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Marazzi M, Gattuso H, Fumanal M, Daniel C, Monari A. Charge-Transfer versus Charge-Separated Triplet Excited States of [Re I (dmp)(CO) 3 (His124)(Trp122)] + in Water and in Modified Pseudomonas aeruginosa Azurin Protein. Chemistry 2019; 25:2519-2526. [PMID: 30379366 DOI: 10.1002/chem.201803685] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2018] [Revised: 10/17/2018] [Indexed: 12/20/2022]
Abstract
A computational investigation of the triplet excited states of a rhenium complex electronically coupled with a tryptophan side chain and bound to an azurin protein is presented. In particular, by using high-level molecular modeling, evidence is provided for how the electronic properties of the excited-state manifolds strongly depend on coupling with the environment. Indeed, only upon explicitly taking into account the protein environment can two stable triplet states of metal-to-ligand charge transfer or charge-separated nature be recovered. In addition, it is also demonstrated how the rhenium complex plus tryptophan system in an aqueous environment experiences too much flexibility, which prevents the two chromophores from being electronically coupled. This occurrence disables the formation of a charge-separated state. The successful strategy requires a multiscale approach of combining molecular dynamics and quantum chemistry. In this context, the strategy used to parameterize the force fields for the electronic triplet states of the metal complex is also presented.
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Affiliation(s)
- Marco Marazzi
- Université de Lorraine, CNRS, LPCT UMR 7019, Boulevard des Aiguillettes, Vandoeuvre-lès-Nancy, 54000, Nancy, France.,Departamento de Química, Centro de Investigacíon en Síntesis Química (CISQ), Universidad de La Rioja, Madre de Dios, 53, 26006, Logroño, Spain
| | - Hugo Gattuso
- Université de Lorraine, CNRS, LPCT UMR 7019, Boulevard des Aiguillettes, Vandoeuvre-lès-Nancy, 54000, Nancy, France
| | - Maria Fumanal
- Laboratoire de Chimie Quantique, Institut de Chimie Strasbourg, UMR-7177, CNRS/Université de Strasbourg, 1 Rue Blaise Pascal BP 296/R8, 67008, Strasbourg, France
| | - Chantal Daniel
- Laboratoire de Chimie Quantique, Institut de Chimie Strasbourg, UMR-7177, CNRS/Université de Strasbourg, 1 Rue Blaise Pascal BP 296/R8, 67008, Strasbourg, France
| | - Antonio Monari
- Université de Lorraine, CNRS, LPCT UMR 7019, Boulevard des Aiguillettes, Vandoeuvre-lès-Nancy, 54000, Nancy, France
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Marazzi M, Gattuso H, Monari A, Assfeld X. Steady-State Linear and Non-linear Optical Spectroscopy of Organic Chromophores and Bio-macromolecules. Front Chem 2018; 6:86. [PMID: 29666792 PMCID: PMC5891624 DOI: 10.3389/fchem.2018.00086] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2018] [Accepted: 03/12/2018] [Indexed: 01/05/2023] Open
Abstract
Bio-macromolecules as DNA, lipid membranes and (poly)peptides are essential compounds at the core of biological systems. The development of techniques and methodologies for their characterization is therefore necessary and of utmost interest, even though difficulties can be experienced due to their intrinsic complex nature. Among these methods, spectroscopies, relying on optical properties are especially important to determine their macromolecular structures and behaviors, as well as the possible interactions and reactivity with external dyes—often drugs or pollutants—that can (photo)sensitize the bio-macromolecule leading to eventual chemical modifications, thus damages. In this review, we will focus on the theoretical simulation of electronic spectroscopies of bio-macromolecules, considering their secondary structure and including their interaction with different kind of (photo)sensitizers. Namely, absorption, emission and electronic circular dichroism (CD) spectra are calculated and compared with the available experimental data. Non-linear properties will be also taken into account by two-photon absorption, a highly promising technique (i) to enhance absorption in the red and infra-red windows and (ii) to enhance spatial resolution. Methodologically, the implications of using implicit and explicit solvent, coupled to quantum and thermal samplings of the phase space, will be addressed. Especially, hybrid quantum mechanics/molecular mechanics (QM/MM) methods are explored for a comparison with solely QM methods, in order to address the necessity to consider an accurate description of environmental effects on spectroscopic properties of biological systems.
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Affiliation(s)
- Marco Marazzi
- Laboratoire de Physique et Chimie Théoriques, Université de Lorraine-Nancy, UMR 7019, Vandoeuvre-lés-Nancy, France.,Laboratoire de Physique et Chimie Théoriques, Centre National de la Recherche Scientifique, UMR 7019, Vandoeuvre-lès-Nancy, France.,Departamento de Química, Centro de Investigacíon en Síntesis Química (CISQ), Universidad de La Rioja, Logroño, Spain
| | - Hugo Gattuso
- Laboratoire de Physique et Chimie Théoriques, Université de Lorraine-Nancy, UMR 7019, Vandoeuvre-lés-Nancy, France.,Laboratoire de Physique et Chimie Théoriques, Centre National de la Recherche Scientifique, UMR 7019, Vandoeuvre-lès-Nancy, France
| | - Antonio Monari
- Laboratoire de Physique et Chimie Théoriques, Université de Lorraine-Nancy, UMR 7019, Vandoeuvre-lés-Nancy, France.,Laboratoire de Physique et Chimie Théoriques, Centre National de la Recherche Scientifique, UMR 7019, Vandoeuvre-lès-Nancy, France
| | - Xavier Assfeld
- Laboratoire de Physique et Chimie Théoriques, Université de Lorraine-Nancy, UMR 7019, Vandoeuvre-lés-Nancy, France.,Laboratoire de Physique et Chimie Théoriques, Centre National de la Recherche Scientifique, UMR 7019, Vandoeuvre-lès-Nancy, France
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Morzan UN, Alonso de Armiño DJ, Foglia NO, Ramírez F, González Lebrero MC, Scherlis DA, Estrin DA. Spectroscopy in Complex Environments from QM–MM Simulations. Chem Rev 2018; 118:4071-4113. [DOI: 10.1021/acs.chemrev.8b00026] [Citation(s) in RCA: 97] [Impact Index Per Article: 16.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Affiliation(s)
- Uriel N. Morzan
- Departamento de Química Inorgánica, Analítica y Química Física/INQUIMAE-CONICET, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Ciudad Universitaria, Pab. II, C1428EHA Buenos Aires, Argentina
| | - Diego J. Alonso de Armiño
- Departamento de Química Inorgánica, Analítica y Química Física/INQUIMAE-CONICET, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Ciudad Universitaria, Pab. II, C1428EHA Buenos Aires, Argentina
| | - Nicolás O. Foglia
- Departamento de Química Inorgánica, Analítica y Química Física/INQUIMAE-CONICET, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Ciudad Universitaria, Pab. II, C1428EHA Buenos Aires, Argentina
| | - Francisco Ramírez
- Departamento de Química Inorgánica, Analítica y Química Física/INQUIMAE-CONICET, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Ciudad Universitaria, Pab. II, C1428EHA Buenos Aires, Argentina
| | - Mariano C. González Lebrero
- Departamento de Química Inorgánica, Analítica y Química Física/INQUIMAE-CONICET, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Ciudad Universitaria, Pab. II, C1428EHA Buenos Aires, Argentina
| | - Damián A. Scherlis
- Departamento de Química Inorgánica, Analítica y Química Física/INQUIMAE-CONICET, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Ciudad Universitaria, Pab. II, C1428EHA Buenos Aires, Argentina
| | - Darío A. Estrin
- Departamento de Química Inorgánica, Analítica y Química Física/INQUIMAE-CONICET, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Ciudad Universitaria, Pab. II, C1428EHA Buenos Aires, Argentina
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Rivail JL, Monari A, Assfeld X. The Non Empirical Local Self Consistent Field Method: Application to Quantum Mechanics/Molecular Mechanics (QM/MM) Modeling of Large Biomolecular Systems. CHALLENGES AND ADVANCES IN COMPUTATIONAL CHEMISTRY AND PHYSICS 2015. [DOI: 10.1007/978-3-319-21626-3_13] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
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Etienne T, Assfeld X, Monari A. QM/MM calculation of absorption spectra of complex systems: The case of human serum albumin. COMPUT THEOR CHEM 2014. [DOI: 10.1016/j.comptc.2014.01.009] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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QM/MM modeling of Harmane cation fluorescence spectrum in water solution and interacting with DNA. COMPUT THEOR CHEM 2014. [DOI: 10.1016/j.comptc.2014.03.026] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
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UV–vis absorption spectrum of a novel Ru(II) complex intercalated in DNA: [Ru(2,2′-bipy)(dppz)(2,2′-ArPy)]+. J Mol Model 2014; 20:2082. [DOI: 10.1007/s00894-014-2082-2] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2013] [Accepted: 10/09/2013] [Indexed: 12/26/2022]
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Chantzis A, Very T, Daniel C, Monari A, Assfeld X. Theoretical evidence of photo-induced charge transfer from DNA to intercalated ruthenium (II) organometallic complexes. Chem Phys Lett 2013. [DOI: 10.1016/j.cplett.2013.05.068] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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Do H, Deeth RJ, Besley NA. Computational study of the structure and electronic circular dichroism spectroscopy of blue copper proteins. J Phys Chem B 2013; 117:8105-12. [PMID: 23773120 DOI: 10.1021/jp404107j] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The calculation of the electronic circular dichroism (CD) spectra of the oxidized form of the blue copper proteins plastocyanin and cucumber basic protein and the relationship between the observed spectral features and the structure of the active site of the protein is investigated. Excitation energies and transition strengths are computed using multireference configuration interaction, and it is shown that computed spectra based on coordinates from the crystal structure or a single structure optimized in quantum mechanics/molecular mechanics (QM/MM) or ligand field molecular mechanics (LFMM) are qualitatively incorrect. In particular, the rotational strength of the ligand to metal charge transfer band is predicted to be too small or have the incorrect sign. By considering calculations on active site models with modified structures, it is shown that the intensity of this band is sensitive to the nonplanarity of the histidine and cysteine ligands coordinated to copper. Calculation of the ultraviolet absorption and CD spectra based upon averaging over many structures drawn from a LFMM molecular dynamics simulation are in good agreement with experiment, and superior to analogous calculations based upon structures from a classical molecular dynamics simulation. This provides evidence that the LFMM force field provides an accurate description of the molecular dynamics of these proteins.
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Affiliation(s)
- Hainam Do
- School of Chemistry, University of Nottingham, University Park, Nottingham, NG7 2RD, UK
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Monari A, Rivail JL, Assfeld X. Theoretical modeling of large molecular systems. Advances in the local self consistent field method for mixed quantum mechanics/molecular mechanics calculations. Acc Chem Res 2013; 46:596-603. [PMID: 23249409 DOI: 10.1021/ar300278j] [Citation(s) in RCA: 86] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Molecular mechanics methods can efficiently compute the macroscopic properties of a large molecular system but cannot represent the electronic changes that occur during a chemical reaction or an electronic transition. Quantum mechanical methods can accurately simulate these processes, but they require considerably greater computational resources. Because electronic changes typically occur in a limited part of the system, such as the solute in a molecular solution or the substrate within the active site of enzymatic reactions, researchers can limit the quantum computation to this part of the system. Researchers take into account the influence of the surroundings by embedding this quantum computation into a calculation of the whole system described at the molecular mechanical level, a strategy known as the mixed quantum mechanics/molecular mechanics (QM/MM) approach. The accuracy of this embedding varies according to the types of interactions included, whether they are purely mechanical or classically electrostatic. This embedding can also introduce the induced polarization of the surroundings. The difficulty in QM/MM calculations comes from the splitting of the system into two parts, which requires severing the chemical bonds that link the quantum mechanical subsystem to the classical subsystem. Typically, researchers replace the quantoclassical atoms, those at the boundary between the subsystems, with a monovalent link atom. For example, researchers might add a hydrogen atom when a C-C bond is cut. This Account describes another approach, the Local Self Consistent Field (LSCF), which was developed in our laboratory. LSCF links the quantum mechanical portion of the molecule to the classical portion using a strictly localized bond orbital extracted from a small model molecule for each bond. In this scenario, the quantoclassical atom has an apparent nuclear charge of +1. To achieve correct bond lengths and force constants, we must take into account the inner shell of the atom: for an sp(3) carbon atom, we consider the two core 1s electrons and treat that carbon as an atom with three electrons. This results in an LSCF+3 model. Similarly, a nitrogen atom with a lone pair of electrons available for conjugation is treated as an atom with five electrons (LSCF+5). This approach is particularly well suited to splitting peptide bonds and other bonds that include carbon or nitrogen atoms. To embed the induced polarization within the calculation, researchers must use a polarizable force field. However, because the parameters of the usual force fields include an average of the induction effects, researchers typically can obtain satisfactory results without explicitly introducing the polarization. When considering electronic transitions, researchers must take into account the changes in the electronic polarization. One approach is to simulate the electronic cloud of the surroundings by a continuum whose dielectric constant is equal to the square of the refractive index. This Electronic Response of the Surroundings (ERS) methodology allows researchers to model the changes in induced polarization easily. We illustrate this approach by modeling the electronic absorption of tryptophan in human serum albumin (HSA).
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Affiliation(s)
- Antonio Monari
- Théorie Modélisation Simulation, Université de Lorraine, SRSMC UMR 7565, Vandœuvre-lès-Nancy F-54506, France
- Théorie Modélisation Simulation, CNRS, SRSMC UMR 7565, Vandœuvre-lès-Nancy F-54506, France
| | - Jean-Louis Rivail
- Théorie Modélisation Simulation, Université de Lorraine, SRSMC UMR 7565, Vandœuvre-lès-Nancy F-54506, France
- Théorie Modélisation Simulation, CNRS, SRSMC UMR 7565, Vandœuvre-lès-Nancy F-54506, France
| | - Xavier Assfeld
- Théorie Modélisation Simulation, Université de Lorraine, SRSMC UMR 7565, Vandœuvre-lès-Nancy F-54506, France
- Théorie Modélisation Simulation, CNRS, SRSMC UMR 7565, Vandœuvre-lès-Nancy F-54506, France
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Zanna N, Monari A, Assfeld X. Theoretical Study of the Absorption Spectrum of a Photoisomerizable Iron Complex. J Phys Chem A 2012; 116:11905-12. [DOI: 10.1021/jp310171r] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Affiliation(s)
- Nicola Zanna
- Dipartimento di Chimica Organica
A. Mangini, Università di Bologna, Viale Risorgimento 4, 40136 Bologna, Italy
| | - Antonio Monari
- Université de Lorraine Nancy, Théorie Modélisation
Simulations, Photosens Laboratoire SRSMC, Boulevard des Aiguillettes,
54506 Vandoeuvre-lès-Nancy, France
- CNRS, Théorie Modélisation
Simulations, Photosens Laboratoire
SRSMC, Boulevard des Aiguillettes, 54506 Vandoeuvre-lès-Nancy,
France
| | - Xavier Assfeld
- Université de Lorraine Nancy, Théorie Modélisation
Simulations, Photosens Laboratoire SRSMC, Boulevard des Aiguillettes,
54506 Vandoeuvre-lès-Nancy, France
- CNRS, Théorie Modélisation
Simulations, Photosens Laboratoire
SRSMC, Boulevard des Aiguillettes, 54506 Vandoeuvre-lès-Nancy,
France
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Lachaud F, Jeandon C, Beley M, Ruppert R, Gros PC, Monari A, Assfeld X. Ground and Excited State Properties of New Porphyrin Based Dyads: A Combined Theoretical and Experimental Study. J Phys Chem A 2012; 116:10736-44. [DOI: 10.1021/jp307452d] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Affiliation(s)
| | - Christophe Jeandon
- Laboratoire CLAC, UMR 7177 du
CNRS, Université de Strasbourg,
1 rue Blaise Pascal, BP 296 R8, 67008 Strasbourg Cedex, France
| | | | - Romain Ruppert
- Laboratoire CLAC, UMR 7177 du
CNRS, Université de Strasbourg,
1 rue Blaise Pascal, BP 296 R8, 67008 Strasbourg Cedex, France
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