1
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Initial Maximum Overlap Method Embedded with Extremely Localized Molecular Orbitals for Core-Ionized States of Large Systems. MOLECULES (BASEL, SWITZERLAND) 2022; 28:molecules28010136. [PMID: 36615331 PMCID: PMC9822432 DOI: 10.3390/molecules28010136] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/29/2022] [Revised: 12/21/2022] [Accepted: 12/22/2022] [Indexed: 12/28/2022]
Abstract
Despite great advances in X-ray absorption spectroscopy for the investigation of small molecule electronic structure, the application to biosystems of experimental techniques developed within this research field remains a challenge. To partially circumvent the problem, users resort to theoretical methods to interpret or predict the X-ray absorption spectra of large molecules. To accomplish this task, only low-cost computational strategies can be exploited. For this reason, some of them are single Slater determinant wavefunction approaches coupled with multiscale embedding techniques designed to treat large systems of biological interest. Therefore, in this work, we propose to apply the recently developed IMOM/ELMO embedding method to the determination of core-ionized states. The IMOM/ELMO technique resulted from the combination of the single Slater determinant Δself-consistent-field-initial maximum overlap approach (ΔSCF-IMOM) with the QM/ELMO (quantum mechanics/extremely localized molecular orbital) embedding strategy, a method where only the chemically relevant region of the examined system is treated at fully quantum chemical level, while the rest is described through transferred and frozen extremely localized molecular orbitals (ELMOs). The IMOM/ELMO technique was initially validated by computing core-ionization energies for small molecules, and it was afterwards exploited to study larger biosystems. The obtained results are in line with those reported in previous studies that applied alternative ΔSCF approaches. This makes us envisage a possible future application of the proposed method to the interpretation of X-ray absorption spectra of large molecules.
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2
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Sun H, Jiang H. Combined
DFT
and wave function theory approach to excited states of lanthanide luminescent materials: A case study of
LaF
3
:Ce
3+. J CHIN CHEM SOC-TAIP 2022. [DOI: 10.1002/jccs.202200348] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Affiliation(s)
- Huai‐Yang Sun
- Beijing National Laboratory for Molecular Sciences, College of Chemistry and Molecular Engineering Peking University Beijing PR China
| | - Hong Jiang
- Beijing National Laboratory for Molecular Sciences, College of Chemistry and Molecular Engineering Peking University Beijing PR China
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3
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David G, Irons TJP, Fouda AEA, Furness JW, Teale AM. Self-Consistent Field Methods for Excited States in Strong Magnetic Fields: a Comparison between Energy- and Variance-Based Approaches. J Chem Theory Comput 2021; 17:5492-5508. [PMID: 34517708 DOI: 10.1021/acs.jctc.1c00236] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Self-consistent field methods for excited states offer an attractive low-cost route to study not only excitation energies but also properties of excited states. Here, we present the generalization of two self-consistent field methods, the maximum overlap method (MOM) and the σ-SCF method, to calculate excited states in strong magnetic fields and investigate their stability and accuracy in this context. These methods use different strategies to overcome the well-known variational collapse of energy-based optimizations to the lowest solution of a given symmetry. The MOM tackles this problem in the definition of the orbital occupations to constrain the self-consistent field procedure to converge on excited states, while the σ-SCF method is based on the minimization of the variance instead of the energy. To overcome the high computational cost of the variance minimization, we present a new implementation of the σ-SCF method with the resolution of identity approximation, allowing the use of large basis sets, which is an important requirement for calculations in strong magnetic fields. The accuracy of these methods is assessed by comparison with the benchmark literature data for He, H2, and CH+. The results reveal severe limitations of the variance-based scheme, which become more acute in large basis sets. In particular, many states are not accessible using variance optimization. Detailed analysis shows that this is a general feature of variance optimization approaches due to the masking of local minima in the optimization. In contrast, the MOM shows promising performance for computing excited states under these conditions, yielding results consistent with available benchmark data for a diverse range of electronic states.
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Affiliation(s)
- Grégoire David
- School of Chemistry, University of Nottingham, Nottingham NG7 2RD, U.K
| | - Tom J P Irons
- School of Chemistry, University of Nottingham, Nottingham NG7 2RD, U.K
| | - Adam E A Fouda
- School of Chemistry, University of Nottingham, Nottingham NG7 2RD, U.K.,Chemical Sciences and Engineering Division, Argonne National Laboratory, 9700 S Cass Avenue, Lemont, Illinois 60439, United States
| | - James W Furness
- Department of Physics and Engineering Physics, Tulane University, New Orleans, Louisiana 70118, United States
| | - Andrew M Teale
- School of Chemistry, University of Nottingham, Nottingham NG7 2RD, U.K.,Hylleraas Centre for Quantum Molecular Sciences, Department of Chemistry, University of Oslo, P.O. Box 1033, Blindern, Oslo N-0315, Norway
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4
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Halbert L, Vidal ML, Shee A, Coriani S, Severo Pereira Gomes A. Relativistic EOM-CCSD for Core-Excited and Core-Ionized State Energies Based on the Four-Component Dirac-Coulomb(-Gaunt) Hamiltonian. J Chem Theory Comput 2021; 17:3583-3598. [PMID: 33944570 DOI: 10.1021/acs.jctc.0c01203] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
We report an implementation of the core-valence separation approach to the four-component relativistic Hamiltonian-based equation-of-motion coupled-cluster with singles and doubles theory (CVS-EOM-CCSD) for the calculation of relativistic core-ionization potentials and core-excitation energies. With this implementation, which is capable of exploiting double group symmetry, we investigate the effects of the different CVS-EOM-CCSD variants and the use of different Hamiltonians based on the exact two-component (X2C) framework on the energies of different core-ionized and -excited states in halogen- (CH3I, HX, and X-, X = Cl-At) and xenon-containing (Xe, XeF2) species. Our results show that the X2C molecular mean-field approach [Sikkema, J.; J. Chem. Phys. 2009, 131, 124116], based on four-component Dirac-Coulomb mean-field calculations (2DCM), is capable of providing core excitations and ionization energies that are nearly indistinguishable from the reference four-component energies for up to and including fifth-row elements. We observe that two-electron integrals over the small-component basis sets lead to non-negligible contributions to core binding energies for the K and L edges for atoms such as iodine or astatine and that the approach based on Dirac-Coulomb-Gaunt mean-field calculations (2DCGM) are significantly more accurate than X2C calculations for which screened two-electron spin-orbit interactions are included via atomic mean-field integrals.
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Affiliation(s)
- Loïc Halbert
- CNRS, UMR 8523-PhLAM-Physique des Lasers, Atomes et Molécules, Université de Lille, F-59000 Lille, France
| | - Marta L Vidal
- DTU Chemistry-Department of Chemistry, Technical University of Denmark, DK-2800 Kongens Lyngby, Denmark
| | - Avijit Shee
- Department of Chemistry, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Sonia Coriani
- DTU Chemistry-Department of Chemistry, Technical University of Denmark, DK-2800 Kongens Lyngby, Denmark
| | - André Severo Pereira Gomes
- CNRS, UMR 8523-PhLAM-Physique des Lasers, Atomes et Molécules, Université de Lille, F-59000 Lille, France
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5
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Klein BP, Hall SJ, Maurer RJ. The nuts and bolts of core-hole constrained ab initiosimulation for K-shell x-ray photoemission and absorption spectra. JOURNAL OF PHYSICS. CONDENSED MATTER : AN INSTITUTE OF PHYSICS JOURNAL 2021; 33. [PMID: 33682682 DOI: 10.1088/1361-648x/abdf00] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/20/2020] [Accepted: 01/22/2021] [Indexed: 05/13/2023]
Abstract
X-ray photoemission (XPS) and near edge x-ray absorption fine structure (NEXAFS) spectroscopy play an important role in investigating the structure and electronic structure of materials and surfaces.Ab initiosimulations provide crucial support for the interpretation of complex spectra containing overlapping signatures. Approximate core-hole simulation methods based on density functional theory (DFT) such as the delta-self-consistent-field (ΔSCF) method or the transition potential (TP) method are widely used to predictK-shell XPS and NEXAFS signatures of organic molecules, inorganic materials and metal-organic interfaces at reliable accuracy and affordable computational cost. We present the numerical and technical details of our variants of the ΔSCF and TP method (coined ΔIP-TP) to simulate XPS and NEXAFS transitions. Using exemplary molecules in gas-phase, in bulk crystals, and at metal-organic interfaces, we systematically assess how practical simulation choices affect the stability and accuracy of simulations. These include the choice of exchange-correlation functional, basis set, the method of core-hole localization, and the use of periodic boundary conditions (PBC). We particularly focus on the choice of aperiodic or periodic description of systems and how spurious charge effects in periodic calculations affect the simulation outcomes. For the benefit of practitioners in the field, we discuss sensible default choices, limitations of the methods, and future prospects.
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Affiliation(s)
- Benedikt P Klein
- Department of Chemistry, University of Warwick, Gibbet Hill Rd, Coventry, CV4 7AL, United Kingdom
- Diamond Light Source, Harwell Science and Innovation Campus, Didcot, OX11 0DE, United Kingdom
| | - Samuel J Hall
- Department of Chemistry, University of Warwick, Gibbet Hill Rd, Coventry, CV4 7AL, United Kingdom
- MAS CDT, Senate House, University of Warwick, Gibbet Hill Rd, Coventry, CV4 7AL, United Kingdom
| | - Reinhard J Maurer
- Department of Chemistry, University of Warwick, Gibbet Hill Rd, Coventry, CV4 7AL, United Kingdom
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6
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Bao P, Hettich CP, Shi Q, Gao J. Block-Localized Excitation for Excimer Complex and Diabatic Coupling. J Chem Theory Comput 2020; 17:240-254. [PMID: 33370101 DOI: 10.1021/acs.jctc.0c01015] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
We describe a block-localized excitation (BLE) method to carry out constrained optimization of block-localized orbitals for constructing valence bond-like, diabatic excited configurations using multistate density functional theory (MSDFT). The method is an extension of the previous block-localized wave function method through a fragment-based ΔSCF approach to optimize excited determinants within a molecular complex. In BLE, both the number of electrons and the electronic spin of different fragments in a whole system can be constrained, whereas electrostatic, exchange, and polarization interactions among different blocks can be fully taken into account of. To avoid optimization collapse to unwanted states, a ΔSCF projection scheme and a maximum overlap of wave function approach have been presented. The method is illustrated by the excimer complex of two naphthalene molecules. With a minimum of eight spin-adapted configurational state functions, it was found that the inversion of La- and Lb- states near the optimal structure of the excimer complex is correctly produced, which is in quantitative agreement with DMRG-CASPT2 calculations and experiments. Trends in the computed transfer integrals associated with excited-state energy transfer both in the singlet and triplet states are discussed. The results suggest that MSDFT may be used as an efficient approach to treat intermolecular interactions in excited states with a minimal active space (MAS) for interpretation of the results and for dynamic simulations, although the selection of a small active space is often system dependent.
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Affiliation(s)
- Peng Bao
- Beijing National Laboratory for Molecular Sciences, State Key Laboratory for Structural Chemistry of Unstable and Stable Species, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, China
| | - Christian P Hettich
- Department of Chemistry and Supercomputing Institute, University of Minnesota, Minneapolis, Minnesota 55455, United States
| | - Qiang Shi
- Beijing National Laboratory for Molecular Sciences, State Key Laboratory for Structural Chemistry of Unstable and Stable Species, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, China.,University of the Chinese Academy of Sciences, Beijing 100049, China
| | - Jiali Gao
- Department of Chemistry and Supercomputing Institute, University of Minnesota, Minneapolis, Minnesota 55455, United States.,Institute of Systems and Physical Biology, Shenzhen Bay Laboratory, Shenzhen 518055, China.,Beijing University Shenzhen Graduate School, Shenzhen 518055, China
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7
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Zheng X, Liu J, Doumy G, Young L, Cheng L. Hetero-site Double Core Ionization Energies with Sub-electronvolt Accuracy from Delta-Coupled-Cluster Calculations. J Phys Chem A 2020; 124:4413-4426. [DOI: 10.1021/acs.jpca.0c00901] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Xuechen Zheng
- Department of Chemistry, The Johns Hopkins University, Baltimore, Maryland 21218, United States
| | - Junzi Liu
- Department of Chemistry, The Johns Hopkins University, Baltimore, Maryland 21218, United States
| | - Gilles Doumy
- Chemical Sciences and Engineering Division, Argonne National Laboratory, Lemont, Illinois 60439, United States
| | - Linda Young
- Chemical Sciences and Engineering Division, Argonne National Laboratory, Lemont, Illinois 60439, United States
| | - Lan Cheng
- Department of Chemistry, The Johns Hopkins University, Baltimore, Maryland 21218, United States
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8
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Terenzi A, Gattuso H, Spinello A, Keppler BK, Chipot C, Dehez F, Barone G, Monari A. Targeting G-quadruplexes with Organic Dyes: Chelerythrine-DNA Binding Elucidated by Combining Molecular Modeling and Optical Spectroscopy. Antioxidants (Basel) 2019; 8:antiox8100472. [PMID: 31658666 PMCID: PMC6826623 DOI: 10.3390/antiox8100472] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2019] [Revised: 10/05/2019] [Accepted: 10/07/2019] [Indexed: 01/24/2023] Open
Abstract
The DNA-binding of the natural benzophenanthridine alkaloid chelerythrine (CHE) has been assessed by combining molecular modeling and optical absorption spectroscopy. Specifically, both double-helical (B-DNA) and G-quadruplex sequences—representative of different topologies and possessing biological relevance, such as telomeric or regulatory sequences—have been considered. An original multiscale protocol, making use of molecular dynamics (MD) simulations and quantum mechanics/molecular mechanics (QM/MM) calculations, allowed us to compare the theoretical and experimental circular dichroism spectra of the different DNA topologies, readily providing atomic-level details of the CHE–DNA binding modes. The binding selectivity towards G-quadruplexes is confirmed by both experimental and theoretical determination of the binding free energies. Overall, our mixed computational and experimental approach is able to shed light on the interaction of small molecules with different DNA conformations. In particular, CHE may be seen as the building block of promising drug candidates specifically targeting G-quadruplexes for both antitumoral and antiviral purposes.
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Affiliation(s)
- Alessio Terenzi
- Institute of Inorganic Chemistry, University of Vienna, Währingerstrasse 42, A-1090 Vienna, Austria.
- Donostia International Physics Center, Paseo Manuel de Lardizabal 4, 20018 Donostia, Spain.
| | - Hugo Gattuso
- Université de Lorraine and CNRS, LPCT UMR 7019, F54000 Nancy, France.
| | - Angelo Spinello
- CNR-IOM DEMOCRITOS c/o International School for Advanced Studies (SISSA), 34136 Trieste, Italy.
| | - Bernhard K Keppler
- Institute of Inorganic Chemistry, University of Vienna, Währingerstrasse 42, A-1090 Vienna, Austria.
| | - Christophe Chipot
- Université de Lorraine and CNRS, LPCT UMR 7019, F54000 Nancy, France.
- Laboratoire International Associé Centre National de la Recherche Scientifique et University of Illinois at Urbana-Champaign, Urbana, IL 61820, USA.
- Department of Physics, University of Illinois at Urbana-Champaign, 1110 West Green Street, Urbana, IL 61801, USA.
| | - François Dehez
- Université de Lorraine and CNRS, LPCT UMR 7019, F54000 Nancy, France.
- Laboratoire International Associé Centre National de la Recherche Scientifique et University of Illinois at Urbana-Champaign, Urbana, IL 61820, USA.
| | - Giampaolo Barone
- Dipartimento di Scienze Biologiche, Chimiche e Farmaceutiche, Università di Palermo, Viale delle Scienze, 90128 Palermo, Italy.
| | - Antonio Monari
- Université de Lorraine and CNRS, LPCT UMR 7019, F54000 Nancy, France.
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9
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Zheng X, Cheng L. Performance of Delta-Coupled-Cluster Methods for Calculations of Core-Ionization Energies of First-Row Elements. J Chem Theory Comput 2019; 15:4945-4955. [DOI: 10.1021/acs.jctc.9b00568] [Citation(s) in RCA: 36] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Xuechen Zheng
- Department of Chemistry, The Johns Hopkins University, Baltimore, Maryland 21218, United States
| | - Lan Cheng
- Department of Chemistry, The Johns Hopkins University, Baltimore, Maryland 21218, United States
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10
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Bokarev SI, Kühn O. Theoretical X‐ray spectroscopy of transition metal compounds. WILEY INTERDISCIPLINARY REVIEWS-COMPUTATIONAL MOLECULAR SCIENCE 2019. [DOI: 10.1002/wcms.1433] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Affiliation(s)
| | - Oliver Kühn
- Institut für Physik Universität Rostock Rostock Germany
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11
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Glushkov VN, Assfeld X. On the orthogonality of states with approximate wavefunctions. J Mol Model 2019; 25:148. [PMID: 31065814 DOI: 10.1007/s00894-019-4019-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2018] [Accepted: 03/29/2019] [Indexed: 11/29/2022]
Abstract
A variational solution to the eigenvalue problem for the Hamiltonian H, with orthogonality restrictions on eigenvectors of H to the vector H ∣ Φ0〉, where ∣Φ0〉 is an approximate ground-state vector, is proposed as a means to calculate excited states. The asymptotic projection (AP) method proposed previously is further developed and applied to solve this problem in a simple way. We demonstrate that the AP methodology does not require an evaluation of the matrix elements of operator H2, whereas conventional approaches-such as the elimination of off-diagonal Lagrange multipliers method, projection operator techniques, and other methods-do. It is shown, based on the results obtained for the single-electron molecular ions H2+, HeH2+, and H32+, that applying the new method to determine excited-state wavefunctions yields the upper bounds for excited-state energies. We demonstrate that regardless of whether the orthogonality constraint for states (〈Φ| Φ0〉 = 0) is applied, the zero-coupling constraint (〈Φ| H| Φ0〉 = 0) is imposed, or both of these restrictions are enforced simultaneously, practically the same excited-state energy is obtained if the basis set is almost complete. For the systems considered here, all schemes are capable of giving a sub-μhartree level of accuracy for the ground and excited states computed with different basis sets.
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Affiliation(s)
- V N Glushkov
- Department of Chemistry, Dnipropetrovsk National University, Dnipropetrovsk, Ukraine.
| | - X Assfeld
- CNRS, Laboratoire de Physique et Chimie Théoriques, UMR 7019, Université de Lorraine, 54506, Vandoeuvre-les-Nancy Cedex, France
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12
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Michelitsch GS, Reuter K. Efficient simulation of near-edge x-ray absorption fine structure (NEXAFS) in density-functional theory: Comparison of core-level constraining approaches. J Chem Phys 2019; 150:074104. [DOI: 10.1063/1.5083618] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- Georg S. Michelitsch
- Chair for Theoretical Chemistry and Catalysis Research Center, Technische Universität München, Lichtenbergstr. 4, D-85748 Garching, Germany
| | - Karsten Reuter
- Chair for Theoretical Chemistry and Catalysis Research Center, Technische Universität München, Lichtenbergstr. 4, D-85748 Garching, Germany
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13
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Carbone JP, Cheng L, Myhre RH, Matthews D, Koch H, Coriani S. An analysis of the performance of coupled cluster methods for K-edge core excitations and ionizations using standard basis sets. ADVANCES IN QUANTUM CHEMISTRY 2019. [DOI: 10.1016/bs.aiq.2019.05.005] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/03/2022]
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14
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Affiliation(s)
- Pablo Ramos
- Department of Chemistry, Rutgers University, Newark, New Jersey 07102, USA
| | - Michele Pavanello
- Department of Chemistry, Rutgers University, Newark, New Jersey 07102, USA
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15
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Rebolini E, Teale AM, Helgaker T, Savin A, Toulouse J. Excitation energies from Görling–Levy perturbation theory along the range-separated adiabatic connection. Mol Phys 2018. [DOI: 10.1080/00268976.2017.1422811] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Affiliation(s)
| | - Andrew M. Teale
- School of Chemistry, University of Nottingham, Nottingham, United Kingdom
- Hylleraas Centre for Quantum Molecular Sciences, Department of Chemistry, University of Oslo, Oslo, Norway
- Centre for Advanced Study at the Norwegian Academy of Science and Letters, Oslo, Norway
| | - Trygve Helgaker
- Hylleraas Centre for Quantum Molecular Sciences, Department of Chemistry, University of Oslo, Oslo, Norway
- Centre for Advanced Study at the Norwegian Academy of Science and Letters, Oslo, Norway
| | - Andreas Savin
- Laboratoire de Chimie Théorique, Université Pierre et Marie Curie, CNRS, Sorbonne Universités, Paris, France
| | - Julien Toulouse
- Laboratoire de Chimie Théorique, Université Pierre et Marie Curie, CNRS, Sorbonne Universités, Paris, France
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16
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Gattuso H, García-Iriepa C, Sampedro D, Monari A, Marazzi M. Simulating the Electronic Circular Dichroism Spectra of Photoreversible Peptide Conformations. J Chem Theory Comput 2017; 13:3290-3296. [DOI: 10.1021/acs.jctc.7b00163] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Affiliation(s)
- Hugo Gattuso
- Théorie-Modélisation-Simulation, Université de Lorraine − Nancy, SRSMC, Boulevard des Aiguillettes, 54506 Vandoeuvre-lès-Nancy, Nancy, France
- Théorie-Modélisation-Simulation,
CNRS, SRSMC, Boulevard des Aiguillettes, 54506 Vandoeuvre-lès-Nancy, Nancy, France
| | - Cristina García-Iriepa
- Departamento
de Química, Centro de Investigación en Síntesis
Química (CISQ), Universidad de La Rioja, Madre de Dios
53, E-26006 Logroño, Spain
- Unidad
Docente de Química Física, Universidad de Alcalá, E-28871 Alcalá de Henares, Madrid, Spain
| | - Diego Sampedro
- Departamento
de Química, Centro de Investigación en Síntesis
Química (CISQ), Universidad de La Rioja, Madre de Dios
53, E-26006 Logroño, Spain
| | - Antonio Monari
- Théorie-Modélisation-Simulation, Université de Lorraine − Nancy, SRSMC, Boulevard des Aiguillettes, 54506 Vandoeuvre-lès-Nancy, Nancy, France
- Théorie-Modélisation-Simulation,
CNRS, SRSMC, Boulevard des Aiguillettes, 54506 Vandoeuvre-lès-Nancy, Nancy, France
| | - Marco Marazzi
- Théorie-Modélisation-Simulation, Université de Lorraine − Nancy, SRSMC, Boulevard des Aiguillettes, 54506 Vandoeuvre-lès-Nancy, Nancy, France
- Théorie-Modélisation-Simulation,
CNRS, SRSMC, Boulevard des Aiguillettes, 54506 Vandoeuvre-lès-Nancy, Nancy, France
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17
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Gattuso H, Monari A, Marazzi M. Photophysics of chlorin e6: from one- and two-photon absorption to fluorescence and phosphorescence. RSC Adv 2017. [DOI: 10.1039/c6ra28616j] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
Linear and non-linear optical properties of a known photosensitizer producing singlet oxygen, chlorin e6, have been studied, including dynamics effects.
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Affiliation(s)
- Hugo Gattuso
- Université de Lorraine – Nancy
- Theory-Modeling-Simulation SRSMC
- Vandoeuvre-les-Nancy
- France
- CNRS
| | - Antonio Monari
- Université de Lorraine – Nancy
- Theory-Modeling-Simulation SRSMC
- Vandoeuvre-les-Nancy
- France
- CNRS
| | - Marco Marazzi
- Université de Lorraine – Nancy
- Theory-Modeling-Simulation SRSMC
- Vandoeuvre-les-Nancy
- France
- CNRS
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18
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Gattuso H, Besancenot V, Grandemange S, Marazzi M, Monari A. From non-covalent binding to irreversible DNA lesions: nile blue and nile red as photosensitizing agents. Sci Rep 2016; 6:28480. [PMID: 27329409 PMCID: PMC4916457 DOI: 10.1038/srep28480] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2016] [Accepted: 06/03/2016] [Indexed: 12/15/2022] Open
Abstract
We report a molecular modeling study, coupled with spectroscopy experiments, on the behavior of two well known organic dyes, nile blue and nile red, when interacting with B-DNA. In particular, we evidence the presence of two competitive binding modes, for both drugs. However their subsequent photophysical behavior is different and only nile blue is able to induce DNA photosensitization via an electron transfer mechanism. Most notably, even in the case of nile blue, its sensitization capabilities strongly depend on the environment resulting in a single active binding mode: the minor groove. Fluorescence spectroscopy confirms the presence of competitive interaction modes for both sensitizers, while the sensitization via electron transfer, is possible only in the case of nile blue.
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Affiliation(s)
- Hugo Gattuso
- Université de Lorraine – Nancy, Theory-Modeling-Simulation SRSMC, Vandoeuvre-lès-Nancy, France
- CNRS, Theory-Modeling-Simulation SRSMC, Vandoeuvre-lès-Nancy, France
| | - Vanessa Besancenot
- Université de Lorraine – Nancy Santé, Biologie, Signal - CRAN, Vandoeuvre-lès-Nancy, France
- CNRS, Santé, Biologie, Signal, CRAN, Vandoeuvre-lès-Nancy, France
| | - Stéphanie Grandemange
- Université de Lorraine – Nancy Santé, Biologie, Signal - CRAN, Vandoeuvre-lès-Nancy, France
- CNRS, Santé, Biologie, Signal, CRAN, Vandoeuvre-lès-Nancy, France
| | - Marco Marazzi
- Université de Lorraine – Nancy, Theory-Modeling-Simulation SRSMC, Vandoeuvre-lès-Nancy, France
- CNRS, Theory-Modeling-Simulation SRSMC, Vandoeuvre-lès-Nancy, France
| | - Antonio Monari
- Université de Lorraine – Nancy, Theory-Modeling-Simulation SRSMC, Vandoeuvre-lès-Nancy, France
- CNRS, Theory-Modeling-Simulation SRSMC, Vandoeuvre-lès-Nancy, France
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19
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Gattuso H, Spinello A, Terenzi A, Assfeld X, Barone G, Monari A. Circular Dichroism of DNA G-Quadruplexes: Combining Modeling and Spectroscopy To Unravel Complex Structures. J Phys Chem B 2016; 120:3113-21. [DOI: 10.1021/acs.jpcb.6b00634] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Hugo Gattuso
- Theory-Modeling-Simulation,
SRSMC, Université de Lorraine Nancy, Boulevard des Aiguillettes, 54506 Vandoeuvre-lès-Nancy, France
- CNRS, Theory-Modeling-Simulation, SRSMC, Boulevard des Aiguillettes, 54506 Vandoeuvre-lès-Nancy, France
| | - Angelo Spinello
- Dipartimento
di Scienze Biologiche, Chimiche e Farmaceutiche, Universitá di Palermo, Viale delle Scienze, Palermo, Italy
| | - Alessio Terenzi
- Dipartimento
di Scienze Biologiche, Chimiche e Farmaceutiche, Universitá di Palermo, Viale delle Scienze, Palermo, Italy
- Institute
of Inorganic Chemistry, University of Vienna, Währingerstrasse 42, Vienna, Austria
| | - Xavier Assfeld
- Theory-Modeling-Simulation,
SRSMC, Université de Lorraine Nancy, Boulevard des Aiguillettes, 54506 Vandoeuvre-lès-Nancy, France
- CNRS, Theory-Modeling-Simulation, SRSMC, Boulevard des Aiguillettes, 54506 Vandoeuvre-lès-Nancy, France
| | - Giampaolo Barone
- Dipartimento
di Scienze Biologiche, Chimiche e Farmaceutiche, Universitá di Palermo, Viale delle Scienze, Palermo, Italy
| | - Antonio Monari
- Theory-Modeling-Simulation,
SRSMC, Université de Lorraine Nancy, Boulevard des Aiguillettes, 54506 Vandoeuvre-lès-Nancy, France
- CNRS, Theory-Modeling-Simulation, SRSMC, Boulevard des Aiguillettes, 54506 Vandoeuvre-lès-Nancy, France
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20
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Gattuso H, Dumont E, Marazzi M, Monari A. Two-photon-absorption DNA sensitization via solvated electron production: unraveling photochemical pathways by molecular modeling and simulation. Phys Chem Chem Phys 2016; 18:18598-606. [DOI: 10.1039/c6cp02592g] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Infrared optical properties and photochemistry of a potential therapeutic dye interacting with DNA: a multiscale computational approach.
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Affiliation(s)
- Hugo Gattuso
- Université de Lorraine – Nancy
- Theory-Modeling-Simulation SRSMC
- Vandoeuvre-les-Nancy
- France
- CNRS
| | - Elise Dumont
- Ecole Normale Supérieure de Lyon and CNRS
- Laboratoire de Chimie
- Lyon
- France
| | - Marco Marazzi
- Université de Lorraine – Nancy
- Theory-Modeling-Simulation SRSMC
- Vandoeuvre-les-Nancy
- France
- CNRS
| | - Antonio Monari
- Université de Lorraine – Nancy
- Theory-Modeling-Simulation SRSMC
- Vandoeuvre-les-Nancy
- France
- CNRS
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21
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Marazzi M, Wibowo M, Gattuso H, Dumont E, Roca-Sanjuán D, Monari A. Hydrogen abstraction by photoexcited benzophenone: consequences for DNA photosensitization. Phys Chem Chem Phys 2016; 18:7829-36. [DOI: 10.1039/c5cp07938a] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
We report a computational investigation of the hydrogen abstraction (H-abstraction) induced by triplet benzophenone (3BP) on thymine nucleobase and backbone sugar.
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Affiliation(s)
- Marco Marazzi
- Université de Lorraine - Nancy
- Theory-Modeling-Simulation SRSMC
- Vandoeuvre-les-Nancy
- France
- CNRS
| | - Meilani Wibowo
- Instituto de Ciencia Molecular
- Universitat de Valencia
- Valencia
- Spain
| | - Hugo Gattuso
- Université de Lorraine - Nancy
- Theory-Modeling-Simulation SRSMC
- Vandoeuvre-les-Nancy
- France
- CNRS
| | - Elise Dumont
- Ecole Normale Supérieure de Lyon and CNRS
- Laboratoire de Chimie
- Lyon
- France
| | | | - Antonio Monari
- Université de Lorraine - Nancy
- Theory-Modeling-Simulation SRSMC
- Vandoeuvre-les-Nancy
- France
- CNRS
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22
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Li C, Lu J, Yang W. Gentlest ascent dynamics for calculating first excited state and exploring energy landscape of Kohn-Sham density functionals. J Chem Phys 2015; 143:224110. [PMID: 26671361 DOI: 10.1063/1.4936411] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
We develop the gentlest ascent dynamics for Kohn-Sham density functional theory to search for the index-1 saddle points on the energy landscape of the Kohn-Sham density functionals. These stationary solutions correspond to excited states in the ground state functionals. As shown by various examples, the first excited states of many chemical systems are given by these index-1 saddle points. Our novel approach provides an alternative, more robust way to obtain these excited states, compared with the widely used ΔSCF approach. The method can be easily generalized to target higher index saddle points. Our results also reveal the physical interest and relevance of studying the Kohn-Sham energy landscape.
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Affiliation(s)
- Chen Li
- Department of Chemistry, Duke University, Durham, North Carolina 27708, USA
| | - Jianfeng Lu
- Department of Chemistry, Duke University, Durham, North Carolina 27708, USA
| | - Weitao Yang
- Department of Chemistry, Duke University, Durham, North Carolina 27708, USA
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23
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Glushkov VN, Assfeld X. Orthogonality-constrained Hartree–Fock and perturbation theory for high-spin open-shell excited states. Theor Chem Acc 2015. [DOI: 10.1007/s00214-015-1759-7] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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24
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Loos PF, Preat J, Laurent AD, Michaux C, Jacquemin D, Perpète EA, Assfeld X. Theoretical Investigation of the Geometries and UV-vis Spectra of Poly(l-glutamic acid) Featuring a Photochromic Azobenzene Side Chain. J Chem Theory Comput 2015; 4:637-45. [PMID: 26620938 DOI: 10.1021/ct700188w] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The geometries and UV-vis spectra of azobenzene dyes grafted as a side chain on poly(l-glutamic acid) have been investigated using a combination of quantum mechanics/molecular mechanics (QM/MM) and time-dependent density functional theory (TD-DFT) methods at the TD-PBE0/6-311+G(d,p)//B3LYP/6-311G(d,p):Amber ff99 level of theory. The influence of the secondary structure of the polypeptide on the electronic properties of both the trans and cis conformations of azobenzene dyes has been studied. It turns out that the grafted dyes exhibit a red-shift of the π → π* absorption energies mainly due to the auxochromic shift induced by the peptidic group used to link the chromophoric unit to the polypeptide and that specific interactions between the glutamic side chain and the azobenzene moiety lead to a large blue-shift of the n → π* transition.
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Affiliation(s)
- Pierre-François Loos
- Equipe de Chimie et Biochimie Théoriques, UMR 7565 CNRS-UHP, Institut Jean Barriol (FR CNRS 2843), Faculté des Sciences et Techniques, Nancy-Université, B.P. 239,54506 Vandoeuvre-les-Nancy Cedex, France, and Groupe de Chimie Physique Théorique et Structurale, Facultés Universitaires Notre-Dame de la Paix, rue de Bruxelles, 61, B-5000 Namur, Belgium
| | - Julien Preat
- Equipe de Chimie et Biochimie Théoriques, UMR 7565 CNRS-UHP, Institut Jean Barriol (FR CNRS 2843), Faculté des Sciences et Techniques, Nancy-Université, B.P. 239,54506 Vandoeuvre-les-Nancy Cedex, France, and Groupe de Chimie Physique Théorique et Structurale, Facultés Universitaires Notre-Dame de la Paix, rue de Bruxelles, 61, B-5000 Namur, Belgium
| | - Adèle D Laurent
- Equipe de Chimie et Biochimie Théoriques, UMR 7565 CNRS-UHP, Institut Jean Barriol (FR CNRS 2843), Faculté des Sciences et Techniques, Nancy-Université, B.P. 239,54506 Vandoeuvre-les-Nancy Cedex, France, and Groupe de Chimie Physique Théorique et Structurale, Facultés Universitaires Notre-Dame de la Paix, rue de Bruxelles, 61, B-5000 Namur, Belgium
| | - Catherine Michaux
- Equipe de Chimie et Biochimie Théoriques, UMR 7565 CNRS-UHP, Institut Jean Barriol (FR CNRS 2843), Faculté des Sciences et Techniques, Nancy-Université, B.P. 239,54506 Vandoeuvre-les-Nancy Cedex, France, and Groupe de Chimie Physique Théorique et Structurale, Facultés Universitaires Notre-Dame de la Paix, rue de Bruxelles, 61, B-5000 Namur, Belgium
| | - Denis Jacquemin
- Equipe de Chimie et Biochimie Théoriques, UMR 7565 CNRS-UHP, Institut Jean Barriol (FR CNRS 2843), Faculté des Sciences et Techniques, Nancy-Université, B.P. 239,54506 Vandoeuvre-les-Nancy Cedex, France, and Groupe de Chimie Physique Théorique et Structurale, Facultés Universitaires Notre-Dame de la Paix, rue de Bruxelles, 61, B-5000 Namur, Belgium
| | - Eric A Perpète
- Equipe de Chimie et Biochimie Théoriques, UMR 7565 CNRS-UHP, Institut Jean Barriol (FR CNRS 2843), Faculté des Sciences et Techniques, Nancy-Université, B.P. 239,54506 Vandoeuvre-les-Nancy Cedex, France, and Groupe de Chimie Physique Théorique et Structurale, Facultés Universitaires Notre-Dame de la Paix, rue de Bruxelles, 61, B-5000 Namur, Belgium
| | - Xavier Assfeld
- Equipe de Chimie et Biochimie Théoriques, UMR 7565 CNRS-UHP, Institut Jean Barriol (FR CNRS 2843), Faculté des Sciences et Techniques, Nancy-Université, B.P. 239,54506 Vandoeuvre-les-Nancy Cedex, France, and Groupe de Chimie Physique Théorique et Structurale, Facultés Universitaires Notre-Dame de la Paix, rue de Bruxelles, 61, B-5000 Namur, Belgium
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25
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Bignon E, Gattuso H, Morell C, Dumont E, Monari A. DNA Photosensitization by an “Insider”: Photophysics and Triplet Energy Transfer of 5‐Methyl‐2‐pyrimidone Deoxyribonucleoside. Chemistry 2015; 21:11509-16. [DOI: 10.1002/chem.201501212] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2015] [Indexed: 12/13/2022]
Affiliation(s)
- Emmanuelle Bignon
- Laboratoire de Chimie, UMR 5182, CNRS Ecole Normale Supérieure de Lyon, Lyon (France)
- Institut des Sciences Analytiques, UMR 5280, Université de Lyon1 (UCBL) CNRS, Lyon (France)
| | - Hugo Gattuso
- Université de Lorraine, Nancy Theory‐Simulation‐Modeling, SRSMC, Vandoeuvre‐les‐Nancy (France)
- CNRS, Nancy Theory‐Simulation‐Modeling, SRSMC, Vandoeuvre‐les‐Nancy (France)
| | - Christophe Morell
- Institut des Sciences Analytiques, UMR 5280, Université de Lyon1 (UCBL) CNRS, Lyon (France)
| | - Elise Dumont
- Laboratoire de Chimie, UMR 5182, CNRS Ecole Normale Supérieure de Lyon, Lyon (France)
| | - Antonio Monari
- Université de Lorraine, Nancy Theory‐Simulation‐Modeling, SRSMC, Vandoeuvre‐les‐Nancy (France)
- CNRS, Nancy Theory‐Simulation‐Modeling, SRSMC, Vandoeuvre‐les‐Nancy (France)
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26
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Gattuso H, Assfeld X, Monari A. Modeling DNA electronic circular dichroism by QM/MM methods and Frenkel Hamiltonian. Theor Chem Acc 2015. [DOI: 10.1007/s00214-015-1640-8] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
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27
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Rebolini E, Toulouse J, Teale AM, Helgaker T, Savin A. Excited states from range-separated density-functional perturbation theory. Mol Phys 2015. [DOI: 10.1080/00268976.2015.1011248] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
Affiliation(s)
- Elisa Rebolini
- Sorbonne Universités, UPMC Univ Paris 06, UMR 7616, Laboratoire de Chimie Théorique, Paris, France
- CNRS, UMR 7616, Laboratoire de Chimie Théorique, Paris, France
- Department of Chemistry, Centre for Theoretical and Computational Chemistry, University of Oslo, Oslo, Norway
| | - Julien Toulouse
- Sorbonne Universités, UPMC Univ Paris 06, UMR 7616, Laboratoire de Chimie Théorique, Paris, France
- CNRS, UMR 7616, Laboratoire de Chimie Théorique, Paris, France
| | - Andrew M. Teale
- School of Chemistry, University of Nottingham, Nottingham, United Kingdom
| | - Trygve Helgaker
- Department of Chemistry, Centre for Theoretical and Computational Chemistry, University of Oslo, Oslo, Norway
| | - Andreas Savin
- Sorbonne Universités, UPMC Univ Paris 06, UMR 7616, Laboratoire de Chimie Théorique, Paris, France
- CNRS, UMR 7616, Laboratoire de Chimie Théorique, Paris, France
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28
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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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29
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Dumont É, Monari A. Interaction of Palmatine with DNA: An Environmentally Controlled Phototherapy Drug. J Phys Chem B 2014; 119:410-9. [DOI: 10.1021/jp5088515] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Affiliation(s)
- Élise Dumont
- Laboratoire
de Chimie, UMR 5182 CNRS, École Normale Supérieure de Lyon, 46, allée d’Italie, 69364 Lyon Cedex 07, France
| | - Antonio Monari
- Théorie-Modélisation-Simulation,
SRSMC, Université de Lorraine Nancy, Boulevard des Aiguillettes 54506, Vandoeuvre-lés-Nancy, France
- Théorie-Modélisation-Simulation,
SRSMC, CNRS, Boulevard des Aiguillettes 54506, Vandoeuvre-lés-Nancy, France
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30
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Huix-Rotllant M, Dumont E, Ferré N, Monari A. Photophysics of acetophenone interacting with DNA: why the road to photosensitization is open. Photochem Photobiol 2014; 91:323-30. [PMID: 25412588 DOI: 10.1111/php.12395] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2014] [Accepted: 11/12/2014] [Indexed: 01/12/2023]
Abstract
Deoxyribonucleic acid photosensitization, i.e. the photoinduced electron- or energy-transfer of chromophores interacting with DNA, is a crucial phenomenon that triggers important DNA lesions such as pyrimidine dimerization, even upon absorption of relatively low-energy radiation. Oxidative lesions may also be produced via the photoinduced production of reactive oxygen species. Aromatic ketones, and acetophenone in particular, are well known for their sensitization effects. In this contribution we model the structural and dynamical properties of the acetophenone/DNA aggregates as well as their spectroscopic and photophysical properties using high-level hybrid quantum mechanics/molecular mechanics methods. We show that the key steps of the photochemistry of acetophenone in gas phase are conserved in the macromolecular environment and thus an ultrafast singlet-triplet conversion of acetophenone is expected prior to the transfer to DNA.
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Affiliation(s)
- Miquel Huix-Rotllant
- Institut fur Physikalische und Theoretische Chemie, Gothe Universitat Frankfurt, Frankfurt am Main, Germany
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31
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Abstract
![]()
A projected hybrid orbital (PHO)
method was described to model
the covalent boundary in a hybrid quantum mechanical and molecular
mechanical (QM/MM) system. The PHO approach can be used in ab initio
wave function theory and in density functional theory with any basis
set without introducing system-dependent parameters. In this method,
a secondary basis set on the boundary atom is introduced to formulate
a set of hybrid atomic orbtials. The primary basis set on the boundary
atom used for the QM subsystem is projected onto the secondary basis
to yield a representation that provides a good approximation to the
electron-withdrawing power of the primary basis set to balance electronic
interactions between QM and MM subsystems. The PHO method has been
tested on a range of molecules and properties. Comparison with results
obtained from QM calculations on the entire system shows that the
present PHO method is a robust and balanced QM/MM scheme that preserves
the structural and electronic properties of the QM region.
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Affiliation(s)
- Yingjie Wang
- Theoretical Chemistry Institute, State Key Laboratory of Theoretical and Computational Chemistry, Jilin University , Changchun, Jilin Province 130028, People's Republic of China
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32
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Laurent AD, Glushkov VN, Very T, Assfeld X. Toward the understanding of the environmental effects on core ionizations. J Comput Chem 2014; 35:1131-9. [PMID: 24752947 DOI: 10.1002/jcc.23604] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2013] [Revised: 02/06/2014] [Accepted: 03/10/2014] [Indexed: 11/10/2022]
Affiliation(s)
- Adèle D. Laurent
- CEISAM, UMR CNRS 6230, BP 92208, Université de Nantes; 2, Rue de la Houssinière, 44322 Nantes, Cedex 3 France
| | - Vitaly N. Glushkov
- Department of Physics; Electronics and Computer Systems; Oles Gonchar Dnipropetrovsk National University; Ukraine
| | - Thibaut Very
- Université de Lorraine, CNRS, Théorie-Modélisation-Simulation; SRSMC UMR 7565, Vandoeuvre-lès-Nancy, F-54506 France
| | - Xavier Assfeld
- Université de Lorraine, CNRS, Théorie-Modélisation-Simulation; SRSMC UMR 7565, Vandoeuvre-lès-Nancy, F-54506 France
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33
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Glushkov VN, Assfeld X. Multireference space without first solving the configuration interaction problem. J Comput Chem 2014; 35:313-23. [PMID: 24403018 DOI: 10.1002/jcc.23502] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2013] [Revised: 10/10/2013] [Accepted: 11/10/2013] [Indexed: 11/07/2022]
Abstract
We further develop an idea to generate a compact multireference space without first solving the configuration interaction problem previously proposed for the ground state (GS) (Glushkov, Chem. Phys. Lett. 1995, 244, 1). In the present contribution, our attention is focused on low-lying excited states (ESs) with the same symmetry as the GS which can be adequately described in terms of an high-spin open-shell formalism. Two references Møller-Plesset (MP) like perturbation theory for ESs is developed. It is based on: (1) a main reference configuration constructed from the parent molecular orbitals adjusted to a given ES and (2) secondary double excitation configuration built on the GS like orbitals determined by the Hartree-Fock equations subject to some orthogonality constraints. It is shown how to modify the MP zeroth-order Hamiltonian so that the reference configurations and corresponding excitations are eigenfunctions of it and are compatible with orthogonality conditions for the GS and ES. Intruder states appearance is also discussed. The proposed scheme is applied to the GS, ES, and excitation energies of small molecules to illustrate and calibrate our calculations.
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Affiliation(s)
- Vitaly N Glushkov
- Department of Physics, Electronics and Computer Systems, Oles Gonchar Dnipropetrovsk National University, Dnipropetrovsk, Ukraine
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34
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Evangelista FA, Shushkov P, Tully JC. Orthogonality constrained density functional theory for electronic excited states. J Phys Chem A 2013; 117:7378-92. [PMID: 23590595 DOI: 10.1021/jp401323d] [Citation(s) in RCA: 70] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
We report a novel scheme for computing electronic excitation energies within the framework of density functional theory (DFT) based on a time-independent variational formulation of DFT. The excited state density functional is recast as a Kohn-Sham functional, which is further simplified by an adiabatic approximation of the exchange-correlation functional. Under the adiabatic approximation, the minimization of the excited state Kohn-Sham functional is shown to be equivalent to a ground state DFT computation augmented with orthogonality constraints with respect to the ground state Kohn-Sham determinant. An algorithm for the optimization of the energy subject to orthogonality constraints, which does not suffer from variational collapse, is described and implemented. A benchmark test set containing 28 organic molecules (Schreiber, M. J. Chem. Phys. 2008, 128, 134110) was used to assess the quality of the excitation energies obtained. Two novel approaches to spin-adapt the resulting excitation energies are discussed and found to provide results with error metrics similar to those of time-dependent DFT. Similarities and differences with respect to other time-independent DFT approaches are highlighted and some of the advantages of our scheme-including the ability to correctly describe charge-transfer excitations-are critically assessed.
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35
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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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36
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Glushkov VN, Assfeld X. On orthogonality constrained multiple core-hole states and optimized effective potential method. J Comput Chem 2012; 33:2058-66. [PMID: 22696265 DOI: 10.1002/jcc.23041] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2012] [Revised: 05/09/2012] [Accepted: 05/13/2012] [Indexed: 01/24/2023]
Abstract
An attempt to construct a multiple core-hole state within the optimized effective potential (OEP) methodology is presented. In contrast to the conventional Δ-self-consistent field method for hole states, the effects of removing an electron is achieved using some orthogonality constraints imposed on the orbitals so that a Slater determinant describing a hole state is constrained to be orthogonal to that of a neutral system. It is shown that single, double, and multiple core-hole states can be treated within a unified framework and can be easily implemented for atoms and molecules. For this purpose, a constrained OEP method proposed earlier for excited states (Glushkov and Levy, J. Chem. Phys. 2007, 126, 174106) is further developed to calculate single and double core ionization energies using a local effective potential expressed as a direct mapping of the external potential. The corresponding equations, determining core-hole orbitals from a one-particle Schrödinger equation with a local potential as well as correlation corrections derived from the second-order many-body perturbation theory are given. One of the advantages of the present direct mapping formulation is that the effective potential, which plays the role of the Kohn-Sham potential, has the symmetry of the external potential. Single and double core ionization potentials computed with the presented scheme were found to be in agreement with data available from experiment and other calculations. We also discuss core-hole state local potentials for the systems studied.
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Affiliation(s)
- V N Glushkov
- Department of Physics,, Electronics and Computer Systems, Dnipropetrovsk National University, Ukraine.
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Coulaud E, Guihéry N, Malrieu JP, Hagebaum-Reignier D, Siri D, Ferré N. Analysis of the physical contributions to magnetic couplings in broken symmetry density functional theory approach. J Chem Phys 2012; 137:114106. [DOI: 10.1063/1.4752412] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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Glushkov VN, Assfeld X. Doubly, triply, and multiply excited states from a constrained optimized effective potential method. J Chem Phys 2010; 132:204106. [PMID: 20515087 DOI: 10.1063/1.3443777] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023] Open
Abstract
This article further develops and applies a constrained optimized effective potential (COEP) approach for the practical calculations of doubly and multiply excited states of atoms and molecules. The COEP method uses the time-independent theory of pure excited states and implements a simple asymptotic projection method to take orthogonality constraints into account. We show that, in contrast with the common time-dependent density functional method, the COEP methodology is capable of treating doubly, triply, and multiply excited states and can be easily applied to both atoms and molecules. In particular, doubly excited energies of each state are calculated through a constrained minimization procedure including constraints that make its Slater determinantal functions orthogonal to those of the ground and all lower-lying doubly excited states. The performance of the proposed method is examined by calculations of doubly excited state energies for the He atom and H(2) molecule at exchange-only and exchange-correlation level of approximation.
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Affiliation(s)
- V N Glushkov
- Department of Physics, Electronics and Computer Systems, National University, per Nauchny 13, Dnepropetrovsk 49050, Ukraine.
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Frozen core orbitals as an alternative to specific frontier bond potential in hybrid Quantum Mechanics/Molecular Mechanics methods. Chem Phys Lett 2006. [DOI: 10.1016/j.cplett.2006.06.095] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
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Fornili A, Moreau Y, Sironi M, Assfeld X. On the suitability of strictly localized orbitals for hybrid QM/MM calculations. J Comput Chem 2006; 27:515-23. [PMID: 16444700 DOI: 10.1002/jcc.20366] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
In the QM/MM method we have developed (LSCF/MM), the QM and the MM parts are held together by means of strictly localized bonding orbitals (SLBOs). Generally these SLBOs are derived from localized bond orbitals (LBOs) that undergo tails deletion, resulting in a nonpredictable change of their properties. An alternative set of SLBOs is provided by the extremely localized molecular orbitals (ELMOs) approach, where the orbitals are rigorously localized on some prefixed atoms without tails on the other atoms of the molecule. A comparative study of SLBOs arising from various localization schemes and ELMOs is presented to test the reliability and the transferability of these functions within the Local Self-Consistent Field (LSCF) framework. Two types of chemical bonds were considered: C--C and C--O single bonds. The localized functions are obtained on the ethane and the methanol molecules, and are tested on beta-alanine and diethyl ether molecules. Moreover, the various protonation forms of beta-alanine have been investigated to illustrate how well the polarity variation of the chemical bond can be handled throughout a chemical process. At last, rotation energy profiles around C--C and C--O bonds are reproduced for butane and fluoromethanol. Energetic, geometric, as well as electronic factors all indicate that ELMO functions are much more transferable from one molecule to another, leading to results closer to the usual SCF reference than any other calculations involving any other localized orbitals. When the shape of the orbital is the most important factor then ELMO functions will perform as well as any other localized orbital.
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Affiliation(s)
- Arianna Fornili
- Dipartimento di Chimica Fisica ed Elettrochimica, Università degli Studi di Milano, Via Golgi 19, 20133 Milano, Milan, Italy
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Ferré N, Assfeld X. A new three-layer hybrid method (LSCF/MM/Madelung) devoted to the study of chemical reactivity in zeolites. Preliminary results. ACTA ACUST UNITED AC 2003. [DOI: 10.1016/s0166-1280(03)00290-2] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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Thiel A, Schirmer J, Köppel H. An intermediate state representation approach to K-shell ionization in molecules. II. Computational tests. J Chem Phys 2003. [DOI: 10.1063/1.1584658] [Citation(s) in RCA: 39] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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