1
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Dellai A, Naim C, Cerezo J, Prampolini G, Castet F. Dynamic effects on the nonlinear optical properties of donor acceptor stenhouse adducts: insights from combined MD + QM simulations. Phys Chem Chem Phys 2024; 26:13639-13654. [PMID: 38511505 DOI: 10.1039/d4cp00310a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/22/2024]
Abstract
The second-order nonlinear optical (NLO) responses of a donor-acceptor stenhouse adduct (DASA) are investigated by using a computational approach combining molecular dynamics simulations and density functional theory (DFT) calculations. Specific force fields for the open and closed photoswitching forms are first parameterized and validated according to the Joyce protocol, in order to finely reproduce the geometrical features and potential energy surfaces of both isomers in chloroform solution. Then, DFT calculations are performed on structural snapshots extracted at regular time steps of the MD trajectories to address the influence of the thermalized conformational dynamics on the NLO responses related to hyper-Rayleigh scattering (HRS) experiments. We show that accounting for the structural dynamics largely enhances the HRS hyperpolarizability (βHRS) compared to DFT calculations considering solely equilibrium geometries, and greatly improves the agreement with experimental measurements. Furthermore, we show that the NLO responses of the NLO-active open form are correlated with the bond order alternation along the triene bridge connecting the donor and acceptor moieties, which is rationalized using simple essential state models.
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Affiliation(s)
- Angela Dellai
- Univ. Bordeaux, CNRS, Bordeaux INP, Institut des Sciences Moléculaires, UMR 5255, F-33400 Talence, France.
| | - Carmelo Naim
- Univ. Bordeaux, CNRS, Bordeaux INP, Institut des Sciences Moléculaires, UMR 5255, F-33400 Talence, France.
- Donostia International Physics Center (DIPC), Manuel Lardizabal Ibilbidea 4, 20018 Donostia, Euskadi, Spain
| | - Javier Cerezo
- Departamento de Química and Institute for Advanced Research in Chemical Sciences (IAdChem), Universidad Autónoma de Madrid, 28049 Madrid, Spain
| | | | - Frédéric Castet
- Univ. Bordeaux, CNRS, Bordeaux INP, Institut des Sciences Moléculaires, UMR 5255, F-33400 Talence, France.
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2
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Aarabi M, Aranda D, Gholami S, Meena SK, Lerouge F, Bretonniere Y, Gürol I, Baldeck P, Parola S, Dumoulin F, Cerezo J, Garavelli M, Santoro F, Rivalta I. Quantum-Classical Protocol for Efficient Characterization of Absorption Lineshape and Fluorescence Quenching upon Aggregation: The Case of Zinc Phthalocyanine Dyes. J Chem Theory Comput 2023; 19:5938-5957. [PMID: 37641958 PMCID: PMC10500990 DOI: 10.1021/acs.jctc.3c00446] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2023] [Indexed: 08/31/2023]
Abstract
A quantum-classical protocol that incorporates Jahn-Teller vibronic coupling effects and cluster analysis of molecular dynamics simulations is reported, providing a tool for simulations of absorption spectra and ultrafast nonadiabatic dynamics in large molecular photosystems undergoing aggregation in solution. Employing zinc phthalocyanine dyes as target systems, we demonstrated that the proposed protocol provided fundamental information on vibronic, electronic couplings and thermal dynamical effects that mostly contribute to the absorption spectra lineshape and the fluorescence quenching processes upon dye aggregation. Decomposing the various effects arising upon dimer formation, the structure-property relations associated with their optical responses have been deciphered at atomistic resolution.
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Affiliation(s)
- Mohammad Aarabi
- Dipartimento
di Chimica Industriale “Toso Montanari”, Universitá degli Studi di Bologna, Viale del Risorgimento 4, I-40136 Bologna, Italy
| | - Daniel Aranda
- Consiglio
Nazionale delle Ricerche, Istituto di Chimica
dei Composti Organo Metallici (ICCOM-CNR), I-56124 Pisa, Italy
- Instituto
de Ciencia Molecular (ICMol), Universidad
de Valencia, Catedrático
J. Beltrán 2, 46980 Paterna, Valencia, Spain
| | - Samira Gholami
- Dipartimento
di Chimica Industriale “Toso Montanari”, Universitá degli Studi di Bologna, Viale del Risorgimento 4, I-40136 Bologna, Italy
| | - Santosh Kumar Meena
- Department
of Chemical Engineering, Indian Institute
of Technology Ropar, Rupnagar, 140001 Punjab, India
| | - Frederic Lerouge
- ENSL,
CNRS, Laboratoire de Chimie UMR 5182, 46 Allée d’Italie, 69364 Lyon, France
| | - Yann Bretonniere
- ENSL,
CNRS, Laboratoire de Chimie UMR 5182, 46 Allée d’Italie, 69364 Lyon, France
| | - Ilke Gürol
- TÜBITAK
Marmara Research Center, Materials Technologies, Gebze, 41470 Kocaeli, Türkiye
| | - Patrice Baldeck
- ENSL,
CNRS, Laboratoire de Chimie UMR 5182, 46 Allée d’Italie, 69364 Lyon, France
| | - Stephane Parola
- ENSL,
CNRS, Laboratoire de Chimie UMR 5182, 46 Allée d’Italie, 69364 Lyon, France
| | - Fabienne Dumoulin
- Department
of Biomedical Engineering, Faculty of Engineering and Natural Sciences, Acibadem Mehmet Ali Aydinlar University, 34752 Istanbul, Türkiye
| | - Javier Cerezo
- Consiglio
Nazionale delle Ricerche, Istituto di Chimica
dei Composti Organo Metallici (ICCOM-CNR), I-56124 Pisa, Italy
- Departamento
de Química and Institute for Advanced Research in Chemical
Sciences (IAdChem), Universidad Autónoma
de Madrid, 28049 Madrid, Spain
| | - Marco Garavelli
- Dipartimento
di Chimica Industriale “Toso Montanari”, Universitá degli Studi di Bologna, Viale del Risorgimento 4, I-40136 Bologna, Italy
| | - Fabrizio Santoro
- Consiglio
Nazionale delle Ricerche, Istituto di Chimica
dei Composti Organo Metallici (ICCOM-CNR), I-56124 Pisa, Italy
| | - Ivan Rivalta
- Dipartimento
di Chimica Industriale “Toso Montanari”, Universitá degli Studi di Bologna, Viale del Risorgimento 4, I-40136 Bologna, Italy
- ENSL,
CNRS, Laboratoire de Chimie UMR 5182, 46 Allée d’Italie, 69364 Lyon, France
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3
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Cerezo J, Gao S, Armaroli N, Ingrosso F, Prampolini G, Santoro F, Ventura B, Pastore M. Non-Phenomenological Description of the Time-Resolved Emission in Solution with Quantum-Classical Vibronic Approaches-Application to Coumarin C153 in Methanol. Molecules 2023; 28:molecules28093910. [PMID: 37175320 PMCID: PMC10180259 DOI: 10.3390/molecules28093910] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2023] [Revised: 04/27/2023] [Accepted: 04/27/2023] [Indexed: 05/15/2023] Open
Abstract
We report a joint experimental and theoretical work on the steady-state spectroscopy and time-resolved emission of the coumarin C153 dye in methanol. The lowest energy excited state of this molecule is characterized by an intramolecular charge transfer thus leading to remarkable shifts of the time-resolved emission spectra, dictated by the methanol reorganization dynamics. We selected this system as a prototypical test case for the first application of a novel computational protocol aimed at the prediction of transient emission spectral shapes, including both vibronic and solvent effects, without applying any phenomenological broadening. It combines a recently developed quantum-classical approach, the adiabatic molecular dynamics generalized vertical Hessian method (Ad-MD|gVH), with nonequilibrium molecular dynamics simulations. For the steady-state spectra we show that the Ad-MD|gVH approach is able to reproduce quite accurately the spectral shapes and the Stokes shift, while a ∼0.15 eV error is found on the prediction of the solvent shift going from gas phase to methanol. The spectral shape of the time-resolved emission signals is, overall, well reproduced, although the simulated spectra are slightly too broad and asymmetric at low energies with respect to experiments. As far as the spectral shift is concerned, the calculated spectra from 4 ps to 100 ps are in excellent agreement with experiments, correctly predicting the end of the solvent reorganization after about 20 ps. On the other hand, before 4 ps solvent dynamics is predicted to be too fast in the simulations and, in the sub-ps timescale, the uncertainty due to the experimental time resolution (300 fs) makes the comparison less straightforward. Finally, analysis of the reorganization of the first solvation shell surrounding the excited solute, based on atomic radial distribution functions and orientational correlations, indicates a fast solvent response (≈100 fs) characterized by the strengthening of the carbonyl-methanol hydrogen bond interactions, followed by the solvent reorientation, occurring on the ps timescale, to maximize local dipolar interactions.
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Affiliation(s)
- Javier Cerezo
- Departamento de Química and Institute for Advanced Research in Chemical Sciences (IAdChem), Universidad Autónoma de Madrid, 28049 Madrid, Spain
- Institute of Chemistry of OrganoMetallic Compounds (ICCOM), National Research Council of Italy (CNR), Area di Ricerca di Pisa, Via Moruzzi 1, I-56124 Pisa, Italy
| | - Sheng Gao
- Institute for Organic Synthesis and Photoreactivity (ISOF), National Research Council of Italy (CNR), Via P. Gobetti 101, I-40129 Bologna, Italy
| | - Nicola Armaroli
- Institute for Organic Synthesis and Photoreactivity (ISOF), National Research Council of Italy (CNR), Via P. Gobetti 101, I-40129 Bologna, Italy
| | - Francesca Ingrosso
- Université de Lorraine & CNRS, Laboratoire de Physique et Chimie Théoriques (LPCT), F-54000 Nancy, France
| | - Giacomo Prampolini
- Institute of Chemistry of OrganoMetallic Compounds (ICCOM), National Research Council of Italy (CNR), Area di Ricerca di Pisa, Via Moruzzi 1, I-56124 Pisa, Italy
| | - Fabrizio Santoro
- Institute of Chemistry of OrganoMetallic Compounds (ICCOM), National Research Council of Italy (CNR), Area di Ricerca di Pisa, Via Moruzzi 1, I-56124 Pisa, Italy
| | - Barbara Ventura
- Institute for Organic Synthesis and Photoreactivity (ISOF), National Research Council of Italy (CNR), Via P. Gobetti 101, I-40129 Bologna, Italy
| | - Mariachiara Pastore
- Université de Lorraine & CNRS, Laboratoire de Physique et Chimie Théoriques (LPCT), F-54000 Nancy, France
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4
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Xu Q, Liu Y, Wang M, Cerezo J, Improta R, Santoro F. The Resonance Raman Spectrum of Cytosine in Water: Analysis of the Effect of Specific Solute-Solvent Interactions and Non-Adiabatic Couplings. Molecules 2023; 28:molecules28052286. [PMID: 36903532 PMCID: PMC10005559 DOI: 10.3390/molecules28052286] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2023] [Revised: 02/21/2023] [Accepted: 02/22/2023] [Indexed: 03/06/2023] Open
Abstract
In this contribution, we report a computational study of the vibrational Resonance Raman (vRR) spectra of cytosine in water, on the grounds of potential energy surfaces (PES) computed by time-dependent density functional theory (TD-DFT) and CAM-B3LYP and PBE0 functionals. Cytosine is interesting because it is characterized by several close-lying and coupled electronic states, challenging the approach commonly used to compute the vRR for systems where the excitation frequency is in quasi-resonance with a single state. We adopt two recently developed time-dependent approaches, based either on quantum dynamical numerical propagations of vibronic wavepackets on coupled PES or on analytical correlation functions for cases in which inter-state couplings were neglected. In this way, we compute the vRR spectra, considering the quasi-resonance with the eight lowest-energy excited states, disentangling the role of their inter-state couplings from the mere interference of their different contributions to the transition polarizability. We show that these effects are only moderate in the excitation energy range explored by experiments, where the spectral patterns can be rationalized from the simple analysis of displacements of the equilibrium positions along the different states. Conversely, at higher energies, interference and inter-state couplings play a major role, and the adoption of a fully non-adiabatic approach is strongly recommended. We also investigate the effect of specific solute-solvent interactions on the vRR spectra, by considering a cluster of cytosine, hydrogen-bonded by six water molecules, and embedded in a polarizable continuum. We show that their inclusion remarkably improves the agreement with the experiments, mainly altering the composition of the normal modes, in terms of internal valence coordinates. We also document cases, mostly for low-frequency modes, in which a cluster model is not sufficient, and more elaborate mixed quantum classical approaches, in explicit solvent models, need to be applied.
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Affiliation(s)
- Qiushuang Xu
- School of Physics Engineering, Qufu Normal University, Qufu 273165, China
- School of Physics and Optoelectronics Engineering, Ludong University, Yantai 264025, China
- Consiglio Nazionale delle Ricerche, Istituto di Chimica dei Composti Organo Metallici (ICCOM-CNR), SS di Pisa, Area della Ricerca, Via G. Moruzzi 1, I-56124 Pisa, Italy
| | - Yanli Liu
- School of Physics and Optoelectronics Engineering, Ludong University, Yantai 264025, China
| | - Meishan Wang
- School of Physics Engineering, Qufu Normal University, Qufu 273165, China
- School of Physics and Optoelectronics Engineering, Ludong University, Yantai 264025, China
| | - Javier Cerezo
- Consiglio Nazionale delle Ricerche, Istituto di Chimica dei Composti Organo Metallici (ICCOM-CNR), SS di Pisa, Area della Ricerca, Via G. Moruzzi 1, I-56124 Pisa, Italy
- Departamento de Química and Institute for Advanced Research in Chemical Sciences (IAdChem), Universidad Autónoma de Madrid, 28049 Madrid, Spain
| | - Roberto Improta
- Consiglio Nazionale delle Ricerche, Istituto di Biostrutture e Bioimmagini (IBB-CNR), Via De Amicis 95, I-80145 Napoli, Italy
- Correspondence: (R.I.); (F.S.)
| | - Fabrizio Santoro
- Consiglio Nazionale delle Ricerche, Istituto di Chimica dei Composti Organo Metallici (ICCOM-CNR), SS di Pisa, Area della Ricerca, Via G. Moruzzi 1, I-56124 Pisa, Italy
- Correspondence: (R.I.); (F.S.)
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5
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Horz M, Masood HMA, Brunst H, Cerezo J, Picconi D, Vormann H, Niraghatam MS, van Wilderen LJGW, Bredenbeck J, Santoro F, Burghardt I. Vibrationally resolved two-photon electronic spectra including vibrational pre-excitation: Theory and application to VIPER spectroscopy with two-photon excitation. J Chem Phys 2023; 158:064201. [PMID: 36792506 DOI: 10.1063/5.0132608] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023] Open
Abstract
Following up on our previous work on vibrationally resolved electronic absorption spectra including the effect of vibrational pre-excitation [von Cosel et al., J. Chem. Phys. 147, 164116 (2017)], we present a combined theoretical and experimental study of two-photon-induced vibronic transitions in polyatomic molecules that are probed in the VIbrationally Promoted Electronic Resonance experiment using two-photon excitation (2P-VIPER). In order to compute vibronic spectra, we employ time-independent and time-dependent methods based on the evaluation of Franck-Condon overlap integrals and Fourier transformations of time-domain correlation functions, respectively. The time-independent approach uses a generalized version of the FCclasses method, while the time-dependent approach relies on the analytical evaluation of Gaussian moments within the harmonic approximation, including Duschinsky rotation effects. For the Coumarin 6 dye, two-dimensional 2P-VIPER experiments involving excitation to the lowest-lying singlet excited state (S1) are presented and compared with corresponding one-photon VIPER spectra. In both cases, coumarin ring modes and a CO stretch mode show VIPER activity, albeit with different relative intensities. Selective pre-excitation of these modes leads to a pronounced redshift of the low-frequency edge of the electronic absorption spectrum, which is a prerequisite for the VIPER experiment. Theoretical analysis underscores the role of interference between Franck-Condon and Herzberg-Teller effects in the two-photon experiment, which is at the root of the observed intensity distribution.
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Affiliation(s)
- Maximiliane Horz
- Institute of Physical and Theoretical Chemistry, Goethe University Frankfurt, Max-von-Laue-Str. 7, 60438 Frankfurt, Germany
| | - Hafiz M A Masood
- Institute of Biophysics, Goethe University Frankfurt, Max-von-Laue-Str. 1, 60438 Frankfurt, Germany
| | - Hendrik Brunst
- Institute of Biophysics, Goethe University Frankfurt, Max-von-Laue-Str. 1, 60438 Frankfurt, Germany
| | - Javier Cerezo
- Departamento de Química and Institute for Advanced Research in Chemical Sciences (IAdChem), Universidad Autónoma de Madrid, 28049 Madrid, Spain
| | - David Picconi
- Institute of Physical and Theoretical Chemistry, Goethe University Frankfurt, Max-von-Laue-Str. 7, 60438 Frankfurt, Germany
| | - Hannah Vormann
- Institute of Physical and Theoretical Chemistry, Goethe University Frankfurt, Max-von-Laue-Str. 7, 60438 Frankfurt, Germany
| | - Madhava Shyam Niraghatam
- Institute of Physical and Theoretical Chemistry, Goethe University Frankfurt, Max-von-Laue-Str. 7, 60438 Frankfurt, Germany
| | - Luuk J G W van Wilderen
- Institute of Biophysics, Goethe University Frankfurt, Max-von-Laue-Str. 1, 60438 Frankfurt, Germany
| | - Jens Bredenbeck
- Institute of Biophysics, Goethe University Frankfurt, Max-von-Laue-Str. 1, 60438 Frankfurt, Germany
| | - Fabrizio Santoro
- Consiglio Nazionale delle Ricerche - CNR, Istituto di Chimica dei Composti Organo Metallici (ICCOM-CNR), SS di Pisa, Via G. Moruzzi 1, I-56124 Pisa, Italy
| | - Irene Burghardt
- Institute of Physical and Theoretical Chemistry, Goethe University Frankfurt, Max-von-Laue-Str. 7, 60438 Frankfurt, Germany
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Cerezo J, García-Iriepa C, Santoro F, Navizet I, Prampolini G. Unraveling the contributions to the spectral shape of flexible dyes in solution: insights on the absorption spectrum of an oxyluciferin analogue. Phys Chem Chem Phys 2023; 25:5007-5020. [PMID: 36722876 DOI: 10.1039/d2cp05701h] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
We present a computational investigation of the absorption spectrum in water of 5,5-spirocyclopropyl-oxyluciferin (5,5-CprOxyLH), an analogue of the emitter compound responsible for the bioluminescence in fireflies. Several factors participate in determining the 5,5-CprOxyLH's spectral shape: (i) the contribution of the four close-energy excited states, which show significant non-adiabatic couplings, (ii) the flexible molecular structure and (iii) the specific interactions established with the surrounding environment, which strongly couple the protic solvent dynamics with the dye's spectral response. To tackle the challenge to capture and dissect the role of all these effects we preliminarily investigate the role of non-adiabatic couplings with quantum dynamics simulations and a linear vibronic coupling model in the gas phase. Then, we account for both the molecular flexibility and solvent interactions by resorting to a mixed quantum classical protocol, named Adiabatic Molecular Dynamics generalized Vertical Gradient (Ad-MD|gVG), which is built on a method recently proposed by some of us. It is rooted in the partition between stiff degrees of freedom of the dye, accounted for at the vibronic level within the harmonic approximation, and flexible degrees of freedom of the solute (and of the solvent), described classically through a sampling based on Molecular Dynamics (MD). Ad-MD|gVG avoids spurious effects arising in the excited state Hessians due to non-adiabatic couplings, and can therefore be applied to account for the contributions of the first four excited states to the 5,5-CprOxyLH absorption spectrum. The final simulated spectrum is in very good agreement with the experiment, especially when the MD is driven by a refined quantum-mechanically derived force-field. More importantly, the origin of each separate contribution to the spectral shape is appropriately accounted for, paving the way to future applications of the method to more complex systems or alternative spectroscopies, as emission or circular dichroism.
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Affiliation(s)
- Javier Cerezo
- Departamento de Química and Institute for Advanced Research in Chemical Sciences (IAdChem), Universidad Autónoma de Madrid, 28049 Madrid, Spain. .,CNR - Consiglio Nazionale delle Ricerche, Istituto di Chimica dei Composti Organo Metallici (ICCOM-CNR), SS di Pisa, Area della Ricerca, via G. Moruzzi 1, I-56124 Pisa, Italy.
| | - Cristina García-Iriepa
- Universidad de Alcalá, Departamento de Química Analítica, Química Física e Ingeniería Química, Grupo de Reactividad y Estructura Molecular (RESMOL), 28806 Alcalá de Henares (Madrid), Spain. .,Universidad de Alcalá, Instituto de Investigación Química "Andrés M. del Río" (IQAR), 28806 Alcalá de Henares (Madrid), Spain
| | - Fabrizio Santoro
- CNR - Consiglio Nazionale delle Ricerche, Istituto di Chimica dei Composti Organo Metallici (ICCOM-CNR), SS di Pisa, Area della Ricerca, via G. Moruzzi 1, I-56124 Pisa, Italy.
| | - Isabelle Navizet
- Univ Gustave Eiffel, Univ Paris Est Creteil, CNRS, UMR 8208, MSME, F-77454 Marne-la-Vallée, France
| | - Giacomo Prampolini
- CNR - Consiglio Nazionale delle Ricerche, Istituto di Chimica dei Composti Organo Metallici (ICCOM-CNR), SS di Pisa, Area della Ricerca, via G. Moruzzi 1, I-56124 Pisa, Italy.
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Cerezo J, Santoro F. FCclasses3: Vibrationally-resolved spectra simulated at the edge of the harmonic approximation. J Comput Chem 2023; 44:626-643. [PMID: 36380723 PMCID: PMC10100349 DOI: 10.1002/jcc.27027] [Citation(s) in RCA: 30] [Impact Index Per Article: 30.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2022] [Revised: 10/03/2022] [Accepted: 10/16/2022] [Indexed: 11/17/2022]
Abstract
We introduce FCclasses3, a code to carry out vibronic simulations of electronic spectra and nonradiative rates, based on the harmonic approximation. Key new features are: implementation of the full family of vertical and adiabatic harmonic models, vibrational analysis in curvilinear coordinates, extension to several electronic spectroscopies and implementation of time-dependent approaches. The use of curvilinear valence internal coordinates allows the adoption of quadratic model potential energy surfaces (PES) of the initial and final states expanded at arbitrary configurations. Moreover, the implementation of suitable projectors provides a robust framework for defining reduced-dimensionality models by sorting flexible coordinates out of the harmonic subset, so that they can then be treated at anharmonic level, or with mixed quantum classical approaches. A set of tools to facilitate input preparation and output analysis is also provided. We show the program at work in the simulation of different spectra (one and two-photon absorption, emission and resonance Raman) and internal conversion rate of a typical rigid molecule, anthracene. Then, we focus on absorption and emission spectra of a series of flexible polyphenyl molecules, highlighting the relevance of some of the newly implemented features. The code is freely available at http://www.iccom.cnr.it/en/fcclasses/.
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Affiliation(s)
- Javier Cerezo
- Departamento de Química and Institute for Advanced Research in Chemical Sciences (IAdChem)Universidad Autónoma de MadridMadridSpain
- Consiglio Nazionale delle RicercheIstituto di Chimica dei Composti Organo Metallici (ICCOM‐CNR)PisaItaly
| | - Fabrizio Santoro
- Consiglio Nazionale delle RicercheIstituto di Chimica dei Composti Organo Metallici (ICCOM‐CNR)PisaItaly
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8
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Xu Q, Aranda D, Yaghoubi Jouybari M, Liu Y, Wang M, Cerezo J, Improta R, Santoro F. Nonadiabatic Vibrational Resonance Raman Spectra from Quantum Dynamics Propagations with LVC Models. Application to Thymine. J Phys Chem A 2022; 126:7468-7479. [PMID: 36099554 PMCID: PMC9596142 DOI: 10.1021/acs.jpca.2c05271] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
![]()
We present a viable protocol to compute vibrational resonance
Raman
(vRR) spectra for systems with several close-lying and potentially
coupled electronic states. It is based on the parametrization of linear
vibronic coupling (LVC) models from time-dependent density functional
theory (TD-DFT) calculations and quantum dynamics propagations of
vibronic wavepackets with the multilayer version of the multiconfiguration
time-dependent Hartree (ML-MCTDH) method. Our approach is applied
to thymine considering seven coupled electronic states, comprising
the three lowest bright states, and all vibrational coordinates. Computed
vRR at different excitation wavelengths are in good agreement with
the available experimental data. Up to 250 nm the signal is dominated
by the lowest HOMO → LUMO transition, whereas at 233 nm, in
the valley between the two lowest energy absorption bands, the contributions
of all the three bright states, and their interferences and couplings,
are important. Inclusion of solvent (water) effects improves the agreement
with experiment, reproducing the coalescence of vibrational bands
due to CC and C=O stretchings. With our approach we disentangle
and assess the effect of interferences between the contribution of
different quasi-resonant states to the transition polarizability and
the effect of interstate couplings. Our findings strongly suggest
that in cases of close-lying and potentially coupled states a simple
inclusion of interference effects is not sufficient, and a fully nonadiabatic
computation should instead be performed. We also document that for
systems with strong couplings and quasi-degenerate states, the use
of HT perturbative approach, not designed for these cases, may lead
to large artifacts.
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Affiliation(s)
- Qiushuang Xu
- School of Physics and Optoelectronics Engineering, Ludong University, 264025 Yantai, Shandong, PR China.,School of Physics Engineering, Qufu Normal University, 2673100 Qufu, Shandong, PR China.,Consiglio Nazionale delle Ricerche, Istituto di Chimica dei Composti Organo Metallici (ICCOM-CNR), SS di Pisa, Area della Ricerca, via G. Moruzzi 1, I-56124 Pisa, Italy
| | - Daniel Aranda
- Instituto de Ciencia Molecular (ICMol)., Universidad de Valencia, c/Catedrático José Beltrán, 2, 46980 Paterna, Spain
| | - Martha Yaghoubi Jouybari
- Consiglio Nazionale delle Ricerche, Istituto di Chimica dei Composti Organo Metallici (ICCOM-CNR), SS di Pisa, Area della Ricerca, via G. Moruzzi 1, I-56124 Pisa, Italy
| | - Yanli Liu
- School of Physics and Optoelectronics Engineering, Ludong University, 264025 Yantai, Shandong, PR China
| | - Meishan Wang
- School of Physics and Optoelectronics Engineering, Ludong University, 264025 Yantai, Shandong, PR China
| | - Javier Cerezo
- Consiglio Nazionale delle Ricerche, Istituto di Chimica dei Composti Organo Metallici (ICCOM-CNR), SS di Pisa, Area della Ricerca, via G. Moruzzi 1, I-56124 Pisa, Italy.,Departamento de Química, Universidad Autónoma de Madrid, 28049 Madrid, Spain
| | - Roberto Improta
- Consiglio Nazionale delle Ricerche, Istituto di Biostrutture e Bioimmagini (IBB-CNR), Via De Amicis 95, I-80145 Napoli, Italy.,DTU Chemistry, Technical University of Denmark, Kemitorvet Bldg 207, DK-2800 Kongens Lyngby, Denmark
| | - Fabrizio Santoro
- Consiglio Nazionale delle Ricerche, Istituto di Chimica dei Composti Organo Metallici (ICCOM-CNR), SS di Pisa, Area della Ricerca, via G. Moruzzi 1, I-56124 Pisa, Italy
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9
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Sahu S, Sikdar Y, Bag R, Cerezo J, Cerón-Carrasco JP, Goswami S. Turn on Fluorescence Sensing of Zn2+ Based on Fused Isoindole-Imidazole Scaffold. Molecules 2022; 27:molecules27092859. [PMID: 35566211 PMCID: PMC9103770 DOI: 10.3390/molecules27092859] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2022] [Revised: 04/13/2022] [Accepted: 04/25/2022] [Indexed: 02/05/2023] Open
Abstract
Optical chemosensors caused a revolution in the field of sensing due to their high specificity, sensitivity, and fast detection features. Imidazole derivatives have offered promising features in the literature as they bear suitable donor/acceptor groups for the selective analytes in the skeleton. In this work, an isoindole-imidazole containing a Schiff base chemosensor (1-{3-[(2-Diethylamino-ethylimino)-methyl]-2-hydroxy-5-methyl-phenyl}-2H-imidazo[5,1-a]isoindole-3,5-dione) was designed and synthesized. The complete sensing phenomena have been investigated by means of UV-Vis, fluorescence, lifetime measurement, FT-IR, NMR and ESI-MS spectroscopic techniques. The optical properties of the synthesized ligand were investigated in 3:7 HEPES buffer:DMSO medium and found to be highly selective and sensitive toward Zn2+ ion through a fluorescence turn-on response with detection limit of 0.073 μm. Furthermore, this response is effective in gel form also. The competition studies reveal that the response of the probe for Zn2+ ion is unaffected by other relevant metal ions. The stoichiometric binding study was performed utilizing Job’s method which indicated a 1:1 sensor–Zn2+ ensemble. Computational calculations were performed to pinpoint the mechanism of sensing.
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Affiliation(s)
- Sutapa Sahu
- Department of Chemistry, University of Calcutta, 92, A.P.C. Road, Kolkata 700009, India; (S.S.); (R.B.)
| | - Yeasin Sikdar
- Department of Chemistry, The Bhawanipur Education Society College, 5, LalaLajpat Rai Sarani, Kolkata 700020, India;
| | - Riya Bag
- Department of Chemistry, University of Calcutta, 92, A.P.C. Road, Kolkata 700009, India; (S.S.); (R.B.)
| | - Javier Cerezo
- Departamento de Química, Universidad Autónoma de Madrid, 28049 Madrid, Spain;
| | - José P. Cerón-Carrasco
- Centro Universitario de la Defensa, Academia General del Aire, Universidad Politécnica de Cartagena, C/Coronel López Peña S/N, Santiago de La Ribera, 30720 Murcia, Spain
- Correspondence: (J.P.C.-C.); (S.G.)
| | - Sanchita Goswami
- Department of Chemistry, University of Calcutta, 92, A.P.C. Road, Kolkata 700009, India; (S.S.); (R.B.)
- Correspondence: (J.P.C.-C.); (S.G.)
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10
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Abstract
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In this work, we
calculate the partition functions and thermodynamic
quantities of molecular hydrogen isotopologues using the rovibrational
energy levels provided by the highly accurate ab initio adiabatic potential energy functions recently determined by Pachucki
and Komasa (Pachucki, K.; Komasa, J. J. Chem. Phys.2014, 141, 224103). The partition
functions are calculated by including all bound energy levels of the
isotopologues, up to their dissociation limits, plus the quasi-bound
levels lying below the centrifugal potential barriers. For the homonuclear
isotopologues, H2, D2, and T2, we
also determine the partition functions and thermodynamic quantities
of the normal mixtures using the statistical treatment recently proposed
by Colonna et al. (Colonna, G.; D’Angola, A.; Capitelli, M. Int. J. Hydrogen Energy2012, 37, 9656) based on the definition of the partition function of the
mixture, which avoids inconsistencies in the values of the thermodynamic
quantities depending directly on the internal partition function,
in the high-temperature limit.
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Affiliation(s)
- José Zúñiga
- Departamento de Química Física, Universidad de Murcia, 30100 Murcia, Spain
| | - Adolfo Bastida
- Departamento de Química Física, Universidad de Murcia, 30100 Murcia, Spain
| | - Alberto Requena
- Departamento de Química Física, Universidad de Murcia, 30100 Murcia, Spain
| | - Javier Cerezo
- Departamento de Química, Universidad Autónoma de Madrid, 28049 Madrid, Spain
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11
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Santoro F, Green JA, Martinez-Fernandez L, Cerezo J, Improta R. Quantum and semiclassical dynamical studies of nonadiabatic processes in solution: achievements and perspectives. Phys Chem Chem Phys 2021; 23:8181-8199. [PMID: 33875988 DOI: 10.1039/d0cp05907b] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
We concisely review the main methodological approaches to model nonadiabatic dynamics in isotropic solutions and their applications. Three general classes of models are identified as the most used to include solvent effects in the simulations. The first model describes the solvent as a set of harmonic collective modes coupled to the solute degrees of freedom, and the second as a continuum, while the third explicitly includes solvent molecules in the calculations. The issues related to the use of these models in semiclassical and quantum dynamical simulations are discussed, as well as the main limitations and perspectives of each approach.
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Affiliation(s)
- Fabrizio Santoro
- CNR-Consiglio Nazionale delle Ricerche, Istituto di Chimica dei Composti Organo Metallici (ICCOM-CNR), SS di Pisa, Area della Ricerca, via G. Moruzzi 1, I-56124 Pisa, Italy.
| | - James A Green
- CNR-Consiglio Nazionale delle Ricerche, Istituto di Biostrutture e Bioimmagini (IBB-CNR), via Mezzocannone 16, I-80136 Napoli, Italy.
| | - Lara Martinez-Fernandez
- Departamento de Química, Facultad de Ciencias and Institute for Advanced Research in Chemistry (IADCHEM), Universidad Autónoma de Madrid, Campus de Excelencia UAM-CSIC, 28049 Madrid, Spain
| | - Javier Cerezo
- Departamento de Química, Facultad de Ciencias and Institute for Advanced Research in Chemistry (IADCHEM), Universidad Autónoma de Madrid, Campus de Excelencia UAM-CSIC, 28049 Madrid, Spain
| | - Roberto Improta
- CNR-Consiglio Nazionale delle Ricerche, Istituto di Biostrutture e Bioimmagini (IBB-CNR), via Mezzocannone 16, I-80136 Napoli, Italy.
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12
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Abstract
Protein folding evolves by exploring the conformational space with a subtle balance between enthalpy and entropy changes which eventually leads to a decrease of free energy upon reaching the folded structure. A complete understanding of this process requires, therefore, a deep insight into both contributions to free energy. In this work, we clarify the role of entropy in favoring the stabilization of folded structures in polyalanine peptides with up to 12 residues. We use a novel method referred to as K2V that allows us to obtain the potential-energy landscapes in terms of residue conformations extracted from molecular dynamics simulations at conformational equilibrium and yields folding thermodynamic magnitudes, which are in agreement with the experimental data available. Our results demonstrate that the folded structures of the larger polyalanine chains are stabilized with respect to the folded structures of the shorter chains by both an energetic contribution coming from the formation of the intramolecular hydrogen bonds and an entropic contribution coming from an increase of the entropy of the solvent with approximate weights of 60 and 40%, respectively, thus unveiling a key piece in the puzzle of protein folding. In addition, the ability of the K2V method to provide the enthalpic and entropic contributions for individual residues along the peptide chain makes it clear that the energetic and entropic stabilizations are basically governed by the nearest neighbor residue conformations, with the folding propensity being rationalized in terms of triads of residues.
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Affiliation(s)
- Adolfo Bastida
- Departamento de Química Física, Universidad de Murcia, 30100 Murcia, Spain
| | - José Zúñiga
- Departamento de Química Física, Universidad de Murcia, 30100 Murcia, Spain
| | - Alberto Requena
- Departamento de Química Física, Universidad de Murcia, 30100 Murcia, Spain
| | - Beatriz Miguel
- Departamento de Ingeniería Química y Ambiental, Universidad Politécnica de Cartagena, 30203 Cartagena, Spain
| | - Javier Cerezo
- Departamento de Química, Universidad Autónoma de Madrid, 28049 Madrid, Spain
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13
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Segalina A, Cerezo J, Prampolini G, Santoro F, Pastore M. Accounting for Vibronic Features through a Mixed Quantum-Classical Scheme: Structure, Dynamics, and Absorption Spectra of a Perylene Diimide Dye in Solution. J Chem Theory Comput 2020; 16:7061-7077. [DOI: 10.1021/acs.jctc.0c00919] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Affiliation(s)
- Alekos Segalina
- Université de Lorraine & CNRS, LPCT, UMR 7019, F-54000 Nancy, France
| | - Javier Cerezo
- Departamento de Química and Institute for Advanced Research in Chemical Sciences (IAdChem), Universidad Autónoma de Madrid, 28049 Madrid, Spain
| | - Giacomo Prampolini
- Istituto di Chimica dei Composti Organo Metallici, Consiglio Nazionale delle Ricerche, (ICCOM-CNR) SS di Pisa, Area della Ricerca, via G. Moruzzi 1, I-56124 Pisa, Italy
| | - Fabrizio Santoro
- Istituto di Chimica dei Composti Organo Metallici, Consiglio Nazionale delle Ricerche, (ICCOM-CNR) SS di Pisa, Area della Ricerca, via G. Moruzzi 1, I-56124 Pisa, Italy
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14
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Humeniuk A, Bužančić M, Hoche J, Cerezo J, Mitrić R, Santoro F, Bonačić-Koutecký V. Predicting fluorescence quantum yields for molecules in solution: A critical assessment of the harmonic approximation and the choice of the lineshape function. J Chem Phys 2020; 152:054107. [DOI: 10.1063/1.5143212] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- Alexander Humeniuk
- Institut für Physikalische und Theoretische Chemie, Universität Würzburg, Am Hubland, 97074 Würzburg, Germany
| | - Margarita Bužančić
- Center of Excellence for Science and Technology-Integration of Mediterranean Region (STIM), Faculty of Science, University of Split, Poljička cesta 35, 2100 Split, Croatia
| | - Joscha Hoche
- Institut für Physikalische und Theoretische Chemie, Universität Würzburg, Am Hubland, 97074 Würzburg, Germany
| | - Javier Cerezo
- Departamento de Química, Facultad de Ciencias, Universidad Autónoma de Madrid, 28049 Madrid, Spain
| | - Roland Mitrić
- Institut für Physikalische und Theoretische Chemie, Universität Würzburg, Am Hubland, 97074 Würzburg, Germany
| | - Fabrizio Santoro
- Istituto di Chimica dei Composti Organometallici (ICCOM–CNR), Area della Ricerca del CNR, Via Moruzzi 1, I-56124 Pisa, Italy
| | - Vlasta Bonačić-Koutecký
- Center of Excellence for Science and Technology-Integration of Mediterranean Region (STIM), Faculty of Science, University of Split, Poljička cesta 35, 2100 Split, Croatia
- Department of Chemistry, Humboldt Universität zu Berlin, Brook-Taylor-Strasse 2, 12489 Berlin, Germany
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15
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Eskandari M, Roldao JC, Cerezo J, Milián-Medina B, Gierschner J. Counterion-Mediated Crossing of the Cyanine Limit in Crystals and Fluid Solution: Bond Length Alternation and Spectral Broadening Unveiled by Quantum Chemistry. J Am Chem Soc 2020; 142:2835-2843. [DOI: 10.1021/jacs.9b10686] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Affiliation(s)
- Morteza Eskandari
- Madrid Institute for Advanced Studies, IMDEA Nanoscience, C/Faraday 9, Ciudad Universitaria de Cantoblanco, 28049 Madrid, Spain
- Department of Chemistry, Institute for Advanced Studies in Basic Sciences, Zanjan, 45137-66731 Iran
| | - Juan Carlos Roldao
- Madrid Institute for Advanced Studies, IMDEA Nanoscience, C/Faraday 9, Ciudad Universitaria de Cantoblanco, 28049 Madrid, Spain
| | - Javier Cerezo
- Departamento de Química, Facultad de Ciencias, Universidad Autónoma de Madrid, 28049 Madrid, Spain
| | - Begoña Milián-Medina
- Department for Physical Chemistry, Faculty of Chemistry, University of Valencia, Avenida Dr. Moliner 50, 46100 Burjassot, Valencia, Spain
| | - Johannes Gierschner
- Madrid Institute for Advanced Studies, IMDEA Nanoscience, C/Faraday 9, Ciudad Universitaria de Cantoblanco, 28049 Madrid, Spain
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16
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Cerezo J, Aranda D, Avila Ferrer FJ, Prampolini G, Santoro F. Adiabatic-Molecular Dynamics Generalized Vertical Hessian Approach: A Mixed Quantum Classical Method To Compute Electronic Spectra of Flexible Molecules in the Condensed Phase. J Chem Theory Comput 2020; 16:1215-1231. [PMID: 31855424 DOI: 10.1021/acs.jctc.9b01009] [Citation(s) in RCA: 36] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
We present a general mixed quantum classical method that couples classical molecular dynamics (MD) and vibronic models to compute the shape of electronic spectra of flexible molecules in the condensed phase without, in principle, any phenomenological broadening. It is based on a partition of the nuclear motions of the solute + solvent system in "soft" and "stiff" vibrational modes and an adiabatic hypothesis that assumes that stiff modes are much faster than soft ones. In this framework, the spectrum is rigorously expressed as a conformational integral of quantum vibronic spectra along the stiff coordinates only. Soft modes enter at the classical level through the conformational distribution that is sampled with classical MD runs. In each configuration, reduced-dimensionality quadratic Hamiltonians are built in the space of the stiff coordinates only, thanks to a generalization of the Vertical Hessian harmonic model and an iterative application of projectors in internal coordinates to remove soft modes. Quantum vibronic spectra, specific for each sampled configuration of the soft coordinates, are then computed at the desired temperature with efficient time-dependent techniques, and the global spectrum simply arises from their average. For consistency of the whole procedure, classical MD runs are performed with quantum-mechanically derived force fields, parameterized at the same level of theory selected for generating the quadratic Hamiltonians along the stiff coordinates. Application to N-methyl-6-oxyquinolinium betaine in water, dithiophene in ethanol, and cyanidine in water is presented to show the performance of the method.
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Affiliation(s)
| | - Daniel Aranda
- CNR-Consiglio Nazionale delle Ricerche, Istituto di Chimica dei Composti Organo Metallici (ICCOM-CNR), SS di Pisa , Area della Ricerca, via G. Moruzzi 1 , I-56124 Pisa , Italy.,Departamento de Química Física, Facultad de Ciencias, Andalucía Tech , Universidad de Málaga , E-29071 Málaga , Spain
| | - Francisco José Avila Ferrer
- Departamento de Química Física, Facultad de Ciencias, Andalucía Tech , Universidad de Málaga , E-29071 Málaga , Spain
| | - Giacomo Prampolini
- CNR-Consiglio Nazionale delle Ricerche, Istituto di Chimica dei Composti Organo Metallici (ICCOM-CNR), SS di Pisa , Area della Ricerca, via G. Moruzzi 1 , I-56124 Pisa , Italy
| | - Fabrizio Santoro
- CNR-Consiglio Nazionale delle Ricerche, Istituto di Chimica dei Composti Organo Metallici (ICCOM-CNR), SS di Pisa , Area della Ricerca, via G. Moruzzi 1 , I-56124 Pisa , Italy
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17
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Abstract
We investigate the interresidual and intraresidual correlations between dihedral displacements of adjacent residues within model polyalanine peptides by analyzing extensive molecular dynamics trajectories. Correlations are evaluated individually at different residue conformations covering the whole (ϕi,ψi)-space. From these, we draw maps that unveil an unprecedented strong intramolecular correlation displaying opposite (correlated/anticorrelated) behaviors at different conformations. Both interresidual and intraresidual correlations arise from the propensity of the peptide to minimize the overall atomic displacements.
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Affiliation(s)
- Adolfo Bastida
- Departamento de Química Física , Universidad de Murcia , 30100 Murcia , Spain
| | | | - José Zúñiga
- Departamento de Química Física , Universidad de Murcia , 30100 Murcia , Spain
| | - Alberto Requena
- Departamento de Química Física , Universidad de Murcia , 30100 Murcia , Spain
| | - Javier Cerezo
- Departamento de Química , Universidad Autónoma de Madrid , 28049 Madrid , Spain
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18
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Abstract
A novel energetic route driving the folding of a polyalanine peptide from an extended conformation to its α-helix native conformation is described, supported by a new method to compute mean potential energy surfaces accurately in terms of the dihedral angles of the peptide chain from extensive molecular dynamics simulations. The energetic self-folding (ESF) route arises specifically from the balance between the intrinsic propensity of alanine residues toward the αR conformation and two, opposite, effects: the destabilizing interaction with neighbor residues and the stabilizing formation of native hydrogen bonds, with the latter being dominant for large peptide lengths. The ESF mechanism provides simple but robust support to the nucleation-elongation or zipper models and offers a quantitative energetic funnel picture of the folding process. The mechanism is validated by the reasonable agreement between the computed folding energies and the experimental values.
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Affiliation(s)
- Adolfo Bastida
- Departamento de Química Física , Universidad de Murcia , 30100 Murcia , Spain
| | - José Zúñiga
- Departamento de Química Física , Universidad de Murcia , 30100 Murcia , Spain
| | - Alberto Requena
- Departamento de Química Física , Universidad de Murcia , 30100 Murcia , Spain
| | - Javier Cerezo
- Departamento de Química Física , Universidad de Murcia , 30100 Murcia , Spain
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19
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Frati F, de Groot F, Cerezo J, Santoro F, Cheng L, Faber R, Coriani S. Coupled cluster study of the x-ray absorption spectra of formaldehyde derivatives at the oxygen, carbon, and fluorine K-edges. J Chem Phys 2019. [DOI: 10.1063/1.5097650] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- Federica Frati
- Debye Institute for Nanomaterials Science, Utrecht University, Universiteitsweg 99, 3584 GC Utrecht, The Netherlands
| | - Frank de Groot
- Debye Institute for Nanomaterials Science, Utrecht University, Universiteitsweg 99, 3584 GC Utrecht, The Netherlands
| | - Javier Cerezo
- Departamento de Química, Facultad de Ciencias, Universidad Autónoma de Madrid, 28049 Madrid, Spain
| | - Fabrizio Santoro
- Istituto di Chimica dei Composti Organometallici (ICCOM–CNR), Area della Ricerca del CNR, Via Moruzzi 1, I-56124 Pisa, Italy
| | - Lan Cheng
- Department of Chemistry, Krieger School of Arts and Sciences, Johns Hopkins University, Baltimore, Maryland 21218, USA
| | - Rasmus Faber
- DTU Chemistry, Technical University of Denmark, DK-2800 Kongens Lyngby, Denmark
| | - Sonia Coriani
- DTU Chemistry, Technical University of Denmark, DK-2800 Kongens Lyngby, Denmark
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20
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Martínez Fernández L, Cerezo J, Asha H, Santoro F, Coriani S, Improta R. The Absorption Spectrum of Guanine Based Radicals: a Comparative Computational Analysis. CHEMPHOTOCHEM 2019. [DOI: 10.1002/cptc.201900107] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Affiliation(s)
- Lara Martínez Fernández
- Departamento de Química, Facultad de Ciencias, Mòdulo13Universidad Autónoma de Madrid, Campus de Excelencia UAM-CSIC Cantoblanco 28049 Madrid Spain
| | - Javier Cerezo
- Departamento de Química, Facultad de Ciencias, Mòdulo13Universidad Autónoma de Madrid, Campus de Excelencia UAM-CSIC Cantoblanco 28049 Madrid Spain
| | - Haritha Asha
- Istituto di Biostrutture e Bioimmagini-CNR Via Mezzocannone 6 I-80134 Napoli
| | - Fabrizio Santoro
- Istituto di Chimica dei Composti Organometallici (ICCOM-CNR)Area della Ricerca del CNR Via Moruzzi 1 I-56124 Pisa
| | - Sonia Coriani
- DTU ChemistryTechnical University of Denmark, Kemitorvet Building 207 DK-2800 Kongens Lyngby Denmark
| | - Roberto Improta
- Istituto di Biostrutture e Bioimmagini-CNR Via Mezzocannone 6 I-80134 Napoli
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21
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Avila Ferrer FJ, Angeli C, Cerezo J, Coriani S, Ferretti A, Santoro F. The Intriguing Case of the One‐Photon and Two‐Photon Absorption of a Prototypical Symmetric Squaraine: Comparison of TDDFT and Wave‐Function Methods. CHEMPHOTOCHEM 2019. [DOI: 10.1002/cptc.201900121] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Affiliation(s)
| | - Celestino Angeli
- Dipartimento di Scienze Chimiche e FarmaceuticheUniversità di Ferrara via Borsari 46 44121 Ferrara Italy
| | - Javier Cerezo
- Departamento de Química, Facultad de Ciencias, Módulo 13Universidad Autónoma de Madrid, Campus de Excelencia UAM-CSIC, Cantoblanco 28049 Madrid Spain
| | - Sonia Coriani
- DTU ChemistryTechnical University of Denmark, Kemitorvet Building 207 DK-2800 Kongens Lyngby Denmark
| | - Alessandro Ferretti
- Istituto di Chimica dei Composti Organometallici (ICCOM-CNR) Area della Ricerca del CNR, Via Moruzzi 1 I-56124 Pisa
| | - Fabrizio Santoro
- Istituto di Chimica dei Composti Organometallici (ICCOM-CNR) Area della Ricerca del CNR, Via Moruzzi 1 I-56124 Pisa
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22
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Prampolini G, Ingrosso F, Cerezo J, Iagatti A, Foggi P, Pastore M. Short- and Long-Range Solvation Effects on the Transient UV-Vis Absorption Spectra of a Ru(II)-Polypyridine Complex Disentangled by Nonequilibrium Molecular Dynamics. J Phys Chem Lett 2019; 10:2885-2891. [PMID: 31082237 DOI: 10.1021/acs.jpclett.9b00944] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Evidence of subtle effects in the dynamic reorganization of a protic solvent in its first- and farther-neighbor shells, in response to the sudden change in the solute's electronic distribution upon excitation, is unveiled by a multilevel computational approach. Through the combination of nonequilibrium molecular dynamics and quantum mechanical calculations, the experimental time evolution of the transient T1 absorption spectra of a heteroleptic Ru(II)-polypyridine complex in ethanol or dimethyl sulfoxide solution is reproduced and rationalized in terms of both fast and slow solvent re-equilibration processes, which are found responsible for the red shift and broadening experimentally observed only in the protic medium. Solvent orientational correlation functions and a time-dependent analysis of the solvation structure confirm that the initial, fast observed red shift can be traced back to the destruction-formation of hydrogen bond networks in the first-neighbor shell, whereas the subsequent shift, evident in the [20-500] ps range and accompanied by a large broadening of the signal, is connected to a collective reorientation of the second and farther solvation shells, which significantly changes the electrostatic embedding felt by the excited solute.
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Affiliation(s)
- Giacomo Prampolini
- Istituto di Chimica dei Composti OrganoMetallici (ICCOM-CNR) , Area della Ricerca, via G. Moruzzi 1 , I-56124 Pisa , Italy
| | - Francesca Ingrosso
- Université de Lorraine & CNRS , Laboratoire de Physique et Chimie Théoriques (LPCT) , F-54000 Nancy , France
| | - Javier Cerezo
- Departamento de Química, Facultad de Ciencias , Universidad Autonoma de Madrid , 28049 Madrid , Spain
| | - Alessandro Iagatti
- European Laboratory for Non Linear Spectroscopy (LENS) , Università di Firenze , Via Nello Carrara 1 , I-50019 Sesto Fiorentino, Florence , Italy
- INO-CNR, Istituto Nazionale di Ottica , Consiglio Nazionale delle Ricerche , Largo Fermi 6 , I-50125 Florence , Italy
| | - Paolo Foggi
- European Laboratory for Non Linear Spectroscopy (LENS) , Università di Firenze , Via Nello Carrara 1 , I-50019 Sesto Fiorentino, Florence , Italy
- INO-CNR, Istituto Nazionale di Ottica , Consiglio Nazionale delle Ricerche , Largo Fermi 6 , I-50125 Florence , Italy
- Dipartimento di Chimica, Biologia e Biotecnologie , Università di Perugia , Via Elce di Sotto 8 , I-06123 Perugia , Italy
| | - Mariachiara Pastore
- Université de Lorraine & CNRS , Laboratoire de Physique et Chimie Théoriques (LPCT) , F-54000 Nancy , France
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23
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Liu Y, Martínez-Fernández L, Cerezo J, Prampolini G, Improta R, Santoro F. Multistate coupled quantum dynamics of photoexcited cytosine in gas-phase: Nonadiabatic absorption spectrum and ultrafast internal conversions. Chem Phys 2018. [DOI: 10.1016/j.chemphys.2018.08.030] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
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24
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Martinez-Fernandez L, Prampolini G, Cerezo J, Liu Y, Santoro F, Improta R. Solvent effect on the energetics of proton coupled electron transfer in guanine-cytosine pair in chloroform by mixed explicit and implicit solvation models. Chem Phys 2018. [DOI: 10.1016/j.chemphys.2018.07.012] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
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25
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Aranda D, Cerezo J, Pescitelli G, Avila Ferrer FJ, Soto J, Santoro F. A computational study of the vibrationally-resolved electronic circular dichroism spectra of single-chain transoid and cisoid oligothiophenes in chiral conformations. Phys Chem Chem Phys 2018; 20:21864-21880. [PMID: 30105334 DOI: 10.1039/c8cp03482f] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
We simulate the vibronic profile of the electronic circular dichroism (ECD) spectra of oligothiophenes in cisoid and transoid chiral arrangements. We consider oligomers of different lengths, from two to fifteen units, and investigate extensively how the ECD spectral shapes depend on the inter-ring torsions. In general, the molecular structures we consider are not stationary points of the ground state potential energy surface. Therefore, in order to perform vibronic calculations, we present a new computational protocol able to define reduced-dimensionality models where the effect of the off-equilibrium modes is removed. This is done adopting a description of the vibrational motions in curvilinear internal coordinates, and vertical harmonic models coupled with an iterative application of projectors to define energy Hessians, and therefore effective normal modes, in the space complementary to the one of the off-equilibrium coordinates. Although we consider both Franck-Condon and Herzberg-Teller contributions, the results show that transoid twisted ribbons always give rise to monosignated ECD spectra, while bi-signated and multi-signated spectra are expected for cisoid helices. These findings are explained on the basis of the different transition strengths of the lowest electronic states imparted by the different spatial arrangement, that is almost linear for transoid structures and more globular for cisoid ones. We predicted the chiroptical response of a large number of possible molecular arrangements. These data are employed to critically discuss the experimental ECD of polythiophenes in different experimental conditions, forming either aggregates or host-guest complexes. The method here proposed to perform vibronic calculations in reduced-dimensionality models is of general applicability and its potential interest goes beyond the practical application presented here.
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Affiliation(s)
- Daniel Aranda
- Department of Physical Chemistry, Faculty of Science, University of Málaga, E-29071-Málaga, Spain
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Galván I, Cerezo J, Jorge A, Wakamatsu K. Molecular vibration as a novel explanatory mechanism for the expression of animal colouration. Integr Biol (Camb) 2018; 10:464-473. [PMID: 29951656 DOI: 10.1039/c8ib00100f] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Animal colouration is characterized by the concentration of pigments in integumentary structures and by the nanoscale arrangement of constitutive elements. However, the influence of molecular vibration on colour expression has been overlooked in biology. Molecular vibration occurs in the infrared spectral region, but vibrational and electronic properties can influence each other. Thus, the vibration of pigment molecules may also affect their absorption properties and the resulting colours. We calculated for the first time the relative contribution of molecular vibration (by means of Raman spectroscopy) and concentration (by means of HPLC) of melanin polymers, the most common animal pigments, to generate diversity in plumage colour in 47 species of birds. Vibrational characteristics explained >9 times more variance in colour expression than the concentration of melanins. Additionally, we modelled melanin Raman spectra on the basis of the chemical structure of their constituent monomers and calculated the Huang-Rhys factors for each vibrational mode, which indicate the contribution of these modes to the electronic spectra responsible for the resulting colours. High Huang-Rhys factors frequently coincided with the vibrational modes of melanin monomers. Our results can be explained by the influence of molecular vibration on the absorption properties of melanins. The colour of organisms may thus mainly result from the vibrational properties of their molecules and only residually from their concentration. As a given melanin concentration can give rise to different colours because different structural melanin conformations can present different vibrational characteristics, vibrational effects may favour phenotypic plasticity and thus constitute an important evolutionary force.
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Affiliation(s)
- Ismael Galván
- Department of Evolutionary Ecology, Doñana Biological Station, CSIC, 41092 Sevilla, Spain.
| | - Javier Cerezo
- Department of Physical Chemistry, University of Murcia, Campus Espinardo, 30100 Murcia, Spain
| | - Alberto Jorge
- Laboratory of Non-Destructive Analytical Techniques, National Museum of Natural Sciences, CSIC, 28006 Madrid, Spain
| | - Kazumasa Wakamatsu
- Department of Chemistry, Fujita Health University School of Health Sciences, Toyoake, Aichi 470-1192, Japan
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27
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Cerezo J, Prampolini G, Cacelli I. Developing accurate intramolecular force fields for conjugated systems through explicit coupling terms. Theor Chem Acc 2018. [DOI: 10.1007/s00214-018-2254-8] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
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Cerezo J, Aranda D, Avila Ferrer FJ, Prampolini G, Mazzeo G, Longhi G, Abbate S, Santoro F. Toward a general mixed quantum/classical method for the calculation of the vibronic ECD of a flexible dye molecule with different stable conformers: Revisiting the case of 2,2,2-trifluoro-anthrylethanol. Chirality 2018; 30:730-743. [DOI: 10.1002/chir.22853] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2018] [Revised: 02/19/2018] [Accepted: 02/20/2018] [Indexed: 12/30/2022]
Affiliation(s)
- Javier Cerezo
- Departamento de Química Física; Universidad de Murcia; Murcia Spain
| | - Daniel Aranda
- Consiglio Nazionale delle Ricerche-Istituto di Chimica dei Composti Organometallici (ICCOM-CNR); Pisa Italy
- Departamento de Química Física; Universidad de Málaga; Málaga Spain
| | | | - Giacomo Prampolini
- Consiglio Nazionale delle Ricerche-Istituto di Chimica dei Composti Organometallici (ICCOM-CNR); Pisa Italy
| | - Giuseppe Mazzeo
- Dipartimento di Medicina Molecolare e Traslazionale; Università di Brescia; Brescia Italy
| | - Giovanna Longhi
- Dipartimento di Medicina Molecolare e Traslazionale; Università di Brescia; Brescia Italy
| | - Sergio Abbate
- Dipartimento di Medicina Molecolare e Traslazionale; Università di Brescia; Brescia Italy
| | - Fabrizio Santoro
- Consiglio Nazionale delle Ricerche-Istituto di Chimica dei Composti Organometallici (ICCOM-CNR); Pisa Italy
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Cerezo J, Liu Y, Lin N, Zhao X, Improta R, Santoro F. Mixed Quantum/Classical Method for Nonadiabatic Quantum Dynamics in Explicit Solvent Models: The ππ*/nπ* Decay of Thymine in Water as a Test Case. J Chem Theory Comput 2018; 14:820-832. [PMID: 29207245 DOI: 10.1021/acs.jctc.7b01015] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
We present a novel mixed quantum classical dynamical method to include solvent effects on internal conversion (IC) processes. All the solute degrees of freedom are represented by a wavepacket moving according to nonadiabatic quantum dynamics, while the motion of an explicit solvent model is described by an ensemble of classical trajectories. The mutual coupling of the solute and solvent dynamics is included within a mean-field framework and the quantum and classical equations of motions are solved simultaneously. As a test case we apply our method to the ultrafast ππ* → nπ* decay of thymine in water. Solvent dynamical response modifies IC yield already on the 50 fs time scale. This effect is due to water librational motions that stabilize the most populated state. Pure static disorder, that is, the existence of different solvent configurations when photoexcitation takes place, also has a remarkable impact on the dynamics.
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Affiliation(s)
- Javier Cerezo
- CNR-Consiglio Nazionale delle Ricerche, Istituto di Chimica dei Composti Organo Metallici (ICCOM-CNR) , SS di Pisa, Area della Ricerca, via G. Moruzzi 1, I-56124 Pisa, Italy.,Departamento de Química Física, Universidad de Murcia , 30100 Murcia, Spain
| | - Yanli Liu
- CNR-Consiglio Nazionale delle Ricerche, Istituto di Chimica dei Composti Organo Metallici (ICCOM-CNR) , SS di Pisa, Area della Ricerca, via G. Moruzzi 1, I-56124 Pisa, Italy.,School of Physics and Optoelectronics Engineering, Ludong University , 264025 Yantai, P. R. China
| | - Na Lin
- State Key Laboratory of Crystal Materials, Shandong University , 250100 Jinan, Shandong, P. R. China
| | - Xian Zhao
- State Key Laboratory of Crystal Materials, Shandong University , 250100 Jinan, Shandong, P. R. China
| | - Roberto Improta
- CNR-Consiglio Nazionale delle Ricerche, Istituto di Biostrutture e Bioimmagini (IBB-CNR) , via Mezzocannone 16, I-80136 Napoli, Italy.,LIDYL, CEA, CNRS, Université Paris-Saclay , F-91191 Gif-sur-Yvette, France
| | - Fabrizio Santoro
- CNR-Consiglio Nazionale delle Ricerche, Istituto di Chimica dei Composti Organo Metallici (ICCOM-CNR) , SS di Pisa, Area della Ricerca, via G. Moruzzi 1, I-56124 Pisa, Italy
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von Cosel J, Cerezo J, Kern-Michler D, Neumann C, van Wilderen LJGW, Bredenbeck J, Santoro F, Burghardt I. Vibrationally resolved electronic spectra including vibrational pre-excitation: Theory and application to VIPER spectroscopy. J Chem Phys 2017; 147:164116. [DOI: 10.1063/1.4999455] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Affiliation(s)
- Jan von Cosel
- Institute of Physical and Theoretical Chemistry, Goethe University Frankfurt, Max-von-Laue-Str. 7, 60438 Frankfurt, Germany
| | - Javier Cerezo
- Departamento de Química Física, Universidad de Murcia, E-30071 Murcia, Spain
| | - Daniela Kern-Michler
- Institute of Biophysics, Goethe University Frankfurt, Max-von-Laue-Str. 1, 60438 Frankfurt, Germany
| | - Carsten Neumann
- Institute of Biophysics, Goethe University Frankfurt, Max-von-Laue-Str. 1, 60438 Frankfurt, Germany
| | | | - Jens Bredenbeck
- Institute of Biophysics, Goethe University Frankfurt, Max-von-Laue-Str. 1, 60438 Frankfurt, Germany
| | - Fabrizio Santoro
- Consiglio Nazionale delle Ricerche–CNR, Istituto di Chimica dei Composti Organo Metallici (ICCOM-CNR), UOS di Pisa, Via G. Moruzzi 1, I-56124 Pisa, Italy
| | - Irene Burghardt
- Institute of Physical and Theoretical Chemistry, Goethe University Frankfurt, Max-von-Laue-Str. 7, 60438 Frankfurt, Germany
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Cerezo J, Requena A, Zúñiga J, Piernas MJ, Santana MD, Pérez J, García L. Structure, Spectra, and DFT Simulation of Nickel Benzazolate Complexes with Tris(2-aminoethyl)amine Ligand. Inorg Chem 2017; 56:3663-3673. [DOI: 10.1021/acs.inorgchem.7b00059] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Javier Cerezo
- Departamento de
Química Física, Universidad de Murcia, E-30071 Murcia, Spain
| | - Alberto Requena
- Departamento de
Química Física, Universidad de Murcia, E-30071 Murcia, Spain
| | - José Zúñiga
- Departamento de
Química Física, Universidad de Murcia, E-30071 Murcia, Spain
| | - María José Piernas
- Departamento de Química Inorgánica, Universidad de Murcia, E-30071 Murcia, Spain
| | - M. Dolores Santana
- Departamento de Química Inorgánica, Universidad de Murcia, E-30071 Murcia, Spain
| | - José Pérez
- Departamento de
Ingeniería Minera, Geológica y Cartográfica,
Área de Química Inorgánica, Universidad Politécnica de Cartagena, E-30203 Cartagena, Spain
| | - Luís García
- Departamento de
Ingeniería Minera, Geológica y Cartográfica,
Área de Química Inorgánica, Universidad Politécnica de Cartagena, E-30203 Cartagena, Spain
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Cerezo J, Bernabé M, Lisbona A, Palací FJ. [Health personnel socialization and the role of resilience in the development of occupational well-being]. Rev Calid Asist 2017; 32:27-32. [PMID: 27544019 DOI: 10.1016/j.cali.2016.06.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/25/2015] [Revised: 05/30/2016] [Accepted: 06/01/2016] [Indexed: 06/06/2023]
Abstract
INTRODUCTION Socialization during the training of specialists is a key step in the subsequent adjustment and occupational well-being of health professionals in the hospital organisation. OBJECTIVE To analyse the relationship of socialization and resilience with the engagement responses of specialists in training. METHOD Convenience sampling was used, with 110 professionals from six teaching units of different hospitals participating in the study. Descriptive and mediational analysis of the study variables were performed using SPSS 21 and Macro Preacher and Hayes (2004). RESULTS The results show statistically significant relationships between socialization, resilience, and engagement. The mediating role of resilience is also shown (β=0.10; se=0.12; p<0.05, 95% CI: [0.02-0.23]) to generate engagement in health professionals. CONCLUSIONS An interaction effect is observed between socialization, and specialty moderates resilience. Therefore it can be seen that positive socialization and resilience can promote good performance.
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Affiliation(s)
- J Cerezo
- Agencia de Calidad Sanitaria de Andalucía
| | - M Bernabé
- Centro Universitario de la Defensa, Academia General Militar, Zaragoza, España
| | - A Lisbona
- Departamento de Psicología Social y de las Organizaciones, Universidad Nacional de Educación a Distancia, Madrid, España
| | - F J Palací
- Departamento de Psicología Social y de las Organizaciones, Universidad Nacional de Educación a Distancia, Madrid, España.
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Padula D, Cerezo J, Pescitelli G, Santoro F. The shape of the electronic circular dichroism spectrum of (2,6-dimethylphenyl)(phenyl)methanol: interplay between conformational equilibria and vibronic effects. Phys Chem Chem Phys 2017; 19:32349-32360. [DOI: 10.1039/c7cp06369e] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
Analysis of the interplay between conformational equilibria, solvent effects and vibronic contributions in the ECD spectra.
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Affiliation(s)
- Daniele Padula
- Department of Chemistry
- University of Liverpool
- Liverpool L69 7ZD
- UK
| | - Javier Cerezo
- Departamento de Química Física
- Universidad de Murcia
- 30100 Murcia
- Spain
| | - Gennaro Pescitelli
- Università di Pisa
- Dipartimento di Chimica e Chimica Industriale
- I-56124 Pisa
- Italy
| | - Fabrizio Santoro
- Consiglio Nazionale delle Ricerche – CNR
- Istituto di Chimica dei Composti Organo Metallici (ICCOM-CNR)
- Pisa
- Italy
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Cerezo J, Mazzeo G, Longhi G, Abbate S, Santoro F. Quantum-Classical Calculation of Vibronic Spectra along a Reaction Path: The Case of the ECD of Easily Interconvertible Conformers with Opposite Chiral Responses. J Phys Chem Lett 2016; 7:4891-4897. [PMID: 27934048 DOI: 10.1021/acs.jpclett.6b02484] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
We present a novel mixed method suitable for computing the low-to-middle resolution spectra of systems characterized by a large-amplitude motion s (defined by either a reaction or an internal path) coupled to a bath of harmonic oscillators r, which change with s. The method is based on an adiabatic approximation whereby s is considered much slower than r degrees of freedom and is treated classically. We show that the spectrum can be obtained by a suitable average of quantum vibronic spectra of the fast coordinates computed at representative values of the slow coordinate along the path. By our method we calculate the electronic circular dichroism (ECD) of 2,2,2-trifluoro-anthryl-ethanol, which possesses two conformers with opposite chirality separated by a low-energy barrier. Path-averaged spectra are significantly different from those obtained only at the stable minima: Agreement with experiment is improved. The method represents a generalization of those currently based on harmonic approximation.
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Affiliation(s)
- Javier Cerezo
- CNR-Consiglio Nazionale delle Ricerche, Istituto di Chimica dei Composti Organo Metallici (ICCOM-CNR), SS di Pisa, Area della Ricerca, via G. Moruzzi 1, I-56124 Pisa, Italy
| | - Giuseppe Mazzeo
- Dipartimento di Medicina Molecolare e Traslazionale, Università di Brescia , Viale Europa 11, I-25123 Brescia, Italy
| | - Giovanna Longhi
- Dipartimento di Medicina Molecolare e Traslazionale, Università di Brescia , Viale Europa 11, I-25123 Brescia, Italy
| | - Sergio Abbate
- Dipartimento di Medicina Molecolare e Traslazionale, Università di Brescia , Viale Europa 11, I-25123 Brescia, Italy
| | - Fabrizio Santoro
- CNR-Consiglio Nazionale delle Ricerche, Istituto di Chimica dei Composti Organo Metallici (ICCOM-CNR), SS di Pisa, Area della Ricerca, via G. Moruzzi 1, I-56124 Pisa, Italy
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35
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Cerezo J, Petrone A, Ferrer FJA, Donati G, Santoro F, Improta R, Rega N. Electronic spectroscopy of a solvatochromic dye in water: comparison of static cluster/implicit and dynamical/explicit solvent models on structures and energies. Theor Chem Acc 2016. [DOI: 10.1007/s00214-016-2009-3] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
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Cerezo J, Santoro F. Revisiting Vertical Models To Simulate the Line Shape of Electronic Spectra Adopting Cartesian and Internal Coordinates. J Chem Theory Comput 2016; 12:4970-4985. [PMID: 27586086 DOI: 10.1021/acs.jctc.6b00442] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Abstract
Vertical models for the simulation of spectroscopic line shapes expand the potential energy surface (PES) of the final state around the equilibrium geometry of the initial state. These models provide, in principle, a better approximation of the region of the band maximum. At variance, adiabatic models expand each PES around its own minimum. In the harmonic approximation, when the minimum energy structures of the two electronic states are connected by large structural displacements, adiabatic models can breakdown and are outperformed by vertical models. However, the practical application of vertical models faces the issues related to the necessity to perform a frequency analysis at a nonstationary point. In this contribution we revisit vertical models in harmonic approximation adopting both Cartesian (x) and valence internal curvilinear coordinates (s). We show that when x coordinates are used, the vibrational analysis at nonstationary points leads to a deficient description of low-frequency modes, for which spurious imaginary frequencies may even appear. This issue is solved when s coordinates are adopted. It is however necessary to account for the second derivative of s with respect to x, which here we compute analytically. We compare the performance of the vertical model in the s-frame with respect to adiabatic models and previously proposed vertical models in x- or Q1-frame, where Q1 are the normal coordinates of the initial state computed as combination of Cartesian coordinates. We show that for rigid molecules the vertical approach in the s-frame provides a description of the final state very close to the adiabatic picture. For sizable displacements it is a solid alternative to adiabatic models, and it is not affected by the issues of vertical models in x- and Q1-frames, which mainly arise when temperature effects are included. In principle the G matrix depends on s, and this creates nonorthogonality problems of the Duschinsky matrix connecting the normal modes of initial and final states in adiabatic approaches. We highlight that such a dependence of G on s is also an issue in vertical models, due to the necessity to approximate the kinetic term in the Hamiltonian when setting up the so-called GF problem. When large structural differences exist between the initial and the final-state minima, the changes in the G matrix can become too large to be disregarded.
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Affiliation(s)
- Javier Cerezo
- Istituto di Chimica dei Composti OrganoMetallici, Consiglio Nazionale delle Richerche (ICCOM-CNR) , Area della Ricerca, via G. Moruzzi 1, I-56124 Pisa, Italy
| | - Fabrizio Santoro
- Istituto di Chimica dei Composti OrganoMetallici, Consiglio Nazionale delle Richerche (ICCOM-CNR) , Area della Ricerca, via G. Moruzzi 1, I-56124 Pisa, Italy
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Cerezo J, Martínez-Fernández L, Improta R, Santoro F. Vibronic approach to the calculation of the decay rate of the photoexcited charge-transfer state of Guanine–Cytosine stacked dimer in water solution. Theor Chem Acc 2016. [DOI: 10.1007/s00214-016-1955-0] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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Liu Y, Cerezo J, Mazzeo G, Lin N, Zhao X, Longhi G, Abbate S, Santoro F. Vibronic Coupling Explains the Different Shape of Electronic Circular Dichroism and of Circularly Polarized Luminescence Spectra of Hexahelicenes. J Chem Theory Comput 2016; 12:2799-819. [DOI: 10.1021/acs.jctc.6b00109] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Affiliation(s)
- Yanli Liu
- State
Key Laboratory of Crystal Materials, Shandong University, 250100 Jinan, Shandong, People’s Republic of China
- 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
| | - Javier Cerezo
- 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
| | - Giuseppe Mazzeo
- Dipartimento
di Medicina Molecolare e Traslazionale, Universitá di Brescia, Viale Europa 11, 25123 Brescia, Italy
| | - Na Lin
- State
Key Laboratory of Crystal Materials, Shandong University, 250100 Jinan, Shandong, People’s Republic of China
| | - Xian Zhao
- State
Key Laboratory of Crystal Materials, Shandong University, 250100 Jinan, Shandong, People’s Republic of China
| | - Giovanna Longhi
- Dipartimento
di Medicina Molecolare e Traslazionale, Universitá di Brescia, Viale Europa 11, 25123 Brescia, Italy
| | - Sergio Abbate
- Dipartimento
di Medicina Molecolare e Traslazionale, Universitá di Brescia, Viale Europa 11, 25123 Brescia, Italy
| | - 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
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Cerezo J, Santoro F, Prampolini G. Comparing classical approaches with empirical or quantum-mechanically derived force fields for the simulation electronic lineshapes: application to coumarin dyes. Theor Chem Acc 2016. [DOI: 10.1007/s00214-016-1888-7] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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40
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Liu Y, Cerezo J, Santoro F, Rizzo A, Lin N, Zhao X. Theoretical investigation of the broad one-photon absorption line-shape of a flexible symmetric carbazole derivative. Phys Chem Chem Phys 2016; 18:22889-905. [DOI: 10.1039/c6cp04162k] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The one-photon absorption spectrum of a carbazole derivative has been studied by employing density functional response theory combined with a mixed quantum/classical approach to simulate the spectral shape.
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Affiliation(s)
- Yanli Liu
- State Key Laboratory of Crystal Materials
- Shandong University
- 250100 Jinan
- P. R. China
- CNR – Consiglio Nazionale delle Ricerche
| | - Javier Cerezo
- CNR – Consiglio Nazionale delle Ricerche
- Istituto di Chimica dei Composti Organo Metallici (ICCOM-CNR)
- I-56124 Pisa
- Italy
| | - Fabrizio Santoro
- CNR – Consiglio Nazionale delle Ricerche
- Istituto di Chimica dei Composti Organo Metallici (ICCOM-CNR)
- I-56124 Pisa
- Italy
| | - Antonio Rizzo
- CNR – Consiglio Nazionale delle Ricerche
- Istituto per i Processi Chimico Fisici (IPCF-CNR)
- I-56124 Pisa
- Italy
| | - Na Lin
- State Key Laboratory of Crystal Materials
- Shandong University
- 250100 Jinan
- P. R. China
| | - Xian Zhao
- State Key Laboratory of Crystal Materials
- Shandong University
- 250100 Jinan
- P. R. China
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Chantzis A, Cerezo J, Perrier A, Santoro F, Jacquemin D. Optical Properties of Diarylethenes with TD-DFT: 0-0 Energies, Fluorescence, Stokes Shifts, and Vibronic Shapes. J Chem Theory Comput 2015; 10:3944-57. [PMID: 26588538 DOI: 10.1021/ct500371u] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
This contribution is an investigation of both the structures and optical properties of a set of 14 diverse, recently synthesized diarylethenes using Time-Dependent Density Functional Theory (TD-DFT) at the ωB97X-D/6-31G(d) level of theory. The linear response (LR) and state-specific (SS) versions of the Polarizable Continuum Model (PCM) have been adopted to account for the bulk solvation effects and their relative performances were critically accessed. It is shown, for the first time in the case of nontrivial diarylethenes, that TD-DFT provides good agreement between the experimental absorption-fluorescence crossing points (AFCPs) and their theoretical counterparts when a robust model accounting for both geometrical relaxation and vibrational corrections is used instead of the vertical approximation. On the other hand, the theoretical estimates for the Stokes shifts based on the vertical transition energies were found to be in disagreement with respect to experiment, prompting us to simulate the absorption/emission vibronic band shapes. It is proved that difficulties associated with the breakdown of the harmonic approximation in Cartesian coordinates exist for the investigated system, and we show how they can be at least partially overcome by means of a vertical approach including Duschinsky effects. Our results provide a valuable basis to rationalize the experimental vibronic structure of both emission and absorption bands and are expected to be a significant asset to the understanding of the optical properties of diarylethene derivatives.
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Affiliation(s)
- Agisilaos Chantzis
- Laboratoire CEISAM - UMR CNR 6230, Université de Nantes , 2 Rue de la Houssiniére, BP 92208, 44322 Nantes Cedex 3, France
| | - Javier Cerezo
- Departamento de Química Física, Universidad de Murcia , 30110 Murcia, Spain
| | - Aurélie Perrier
- ITODYS, UMR 7086, Université Paris Diderot, Sorbonne Paris Cité , 15 Rue Jean Antoine de Baif, 75205 Paris Cedex 13, France
| | - Fabrizio Santoro
- CNR-Consiglio Nazionale delle Ricerche, Istituto di Chimica dei Composti OrganoMetallici (ICCOM-CNR), UOS di Pisa , Area della Ricerca, via G. Moruzzi 1, I-56124 Pisa, Italy
| | - Denis Jacquemin
- Laboratoire CEISAM - UMR CNR 6230, Université de Nantes , 2 Rue de la Houssiniére, BP 92208, 44322 Nantes Cedex 3, France.,Institut Universitaire de France, 103, bd Saint-Michel, F-75005 Paris Cedex 05, France
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Cerezo J, Avila Ferrer FJ, Prampolini G, Santoro F. Modeling Solvent Broadening on the Vibronic Spectra of a Series of Coumarin Dyes. From Implicit to Explicit Solvent Models. J Chem Theory Comput 2015; 11:5810-25. [DOI: 10.1021/acs.jctc.5b00870] [Citation(s) in RCA: 56] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Affiliation(s)
- Javier Cerezo
- Istituto
di Chimica dei Composti OrganoMetallici, Consiglio Nazionale delle Richerche (ICCOM-CNR), Area della Ricerca, via G. Moruzzi 1, I-56124 Pisa, Italy
| | - Francisco J. Avila Ferrer
- Istituto
di Chimica dei Composti OrganoMetallici, Consiglio Nazionale delle Richerche (ICCOM-CNR), Area della Ricerca, via G. Moruzzi 1, I-56124 Pisa, Italy
- Physical
Chemistry, Faculty of Science, University of Málaga, Málaga 29071, Spain
| | - Giacomo Prampolini
- Istituto
di Chimica dei Composti OrganoMetallici, Consiglio Nazionale delle Richerche (ICCOM-CNR), Area della Ricerca, via G. Moruzzi 1, I-56124 Pisa, Italy
| | - Fabrizio Santoro
- Istituto
di Chimica dei Composti OrganoMetallici, Consiglio Nazionale delle Richerche (ICCOM-CNR), Area della Ricerca, via G. Moruzzi 1, I-56124 Pisa, Italy
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Petrone A, Cerezo J, Ferrer FJA, Donati G, Improta R, Rega N, Santoro F. Absorption and Emission Spectral Shapes of a Prototype Dye in Water by Combining Classical/Dynamical and Quantum/Static Approaches. J Phys Chem A 2015; 119:5426-38. [DOI: 10.1021/jp510838m] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Affiliation(s)
- Alessio Petrone
- Dipartimento di
Scienze Chimiche, Università di Napoli ‘Federico II’, Complesso Universitario di M.S. Angelo, via Cintia, I-80126 Napoli, Italy
| | - Javier Cerezo
- CNR−Consiglio
Nazionale delle Ricerche, Istituto di Chimica dei Composti Organometallici (ICCOM-CNR), UOS di Pisa, Area della Ricerca, via G. Moruzzi 1, I-56124 Pisa, Italy
| | - Francisco J. Avila Ferrer
- CNR−Consiglio
Nazionale delle Ricerche, Istituto di Chimica dei Composti Organometallici (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
| | - Greta Donati
- Dipartimento di
Scienze Chimiche, Università di Napoli ‘Federico II’, Complesso Universitario di M.S. Angelo, via Cintia, I-80126 Napoli, Italy
| | - Roberto Improta
- CNR−Consiglio
Nazionale delle Ricerche, Istituto di Biostrutture e Bioimmagini (IBB-CNR), via Mezzocannone 16, I-80136 Napoli, Italy
| | - Nadia Rega
- Dipartimento di
Scienze Chimiche, Università di Napoli ‘Federico II’, Complesso Universitario di M.S. Angelo, via Cintia, I-80126 Napoli, Italy
- Italian Institute
of Technology, IIT@CRIB Center for Advanced Biomaterials for Healthcare, Largo Barsanti e Matteucci, I-80125 Napoli, Italy
| | - Fabrizio Santoro
- CNR−Consiglio
Nazionale delle Ricerche, Istituto di Chimica dei Composti Organometallici (ICCOM-CNR), UOS di Pisa, Area della Ricerca, via G. Moruzzi 1, I-56124 Pisa, Italy
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Dileep KV, Remya C, Cerezo J, Fassihi A, Pérez-Sánchez H, Sadasivan C. Comparative studies on the inhibitory activities of selected benzoic acid derivatives against secretory phospholipase A2, a key enzyme involved in the inflammatory pathway. Mol BioSyst 2015; 11:1973-9. [DOI: 10.1039/c5mb00073d] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Inhibitory activities of selected benzoic acid derivatives against phospholipase A2.
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Affiliation(s)
- K. V. Dileep
- Department of Biotechnology and Microbiology and Inter University Centre for Biosciences
- Thalassery Campus
- Kannur University
- India
| | - C. Remya
- Department of Biotechnology and Microbiology and Inter University Centre for Biosciences
- Thalassery Campus
- Kannur University
- India
| | - J. Cerezo
- CNR–Consiglio Nazionale delle Ricerche
- Istituto di Chimica dei Composti Organo Metallici (ICCOM-CNR)
- UOS di Pisa
- I-56124 Pisa
- Italy
| | - A. Fassihi
- Bioinformatics and High Performance Computing Research Group (BIO-HPC)
- Computer Science Department
- Universidad Católica San Antonio de Murcia (UCAM)
- 30107 Guadalupe
- Spain
| | - H. Pérez-Sánchez
- Bioinformatics and High Performance Computing Research Group (BIO-HPC)
- Computer Science Department
- Universidad Católica San Antonio de Murcia (UCAM)
- 30107 Guadalupe
- Spain
| | - C. Sadasivan
- Department of Biotechnology and Microbiology and Inter University Centre for Biosciences
- Thalassery Campus
- Kannur University
- India
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Cerezo J, Avila Ferrer FJ, Santoro F. Disentangling vibronic and solvent broadening effects in the absorption spectra of coumarin derivatives for dye sensitized solar cells. Phys Chem Chem Phys 2015; 17:11401-11. [DOI: 10.1039/c5cp00370a] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Abstract
Individuation of vibronic and solvent contributions to the spectra of a family of coumarin dyes helps to understand the main differences in their lineshapes.
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Affiliation(s)
- Javier Cerezo
- CNR–Consiglio Nazionale delle Ricerche
- Istituto di Chimica dei Composti Organo Metallici (ICCOM-CNR)
- UOS di Pisa
- Area della Ricerca
- I-56124 Pisa
| | - Francisco J. Avila Ferrer
- CNR–Consiglio Nazionale delle Ricerche
- Istituto di Chimica dei Composti Organo Metallici (ICCOM-CNR)
- UOS di Pisa
- Area della Ricerca
- I-56124 Pisa
| | - Fabrizio Santoro
- CNR–Consiglio Nazionale delle Ricerche
- Istituto di Chimica dei Composti Organo Metallici (ICCOM-CNR)
- UOS di Pisa
- Area della Ricerca
- I-56124 Pisa
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Cerón-Carrasco JP, Cerezo J, Requena A, Zuñiga J, Contreras-García J, Chavan S, Manrubia-Cobo M, Pérez-Sánchez H. Labelling Herceptin with a novel oxaliplatin derivative: a computational approach towards the selective drug delivery. J Mol Model 2014; 20:2401. [PMID: 25149438 DOI: 10.1007/s00894-014-2401-7] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2014] [Accepted: 07/28/2014] [Indexed: 11/30/2022]
Abstract
The clinical use of platinum(II)-based drugs has serious side effects due to the non-specific reactions with both malignant and normal cells. To circumvent such major drawback, novel metallodrugs might be combined with suitable carrier molecules, as antibodies, to ensure selective attacks on tumours while sparing healthy tissues. In this contribution, we investigate the stability of a novel oxaliplatin derivate drug embedded in Herceptin (trastuzumab), an antibody which is able to recognise breast cancer cells, by using a wide panel of theoretical tools: docking, molecular dynamics and quantum calculations. Our calculations reveal the binding mechanism: the drug initially interacts non-covalently with the Pro40A and Asp167A residues, and the nitrogen of His171B subsequently replaces one of the water molecules coordinated to the platinum center, where the latter step reversibly fixes the drug into the antibody. These data might be used to further rationalise the synthesis of improved drugs beyond classical platinum(II) derivatives by improving the ligand-protein coupling mode.
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Affiliation(s)
- José P Cerón-Carrasco
- Departamento de Química Física, Facultad de Química, Universidad de Murcia, 30100 Campus de Espinardo, Murcia, Spain,
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Cerezo J, Zúñiga J, Requena A, Ávila Ferrer FJ, Santoro F. Erratum: Harmonic Models in Cartesian and Internal Coordinates to Simulate the Absorption Spectra of Carotenoids at Finite Temperatures. J Chem Theory Comput 2014; 10:3586-7. [DOI: 10.1021/ct500588v] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Javier Cerezo
- CNR−Consiglio
Nazionale delle Ricerche, Istituto di Chimica dei Composti Organometallici (ICCOM-CNR), UOS di Pisa, Area della Ricerca, via G. Moruzzi 1, I-56124 Pisa, Italy
- Departamento
de Química Física, Universidad de Murcia, Murcia 30100, Spain
| | - José Zúñiga
- Departamento
de Química Física, Universidad de Murcia, Murcia 30100, Spain
| | - Alberto Requena
- Departamento
de Química Física, Universidad de Murcia, Murcia 30100, Spain
| | - Francisco J. Ávila Ferrer
- CNR−Consiglio
Nazionale delle Ricerche, Istituto di Chimica dei Composti Organometallici (ICCOM-CNR), UOS di Pisa, Area della Ricerca, via G. Moruzzi 1, I-56124 Pisa, Italy
- University of Málaga, Physical Chemistry, Faculty
of Science, Málaga 29071, Spain
| | - Fabrizio Santoro
- CNR−Consiglio
Nazionale delle Ricerche, Istituto di Chimica dei Composti Organometallici (ICCOM-CNR), UOS di Pisa, Area della Ricerca, via G. Moruzzi 1, I-56124 Pisa, Italy
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Avila Ferrer FJ, Cerezo J, Soto J, Improta R, Santoro F. First-principle computation of absorption and fluorescence spectra in solution accounting for vibronic structure, temperature effects and solvent inhomogenous broadening. COMPUT THEOR CHEM 2014. [DOI: 10.1016/j.comptc.2014.03.003] [Citation(s) in RCA: 78] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
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López-Banet L, Santana MD, Piernas MJ, García G, Cerezo J, Requena A, Zúñiga J, Pérez J, García L. Structure and Spectroscopic Properties of Nickel Benzazolate Complexes with Hydrotris(pyrazolyl)borate Ligand. Inorg Chem 2014; 53:5502-14. [DOI: 10.1021/ic5001655] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Affiliation(s)
- Luisa López-Banet
- Departamento
de Química Inorgánica, Universidad de Murcia, E-30071 Murcia, Spain
| | - M. Dolores Santana
- Departamento
de Química Inorgánica, Universidad de Murcia, E-30071 Murcia, Spain
| | - María José Piernas
- Departamento
de Química Inorgánica, Universidad de Murcia, E-30071 Murcia, Spain
| | - Gabriel García
- Departamento
de Química Inorgánica, Universidad de Murcia, E-30071 Murcia, Spain
| | - Javier Cerezo
- Departamento de
Química Física, Universidad de Murcia, E-30071 Murcia, Spain
| | - Alberto Requena
- Departamento de
Química Física, Universidad de Murcia, E-30071 Murcia, Spain
| | - José Zúñiga
- Departamento de
Química Física, Universidad de Murcia, E-30071 Murcia, Spain
| | - José Pérez
- Departamento de Ingeniería
Minera, Geológica y Cartográfica, Área de Química
Inorgánica, Universidad Politécnica de Cartagena, E-30203 Cartagena, Spain
| | - Luís García
- Departamento de Ingeniería
Minera, Geológica y Cartográfica, Área de Química
Inorgánica, Universidad Politécnica de Cartagena, E-30203 Cartagena, Spain
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Cerón-Carrasco JP, Cerezo J, Jacquemin D. How DNA is damaged by external electric fields: selective mutation vs. random degradation. Phys Chem Chem Phys 2014; 16:8243-6. [DOI: 10.1039/c3cp54518k] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
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