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Lima IT, Gomes RFC, Paura ENC, Provasi PF, Gester R, Rodrigues da Cunha A. Exploring the molecular solvatochromism, stability, reactivity, and non-linear optical response of resveratrol. J Mol Model 2024; 30:314. [PMID: 39167248 DOI: 10.1007/s00894-024-06108-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2024] [Accepted: 08/08/2024] [Indexed: 08/23/2024]
Abstract
CONTEXT This work analyzes the isomerization effects and solvent contributions to the stability, electronic excitations, reactivity, and non-linear optical properties (NLO) of resveratrol molecules within the formalism of the Density Functional Theory. The findings suggest that resveratrol solvatochromism is significantly influenced by solvent polarization. The electronic and free energies (E and G) indicate that trans is the most stable conformer. The system is classified as a strong nucleophile. However, the analysis of the Fukui functions and the Mulliken charges indicate that cis-trans isomerization jointly affects the reactive indices of the carbon and hydrogen atoms. The results also suggest that solvent is relevant to solvatochromism and the NLO response. Both cis and trans conformers present strong π - π ∗ excitations that undergo a visible hypsochromic change when the polarity of the solvent increases. Once the absorption spectra are connected to the first hyperpolarization ( β ) by the Oudar and Chemla relation, the hypsochromism of resveratrol is the reason for the drop in the generation of the second harmonic when the ambient polarity decreases. The CAM-B3LYP DFT results suggest that resveratrol is interesting for NLO applications. Depending on the choice of solvent, values ∼ 50 times those observed for urea ( β = 0.34 × 10 - 34 esu), which is a standard NLO material. METHODS The optimized geometries of cis and trans isomers of resveratrol in vacuum were obtained using Density Functional Theory (DFT) with the hybrid exchange-correlation function (CAM-B3LYP) and Pople basis set functions, specifically 6-311++G(d,p). The solvent effect on the geometries of both isomers was included using the polarizable continuum model (PCM) with the same level of QM calculation. Vibrational analysis was conducted to confirm that all optimized geometries correspond to the minimum energy. Various electronic properties, including dipole moments, molecular orbitals, transition energy, dipole polarizabilities, and global reactivity parameters, were calculated using both continuum and discrete solvation models based on the sequential QM/MM methodology. All QM calculations were performed with the Gaussian 09 program and the MC simulations with the DICE program. All NLO analysis was carried out using the Multiwfn code.
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Affiliation(s)
- Igo T Lima
- Coordenação do Bacharelado Interdisciplinar em Ciência e Tecnologia, Campus Dom Delgado, Universidade Federal do Maranhão, UFMA, São Luís, MA, Brazil
| | - Ramon F C Gomes
- Coordenação do Bacharelado Interdisciplinar em Ciência e Tecnologia, Campus Dom Delgado, Universidade Federal do Maranhão, UFMA, São Luís, MA, Brazil
| | - Edson N C Paura
- Universidade Federal do Maranhão, UFMA, Campus Balsas, Balsas, MA, Brazil
| | - Patricio F Provasi
- Department of Physics, IMIT, Northeastern University, CONICET, AV. Libertad 5500, W 3404 AAS, Corrientes, Argentina
| | - Rodrigo Gester
- Faculdade de Física, Universidade Federal do Sul e Sudeste do Pará, UNIFESSPA, Marabá, PA, Brazil
- Instituto de Física, Universidade de São Paulo, USP, Rua do Matão 1371, São Paulo, SP, Brazil
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Kiataki MB, Varella MTDN, Coutinho K, Rabilloud F. Novel Approach for Predicting Vertical Electron Attachment Energies in Bulk-Solvated Molecules. J Chem Theory Comput 2024; 20:4893-4900. [PMID: 38783835 DOI: 10.1021/acs.jctc.4c00256] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/25/2024]
Abstract
When low-energy electrons interact with molecules, they can give rise to transient anion states commonly known as resonances. These states are formed through vertical electron attachment processes and have the potential to induce various forms of DNA lesions, including base damage, single- and double-strand breaks, cross-links, and clustered lesions that are challenging to repair. So far, most experimental and theoretical studies have investigated the formation of resonances of (bio)molecules in the gas phase or in microsolvated environments. Since cellular environments are mainly composed of water molecules, it is crucial to understand how bulk water affects the resonances of (bio)molecules. Given the existing gap in studies on resonances of bulk-solvated molecules, we propose a novel theoretical-computational approach to address this void. Our approach combines the multibasis-set (time-dependent-)density functional theory and self-consistent sequential quantum mechanics/molecular mechanics polarizable electrostatic embedding methods. We apply this combined methodology to predict the vertical electron attachment energies of 1-methyl-5-nitroimidazole (1M5NI), a well-known radiosensitizer model, in bulk water. In addition, we analyze the rapid mutual polarization between the resonances (both shape- and core-excited) of 1M5NI and the surrounding bulk water environment. For comparison, we also studied the isolated and microsolvated 1M5NI. Overall, while the polarization of the environment is clearly sensitive to the solute charge, causing a significant impact on the vertical electron affinity and consequently on the attachment electron energies, it does not have a significant impact on the excitation energies of the anion.
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Affiliation(s)
- Matheus B Kiataki
- Universite Claude Bernard Lyon 1, CNRS, Institut Lumière Matière, UMR5306, Villeurbanne F-69100, France
- Instituto de Física, Universidade de São Paulo, Rua do Matão 1731, São Paulo 05508-090, São Paulo, Brazil
| | - Márcio T do N Varella
- Instituto de Física, Universidade de São Paulo, Rua do Matão 1731, São Paulo 05508-090, São Paulo, Brazil
| | - Kaline Coutinho
- Instituto de Física, Universidade de São Paulo, Rua do Matão 1731, São Paulo 05508-090, São Paulo, Brazil
| | - Franck Rabilloud
- Universite Claude Bernard Lyon 1, CNRS, Institut Lumière Matière, UMR5306, Villeurbanne F-69100, France
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Zhang M, Li S, Yang H, Song G, Wu C, Li Z. Structure and Ultrafast X-ray Diffraction of the Hydrated Metaphosphate. J Phys Chem A 2024; 128:3086-3094. [PMID: 38605669 DOI: 10.1021/acs.jpca.4c00346] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/13/2024]
Abstract
We study the pathway of metaphosphate hydration when a metaphosphate anion is dissolved in liquid water with an explicit water model. For this purpose, we propose a sequential Monte Carlo algorithm incorporated with the ab initio quantum mechanics/molecular mechanics (QM/MM) method, which can reduce the amount of ab initio QM/MM sampling while retaining the accuracy of the simulation. We demonstrate the numerical calculation of the standard enthalpy change for the successive addition reaction PO3-·2H2O + H2O ⇌ PO3-·3H2O in the liquid phase, which helps to clarify the hydration pathway of the metaphosphate. With the obtained hydrated structure of the metaphosphate anion, we perform ab initio calculations for its relaxation dynamics upon vibrational excitation and characterize the energy transfer process in solution with simulated ultrafast X-ray diffraction signals, which can be experimentally implemented with X-ray free-electron lasers.
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Affiliation(s)
- Ming Zhang
- State Key Laboratory for Mesoscopic Physics and Collaborative Innovation Center of Quantum Matter, School of Physics, Peking University, Beijing 100871, China
- Collaborative Innovation Center of Extreme Optics, Shanxi University, Taiyuan, Shanxi 030006, China
| | - Sizhe Li
- College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China
| | - Hanwei Yang
- State Key Laboratory for Mesoscopic Physics and Collaborative Innovation Center of Quantum Matter, School of Physics, Peking University, Beijing 100871, China
- Collaborative Innovation Center of Extreme Optics, Shanxi University, Taiyuan, Shanxi 030006, China
| | - Gaoxing Song
- State Key Laboratory for Mesoscopic Physics and Collaborative Innovation Center of Quantum Matter, School of Physics, Peking University, Beijing 100871, China
- Collaborative Innovation Center of Extreme Optics, Shanxi University, Taiyuan, Shanxi 030006, China
| | - Chengyin Wu
- State Key Laboratory for Mesoscopic Physics and Collaborative Innovation Center of Quantum Matter, School of Physics, Peking University, Beijing 100871, China
- Collaborative Innovation Center of Extreme Optics, Shanxi University, Taiyuan, Shanxi 030006, China
- Peking University Yangtze Delta Institute of Optoelectronics, Nantong, Jiangsu 226010, China
| | - Zheng Li
- State Key Laboratory for Mesoscopic Physics and Collaborative Innovation Center of Quantum Matter, School of Physics, Peking University, Beijing 100871, China
- Collaborative Innovation Center of Extreme Optics, Shanxi University, Taiyuan, Shanxi 030006, China
- Peking University Yangtze Delta Institute of Optoelectronics, Nantong, Jiangsu 226010, China
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Tavares CA, Santos TMR, Gonçalves MA, da Cunha EFF, Ramalho TC. Enhanced Sampling in Molecular Dynamics Simulations: How Many MD Snapshots can be Needed to Reproduce the Biological Behavior? Mini Rev Med Chem 2024; 24:1063-1069. [PMID: 38258786 DOI: 10.2174/0113895575250433231103063707] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2023] [Revised: 08/01/2023] [Accepted: 09/14/2023] [Indexed: 01/24/2024]
Abstract
Since its early days in the 19th century, medicinal chemistry has concentrated its efforts on the treatment of diseases, using tools from areas such as chemistry, pharmacology, and molecular biology. The understanding of biological mechanisms and signaling pathways is crucial information for the development of potential agents for the treatment of diseases mainly because they are such complex processes. Given the limitations that the experimental approach presents, computational chemistry is a valuable alternative for the study of these systems and their behavior. Thus, classical molecular dynamics, based on Newton's laws, is considered a technique of great accuracy, when appropriated force fields are used, and provides satisfactory contributions to the scientific community. However, as many configurations are generated in a large MD simulation, methods such as Statistical Inefficiency and Optimal Wavelet Signal Compression Algorithm are great tools that can reduce the number of subsequent QM calculations. Accordingly, this review aims to briefly discuss the importance and relevance of medicinal chemistry allied to computational chemistry as well as to present a case study where, through a molecular dynamics simulation of AMPK protein (50 ns) and explicit solvent (TIP3P model), a minimum number of snapshots necessary to describe the oscillation profile of the protein behavior was proposed. For this purpose, the RMSD calculation, together with the sophisticated OWSCA method was used to propose the minimum number of snapshots.
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Affiliation(s)
- Camila A Tavares
- Laboratory of Molecular Modelling, Department of Chemistry, Federal University of Lavras, Lavras - MG, 37200-000, Brazil
| | - Taináh M R Santos
- Laboratory of Molecular Modelling, Department of Chemistry, Federal University of Lavras, Lavras - MG, 37200-000, Brazil
| | - Mateus A Gonçalves
- Laboratory of Molecular Modelling, Department of Chemistry, Federal University of Lavras, Lavras - MG, 37200-000, Brazil
| | - Elaine F F da Cunha
- Laboratory of Molecular Modelling, Department of Chemistry, Federal University of Lavras, Lavras - MG, 37200-000, Brazil
| | - Teodorico C Ramalho
- Laboratory of Molecular Modelling, Department of Chemistry, Federal University of Lavras, Lavras - MG, 37200-000, Brazil
- Department of Chemistry, Faculty of Science, University of Hradec Králové, Hradec Králové, 500 03, Czech Republic
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Franco LR, Toledo KCF, Matias TA, Araujo CM, Araki K, Coutinho K. Theoretical investigation of solvent and oxidation/deprotonation effects on the electronic structure of a mononuclear Ru-aqua-polypyridine complex in aqueous solution. Phys Chem Chem Phys 2023; 25:24475-24494. [PMID: 37655780 DOI: 10.1039/d3cp02154h] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/02/2023]
Abstract
Mononuclear polypyridine ruthenium (Ru) complexes can catalyze various reactions, including water splitting, and can also serve as photosensitizers in solar cells. Despite recent progress in their synthesis, accurately modeling their physicochemical properties, particularly in solution, remains challenging. Herein, we conduct a theoretical investigation of the structural and electronic properties of a mononuclear Ru-aqua polypyridine complex in aqueous solution, considering five of its possible oxidation/protonation states species: [RuII(H2O)(py)(bpy)2]2+, [RuII(OH)(py)(bpy)2]+, [RuIII(H2O)(py)(bpy)2]3+, [RuIII(OH)(py)(bpy)2]2+ and [RuIV(O)(py)(bpy)2]2+, where py = pyridine and bpy = 2,2'-bipyridine. At first, we investigate the impact of proton-coupled and non-coupled electron transfer reactions on the geometry and electronic structure of the complexes in vacuum and in solution, using an implicit solvent model. Then, using a sequential multiscale approach that combines quantum mechanics and molecular mechanics (S-QM/MM), we examine the explicit solvent effects on the electronic excitations of the complexes, and compare them with the experimental results. The complexes were synthesized, and their absorption spectra measured in aqueous solution. To accurately describe the QM interactions between the metal center and the aqueous ligand in the MM simulations, we developed new force field parameters for the Ru atom. We analyze the solvent structure around the complexes and account for its explicit influence on the polarization and electronic excitations of the complexes. Notably, accounting for the explicit solvent polarization effects of the first solvation shells is essential to correctly describe the energy of the electronic transitions, and the explicit treatment of the hydrogen bonds at the QM level in the excitation calculations improves the accuracy of the description of the metal-to-ligand charge-transfer bands. Transition density matrix analysis is used to characterize all electronic transitions in the visible and ultraviolet ranges according to their charge-transfer (CT) character. This study elucidates the electronic structure of those ruthenium polypyridyl complexes in aqueous solution and underscores the importance of precisely describing solvent effects, which can be achieved employing the S-QM/MM method.
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Affiliation(s)
- Leandro Rezende Franco
- Instituto de Fisica, Universidade de Sao Paulo, Cidade Universitaria, 05508-090 Sao Paulo, SP, Brazil
- Department of Engineering and Physics, Karlstad University, 65188 Karlstad, Sweden.
| | | | - Tiago Araujo Matias
- Instituto de Quimica, Universidade de Sao Paulo, Av. Lineu Prestes 748, Butanta, 05508-000 Sao Paulo, SP, Brazil
| | - C Moyses Araujo
- Department of Engineering and Physics, Karlstad University, 65188 Karlstad, Sweden.
- Materials Theory Division, Department of Physics and Astronomy, Ångström Laboratory, Uppsala University, 75120 Uppsala, Sweden
| | - Koiti Araki
- Instituto de Quimica, Universidade de Sao Paulo, Av. Lineu Prestes 748, Butanta, 05508-000 Sao Paulo, SP, Brazil
| | - Kaline Coutinho
- Instituto de Fisica, Universidade de Sao Paulo, Cidade Universitaria, 05508-090 Sao Paulo, SP, Brazil
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Junqueira GMA, Ballester MY, Nascimento MAC. Reactivity properties of the HOSO and HSO 2 isomers in liquid medium: a sequential Monte Carlo/quantum mechanics study. J Mol Model 2023; 29:189. [PMID: 37249704 DOI: 10.1007/s00894-023-05514-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2023] [Accepted: 03/13/2023] [Indexed: 05/31/2023]
Abstract
CONTEXT The rationalization of acid rain formation steps is fundamental for mitigating its effects. It is believed the hydroxysulfinyl radical is an intermediate species for the production of atmospheric sulfuric acid. Two stable configurations HOSO and HSO2 have been reported for such a radical in the gas phase. This work aims at studying these isomers in the aqueous medium. The electrical and reactivity quantities - electronic chemical potential ([Formula: see text]), chemical hardness ([Formula: see text]), and electrophilicity ([Formula: see text]) - are here calculated and compared. Considering first solvation shells (15 H2O for HSO2 and 23 H2O for HOSO), an increase of 25% in the dipole moment of HSO2 was obtained, while the dipole moment of HOSO decreases in 11%. Both solvated isomers grow softer ([Formula: see text] decreases) contrasted to the gas phase. METHODS HOSO and HSO2 are studied through a sequential Monte Carlo/quantum mechanics approach. Lennard-Jones plus the Coulomb potentials were used to represent intermolecular potential interaction in the frame of the DICE package. Molecular structure calculations were performed at CASPT2/aug - cc - pV(T + d)Z level of theory using the MOLPRO suite of programs.
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Affiliation(s)
- Geórgia Maria A Junqueira
- Department of Physical Chemistry, Federal University of Rio de Janeiro, Cidade Universitária, Rio de Janeiro, 21941-909, RJ, Brazil.
| | - Maikel Y Ballester
- Department of Physics, Federal University of Juiz de Fora, Campus Universitário, Juiz de Fora, 36015-260, MG, Brazil
| | - Marco Antonio Chaer Nascimento
- Department of Physical Chemistry, Federal University of Rio de Janeiro, Cidade Universitária, Rio de Janeiro, 21941-909, RJ, Brazil
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Ramos TN, Champagne B. Investigation of the Second Harmonic Generation at the Water-Vacuum Interface by Using Multi-Scale Modeling Methods. ChemistryOpen 2023; 12:e202200045. [PMID: 35950561 PMCID: PMC9806952 DOI: 10.1002/open.202200045] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2022] [Revised: 06/16/2022] [Indexed: 01/28/2023] Open
Abstract
The Sequential Quantum Mechanics/Molecular Mechanics scheme has been enacted to perform a systematic investigation of the polarizability (α) and first hyperpolarizability (β) responses at the water-vacuum interface. After performing classical molecular dynamics simulations to provide snapshots of the structures, quantum chemistry calculations of the linear and nonlinear optical responses have been performed for clusters of five water molecules at the time-dependent DFT level in combination with different embedding schemes, ranging from point charges to polarizable point charges, with and without local field effects. When going from the bulk to the interface, the main observations of these calculations encompass i) a modest increase of the average polarizability but an increase by about a factor of two of its anisotropy, ii) an increase by about 20 % of the βHRS response, accompanied by a small increase of its depolarization ratio, and iii) a net increase of the component of the β tensor normal to the interface (βzzz ) as well as of β// . Globally, the interfacial effects on β are localized at the first molecular layer while they are observed up to the fourth molecular layer on α.
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Affiliation(s)
- Tárcius N. Ramos
- Laboratory of Theoretical ChemistryNamur Institute of Structured Matter (NISM)University of NamurRue de Bruxelles, 61B-5000NamurBelgium
| | - Benoît Champagne
- Laboratory of Theoretical ChemistryNamur Institute of Structured Matter (NISM)University of NamurRue de Bruxelles, 61B-5000NamurBelgium
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Gonçalves MA, Gonçalves AS, Franca TCC, Santana MS, da Cunha EFF, Ramalho TC. Improved Protocol for the Selection of Structures from Molecular Dynamics of Organic Systems in Solution: The Value of Investigating Different Wavelet Families. J Chem Theory Comput 2022; 18:5810-5818. [DOI: 10.1021/acs.jctc.2c00593] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Mateus A. Gonçalves
- Chemistry Department, Federal University of Lavras, 37200-000Lavras, MG, Brazil
| | - Arlan S. Gonçalves
- Federal Institute of Education Science and Technology of Espírito Santo, Vila Velha29100-000, Brazil
- Federal Institute of Education Science and Technology of Espírito Santo, Unit Goiabeiras, 29056-264Vitória, Espírito Santo, Brazil
| | - Tanos C. C. Franca
- Laboratory of Molecular Modeling Applied to Chemical and Biological Defense (LMACBD), Military Institute of Engineering (IME), Rio de Janeiro22290-270, Brazil
| | - Mozarte S. Santana
- Chemistry Department, Federal University of Lavras, 37200-000Lavras, MG, Brazil
| | | | - Teodorico C. Ramalho
- Chemistry Department, Federal University of Lavras, 37200-000Lavras, MG, Brazil
- Faculty of Informatics and Management, Center for Basic and Applied Research, University of Hradec Kralove, Hradec Kralove50003, Czech Republic
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Franco LR, Toledo KCF, Matias TA, Benavides PA, Cezar HM, Araujo CM, Coutinho K, Araki K. Unraveling the acid-base characterization and solvent effects on the structural and electronic properties of a bis-bidentate bridging ligand. Phys Chem Chem Phys 2022; 24:10222-10240. [PMID: 35420602 DOI: 10.1039/d1cp03912a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Understanding the interactions and the solvent effects on the distribution of several species in equilibrium and how it can influence the 1H-NMR properties, spectroscopy (UV-vis absorption), and the acid-base equilibria can be especially challenging. This is the case of a bis-bidentate bridging ligand bis(2-pyridyl)-benzo-bis(imidazole), where the two pyridyl and four imidazolyl nitrogen atoms can be protonated in different ways, depending on the solvent, generating many isomeric/tautomeric species. Herein, we report a combined theoretical-experimental approach based on a sequential quantum mechanics/molecular mechanics procedure that was successfully applied to describe in detail the acid-base characterization and its effects on the electronic properties of such a molecule in solution. The calculated free-energies allowed the identification of the main species present in solution as a function of the solvent polarity, and its effects on the magnetic shielding of protons (1H-NMR chemical shifts), the UV-vis absorption spectra, and the acid-base equilibrium constants (pKas) in aqueous solution. Three acid-base equilibrium constants were experimentally/theoretically determined (pKa1 = 1.3/1.2, pKa2 = 2.1/2.2 and pKa5 = 10.1/11.3) involving mono-deprotonated and mono-protonated cis and trans species. Interestingly, other processes with pKa3 = 3.7 and pKa4 = 6.0 were also experimentally determined and assigned to the protonation and deprotonation of dimeric species. The dimerization of the most stable neutral species was investigated by Monte Carlo simulations and its electronic effects were considered for the elucidation of the UV-vis absorption bands, revealing transitions mainly with the charge-transfer characteristic and involving both the monomeric species and the dimeric species. The good matching of the theoretical and experimental results provides an atomistic insight into the solvent effects on the electronic properties of this bis-bidentate bridging ligand.
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Affiliation(s)
- Leandro Rezende Franco
- Instituto de Física, Universidade de São Paulo, Cidade Universitária, 05508-090 São Paulo, SP, Brazil. .,Department of Engineering and Physics, Karlstad University, 65188 Karlstad, Sweden
| | | | - Tiago Araujo Matias
- Instituto de Química, Universidade de São Paulo, Av. Lineu Prestes 748, Butantã, 05508-000 São Paulo, SP, Brazil.
| | - Paola Andrea Benavides
- Instituto de Química, Universidade de São Paulo, Av. Lineu Prestes 748, Butantã, 05508-000 São Paulo, SP, Brazil.
| | - Henrique Musseli Cezar
- Instituto de Física, Universidade de São Paulo, Cidade Universitária, 05508-090 São Paulo, SP, Brazil.
| | - C Moyses Araujo
- Department of Engineering and Physics, Karlstad University, 65188 Karlstad, Sweden.,Materials Theory Division, Department of Physics and Astronomy, Ångström Laboratory, Uppsala University, 75120 Uppsala, Sweden
| | - Kaline Coutinho
- Instituto de Física, Universidade de São Paulo, Cidade Universitária, 05508-090 São Paulo, SP, Brazil.
| | - Koiti Araki
- Instituto de Química, Universidade de São Paulo, Av. Lineu Prestes 748, Butantã, 05508-000 São Paulo, SP, Brazil.
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Extending NMR Quantum Computation Systems by Employing Compounds with Several Heavy Metals as Qubits. MAGNETOCHEMISTRY 2022. [DOI: 10.3390/magnetochemistry8050047] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Nuclear magnetic resonance (NMR) is a spectroscopic method that can be applied to several areas. Currently, this technique is also being used as an experimental quantum simulator, where nuclear spins are employed as quantum bits or qubits. The present work is devoted to studying heavy metal complexes as possible candidates to act as qubit molecules. Nuclei such 113Cd, 199Hg, 125Te, and 77Se assembled with the most common employed nuclei in NMR-QIP implementations (1H, 13C, 19F, 29Si, and 31P) could potentially be used in heteronuclear systems for NMR-QIP implementations. Hence, aiming to contribute to the development of future scalable heteronuclear spin systems, we specially designed four complexes, based on the auspicious qubit systems proposed in our previous work, which will be explored by quantum chemical calculations of their NMR parameters and proposed as suitable qubit molecules. Chemical shifts and spin–spin coupling constants in four complexes were examined using the spin–orbit zeroth-order regular approximation (ZORA) at the density functional theory (DFT) level, as well as the relaxation parameters (T1 and T2). Examining the required spectral properties of NMR-QIP, all the designed complexes were found to be promising candidates for qubit molecules.
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Investigating an efficient and accurate protocol for sampling structures from molecular dynamics simulations: a close look by different wavelet families. Theor Chem Acc 2021. [DOI: 10.1007/s00214-021-02816-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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Cardenuto MH, Cezar HM, Mikkelsen KV, Sauer SPA, Coutinho K, Canuto S. A QM/MM study of the conformation stability and electronic structure of the photochromic switches derivatives of DHA/VHF in acetonitrile solution. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2021; 251:119434. [PMID: 33465576 DOI: 10.1016/j.saa.2021.119434] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/16/2020] [Revised: 12/30/2020] [Accepted: 01/03/2021] [Indexed: 06/12/2023]
Abstract
We present a detailed theoretical study of the electronic absorption spectra and thermochemistry of molecular photoswitches composed of one and two photochromic units of dihydroazulene (DHA)/vinylheptafulvene (VHF) molecules. Six different isomers are considered depending on the ring opening/closure forms of the DHA units. The solvent effect of acetonitrile is investigated using a sequential Molecular Mechanics/Quantum Mechanics approach. The thermochemical investigations of these photochromic molecules were performed using the Free Energy Perturbation method, and the simulations were performed using Configurational Bias Monte Carlo. We show that to open the 5-member ring of the DHA, there is no significant gain in thermal release of energy for the back reaction when a unit or two DHA units are considered. Overall, we found agreement between the solvation free energy based on Monte Carlo simulations and the continuum solvent model. However, the cavitation term in the continuum model is shown to be a source of disagreement when the non-electrostatic terms are compared. The electronic absorption spectra are calculated using TDDFT CAM-B3LYP/cc-pVDZ. Agreement with experiment is obtained within 0.1 eV, considering statistically uncorrelated configurations from the simulations. Inhomogeneous broadening is also considered and found to be well described in all cases.
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Affiliation(s)
- Marcelo Hidalgo Cardenuto
- Instituto de Física, Universidade de São Paulo, Rua do Matão 1371, Cidade Universitária, 05508-090 São Paulo, Brazil
| | - Henrique M Cezar
- Instituto de Física, Universidade de São Paulo, Rua do Matão 1371, Cidade Universitária, 05508-090 São Paulo, Brazil
| | - Kurt V Mikkelsen
- Department of Chemistry, University of Copenhagen, Universitetsparken 5, 2100 Copenhagen, Denmark
| | - Stephan P A Sauer
- Department of Chemistry, University of Copenhagen, Universitetsparken 5, 2100 Copenhagen, Denmark
| | - Kaline Coutinho
- Instituto de Física, Universidade de São Paulo, Rua do Matão 1371, Cidade Universitária, 05508-090 São Paulo, Brazil.
| | - Sylvio Canuto
- Instituto de Física, Universidade de São Paulo, Rua do Matão 1371, Cidade Universitária, 05508-090 São Paulo, Brazil.
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Gonçalves A, Raiol A, da Cunha AR, Manzoni V, Andrade-Filho T, Gester R. Insights on the crossing of the two lowest n-π∗ and π-π∗ absorption lines of thieno[3,4-b]pyrazine in an aqueous environment. Chem Phys Lett 2021. [DOI: 10.1016/j.cplett.2021.138366] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
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Ramos TN, Castet F, Champagne B. Second Harmonic Generation Responses of Ion Pairs Forming Dimeric Aggregates. J Phys Chem B 2021; 125:3386-3397. [PMID: 33769813 DOI: 10.1021/acs.jpcb.1c00939] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
A sequential approach combining molecular dynamics and density functional theory calculations has been worked out to unravel the second harmonic generation responses of anion-cation (AC) pairs when they form dimeric aggregates, where the cation is a stilbazolium derivative and the anions range from small inorganic iodide to medium-size organic p-toluenesulfonate. These complexes showed a strong self-aggregation behavior in molecular dynamics simulations within high-concentration conditions and formed stable dimeric aggregates, (AC)2, which can adopt different structural shapes from stacked, Λ, to head-to-head configurations. These various structures are associated with different symmetries, which are shown to modulate the second- and third-order nonlinear optical (NLO) responses. By consolidating the NLO results of this work with those previously obtained for single AC pairs [ J. Chem. Inf. Model. 2020, 60, 4817-4826], we have been able to explain the experimentally observed variations of the electrical-field-induced second harmonic generation (EFISHG) responses of these complexes as a function of concentration [ ChemPhysChem 2010, 11, 495-507]. Moreover, results have highlighted that (i) the second-order contribution, μβ//, dominates the global EFISHG response; (ii) the μβ// responses of dimers are about half of those computed for the parent AC pairs, while the third-order contributions, γ//, are reduced by only 10%; (iii) these distinct trends are ascribed to the formation of dimers adopting mainly Λ and head-to-head shapes, increasing the centrosymmetric character, in comparison to the monomers, a situation in which the second-order response cancels out as well as influences the dipole moment on μβ//; (iv) the presence of a strong amino donor group in the cation enhances the μβ// response by 1 order of magnitude and γ// by about a factor of 2; and finally, (v) dimeric aggregation has similar effects on the hyper-Rayleigh scattering response, βHRS, as on μβ//, while it reduces the one-dimensional character of βHRS. This work constitutes a step forward for the modeling of the NLO responses of AC aggregates in solution.
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Affiliation(s)
- Tárcius N Ramos
- University of Namur, Theoretical Chemistry Lab, Unit of Theoretical and Structural Physical Chemistry, Namur Institute of Structured Matter, rue de Bruxelles, 61, B-5000 Namur, Belgium
| | - Frédéric Castet
- Université de Bordeaux, Institut des Sciences Moléculaires, UMR 5255 CNRS, cours de la Libération 351, F-33405 Talence Cedex, France
| | - Benoît Champagne
- University of Namur, Theoretical Chemistry Lab, Unit of Theoretical and Structural Physical Chemistry, Namur Institute of Structured Matter, rue de Bruxelles, 61, B-5000 Namur, Belgium
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15
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Value of NMR relaxation parameters of diamagnetic molecules for quantum information processing: optimizing the coherent phase. Theor Chem Acc 2021. [DOI: 10.1007/s00214-020-02706-9] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
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16
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Vequi-Suplicy CC, Orozco-Gonzalez Y, Lamy MT, Canuto S, Coutinho K. A new interpretation of the absorption and the dual fluorescence of Prodan in solution. J Chem Phys 2020; 153:244104. [PMID: 33380080 DOI: 10.1063/5.0025013] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Remarkable interest is associated with the interpretation of the Prodan fluorescent spectrum. A sequential hybrid Quantum Mechanics/Molecular Mechanics method was used to establish that the fluorescent emission occurs from two different excited states, resulting in a broad asymmetric emission spectrum. The absorption spectra in several solvents were measured and calculated using different theoretical models presenting excellent agreement. All theoretical models [semiempirical, time dependent density functional theory and and second-order multiconfigurational perturbation theory] agree that the first observed band at the absorption spectrum in solution is composed of three electronic excitations very close in energy. Then, the electronic excitation around 340 nm-360 nm may populate the first three excited states (π-π*Lb, n-π*, and π-π*La). The ground state S0 and the first three excited states were analyzed using multi-configurational calculations. The corresponding equilibrium geometries are all planar in vacuum. Considering the solvent effects in the electronic structure of the solute and in the solvent relaxation around the solute, it was identified that these three excited states can change the relative order depending on the solvent polarity, and following the minimum path energy, internal conversions may occur. A consistent explanation of the experimental data is obtained with the conclusive interpretation that the two bands observed in the fluorescent spectrum of Prodan, in several solvents, are due to the emission from two independent states. Our results indicate that these are the n-π* S2 state with a small dipole moment at a lower emission energy and the π-π*Lb S1 state with large dipole moment at a higher emission energy.
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Affiliation(s)
- Cíntia C Vequi-Suplicy
- Instituto de Física, Universidade de São Paulo, Rua do Matão, 1371, 05508-090 São Paulo, SP, Brazil
| | - Yoelvis Orozco-Gonzalez
- Instituto de Física, Universidade de São Paulo, Rua do Matão, 1371, 05508-090 São Paulo, SP, Brazil
| | - M Teresa Lamy
- Instituto de Física, Universidade de São Paulo, Rua do Matão, 1371, 05508-090 São Paulo, SP, Brazil
| | - Sylvio Canuto
- Instituto de Física, Universidade de São Paulo, Rua do Matão, 1371, 05508-090 São Paulo, SP, Brazil
| | - Kaline Coutinho
- Instituto de Física, Universidade de São Paulo, Rua do Matão, 1371, 05508-090 São Paulo, SP, Brazil
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17
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Ludwig V, da Costa Ludwig ZM, Valverde D, Georg HC, Canuto S. Free energy gradient for understanding the stability and properties of neutral and charged L-alanine molecule in water. J Mol Liq 2020. [DOI: 10.1016/j.molliq.2020.114109] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
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18
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Theoretical analysis of the influence of C–H$$\cdots $$O bonds on the NMR constants of uracil in DMSO. Theor Chem Acc 2020. [DOI: 10.1007/s00214-020-02670-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
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19
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Cezar HM, Canuto S, Coutinho K. Understanding the absorption spectrum of mesityl oxide dye in solvents of different polarities. J Mol Liq 2020. [DOI: 10.1016/j.molliq.2020.112924] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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20
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Cezar HM, Canuto S, Coutinho K. DICE: A Monte Carlo Code for Molecular Simulation Including the Configurational Bias Monte Carlo Method. J Chem Inf Model 2020; 60:3472-3488. [DOI: 10.1021/acs.jcim.0c00077] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Henrique M. Cezar
- Instituto de Fisica, Universidade de Sao Paulo, 05508-090 Sao Paulo, SP, Brazil
| | - Sylvio Canuto
- Instituto de Fisica, Universidade de Sao Paulo, 05508-090 Sao Paulo, SP, Brazil
| | - Kaline Coutinho
- Instituto de Fisica, Universidade de Sao Paulo, 05508-090 Sao Paulo, SP, Brazil
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21
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Ramos TN, Canuto S, Champagne B. Unraveling the Electric Field-Induced Second Harmonic Generation Responses of Stilbazolium Ion Pairs Complexes in Solution Using a Multiscale Simulation Method. J Chem Inf Model 2020; 60:4817-4826. [DOI: 10.1021/acs.jcim.9b01161] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Tárcius N. Ramos
- Universidade de Sao Paulo, Instituto de Fisica, Rua do Matão 1371, 05508-090, São Paulo, São Paulo, Brazil
- Theoretical Chemistry Lab, Unit of Theoretical and Structural Physical Chemistry, Namur Institute of Structured Matter, University of Namur, rue de Bruxelles, 61, B-5000 Namur, Belgium
| | - Sylvio Canuto
- Universidade de Sao Paulo, Instituto de Fisica, Rua do Matão 1371, 05508-090, São Paulo, São Paulo, Brazil
| | - Benoît Champagne
- Theoretical Chemistry Lab, Unit of Theoretical and Structural Physical Chemistry, Namur Institute of Structured Matter, University of Namur, rue de Bruxelles, 61, B-5000 Namur, Belgium
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22
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Ramos TN, Silva DL, Cabral BJ, Canuto S. On the spectral line width broadening for simulation of the two-photon absorption cross-section of para-Nitroaniline in liquid environment. J Mol Liq 2020. [DOI: 10.1016/j.molliq.2019.112405] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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23
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Cornetta LM, Coutinho K, Varella MTDN. Solvent effects on the π* shape resonances of uracil. J Chem Phys 2020; 152:084301. [DOI: 10.1063/1.5139459] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- L. M. Cornetta
- Instituto de Física, Universidade de São Paulo, Rua do Matão 1371, 05508-090 São Paulo, São Paulo, Brazil
| | - K. Coutinho
- Instituto de Física, Universidade de São Paulo, Rua do Matão 1371, 05508-090 São Paulo, São Paulo, Brazil
| | - M. T. do N. Varella
- Instituto de Física, Universidade de São Paulo, Rua do Matão 1371, 05508-090 São Paulo, São Paulo, Brazil
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24
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Quinoline derivatives as possible lead compounds for anti-malarial drugs: Spectroscopic, DFT and MD study. ARAB J CHEM 2020. [DOI: 10.1016/j.arabjc.2017.07.006] [Citation(s) in RCA: 74] [Impact Index Per Article: 18.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
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25
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Silva JL, Unger I, Matias TA, Franco LR, Damas G, Costa LT, Toledo KCF, Rocha TCR, de Brito AN, Saak CM, Coutinho K, Araki K, Björneholm O, Brena B, Araujo CM. X-ray Photoelectron Fingerprints of High-Valence Ruthenium-Oxo Complexes along the Oxidation Reaction Pathway in an Aqueous Environment. J Phys Chem Lett 2019; 10:7636-7643. [PMID: 31747290 DOI: 10.1021/acs.jpclett.9b02756] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Recent advances in operando-synchrotron-based X-ray techniques are making it possible to address fundamental questions related to complex proton-coupled electron transfer reactions, for instance, the electrocatalytic water splitting process. However, it is still a grand challenge to assess the ability of the different techniques to characterize the relevant intermediates, with minimal interference on the reaction mechanism. To this end, we have developed a novel methodology employing X-ray photoelectron spectroscopy (XPS) in connection with the liquid-jet approach to probe the electrochemical properties of a model electrocatalyst, [RuII(bpy)2(py)(OH2)]2+, in an aqueous environment. There is a unique fingerprint of the extremely important higher-valence ruthenium-oxo species in the XPS spectra along the oxidation reaction pathway. Furthermore, a sequential method combining quantum mechanics and molecular mechanics is used to illuminate the underlying physical chemistry of such systems. This study provides the basis for the future development of in-operando XPS techniques for water oxidation reactions.
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Affiliation(s)
- Jose Luis Silva
- Materials Theory Division, Department of Physics and Astronomy , Uppsala University , Box 516, 75120 Uppsala , Sweden
| | - Isaak Unger
- Molecular and Condensed Matter Physics Division, Department of Physics and Astronomy , Uppsala University , Box 516, 75120 Uppsala , Sweden
| | - Tiago Araujo Matias
- Department of Fundamental Chemistry, Institute of Chemistry , University of São Paulo , Av. Lineu Prestes 748, Cidade Universitária, Butanta , Sao Paulo , SP 05508-000 , Brazil
| | - Leandro Rezende Franco
- Instituto de Física , Universidade de São Paulo , Cidade Universitária , 05508-090 São Paulo , SP , Brazil
| | - Giane Damas
- Materials Theory Division, Department of Physics and Astronomy , Uppsala University , Box 516, 75120 Uppsala , Sweden
| | - Luciano T Costa
- Instituto de Química, Departamento de Físico-química , Universidade Federal Fluminense , Outeiro de São João Batista s/n , CEP, 24020-150 Niterói , RJ , Brazil
| | - Kalil C F Toledo
- Department of Fundamental Chemistry, Institute of Chemistry , University of São Paulo , Av. Lineu Prestes 748, Cidade Universitária, Butanta , Sao Paulo , SP 05508-000 , Brazil
| | - Tulio C R Rocha
- Brazilian Synchrotron Light Laboratory (LNLS) , Brazilian Center for Research on Energy and Materials (CNPEM) , P.O. Box 6192, 13083-970 Campinas , SP , Brazil
| | - Arnaldo Naves de Brito
- Institute of Physics "Gleb Wataghin" , University of Campinas , 13083-859 Campinas , SP , Brazil
| | - Clara-Magdalena Saak
- Molecular and Condensed Matter Physics Division, Department of Physics and Astronomy , Uppsala University , Box 516, 75120 Uppsala , Sweden
| | - Kaline Coutinho
- Instituto de Física , Universidade de São Paulo , Cidade Universitária , 05508-090 São Paulo , SP , Brazil
| | - Koiti Araki
- Department of Fundamental Chemistry, Institute of Chemistry , University of São Paulo , Av. Lineu Prestes 748, Cidade Universitária, Butanta , Sao Paulo , SP 05508-000 , Brazil
| | - Olle Björneholm
- Molecular and Condensed Matter Physics Division, Department of Physics and Astronomy , Uppsala University , Box 516, 75120 Uppsala , Sweden
| | - Barbara Brena
- Materials Theory Division, Department of Physics and Astronomy , Uppsala University , Box 516, 75120 Uppsala , Sweden
| | - C Moyses Araujo
- Materials Theory Division, Department of Physics and Astronomy , Uppsala University , Box 516, 75120 Uppsala , Sweden
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26
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Costa MP, Prates LM, Baptista L, Cruz MT, Ferreira IL. Interaction of polyelectrolyte complex between sodium alginate and chitosan dimers with a single glyphosate molecule: A DFT and NBO study. Carbohydr Polym 2018; 198:51-60. [DOI: 10.1016/j.carbpol.2018.06.052] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2018] [Revised: 05/15/2018] [Accepted: 06/12/2018] [Indexed: 01/08/2023]
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27
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Oliveira LB, Prado RC, Júnior LA, Colherinhas G. The influence of flexibility on the spectroscopic properties for organic molecules in solution: A theoretical study applied to A3R polypeptide. J Mol Liq 2018. [DOI: 10.1016/j.molliq.2018.05.007] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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28
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29
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Venâncio MF, Doctorovich F, Rocha WR. Solvation and Proton-Coupled Electron Transfer Reduction Potential of 2NO• to 1HNO in Aqueous Solution: A Theoretical Investigation. J Phys Chem B 2017. [DOI: 10.1021/acs.jpcb.7b03552] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Mateus F. Venâncio
- Laboratório
de Química Computacional e Modelagem Molecular (LQC-MM), Departamento
de Química, ICEx, Universidade Federal de Minas Gerais, 31270-901, Pampulha, Belo Horizonte, MG, Brazil
| | - Fabio Doctorovich
- Departamento
de Química Inorganica, Analítica y Química Física,
Facultad de Ciencias Exactas y Naturales (INQUIMAE-CONICET), Universidad de Buenos Aires, Ciudad Universitaria, Buenos Aires, Argentina
| | - Willian R. Rocha
- Laboratório
de Química Computacional e Modelagem Molecular (LQC-MM), Departamento
de Química, ICEx, Universidade Federal de Minas Gerais, 31270-901, Pampulha, Belo Horizonte, MG, Brazil
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30
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Cardenuto MH, Coutinho K, Canuto S. Quantum Chemistry with Thermodynamic Condition. A Journey into the Supercritical Region and Approaching the Critical Point. ADVANCES IN QUANTUM CHEMISTRY 2017. [DOI: 10.1016/bs.aiq.2016.06.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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31
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Gonçalves MA, Santos LS, Prata DM, Peixoto FC, da Cunha EFF, Ramalho TC. Optimal wavelet signal compression as an efficient alternative to investigate molecular dynamics simulations: application to thermal and solvent effects of MRI probes. Theor Chem Acc 2016. [DOI: 10.1007/s00214-016-2037-z] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
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32
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Silva MC, Torres JA, Castro AA, da Cunha EF, Alves de Oliveira LC, Corrêa AD, Ramalho TC. Combined experimental and theoretical study on the removal of pollutant compounds by peroxidases: affinity and reactivity toward a bioremediation catalyst. J Biomol Struct Dyn 2016; 34:1839-48. [DOI: 10.1080/07391102.2015.1063456] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
Affiliation(s)
- Maria Cristina Silva
- Department of Chemistry, Federal University of Minas Gerais, 31270-901 Belo Horizonte, Brazil
| | | | - Alexandre A. Castro
- Department of Chemistry, Federal University of Lavras, 37200-000 Lavras, Brazil
| | | | | | | | - Teodorico C. Ramalho
- Department of Chemistry, Federal University of Lavras, 37200-000 Lavras, Brazil
- Center for Basic and Applied Research, University Hradec Kralove, Hradec Kralove, Czech Republic
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33
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GIAODFT isotropic magnetic shielding constants and spinspin coupling of tartaric acid in water solution. Chem Phys Lett 2016. [DOI: 10.1016/j.cplett.2015.12.003] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
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34
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Cardenuto MH, Castet F, Champagne B. Investigating the first hyperpolarizability of liquid carbon tetrachloride. RSC Adv 2016. [DOI: 10.1039/c6ra23187j] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Sequential QMMM calculations have been carried out to investigate the first hyperpolarizability of liquid CCl4.
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Affiliation(s)
- Marcelo Hidalgo Cardenuto
- Laboratoire de Chimie Théorique
- Unité de Chimie Physique Théorique et Structurale
- University of Namur
- B-5000 Namur
- Belgium
| | - Frédéric Castet
- Université de Bordeaux
- Institut des Sciences Moléculaires (ISM)
- UMR 5255 CNRS
- F-33405 Talence Cedex
- France
| | - Benoît Champagne
- Laboratoire de Chimie Théorique
- Unité de Chimie Physique Théorique et Structurale
- University of Namur
- B-5000 Namur
- Belgium
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35
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Nakano H, Sato H. An Ab Initio QM/MM-Based Approach to Efficiently Evaluate Vertical Excitation Energies in Condensed Phases Including the Nonequilibrium Solvation Effect. J Phys Chem B 2015; 120:1670-8. [DOI: 10.1021/acs.jpcb.5b08455] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Affiliation(s)
- Hiroshi Nakano
- Department
of Molecular Engineering, Kyoto University, Kyoto 615-8510, Japan
- Elements
Strategy Initiative for Catalysts and Batteries, Kyoto University, Kyoto 615-8510, Japan
| | - Hirofumi Sato
- Department
of Molecular Engineering, Kyoto University, Kyoto 615-8510, Japan
- Elements
Strategy Initiative for Catalysts and Batteries, Kyoto University, Kyoto 615-8510, Japan
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36
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Probing thermal and solvent effects on hyperfine interactions and spin relaxation rate of δ-FeOOH(100) and [MnH3buea(OH)]2−: Toward new MRI probes. COMPUT THEOR CHEM 2015. [DOI: 10.1016/j.comptc.2015.07.006] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
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37
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Zobel JP, Nogueira JJ, González L. Quenching of Charge Transfer in Nitrobenzene Induced by Vibrational Motion. J Phys Chem Lett 2015; 6:3006-3011. [PMID: 26267195 DOI: 10.1021/acs.jpclett.5b00990] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
Although nitrobenzene is the smallest nitro-aromatic molecule, the nature of its electronic structure is still unclear. Most notably, the lowest-energy absorption band was assessed in numerous studies providing conflicting results regarding its charge-transfer character. In this study, we employ a combination of molecular dynamics and quantum chemical methods to disentangle the nature of the lowest-energy absorption band of nitrobenzene. Surprisingly, the charge-transfer transition from the benzene moiety to the nitro group is found to be quenched by a flow of charge into the opposite direction induced by vibrational motion. Beyond clarifying the charge-transfer character of nitrobenzene, we show that the widely used approach of analyzing the ground-state minimum-energy geometry provides completely wrong conclusions.
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Affiliation(s)
- J Patrick Zobel
- Institute of Theoretical Chemistry, University of Vienna, Währinger Straße 17, A-1090 Vienna, Austria
| | - Juan J Nogueira
- Institute of Theoretical Chemistry, University of Vienna, Währinger Straße 17, A-1090 Vienna, Austria
| | - Leticia González
- Institute of Theoretical Chemistry, University of Vienna, Währinger Straße 17, A-1090 Vienna, Austria
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38
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Modesto-Costa L, Mukherjee PK, Canuto S. Theoretical study of the spectral shift of the absorption line of Rb and Cs in liquid helium. Chem Phys Lett 2015. [DOI: 10.1016/j.cplett.2015.05.065] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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39
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Quertinmont J, Champagne B, Castet F, Hidalgo Cardenuto M. Explicit versus Implicit Solvation Effects on the First Hyperpolarizability of an Organic Biphotochrome. J Phys Chem A 2015; 119:5496-503. [DOI: 10.1021/acs.jpca.5b00631] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Jean Quertinmont
- Laboratoire de
Chimie Théorique, Unité de Chimie Physique Théorique
et Structurale, University of Namur, rue de Bruxelles, 61, B-5000 Namur, Belgium
| | - Benoît Champagne
- Laboratoire de
Chimie Théorique, Unité de Chimie Physique Théorique
et Structurale, University of Namur, rue de Bruxelles, 61, B-5000 Namur, Belgium
| | - Frédéric Castet
- Institut
des Sciences
Moléculaires (ISM), Université de Bordeaux, UMR 5255 CNRS, Cours de la Libération
351, F-33405 Talence
Cedex, France
| | - Marcelo Hidalgo Cardenuto
- Laboratoire de
Chimie Théorique, Unité de Chimie Physique Théorique
et Structurale, University of Namur, rue de Bruxelles, 61, B-5000 Namur, Belgium
- Instituto de Física, Universidade de São Paulo, CP 66318, 05314-970 São Paulo, SP, Brazil
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40
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Hidalgo Cardenuto M, Champagne B. The first hyperpolarizability of nitrobenzene in benzene solutions: investigation of the effects of electron correlation within the sequential QM/MM approach. Phys Chem Chem Phys 2015; 17:23634-42. [DOI: 10.1039/c5cp03455h] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Molecular polarization due to solvation amplifies the impact of electron correlation on the first hyperpolarizability of nitrobenzene.
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Affiliation(s)
- Marcelo Hidalgo Cardenuto
- Laboratoire de Chimie Théorique
- Unité de Chimie Physique Théorique et Structurale
- University of Namur
- B-5000 Namur
- Belgium
| | - Benoît Champagne
- Laboratoire de Chimie Théorique
- Unité de Chimie Physique Théorique et Structurale
- University of Namur
- B-5000 Namur
- Belgium
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41
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Electronic Properties in Supercritical Fluids. ADVANCES IN QUANTUM CHEMISTRY 2015. [DOI: 10.1016/bs.aiq.2015.03.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register]
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42
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Seidler T, Champagne B. Which charge definition for describing the crystal polarizing field and the χ(1) and χ(2) of organic crystals? Phys Chem Chem Phys 2015; 17:19546-56. [DOI: 10.1039/c5cp03248b] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
Crystal optical susceptibilities are probes to assess the performance of the charge definition employed to describe the crystal polarizing field.
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Affiliation(s)
- Tomasz Seidler
- Laboratoire de Chimie Théorique
- University of Namur
- Namur
- Belgium
- Faculty of Chemistry
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Hidalgo Cardenuto M, Champagne B. QM/MM investigation of the concentration effects on the second-order nonlinear optical responses of solutions. J Chem Phys 2014; 141:234104. [DOI: 10.1063/1.4903545] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Affiliation(s)
- Marcelo Hidalgo Cardenuto
- Laboratoire de Chimie Théorique, Unité de Chimie Physique
Théorique et Structurale, University of Namur, rue de
Bruxelles, 61, B-5000 Namur, Belgium
- Instituto de Física, Universidade de São Paulo, CP 66318, 05314-970 São Paulo, SP, Brazil
| | - Benoît Champagne
- Laboratoire de Chimie Théorique, Unité de Chimie Physique
Théorique et Structurale, University of Namur, rue de
Bruxelles, 61, B-5000 Namur, Belgium
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44
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Gonçalves MA, Peixoto FC, da Cunha EF, Ramalho TC. Dynamics, NMR parameters and hyperfine coupling constants of the Fe3O4(1 0 0)–water interface: Implications for MRI probes. Chem Phys Lett 2014. [DOI: 10.1016/j.cplett.2014.06.030] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
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45
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Caputo MC, Provasi PF, Benitez L, Georg HC, Canuto S, Coutinho K. Monte Carlo–Quantum Mechanics Study of Magnetic Properties of Hydrogen Peroxide in Liquid Water. J Phys Chem A 2014; 118:6239-47. [DOI: 10.1021/jp411303n] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Affiliation(s)
- María Cristina Caputo
- Departamento de Fı́sica, FCEN,
UBA and IFIBA, Conicet, Ciudad Universitaria, 1428, Buenos Aires, Argentina
| | - Patricio F. Provasi
- Department of Physics - IMIT, Northeastern University, Av. Libertad 5500, Corrientes, Argentina
| | - Lucía Benitez
- Department of Physics - IMIT, Northeastern University, Av. Libertad 5500, Corrientes, Argentina
| | - Herbert C. Georg
- Instituto
de Fı́sica, Universidade Federal de Goiás, CP 131, 74001-970 Goiânia, GO, Brazil
| | - Sylvio Canuto
- Instituto de Fı́sica, Universidade de São Paulo, CP
66318, 05315-970 São Paulo, Brazil
| | - Kaline Coutinho
- Instituto de Fı́sica, Universidade de São Paulo, CP
66318, 05315-970 São Paulo, Brazil
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Theoretical study of the solvent effect on the aromaticity of benzene: a NICS analysis. J Mol Model 2014; 20:2152. [PMID: 24567161 DOI: 10.1007/s00894-014-2152-5] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2013] [Accepted: 01/21/2014] [Indexed: 10/25/2022]
Abstract
Nucleus-independent chemical shift (NICS) quantities for benzene-benzene and benzene-water species were obtained and are discussed in gas phase and in solution. Besides standard polarizable continuum model (PCM) calculations, sequential Monte Carlo/quantum mechanics (S-MC/QM) were also performed. Benzene was shown to be slightly more aromatic in condensate phase when we considered the average solvent configuration (ASEC) approach with explicit molecules.
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47
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Silva DL, Murugan NA, Kongsted J, Ågren H, Canuto S. Self-aggregation and optical absorption of stilbazolium merocyanine in chloroform. J Phys Chem B 2014; 118:1715-25. [PMID: 24467553 DOI: 10.1021/jp411178h] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Dipolar aggregation is in many cases detrimental for the functioning of optical materials. In this study we investigate self-aggregation and optical absorption of stilbazolium merocyanine (SM) in chloroform solution by performing classical Molecular Dynamics (MD) simulations under ambient conditions. The reversal solvatochromic shift, the large bathochromic shift, and the structured absorption band presented by SM in chloroform solution are all aspects of its optical absorption behavior for which the existence of self-aggregation is yet not completely understood. Moreover, the spectroscopic properties of SM oligomers and their occurrence in solvent of low polarity remain a relevant topic that deserves to be investigated. Our analysis of the aggregation behavior of SM in chloroform verified that the majority of the chromophores are involved in the formation of oligomers in solution, where the whole dimer and part of the trimer populations present a stable π-stacking structure. The optical properties of the monomers and oligomers in solution were evaluated by means of a discrete polarizable embedding quantum mechanical/molecular mechanical (PE-QM/MM) response scheme where the quantum part is described at the level of density functional theory. The visible absorption spectrum of SM in chloroform is simulated using time average values obtained for the monomeric and oligomeric forms of SM from the PE-QM/MM calculations performed on uncorrelated configurations extracted from the classical MD simulations. This study shows that the self-aggregation of SM in chloroform may exist, but it is not essential for reproducing the reversal solvatochromic shift in chloroform and that the process does not contribute to enhance the bathochromic shift nor explain the structure observed in its absorption band. Moreover, it is verified that since the electronic transitions of the monomer and oligomers are close together, changes in the interplane separation between the monomeric units of the stacked oligomers substantially affect the spectral resolution of their contribution to the optical absorption spectrum.
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Affiliation(s)
- Daniel L Silva
- Instituto de Física, Universidade de São Paulo , Caixa Postal 66318, 05314-970 São Paulo, SP, Brazil
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48
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Silva DL, Barreto RC, Lacerda EG, Coutinho K, Canuto S. One- and two-photon absorption of fluorescein dianion in water: a study using S-QM/MM methodology and ZINDO method. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2014; 119:63-75. [PMID: 23669507 DOI: 10.1016/j.saa.2013.04.035] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/23/2013] [Revised: 04/02/2013] [Accepted: 04/06/2013] [Indexed: 06/02/2023]
Abstract
One- and two-photon absorption (1PA and 2PA) of fluorescein dianion (FSD) in water were studied using a combined and sequential Quantum Mechanics/Molecular Dynamics methodology. Different sets of 250 statistically relevant (uncorrelated) configurations composed by the solute and several solvent molecules were sampled from the classical simulation. On these configurations, the electronic properties were calculated a posteriori using the Zerner's intermediate neglect of differential overlap (ZINDO) method. The linear and nonlinear absorption of FSD in water were calculated using discrete and explicit solvent models. In the largest case, the relevant configurations are composed by FSD and 47 explicit water molecules embedded in the electrostatic field of all remaining water molecules. Both INDO/CIS and INDO/CISD calculations were performed to study the absorption processes of FSD and the Sum-Over-States (SOS) model was used to describe the 2PA process. A semi-classical method for spectrum simulations was employed to simulate the 1PA and 2PA cross-section spectra of FSD in water. For comparison purposes, in the case of the 2PA process two approaches, the "full expression" and "resonant expression" methods, were employed to simulate the nonlinear spectrum. The last method assumes resonant conditions and on the computation point of view it represents an interesting option to study the 2PA process. The INDO/CI calculations give a satisfactory description of the 1PA spectrum of FSD and properly describe the unusual blue-shift of its first π→π(*) transition in water. In the case of 2PA, the introduction of doubly excited configuration interactions (INDO/CISD) has proven to be essential for an appropriate description of the process at the higher energy spectral region. It was observed that the solvent effects do not drastically change the cross-sections of both processes. The simulated 2PA cross-section spectrum provided by the "full expression" method presents a better definition of the bands which appear along the experimental spectrum than the one provided by the "resonant expression" method. However, both approaches provide similar description for the effect of the solvent environment on the 2PA process of FSD in water.
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Affiliation(s)
- D L Silva
- Instituto de Física, Universidade de São Paulo, CP 66318, 05314-970 São Paulo, SP, Brazil
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49
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Theoretically describing the 17O magnetic shielding constant of biomolecular systems: uracil and 5-fluorouracil in water environment. Theor Chem Acc 2013. [DOI: 10.1007/s00214-013-1424-y] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
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50
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Kohls E, Mishev A, Pejov L. Solvation of fluoroform and fluoroform-dimethylether dimer in liquid krypton: a theoretical cryospectroscopic study. J Chem Phys 2013; 139:054504. [PMID: 23927267 DOI: 10.1063/1.4816282] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023] Open
Abstract
A hybrid, sequential statistical physics-quantum mechanical electronic-quantum mechanical nuclei approach has been applied to study the C-H stretching frequencies of bare fluoroform dissolved in liquid krypton under cryogenic conditions (at ~130 K), as well as upon blue shifting hydrogen bonding interactions with dimethylether in the same solvent. The structure of the liquid at 130 K was generated by Monte Carlo simulations of cryogenic Kr solutions containing either fluoroform or fluoroform and dimethylether molecules. Statistically uncorrelated configurations were appropriately chosen from the equilibrated MC runs and supermolecular clusters containing solute and solvent molecules (either standalone or embedded in the "bulk" part of the solvent treated as a polarizable continuum) were subjected to quantum mechanical electronic (QMel) and subsequent quantum mechanical nuclei (QMnuc) calculations. QMel calculations were implemented to generate the in-liquid 1D intramolecular C-H stretching vibrational potential of the fluoroform moiety and subsequently in the QMnuc phase the corresponding anharmonic C-H stretching frequency was computed by diagonalization techniques. Finally, the constructed vibrational density of states histograms were compared to the experimental Raman bands. The calculated anharmonic vibrational frequency shifts of the fluoroform C-H stretching mode upon interaction with dimethylether in liquid Kr are in very good agreement with the experimental data (20.3 at MP2 level vs. 16.6 cm(-1) experimentally). Most of this relatively large frequency blue shift is governed by configurations characterized by a direct C-H···O contact between monomers. The second population detected during MC simulations, characterized by reversed orientation of the monomers, has a minor contribution to the spectral appearance. The experimentally observed trend in the corresponding bandwidths is also correctly reproduced by our theoretical approach. Solvation of the fluoroform monomer, according to experiment, results in small C-H stretching frequency red shift (~-2 cm(-1)), while our approach predicts a blue shift of about 10 cm(-1). By a detailed analysis of the anharmonic C-H stretching frequency dependence on the position of the nearest solvent krypton atom and also by analyzing the vibrational Stark effect induced by the local fluctuating field component parallel to the C-H axis, we have derived several conclusions related to these observations. The frequency vs. C···Kr distance dependence shows appreciable fluctuations and even changes in sign at R values close to the maximum of the C···Kr radial distribution function, so that most of the first-shell Kr atoms are located at positions at which the CH frequency shifts acquire either small negative or small positive values. It so happens, therefore, that even the actual sign of the frequency shift is strongly dependent on the correct description of the first solvation shell around CF3H by the Monte Carlo method, much more than the other in-liquid properties calculated by similar approaches.
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Affiliation(s)
- Emilija Kohls
- Institute of Chemistry, Faculty of Science, Ss. Cyril and Methodius University, P.O. Box 162, 1001 Skopje, Republic of Macedonia
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