in aqueous solution gives calculated spectra in remarkable agreement with their experimental counterparts and a substantial improvement with respect to the same spectra calculated with the PCM.
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Affiliation(s)
| | - Marta Olszòwka
- Dipartimento di Chimica e Chimica Industriale, Università di Pisa , Via Moruzzi 13, 56124 Pisa, Italy
| | - Chiara Cappelli
- Scuola Normale Superiore, Piazza dei Cavalieri 7, 56126 Pisa, Italy
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9
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Bloino J, Biczysko M, Barone V. Anharmonic Effects on Vibrational Spectra Intensities: Infrared, Raman, Vibrational Circular Dichroism, and Raman Optical Activity. J Phys Chem A 2015; 119:11862-74. [PMID: 26580121 PMCID: PMC5612400 DOI: 10.1021/acs.jpca.5b10067] [Citation(s) in RCA: 83] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The aim of this paper is 2-fold. First, we want to report the extension of our virtual multifrequency spectrometer (VMS) to anharmonic intensities for Raman optical activity (ROA) with the full inclusion of first- and second-order resonances for both frequencies and intensities in the framework of the generalized second-order vibrational perturbation theory (GVPT2) for all kinds of vibrational spectroscopies. Then, from a more general point of view, we want to present and validate the performance of VMS for the parallel analysis of different vibrational spectra for medium-sized molecules (IR, Raman, VCD, ROA) including both mechanical and electric/magnetic anharmonicity. For the well-known methyloxirane benchmark, careful selection of density functional, basis set, and resonance thresholds permitted us to reach qualitative and quantitative agreement between experimental and computed band positions and shapes. Next, the whole series of halogenated azetidinones is analyzed, showing that it is now possible to interpret different spectra in terms of mass, electronegativity, polarizability, and hindrance variation between closely related substituents, chiral spectroscopies being particular effective in this connection.
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Affiliation(s)
- Julien Bloino
- Consiglio Nazionale delle Ricerche, Istituto di Chimica dei
Composti OrganoMetallici (ICCOM-CNR), UOS di Pisa, Area della Ricerca CNR, Via G.
Moruzzi 1, I-56124 Pisa, Italy
| | - Malgorzata Biczysko
- Consiglio Nazionale delle Ricerche, Istituto di Chimica dei
Composti OrganoMetallici (ICCOM-CNR), UOS di Pisa, Area della Ricerca CNR, Via G.
Moruzzi 1, I-56124 Pisa, Italy
- International Center of Quantum and Molecular Structures,
College of Sciences, Shanghai University, 99 Shangda Road, Shanghai, 200444
China
| | - Vincenzo Barone
- Scuola Normale Superiore, Piazza dei Cavalieri 7, 56126 Pisa,
Italy
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10
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Burgueño-Tapia E, Joseph-Nathan P. Vibrational Circular Dichroism: Recent Advances for the Assignment of the Absolute Configuration of Natural Products. Nat Prod Commun 2015. [DOI: 10.1177/1934578x1501001036] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
Vibrational circular dichroism (VCD) emerged during the last decade as a reliable tool for the absolute configuration (AC) determination of organic compounds. The principles, instrumentation, and methodology applied prior to early 2013 were recently reviewed by us. Since VCD is a very dynamic field, the aim of this review is to update VCD advances for the AC assignment of terpenoids, aromatic compounds, alkaloids, and other natural products for the 2013-2014 period, when VCD was applied to the AC assignment of some 70 natural products. In addition, although discovered in 2012, a brief introduction to the VCD exciton coupling approach and its applications in natural products AC assignment is presented.
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Affiliation(s)
- Eleuterio Burgueño-Tapia
- Departamento de Quimica Orgdnica, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico National, Prolongatión de Carpio y Plan de Ayala, Col. Santo Tomás, México D.F., 11340 Mexico
| | - Pedro Joseph-Nathan
- Departamento de Química, Centro de Investigatión y de Estudios Avanzados del Instituto Politécnico Nacional, Apartado 14-740, México D.F., 07000 Mexico
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11
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Egidi F, Segado M, Koch H, Cappelli C, Barone V. A benchmark study of electronic excitation energies, transition moments, and excited-state energy gradients on the nicotine molecule. J Chem Phys 2015; 141:224114. [PMID: 25494739 DOI: 10.1063/1.4903307] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
In this work, we report a comparative study of computed excitation energies, oscillator strengths, and excited-state energy gradients of (S)-nicotine, chosen as a test case, using multireference methods, coupled cluster singles and doubles, and methods based on time-dependent density functional theory. This system was chosen because its apparent simplicity hides a complex electronic structure, as several different types of valence excitations are possible, including n-π(*), π-π(*), and charge-transfer states, and in order to simulate its spectrum it is necessary to describe all of them consistently well by the chosen method.
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Affiliation(s)
- Franco Egidi
- Scuola Normale Superiore, Piazza dei Cavalieri, 7 I-56126 Pisa, Italy
| | - Mireia Segado
- Scuola Normale Superiore, Piazza dei Cavalieri, 7 I-56126 Pisa, Italy
| | - Henrik Koch
- Department of Chemistry, Norwegian University of Science and Technology, 7491 Trondheim, Norway
| | - Chiara Cappelli
- Dipartimento di Chimica e Chimica Industriale, Università di Pisa, via G. Moruzzi, 3 I-56124 Pisa, Italy
| | - Vincenzo Barone
- Scuola Normale Superiore, Piazza dei Cavalieri, 7 I-56126 Pisa, Italy
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12
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Vidal LN, Egidi F, Barone V, Cappelli C. Origin invariance in vibrational resonance Raman optical activity. J Chem Phys 2015; 142:174101. [DOI: 10.1063/1.4918935] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- Luciano N. Vidal
- Dipartimento di Chimica e Chimica Industriale, Università di Pisa, Via Moruzzi 3, 56124 Pisa, Italy
| | - Franco Egidi
- Department of Chemistry, University of Washington, Seattle, Washington 98195, USA
| | - Vincenzo Barone
- Scuola Normale Superiore, Piazza dei Cavalieri 7, 56126 Pisa, Italy
| | - Chiara Cappelli
- Dipartimento di Chimica e Chimica Industriale, Università di Pisa, Via Moruzzi 3, 56124 Pisa, Italy
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13
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Egidi F, Russo R, Carnimeo I, D'Urso A, Mancini G, Cappelli C. The electronic circular dichroism of nicotine in aqueous solution: a test case for continuum and mixed explicit-continuum solvation approaches. J Phys Chem A 2015; 119:5396-404. [PMID: 25568940 DOI: 10.1021/jp510542x] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
In this paper, we extend an integrated QM/MM/polarizable continuum model (PCM) method, which combines a fluctuating charge (FQ) approach to the MM polarization with the PCM, to describe electronic circular dichroism (ECD) spectra of systems in aqueous solution. The main features of the approach are presented, and then applications to the UV and ECD spectra of neutral (S)-nicotine in aqueous solution are reported. The performance of the QM/FQ/PCM is compared with that of the PCM against newly measured UV ECD spectra, which are in agreement with previous findings. The inclusion of specific solvation effects via the QM/FQ/PCM method leads to an improvement in the calculated spectra compared to the experimental findings, though the pure PCM results are still qualitatively correct and are a useful tool for the characterization of the states.
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Affiliation(s)
- Franco Egidi
- Scuola Normale Superiore, Piazza dei Cavalieri 7, I-56126 Pisa, Italy.,Dipartimento di Chimica e Chimica Industriale, Università di Pisa, via Giuseppe Moruzzi 3, I-56124 Pisa, Italy.,Compunet, Istituto Italiano di Tecnologia (IIT), via Morego 30, I-16163 Genova, Italy.,Scuola Normale Superiore, Piazza dei Cavalieri 7, I-56126 Pisa, Italy.,Department of Chemical Sciences, University of Catania, Viale A. Doria 6, I-95125 Catania, Italy.,Scuola Normale Superiore, Piazza dei Cavalieri 7, I-56126 Pisa, Italy.,Dipartimento di Chimica e Chimica Industriale, Università di Pisa, via Giuseppe Moruzzi 3, I-56124 Pisa, Italy
| | - Rosario Russo
- Scuola Normale Superiore, Piazza dei Cavalieri 7, I-56126 Pisa, Italy.,Dipartimento di Chimica e Chimica Industriale, Università di Pisa, via Giuseppe Moruzzi 3, I-56124 Pisa, Italy.,Compunet, Istituto Italiano di Tecnologia (IIT), via Morego 30, I-16163 Genova, Italy.,Scuola Normale Superiore, Piazza dei Cavalieri 7, I-56126 Pisa, Italy.,Department of Chemical Sciences, University of Catania, Viale A. Doria 6, I-95125 Catania, Italy.,Scuola Normale Superiore, Piazza dei Cavalieri 7, I-56126 Pisa, Italy.,Dipartimento di Chimica e Chimica Industriale, Università di Pisa, via Giuseppe Moruzzi 3, I-56124 Pisa, Italy
| | - Ivan Carnimeo
- Scuola Normale Superiore, Piazza dei Cavalieri 7, I-56126 Pisa, Italy.,Dipartimento di Chimica e Chimica Industriale, Università di Pisa, via Giuseppe Moruzzi 3, I-56124 Pisa, Italy.,Compunet, Istituto Italiano di Tecnologia (IIT), via Morego 30, I-16163 Genova, Italy.,Scuola Normale Superiore, Piazza dei Cavalieri 7, I-56126 Pisa, Italy.,Department of Chemical Sciences, University of Catania, Viale A. Doria 6, I-95125 Catania, Italy.,Scuola Normale Superiore, Piazza dei Cavalieri 7, I-56126 Pisa, Italy.,Dipartimento di Chimica e Chimica Industriale, Università di Pisa, via Giuseppe Moruzzi 3, I-56124 Pisa, Italy
| | - Alessandro D'Urso
- Scuola Normale Superiore, Piazza dei Cavalieri 7, I-56126 Pisa, Italy.,Dipartimento di Chimica e Chimica Industriale, Università di Pisa, via Giuseppe Moruzzi 3, I-56124 Pisa, Italy.,Compunet, Istituto Italiano di Tecnologia (IIT), via Morego 30, I-16163 Genova, Italy.,Scuola Normale Superiore, Piazza dei Cavalieri 7, I-56126 Pisa, Italy.,Department of Chemical Sciences, University of Catania, Viale A. Doria 6, I-95125 Catania, Italy.,Scuola Normale Superiore, Piazza dei Cavalieri 7, I-56126 Pisa, Italy.,Dipartimento di Chimica e Chimica Industriale, Università di Pisa, via Giuseppe Moruzzi 3, I-56124 Pisa, Italy
| | - Giordano Mancini
- Scuola Normale Superiore, Piazza dei Cavalieri 7, I-56126 Pisa, Italy.,Dipartimento di Chimica e Chimica Industriale, Università di Pisa, via Giuseppe Moruzzi 3, I-56124 Pisa, Italy.,Compunet, Istituto Italiano di Tecnologia (IIT), via Morego 30, I-16163 Genova, Italy.,Scuola Normale Superiore, Piazza dei Cavalieri 7, I-56126 Pisa, Italy.,Department of Chemical Sciences, University of Catania, Viale A. Doria 6, I-95125 Catania, Italy.,Scuola Normale Superiore, Piazza dei Cavalieri 7, I-56126 Pisa, Italy.,Dipartimento di Chimica e Chimica Industriale, Università di Pisa, via Giuseppe Moruzzi 3, I-56124 Pisa, Italy
| | - Chiara Cappelli
- Scuola Normale Superiore, Piazza dei Cavalieri 7, I-56126 Pisa, Italy.,Dipartimento di Chimica e Chimica Industriale, Università di Pisa, via Giuseppe Moruzzi 3, I-56124 Pisa, Italy.,Compunet, Istituto Italiano di Tecnologia (IIT), via Morego 30, I-16163 Genova, Italy.,Scuola Normale Superiore, Piazza dei Cavalieri 7, I-56126 Pisa, Italy.,Department of Chemical Sciences, University of Catania, Viale A. Doria 6, I-95125 Catania, Italy.,Scuola Normale Superiore, Piazza dei Cavalieri 7, I-56126 Pisa, Italy.,Dipartimento di Chimica e Chimica Industriale, Università di Pisa, via Giuseppe Moruzzi 3, I-56124 Pisa, Italy
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14
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Bloino J. A VPT2 Route to Near-Infrared Spectroscopy: The Role of Mechanical and Electrical Anharmonicity. J Phys Chem A 2015; 119:5269-87. [DOI: 10.1021/jp509985u] [Citation(s) in RCA: 76] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Affiliation(s)
- Julien Bloino
- Consiglio
Nazionale delle Ricerche, Istituto di Chimica dei Composti OrganoMetallici
(ICCOM-CNR), UOS di Pisa,
Area della Ricerca CNR, Via G. Moruzzi
1, 56124 Pisa, Italy
- Scuola Normale Superiore, piazza dei Cavalieri 7, I-56126 Pisa, Italy
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15
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Ortega PGR, Montejo M, González JJL. Vibrational circular dichroism and theoretical study of the conformational equilibrium in (-)-S-nicotine. Chemphyschem 2014; 16:342-52. [PMID: 25421493 DOI: 10.1002/cphc.201402652] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2014] [Indexed: 11/09/2022]
Abstract
We report an extensive study of the molecular and electronic structure of (-)-S-nicotine, to deduce the phenomenon that controls its conformational equilibrium and to solve its solution-state conformer population. Density functional theory, ab initio, and molecular mechanics calculations were used together with vibrational circular dichroism (VCD) and Fourier transform infrared spectroscopies. Calculations and experiments in solution show that the structure and the conformational energy profile of (-)-S-nicotine are not strongly dependent on the medium, thus suggesting that the conformational equilibrium is dominated by hyperconjugative interactions rather than repulsive electronic effects. The analysis of the first recorded VCD spectra of (-)-S-nicotine confirmed the presence of two main conformers at room temperature. Our results provide further evidence of the hypersensitivity of vibrational optical activity spectroscopies to the three-dimensional structure of chiral samples and prove their suitability for the elucidation of solution-state conformer distribution.
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16
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Licari D, Baiardi A, Biczysko M, Egidi F, Latouche C, Barone V. Implementation of a graphical user interface for the virtual multifrequency spectrometer: The VMS-Draw tool. J Comput Chem 2014; 36:321-34. [DOI: 10.1002/jcc.23785] [Citation(s) in RCA: 76] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2014] [Accepted: 10/12/2014] [Indexed: 11/09/2022]
Affiliation(s)
- Daniele Licari
- Scuola Normale Superiore; piazza dei Cavalieri 7 I-56126 Pisa Italy
| | - Alberto Baiardi
- Scuola Normale Superiore; piazza dei Cavalieri 7 I-56126 Pisa Italy
| | - Malgorzata Biczysko
- Scuola Normale Superiore; piazza dei Cavalieri 7 I-56126 Pisa Italy
- Consiglio Nazionale delle Ricerche, Istituto di Chimica dei Composti OrganoMetallici (ICCOM-CNR), UOS di Pisa, Area della Ricerca CNR; Via G. Moruzzi 1 I-56124 Pisa Italy
| | - Franco Egidi
- Scuola Normale Superiore; piazza dei Cavalieri 7 I-56126 Pisa Italy
| | - Camille Latouche
- Scuola Normale Superiore; piazza dei Cavalieri 7 I-56126 Pisa Italy
| | - Vincenzo Barone
- Scuola Normale Superiore; piazza dei Cavalieri 7 I-56126 Pisa Italy
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17
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Barone V, Baiardi A, Bloino J. New developments of a multifrequency virtual spectrometer: stereo-electronic, dynamical, and environmental effects on chiroptical spectra. Chirality 2014; 26:588-600. [PMID: 24839096 PMCID: PMC4604663 DOI: 10.1002/chir.22325] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2013] [Revised: 01/29/2014] [Accepted: 03/03/2014] [Indexed: 11/09/2022]
Abstract
Computational spectroscopy has recently evolved from a field reserved for specialists toward a general tool allowing interpretations and analyses of experimental results. However, the current practice of providing tables of transitions for rigid geometries, possibly tuned by phenomenological broadening, is by far too naive. In order to improve this situation in the last few years we have been developing a general, robust, and user-friendly virtual spectrometer (VS) able to complement experimental studies for complex systems in condensed phases. The VS is based on flexible graphical pre- and postprocessing tools interfaced with general number-crunching software. This last tool is rooted in several electronic structure methodologies (DFT, TD-DFT, post-Hartree-Fock), powerful discrete/continuum models for describing environmental effects, and general vibrational and vibronic models. These last topics are the main focus of this work, which sketches our latest developments related to effective inclusion of anharmonic contributions, together with time-independent and/or time-dependent descriptions of vibronic transitions including Franck-Condon, Herzberg-Teller, and Duschinsky effects. Some test cases are described in some detail with the aim of showing the role of different effects in ruling vibrational (VCD) and electronic (ECD, CPL) chiral spectroscopies.
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Affiliation(s)
- Vincenzo Barone
- Scuola Normale Superiore, Piazza dei Cavalieri 7, 56126 Pisa, Italy
| | - Alberto Baiardi
- Scuola Normale Superiore, Piazza dei Cavalieri 7, 56126 Pisa, Italy
| | - Julien Bloino
- Scuola Normale Superiore, Piazza dei Cavalieri 7, 56126 Pisa, Italy
- Consiglio Nazionale delle Ricerche, Istituto di Chimica dei Composti Organometallici, UOS di Pisa, Via G. Moruzzi 1, 56124 Pisa, Italy
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18
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Fornaro T, Biczysko M, Monti S, Barone V. Dispersion corrected DFT approaches for anharmonic vibrational frequency calculations: nucleobases and their dimers. Phys Chem Chem Phys 2014; 16:10112-28. [PMID: 24531740 PMCID: PMC4612423 DOI: 10.1039/c3cp54724h] [Citation(s) in RCA: 68] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Abstract
Computational spectroscopy techniques have become in the last few years an effective means to analyze and assign infrared (IR) spectra of molecular systems of increasing dimensions and in different environments. However, transition from compilation of harmonic data to fully anharmonic simulations of spectra is still underway. The most promising results for large systems have been obtained, in our opinion, by perturbative vibrational approaches based on potential energy surfaces computed by hybrid (especially B3LYP) density functionals and medium size (e.g. SNSD) basis sets. In this framework, we are actively developing a comprehensive and robust computational protocol aimed at quantitative reproduction of the spectra of nucleic acid base complexes and their adsorption on solid supports (organic/inorganic). In this contribution we report the essential results of the first step devoted to isolated monomers and dimers. It is well known that in order to model the vibrational spectra of weakly bound molecular complexes dispersion interactions should be taken into proper account. In this work we have chosen two popular and inexpensive approaches to model dispersion interactions, namely the semi-empirical dispersion correction (D3) and pseudopotential based (DCP) methodologies both in conjunction with the B3LYP functional. These have been used for simulating fully anharmonic IR spectra of nucleobases and their dimers through generalized second order vibrational perturbation theory (GVPT2). We have studied, in particular, isolated adenine, hypoxanthine, uracil, thymine and cytosine, the hydrogen-bonded and stacked adenine and uracil dimers, and the stacked adenine-naphthalene heterodimer. Anharmonic frequencies are compared with standard B3LYP results and experimental findings, while the computed interaction energies and structures of complexes are compared to the best available theoretical estimates.
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Affiliation(s)
- Teresa Fornaro
- Scuola Normale Superiore, piazza dei Cavalieri 7, I-56126 Pisa, Italy.
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19
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Barone V, Biczysko M, Bloino J. Fully anharmonic IR and Raman spectra of medium-size molecular systems: accuracy and interpretation. Phys Chem Chem Phys 2014; 16:1759-87. [PMID: 24346191 PMCID: PMC4604664 DOI: 10.1039/c3cp53413h] [Citation(s) in RCA: 295] [Impact Index Per Article: 29.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Computation of full infrared (IR) and Raman spectra (including absolute intensities and transition energies) for medium- and large-sized molecular systems beyond the harmonic approximation is one of the most interesting challenges of contemporary computational chemistry. Contrary to common beliefs, low-order perturbation theory is able to deliver results of high accuracy (actually often better than those issuing from current direct dynamics approaches) provided that anharmonic resonances are properly managed. This perspective sketches the recent developments in our research group toward the development of a robust and user-friendly virtual spectrometer rooted in second-order vibrational perturbation theory (VPT2) and usable also by non-specialists essentially as a black-box procedure. Several examples are explicitly worked out in order to illustrate the features of our computational tool together with the most important ongoing developments.
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Affiliation(s)
- Vincenzo Barone
- Scuola Normale Superiore, piazza dei Cavalieri 7, I-56126 Pisa, Italy.
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20
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Egidi F, Bloino J, Cappelli C, Barone V. A robust and effective time-independent route to the calculation of Resonance Raman spectra of large molecules in condensed phases with the inclusion of Duschinsky, Herzberg-Teller, anharmonic, and environmental effects. J Chem Theory Comput 2013; 10:346-363. [PMID: 26550003 DOI: 10.1021/ct400932e] [Citation(s) in RCA: 62] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Abstract
We present an effective time-independent implementation to model vibrational resonance Raman (RR) spectra of medium-large molecular systems with the inclusion of Franck-Condon (FC) and Herzberg-Teller (HT) effects and a full account of the possible differences between the harmonic potential energy surfaces of the ground and resonant electronic states. Thanks to a number of algorithmic improvements and very effective parallelization, the full computations of fundamentals, overtones, and combination bands can be routinely performed for large systems possibly involving more than two electronic states. In order to improve the accuracy of the results, an effective inclusion of the leading anharmonic effects is also possible, together with environmental contributions under different solvation regimes. Reduced-dimensionality approaches can further enlarge the range of applications of this new tool. Applications to imidazole, pyrene, and chlorophyll a1 in solution are reported, as well as comparisons with available experimental data.
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Affiliation(s)
- Franco Egidi
- Scuola Normale Superiore, Piazza dei Cavalieri 7, 56126 Pisa, Italy
| | - Julien Bloino
- Scuola Normale Superiore, Piazza dei Cavalieri 7, 56126 Pisa, Italy ; Consiglio Nazionale delle Ricerche, Istituto di Chimica dei Composti Organometallici, UOS di Pisa, Via G. Moruzzi 1, 56124 Pisa, Italy
| | - Chiara Cappelli
- Dipartimento di Chimica e Chimica Industriale, Università di Pisa, via Risorgimento 35, 56126 Pisa, Italy
| | - Vincenzo Barone
- Scuola Normale Superiore, Piazza dei Cavalieri 7, 56126 Pisa, Italy
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