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Cherepanov DA, Kurashov V, Gostev FE, Shelaev IV, Zabelin AA, Shen G, Mamedov MD, Aybush A, Shkuropatov AY, Nadtochenko VA, Bryant DA, Golbeck JH, Semenov AY. Femtosecond optical studies of the primary charge separation reactions in far-red photosystem II from Synechococcus sp. PCC 7335. BIOCHIMICA ET BIOPHYSICA ACTA. BIOENERGETICS 2024; 1865:149044. [PMID: 38588942 DOI: 10.1016/j.bbabio.2024.149044] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/22/2023] [Revised: 01/26/2024] [Accepted: 04/02/2024] [Indexed: 04/10/2024]
Abstract
Primary processes of light energy conversion by Photosystem II (PSII) were studied using femtosecond broadband pump-probe absorption difference spectroscopy. Transient absorption changes of core complexes isolated from the cyanobacterium Synechococcus sp. PCC 7335 grown under far-red light (FRL-PSII) were compared with the canonical Chl a containing spinach PSII core complexes upon excitation into the red edge of the Qy band. Absorption changes of FRL-PSII were monitored at 278 K in the 400-800 nm spectral range on a timescale of 0.1-500 ps upon selective excitation at 740 nm of four chlorophyll (Chl) f molecules in the light harvesting antenna, or of one Chl d molecule at the ChlD1 position in the reaction center (RC) upon pumping at 710 nm. Numerical analysis of absorption changes and assessment of the energy levels of the presumed ion-radical states made it possible to identify PD1+ChlD1- as the predominant primary charge-separated radical pair, the formation of which upon selective excitation of Chl d has an apparent time of ∼1.6 ps. Electron transfer to the secondary acceptor pheophytin PheoD1 has an apparent time of ∼7 ps with a variety of excitation wavelengths. The energy redistribution between Chl a and Chl f in the antenna occurs within 1 ps, whereas the energy migration from Chl f to the RC occurs mostly with lifetimes of 60 and 400 ps. Potentiometric analysis suggests that in canonical PSII, PD1+ChlD1- can be partially formed from the excited (PD1ChlD1)* state.
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Affiliation(s)
- Dmitry A Cherepanov
- N.N. Semenov Federal Research Center for Chemical Physics, Russian Academy of Sciences, Kosygina st., 4, 119991 Moscow, Russia; A.N. Belozersky Institute of Physical-Chemical Biology, Lomonosov Moscow State University, Leninskiye Gory, 1, building 40, 119992 Moscow, Russia.
| | - Vasily Kurashov
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, 16802, USA
| | - Fedor E Gostev
- N.N. Semenov Federal Research Center for Chemical Physics, Russian Academy of Sciences, Kosygina st., 4, 119991 Moscow, Russia
| | - Ivan V Shelaev
- N.N. Semenov Federal Research Center for Chemical Physics, Russian Academy of Sciences, Kosygina st., 4, 119991 Moscow, Russia
| | - Alexey A Zabelin
- Institute of Basic Biological Problems of the Russian Academy of Sciences, Federal Research Center "Pushchino Scientific Center for Biological Research of the Russian Academy of Sciences", 142290 Pushchino, Moscow Region, Russia
| | - Gaozhong Shen
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, 16802, USA
| | - Mahir D Mamedov
- A.N. Belozersky Institute of Physical-Chemical Biology, Lomonosov Moscow State University, Leninskiye Gory, 1, building 40, 119992 Moscow, Russia
| | - Arseny Aybush
- N.N. Semenov Federal Research Center for Chemical Physics, Russian Academy of Sciences, Kosygina st., 4, 119991 Moscow, Russia
| | - Anatoly Ya Shkuropatov
- Institute of Basic Biological Problems of the Russian Academy of Sciences, Federal Research Center "Pushchino Scientific Center for Biological Research of the Russian Academy of Sciences", 142290 Pushchino, Moscow Region, Russia
| | - Victor A Nadtochenko
- N.N. Semenov Federal Research Center for Chemical Physics, Russian Academy of Sciences, Kosygina st., 4, 119991 Moscow, Russia; Chemistry Department, Lomonosov Moscow State University, Leninskiye Gory, 1, 119991 Moscow, Russia
| | - Donald A Bryant
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, 16802, USA
| | - John H Golbeck
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, 16802, USA; Department of Chemistry, The Pennsylvania State University, University Park, 16802, USA
| | - Alexey Yu Semenov
- N.N. Semenov Federal Research Center for Chemical Physics, Russian Academy of Sciences, Kosygina st., 4, 119991 Moscow, Russia; A.N. Belozersky Institute of Physical-Chemical Biology, Lomonosov Moscow State University, Leninskiye Gory, 1, building 40, 119992 Moscow, Russia.
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Imuta T, Hara N, Ogasawara S, Tamiaki H. Extra-Annulated Chlorophyll Derivatives by Scholl Reaction. Org Lett 2024; 26:6259-6262. [PMID: 39018048 DOI: 10.1021/acs.orglett.4c02238] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/18/2024]
Abstract
The ferric chloride assisted Scholl reaction of methyl (3,5-dimethoxyphenyl)carbonyl-pyropheophorbide-a produced an extra-annulated, didehydrogenated chlorophyll derivative with a six-membered ring fused at the pyrrole A-ring. The steric interaction of the substituents on the additional tetralone and B-rings induced molecular helicity. The helically cyclized stereoisomers were separated by recrystallization, and their (P/M)-stereochemistry was confirmed by circular dichroism spectra. The distortion of their chlorin π-systems broadened electronic absorption bands to cover all visible regions and reach the near-infrared region.
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Affiliation(s)
- Takuma Imuta
- Graduate School of Life Sciences, Ritsumeikan University, Kusatsu, Shiga 525-8577, Japan
| | - Nobuyuki Hara
- Graduate School of Life Sciences, Ritsumeikan University, Kusatsu, Shiga 525-8577, Japan
| | - Shin Ogasawara
- Graduate School of Life Sciences, Ritsumeikan University, Kusatsu, Shiga 525-8577, Japan
| | - Hitoshi Tamiaki
- Graduate School of Life Sciences, Ritsumeikan University, Kusatsu, Shiga 525-8577, Japan
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Bessong CDRA, Abe MTO, Ntieche Z, Noudem P, Fankam Fankam JB, Ndjaka JMB. Impact of doping with organic dopants and mixed doping with alkali metals and organic dopants on the absorption, electronic, optoelectronic, thermodynamic and nonlinear optical properties of dibenzo[b,def]chrysene in gaseous media: DFT and TD-DFT studies. J Mol Model 2024; 30:240. [PMID: 38954155 DOI: 10.1007/s00894-024-06026-8] [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: 01/17/2024] [Accepted: 06/14/2024] [Indexed: 07/04/2024]
Abstract
CONTEXT In this study, we evaluate the geometrical, absorption, optoelectronic, electronic, nonlinear optical (NLO) and thermodynamic properties of dibenzo[b,def]chrysene molecule derivatives by means of DFT and TD-DFT simulations. In view of the aim of producing new high-performance materials for non-linear optics (NLO) by doping test, two types of doping were used. We obtained six derivatives by doping with organic dopants (Nitro, amide and ticyanoethenyl) and mixed alkali metal (potassium) and organic dopants. Doping with organic dopants produced molecules A, B and C, respectively when substituting one hydrogen with nitro (NO2), amide (CONH2) and tricyanoethenyl (C5N3) groups, while mixed doping involved considering A, B and C and then substituting two hydrogens with two potassiums to obtain compounds D, E and F respectively. The negative values of the various interaction energies calculated for all the doped molecules show that they are all stable, but also that molecules C and F are the most stable in the case of both dopings. The gap energies calculated at the B3LYP level of theory are all below 3 eV, which means that all the molecules obtained are semiconductors. Better still, compounds C and F, with gap energies of 1.852 eV and 1.204 eV, respectively, corresponding to decreases of 35.67% and 58.18% in gap energy compared with the pristine molecule, are more reactive than the other doped molecules. Mixed doping is therefore a highly effective way of narrowing the energy gap and boosting the semiconducting character and reactivity of organic materials. Optoelectronic properties have also been improved, with refractive index values higher than those of the reference material, glass. This shows that our compounds could be used under very high electric field conditions of the order of 4.164 × 109 V.m-1 for C and 7.410 × 109 V.m-1 for F the highest values at the B3LYP level of theory. The maximum first-order hyperpolarizability values for both types of doping are obtained at the CAM-B3LYP level of theory by C:β mol = 92.088 × 10-30esu and by F:β mol = 129.449 × 10-30esu, and second-order values are also given by these same compounds. These values are higher than the reference value, which is urea, making our compounds potential candidates for high-performance NLO applications. In dynamic mode and at a frequency of 1064 nm, at the CAM-B3LYP level of theory, the highest dynamic hyperpolarizability coefficients were obtained by C and F. Hyper-Rayleigh scattering β HRS , coefficients of the electro-optical Pockel effect (EOPE), EFISHG, third-order NLO-response degree four-wave mixingγ DFWM , quadratic nonlinear refractive index n2 were also calculated. The maximum values of n2 are obtained by C (6.13 × 10-20 m2/W) and F (6.60 × 10-20 m2/W), these values are 2.24 times higher than that of fused silica which is the reference for degenerate four-wave mixing so our molecules could also have applications in optoelectronics as wavelength converters, optical pulse modulators and optical switches. METHODS Using the DFT method, we were able to determine the optimized and stable electronic structures of doped dibenzo[b,def]chrysene derivatives in the gas phase. We limited ourselves to using the proven B3LYP and CAMB3LYP levels of theory for calculating electronic properties, and non-linear optics with the 6-311G + + (d,p) basis set, which is a large basis set frequently used for these types of compound. Gaussian 09 software was used to run our calculations, and Gauss View 6.0.16 was used to visualize the output files. TD-DFT was also used to determine absorption properties at the B3LYP level of theory, using the same basis set.
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Affiliation(s)
- C D Ribouem A Bessong
- Faculty of Science, Department of Physics, University of Yaoundé I, P.M.B 812, Yaoundé, Cameroon.
| | - M T Ottou Abe
- Faculty of Science, Department of Physics, University of Yaoundé I, P.M.B 812, Yaoundé, Cameroon.
| | - Zounedou Ntieche
- Faculty of Science, Department of Physics, University of Yaoundé I, P.M.B 812, Yaoundé, Cameroon
- Local Material Promotion Authority (MIPROMALO), P.O. Box 2396, Yaoundé, Cameroon
| | - P Noudem
- Faculty of Science, Department of Physics, University of Yaoundé I, P.M.B 812, Yaoundé, Cameroon
| | - J B Fankam Fankam
- Molecular Sciences Institute, School of Chemistry, University of the Witwatersrand, Johannesburg, 2050, South Africa
| | - J M B Ndjaka
- Faculty of Science, Department of Physics, University of Yaoundé I, P.M.B 812, Yaoundé, Cameroon
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Ganguly G, Havlas Z, Michl J. Ab Initio Calculation of UV-vis Absorption of Parent Mg, Fe, Co, Ni, Cu, and Zn Metalloporphyrins. Inorg Chem 2024; 63:10127-10142. [PMID: 38770816 DOI: 10.1021/acs.inorgchem.3c04460] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/22/2024]
Abstract
Relativistic restricted active space (RAS) second-order multireference perturbation theory (MRPT2) methods, incorporating spin-orbit (SO) coupling perturbatively via state interaction (SO-MRPT2/RASSCF), were used to reproduce the absorption spectra of parent metalloporphyrins containing the Mg2+, Zn2+, Co2+, Ni2+, Cu2+, or FeCl2+ ions in the 12,500-40,000 cm-1 region. Particular attention was paid to the interaction between the porphyrin ring and the metal 3d electrons in states of different multiplicities (we used metal 3d and double d-shell or 3d' orbitals). For this class of compounds, the N-electron valence state perturbation theory (NEVPT2) method is superior to the complete active space perturbation theory (CASPT2) and successfully reproduces the energies of all four characteristic transitions (Q, B, N, and L) of closed-shell metalloporphyrins. Inclusion of SO coupling was found to have very little effect on excitation energies and oscillator strengths. For FeCl2+ porphyrin, we treated ligand-to-metal charge-transfer (LMCT; π,d), metal ligand field (d,d), and metal-to-ligand charge-transfer (MLCT; d,π*) transitions within the same framework. The broad and intense spectral features associated with its B (Soret) band are attributed to multiconfigurational LMCT (d,π*) bands involving strong metal-ligand orbital mixing.
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Affiliation(s)
- Gaurab Ganguly
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Prague 6 16610, Czech Republic
| | - Zdenek Havlas
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Prague 6 16610, Czech Republic
| | - Josef Michl
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Prague 6 16610, Czech Republic
- Department of Chemistry, University of Colorado, Boulder, Colorado 80309, United States
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Buttarazzi E, Inchingolo A, Pedron D, Alberto ME, Collini E, Petrone A. Conformational and environmental effects on the electronic and vibrational properties of dyes for solar cell devices. J Chem Phys 2024; 160:204301. [PMID: 38785282 DOI: 10.1063/5.0207770] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2024] [Accepted: 05/07/2024] [Indexed: 05/25/2024] Open
Abstract
The main challenge for solar cell devices is harvesting photons beyond the visible by reaching the red-edge (650-780 nm). Dye-sensitized solar cell (DSSC) devices combine the optical absorption and the charge separation processes by the association of a sensitizer as a light-absorbing material (dye molecules, whose absorption can be tuned and designed) with a wide band gap nanostructured semiconductor. Conformational and environmental effects (i.e., solvent, pH) can drastically influence the photophysical properties of molecular dyes. This study proposes a combined experimental and computational approach for the comprehensive investigation of the electronic and vibrational properties of a unique class of organic dye compounds belonging to the family of red-absorbing dyes, known as squaraines. Our focus lies on elucidating the intricate interplay between the molecular structure, vibrational dynamics, and optical properties of squaraines using state-of-the-art density functional theory calculations and spectroscopic techniques. Through systematic vibrational and optical analyses, we show that (i) the main absorption peak in the visible range is influenced by the conformational and protonation equilibria, (ii) the solvent polarity tunes the position of the UV-vis absorption, and (iii) the vibrational spectroscopy techniques (infrared and Raman) can be used as informative tools to distinguish between different conformations and protonation states. This comprehensive understanding offers valuable insights into the design and optimization of squaraine-based DSSCs for enhanced solar energy conversion efficiency.
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Affiliation(s)
- Edoardo Buttarazzi
- Scuola Superiore Meridionale, Largo San Marcellino 10, I-80138 Napoli, Italy
- Department of Chemical Sciences, University of Napoli Federico II, Complesso Universitario di Monte S. Angelo, Via Cintia 21, I-80126 Napoli, Italy
| | - Antonio Inchingolo
- Department of Chemical Sciences, University of Padova, Via Marzolo 1, I-35131 Padova, Italy
| | - Danilo Pedron
- Department of Chemical Sciences, University of Padova, Via Marzolo 1, I-35131 Padova, Italy
| | - Marta Erminia Alberto
- Department of Chemical and Chemical Technologies, University of Calabria, Via Pietro Bucci ed. 12/C, I-87036 Arcavacata di Rende, Cosenza, Italy
| | - Elisabetta Collini
- Department of Chemical Sciences, University of Padova, Via Marzolo 1, I-35131 Padova, Italy
| | - Alessio Petrone
- Scuola Superiore Meridionale, Largo San Marcellino 10, I-80138 Napoli, Italy
- Department of Chemical Sciences, University of Napoli Federico II, Complesso Universitario di Monte S. Angelo, Via Cintia 21, I-80126 Napoli, Italy
- Istituto Nazionale Di Fisica Nucleare, Sezione di Napoli, Complesso Universitario di Monte S. Angelo ed. 6, Via Cintia, I-80126 Napoli, Italy
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Cherepanov DA, Milanovsky GE, Neverov KV, Obukhov YN, Maleeva YV, Aybush AV, Kritsky MS, Nadtochenko VA. Exciton interactions of chlorophyll tetramer in water-soluble chlorophyll-binding protein BoWSCP. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2024; 309:123847. [PMID: 38217986 DOI: 10.1016/j.saa.2024.123847] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/31/2023] [Revised: 01/02/2024] [Accepted: 01/03/2024] [Indexed: 01/15/2024]
Abstract
The exciton interaction of four chlorophyll a (Chl a) molecules in a symmetrical tetrameric complex of the water-soluble chlorophyll-binding protein BoWSCP was analyzed in the pH range of 3-11. Exciton splitting ΔE = 232 ± 2 cm-1 of the Qy band of Chl a into two subcomponents with relative intensities of 78.1 ± 0.7 % and 21.9 ± 0.7 % was determined by a joint decomposition of the absorption and circular dichroism spectra into Gaussian functions. The exciton coupling parameters were calculated based on the BoWSCP atomic structure in three approximations: the point dipole model, the distributed atomic monopoles, and direct ab initio calculations in the TDDFT/PCM approximation. The Coulomb interactions of monomers were calculated within the continuum model using three values of optical permittivity. The models based on the properties of free Chl a in solution suffer from significant errors both in estimating the absolute value of the exciton interaction and in the relative intensity of exciton transitions. Calculations within the TDDFT/PCM approximation reproduce the experimentally determined parameters of the exciton splitting and the relative intensities of the exciton bands. The following factors of pigment-protein and pigment-pigment interactions were examined: deviation of the macrocycle geometry from the planar conformation of free Chl; the formation of hydrogen bonds between the macrocycle and water molecules; the overlap of wave functions of monomers at close distances. The most significant factor is the geometrical deformation of the porphyrin macrocycle, which leads to an increase in the dipole moment of Chl monomer from 5.5 to 6.9 D and to a rotation of the dipole moment by 15° towards the cyclopentane ring. The contributions of resonant charge-transfer states to the wave functions of the Chl dimer were determined and the transition dipole moments of the symmetric and antisymmetric charge-transfer states were estimated.
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Affiliation(s)
- D A Cherepanov
- N.N. Semenov Federal Research Center for Chemical Physics, Russian Academy of Sciences, 119991 Moscow, Kosygina str., 4, Russian Federation; A.N. Belozersky Institute Of Physico-Chemical Biology, Moscow State University, 119992 Moscow, Leninskye gory, 1b.40, Russian Federation.
| | - G E Milanovsky
- A.N. Belozersky Institute Of Physico-Chemical Biology, Moscow State University, 119992 Moscow, Leninskye gory, 1b.40, Russian Federation
| | - K V Neverov
- A.N. Bach Institute of Biochemistry, Federal Research Center "Fundamentals of Biotechnology", Russian Academy of Sciences", 119071 Moscow, Leninsky prospect, 33b.2, Russian Federation; Faculty of Biology, Moscow State University, 119234 Moscow, Leninskye gory, 1b.12, Russian Federation
| | - Yu N Obukhov
- A.N. Bach Institute of Biochemistry, Federal Research Center "Fundamentals of Biotechnology", Russian Academy of Sciences", 119071 Moscow, Leninsky prospect, 33b.2, Russian Federation
| | - Yu V Maleeva
- Faculty of Biology, Moscow State University, 119234 Moscow, Leninskye gory, 1b.12, Russian Federation
| | - A V Aybush
- N.N. Semenov Federal Research Center for Chemical Physics, Russian Academy of Sciences, 119991 Moscow, Kosygina str., 4, Russian Federation
| | - M S Kritsky
- A.N. Bach Institute of Biochemistry, Federal Research Center "Fundamentals of Biotechnology", Russian Academy of Sciences", 119071 Moscow, Leninsky prospect, 33b.2, Russian Federation
| | - V A Nadtochenko
- N.N. Semenov Federal Research Center for Chemical Physics, Russian Academy of Sciences, 119991 Moscow, Kosygina str., 4, Russian Federation; Department of Chemistry, Moscow State University, 119991 Moscow, Leninskye gory, 1b.3, Russian Federation
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Coppola F, Cimino P, Petrone A, Rega N. Evidence of Excited-State Vibrational Mode Governing the Photorelaxation of a Charge-Transfer Complex. J Phys Chem A 2024; 128:1620-1633. [PMID: 38381887 DOI: 10.1021/acs.jpca.3c08366] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/23/2024]
Abstract
Modern, nonlinear, time-resolved spectroscopic techniques have opened new doors for investigating the intriguing but complex world of photoinduced ultrafast out-of-equilibrium phenomena and charge dynamics. The interaction between light and matter introduces an additional dimension, where the complex interplay between electronic and vibrational dynamics needs the most advanced theoretical-computational protocols to be fully understood on the molecular scale. In this study, we showcase the capabilities of ab initio molecular dynamics simulation integrated with a multiresolution wavelet protocol to carefully investigate the excited-state relaxation dynamics in a noncovalent complex involving tetramethylbenzene (TMB) and tetracyanoquinodimethane (TCNQ) undergoing charge transfer (CT) upon photoexcitation. Our protocol provides an accurate description that facilitates a direct comparison between transient vibrational analysis and time-resolved spectroscopic signals. This molecular level perspective enhances our understanding of photorelaxation processes confined in the adiabatic regime and offers an improved interpretation of vibrational spectra. Furthermore, it enables the quantification of anharmonic vibrational couplings between high- and low-frequency modes, specifically the TCNQ "rocking" and "bending" modes. Additionally, it identifies the primary vibrational mode that governs the adiabaticity between the ground state and the CT state. This comprehensive understanding of photorelaxation processes holds significant importance in the rational design and precise control of more efficient photovoltaic and sensor devices.
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Affiliation(s)
- Federico Coppola
- Scuola Superiore Meridionale, Largo San Marcellino 10, I-80138 Napoli, Italy
| | - Paola Cimino
- Department of Chemical Sciences, University of Napoli Federico II, Complesso Universitario di M.S. Angelo, 80126 Napoli, Italy
| | - Alessio Petrone
- Scuola Superiore Meridionale, Largo San Marcellino 10, I-80138 Napoli, Italy
- Department of Chemical Sciences, University of Napoli Federico II, Complesso Universitario di M.S. Angelo, 80126 Napoli, Italy
- Istituto Nazionale Di Fisica Nucleare, sezione di Napoli, Complesso Universitario di Monte S. Angelo ed. 6, 80126 Napoli, Italia
| | - Nadia Rega
- Scuola Superiore Meridionale, Largo San Marcellino 10, I-80138 Napoli, Italy
- Department of Chemical Sciences, University of Napoli Federico II, Complesso Universitario di M.S. Angelo, 80126 Napoli, Italy
- Istituto Nazionale Di Fisica Nucleare, sezione di Napoli, Complesso Universitario di Monte S. Angelo ed. 6, 80126 Napoli, Italia
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Crisci L, Coppola F, Petrone A, Rega N. Tuning ultrafast time-evolution of photo-induced charge-transfer states: A real-time electronic dynamics study in substituted indenotetracene derivatives. J Comput Chem 2024; 45:210-221. [PMID: 37706600 DOI: 10.1002/jcc.27231] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2023] [Revised: 08/31/2023] [Accepted: 09/05/2023] [Indexed: 09/15/2023]
Abstract
Photo-induced charge transfer (CT) states are pivotal in many technological and biological processes. A deeper knowledge of such states is mandatory for modeling the charge migration dynamics. Real-time time-dependent density functional theory (RT-TD-DFT) electronic dynamics simulations are employed to explicitly observe the electronic density time-evolution upon photo-excitation. Asymmetrically substituted indenotetracene molecules, given their potential application as n-type semiconductors in organic photovoltaic materials, are here investigated. Effects of substituents with different electron-donating characters are analyzed in terms of the overall electronic energy spacing and resulting ultrafast CT dynamics through linear response (LR-)TD-DFT and RT-TD-DFT based approaches. The combination of the computational techniques here employed provided direct access to the electronic density reorganization in time and to its spatial and rational representation in terms of molecular orbital occupation time evolution. Such results can be exploited to design peculiar directional charge dynamics, crucial when photoactive materials are used for light-harvesting applications.
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Affiliation(s)
- Luigi Crisci
- Department of Chemical Sciences, University of Napoli Federico II, Complesso Universitario di M.S. Angelo, Naples, Italy
- Scuola Normale Superiore di Pisa, Pisa, Italy
| | | | - Alessio Petrone
- Department of Chemical Sciences, University of Napoli Federico II, Complesso Universitario di M.S. Angelo, Naples, Italy
- Scuola Superiore Meridionale, Naples, Italy
- Istituto Nazionale Di Fisica Nucleare, Sezione di Napoli, Complesso Universitario di M.S. Angelo ed. 6, Naples, Italy
| | - Nadia Rega
- Department of Chemical Sciences, University of Napoli Federico II, Complesso Universitario di M.S. Angelo, Naples, Italy
- Scuola Superiore Meridionale, Naples, Italy
- Istituto Nazionale Di Fisica Nucleare, Sezione di Napoli, Complesso Universitario di M.S. Angelo ed. 6, Naples, Italy
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Kosar N, Kanwal S, Sajid H, Ayub K, Gilani MA, Elfaki Ibrahim K, Gatasheh MK, Mary YS, Mahmood T. Frequency-dependent nonlinear optical response and refractive index investigation of lactone-derived thermochromic compounds. J Mol Graph Model 2024; 126:108646. [PMID: 37816302 DOI: 10.1016/j.jmgm.2023.108646] [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: 08/23/2023] [Revised: 09/28/2023] [Accepted: 09/29/2023] [Indexed: 10/12/2023]
Abstract
Nonlinear optical (NLO) switchable materials play a crucial role in the fields of electronics and optoelectronics. The selection of an appropriate switching approach is vital in designing such materials to enhance their NLO response. Among various approaches, thermos-switching materials have shown a 4-fold increase in NLO response compared to other photo-switching materials. In this study, we computationally investigated the geometric, electronic, and nonlinear optical properties of reversible lactone-based thermochromic compounds using the ωB97XD/6-311+G (d,p) level of theory. Molecular orbital studies are employed to analyze the electronic properties of the close and open isomers of these compounds, while time-dependent density functional theory (TD-DFT) analysis is utilized to evaluate their molecular absorption. Our findings reveal that the π-electronic conjugation-induced delocalization significantly influences the ON-OFF switchable nonlinear optical response of the lactone-based thermochromic compounds. Notably, among all compounds, the open isomer of lactone 2 exhibits the highest hyperpolarizability value (6596.69 au). Furthermore, we extended our analysis to investigate the frequency-dependent second and third-order hyperpolarizabilities. The most pronounced frequency-dependent NLO response is observed at 532 nm. Additionally, we calculated the refractive index of these thermochromic compounds to further assess their nonlinear optical response. The open isomer of lactone 1 demonstrates the highest refractive index value (3.99 × 10-14 cm2/W). Overall, our study highlights the excellent potential of reversible thermochromic compounds as NLO molecular thermos-switches for future applications.
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Affiliation(s)
- Naveen Kosar
- Department of Chemistry, University of Management and Technology (UMT), C-11, Johar Town, Lahore, Pakistan
| | - Saba Kanwal
- Department of Chemistry, COMSATS University Islamabad, Abbottabad Campus, Abbottabad, 22060, Pakistan
| | - Hasnain Sajid
- School of Science and Technology, Nottingham Trent University, Clifton Lane, Nottingham, NG11 8NS, UK
| | - Khurshid Ayub
- Department of Chemistry, COMSATS University Islamabad, Abbottabad Campus, Abbottabad, 22060, Pakistan
| | - Mazhar Amjad Gilani
- Department of Chemistry, COMSATS University Islamabad, Lahore Campus, Lahore, Pakistan
| | - Khalid Elfaki Ibrahim
- Department of Zoology, College of Science, King Saud University, P.O. Box 2455, Riyadh, 11451, Saudi Arabia
| | - Mansour K Gatasheh
- Department of Biochemistry, College of Science, King Saud University, P.O. Box 2455, Riyadh, 11451, Saudi Arabia
| | - Y Sheena Mary
- Department of Physics, FMNC, Kollam, Kerala, University of Kerala, India
| | - Tariq Mahmood
- Department of Chemistry, COMSATS University Islamabad, Abbottabad Campus, Abbottabad, 22060, Pakistan; Department of Chemistry, College of Science, University of Bahrain, Sakhir, 32038, Bahrain.
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10
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Levina EO, Tsirelson VG. DFT potentials from a chemical perspective: Anatomy of electron (de)localization in molecules and crystals. J Comput Chem 2023. [PMID: 37183763 DOI: 10.1002/jcc.27131] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2023] [Revised: 04/26/2023] [Accepted: 04/28/2023] [Indexed: 05/16/2023]
Abstract
We introduce a fermionic potential, v f $$ {v}_f $$ , as a comprehensive measure of electron (de)localization in atomic-molecular systems. Unlike other common descriptors as ELF, LOL, etc., it characterizes all physical effects responsible for (de)localization of electrons, namely: an exchange hole depth, its tendency to change, a sensitivity of an exchange correlation hidden in a pair density and kinetic potential to local variations in electron density. Wells in the v f $$ {v}_f $$ distribution correspond to the domains of maximum electron localization, while the potential's barriers prevent delocalization of electrons through them. It also estimates bond orders and successfully reveals the impact of chemical modifications or environmental effects on the delocalization of electrons in molecules and crystals. The v f $$ {v}_f $$ components provide a unique opportunity to compare the influence of the mentioned physical effects on electron (de)localization. This merges physical and chemical views of electron delocalization using functions appearing in density functional theory.
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Affiliation(s)
- Elena O Levina
- N.S. Kurnakov Institute of General and Inorganic Chemistry of the Russian Academy of Sciences, Moscow, Russia
| | - Vladimir G Tsirelson
- D.I. Mendeleev University of Chemical Technology, Moscow, Russia
- Federal Research Centre "Fundamentals of Biotechnology" of the Russian Academy of Sciences, Moscow, Russia
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11
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Xu H, Yu Y, Chen L, Feng Y, Xuan H, He H. A theoretical study of the ESIPT mechanism for the 2-butyl-4-hydroxyisoindoline-1, 3-dione probe. COMPUT THEOR CHEM 2023. [DOI: 10.1016/j.comptc.2023.114104] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/30/2023]
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12
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Saito K, Mitsuhashi K, Tamura H, Ishikita H. Quantum mechanical analysis of excitation energy transfer couplings in photosystem II. Biophys J 2023; 122:470-483. [PMID: 36609140 PMCID: PMC9941724 DOI: 10.1016/j.bpj.2023.01.002] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2022] [Revised: 11/21/2022] [Accepted: 01/04/2023] [Indexed: 01/07/2023] Open
Abstract
We evaluated excitation energy transfer (EET) coupling (J) between all pairs of chlorophylls (Chls) and pheophytins (Pheos) in the protein environment of photosystem II based on the time-dependent density functional theory with a quantum mechanical/molecular mechanics approach. In the reaction center, the EET coupling between Chls PD1 and PD2 is weaker (|J(PD1/PD2)| = 79 cm-1), irrespective of a short edge-to-edge distance of 3.6 Å (Mg-to-Mg distance of 8.1 Å), than the couplings between PD1 and the accessory ChlD1 (|J(PD1/ChlD2)| = 104 cm-1) and between PD2 and ChlD2 (|J(PD2/ChlD1)| = 101 cm-1), suggesting that PD1 and PD2 are two monomeric Chls rather than a "special pair". There exist strongly coupled Chl pairs (|J| > ∼100 cm-1) in the CP47 and CP43 core antennas, which may be candidates for the red-shifted Chls observed in spectroscopic studies. In CP47 and CP43, Chls ligated to CP47-His26 and CP43-His56, which are located in the middle layer of the thylakoid membrane, play a role in the "hub" that mediates the EET from the lumenal to stromal layers. In the stromal layer, Chls ligated to CP47-His466, CP43-His441, and CP43-His444 mediate the EET from CP47 to ChlD2/PheoD2 and from CP43 to ChlD1/PheoD1 in the reaction center. Thus, the excitation energy from both CP47 and CP43 can always be utilized for the charge-separation reaction in the reaction center.
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Affiliation(s)
- Keisuke Saito
- Department of Applied Chemistry, The University of Tokyo, Bunkyo-ku, Tokyo, Japan; Research Center for Advanced Science and Technology, The University of Tokyo, Meguro-ku, Tokyo, Japan.
| | - Koji Mitsuhashi
- Department of Applied Chemistry, The University of Tokyo, Bunkyo-ku, Tokyo, Japan
| | - Hiroyuki Tamura
- Department of Applied Chemistry, The University of Tokyo, Bunkyo-ku, Tokyo, Japan; Research Center for Advanced Science and Technology, The University of Tokyo, Meguro-ku, Tokyo, Japan.
| | - Hiroshi Ishikita
- Department of Applied Chemistry, The University of Tokyo, Bunkyo-ku, Tokyo, Japan; Research Center for Advanced Science and Technology, The University of Tokyo, Meguro-ku, Tokyo, Japan.
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13
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Dindorkar SS, Vardhan Patel R, Yadav A. Adsorption behaviour of graphene, boron nitride and boron carbon nitride nanosheets towards pharmaceutical and personal care products. COMPUT THEOR CHEM 2023. [DOI: 10.1016/j.comptc.2022.113995] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
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14
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Charge transfer Interaction between 2, 3-Diamino-5-bromopyridine and 2, 4-Dinitrophenol: Synthesis, Spectroscopic Characterization, DNA binding analysis, and Density Functional studies. RESULTS IN CHEMISTRY 2023. [DOI: 10.1016/j.rechem.2023.100836] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/09/2023] Open
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15
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Chaudhuri D, Patterson CH. TDDFT versus GW/BSE Methods for Prediction of Light Absorption and Emission in a TADF Emitter. J Phys Chem A 2022; 126:9627-9643. [PMID: 36515973 PMCID: PMC9806837 DOI: 10.1021/acs.jpca.2c06403] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Design concepts for organic light emitting diode (OLED) emitters, which exhibit thermally activated delayed fluorescence (TADF) and thereby achieve quantum yields exceeding 25%, depend on singlet-triplet splitting energies of order kT to allow reverse intersystem crossing at ambient temperatures. Simulation methods for these systems must be able to treat relatively large organic molecules, as well as predict their excited state energies, transition energies, singlet-triplet splittings, and absorption and emission cross sections with reasonable accuracy, in order to prove useful in the design process. Here we compare predictions of TDDFT with M06-2X and ωB97X-D exchange-correlation functionals and a GoWo@HF/BSE method for these quantities in the well-studied DPTZ-DBTO2 TADF emitter molecule. Geometry optimization is performed for ground state (GS) and lowest donor-acceptor charge transfer (CT) state for each functional. Optical absorption and emission cross sections and energies are calculated at these geometries. Relaxation energies are on the order of 0.5 eV, and the importance of obtaining excited state equilibrium geometries in predicting delayed fluorescence is demonstrated. There are clear trends in predictions of GoWo@HF/BSE, and TDDFT/ωB97X-D and M06-2X methods in which the former method favors local exciton (LE) states while the latter favors DA CT states and ωB97X-D makes intermediate predictions. GoWo@HF/BSE suffers from triplet instability for LE states but not CT states relevant for TADF. Shifts in HOMO and LUMO levels on adding a conductor-like polarizable continuum model dielectric background are used to estimate changes in excitation energies on going from the gas phase to a solvated molecule.
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16
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C R A, Jose D, Joy S. DFT Studies on the Molecular Structure, Regioisomerism, Ground and Excited state Charge Transfer Properties of Spiro‐heterocycles. ChemistrySelect 2022. [DOI: 10.1002/slct.202203188] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Affiliation(s)
- Anumol C R
- Department of chemistry Mar Athanasius College Kothamangalam
| | - Densely Jose
- Department of chemistry Mar Athanasius College Kothamangalam
| | - Sherin Joy
- Department of chemistry Baselius College Kottayam
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17
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Lama B, Sarma M. Unraveling the Mechanistic Pathway for the Dual Fluorescence in Green Fluorescent Protein (GFP) Chromophore Analogue: A Detailed Theoretical Investigation. J Phys Chem B 2022; 126:9930-9944. [PMID: 36354358 DOI: 10.1021/acs.jpcb.2c03842] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
The photophysical properties of the para-sulfonamide (p-TsABDI) analogue of the green fluorescent protein (GFP) chromophore with both proton donating and accepting sites have been exploited in polar solvents to understand the origin of the unusual dual fluorescence nature of the chromophore. In the polar solvents, the compound undergoes structural rearrangement upon photoexcitation, leading to the ultrafast excited-state intermolecular proton transfer (ESIPT) phenomenon at the S1 surface. In this work, we employed both the static electronic structure calculations and on-the-fly molecular dynamics simulation to unravel the underlying reason for this peculiar behavior of the p-TsABDI analogue in polar solvents. To represent this adequately and provide extensive information on the ESIPT mechanism mediated by the solvent molecules, we considered explicit solvent molecules using the integral equation formalism variant of polarizable continuum (IEFPCM) model. From the static calculation analysis, we can conclude that the dual emissive behavior of the compound is ascribed to the proton transfer (PT) phenomena in the excited-state. However, based on the static calculation exclusively, it is hard to ascertain the mechanistic pathway of the PT phenomena. Hence, to investigate the dynamics and reaction mechanism for the ESIPT process, we performed the on-the-fly dynamics simulation for p-TsABDI in solvent clusters. Dynamics simulation results reveal that, based on the time lag between all the proton transfer processes, the ESIPT mechanism occurs in a stepwise manner from the benzylidene moiety of the chromophore to its imidazolinone moiety. However, the nonexistence of crossings between the S1- and S0-states confirms the PT characteristics of the reactions.
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Affiliation(s)
- Bittu Lama
- Department of Chemistry, Indian Institute of Technology, Guwahati, Assam781039, India
| | - Manabendra Sarma
- Department of Chemistry, Indian Institute of Technology, Guwahati, Assam781039, India
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18
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Meesala G, Syeda AH, Varukolu M, Tigulla P. The charge transfer complex between 2, 3-diamino-5-bromopyridine and chloranilic acid: Preparation, spectroscopic characterization, DNA binding, and DFT/PCM analysis. J INDIAN CHEM SOC 2022. [DOI: 10.1016/j.jics.2022.100799] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
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19
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Synthesis, Spectroscopic Characterization, DNA binding and DFT/PCM calculations of New Hydrogen-bonded Charge Transfer complex between 4-Dimethylaminopyridine and Chloranilic acid. RESULTS IN CHEMISTRY 2022. [DOI: 10.1016/j.rechem.2022.100694] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
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20
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Förster A, Visscher L. Quasiparticle Self-Consistent GW-Bethe-Salpeter Equation Calculations for Large Chromophoric Systems. J Chem Theory Comput 2022; 18:6779-6793. [PMID: 36201788 PMCID: PMC9648197 DOI: 10.1021/acs.jctc.2c00531] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
![]()
The GW-Bethe–Salpeter equation
(BSE) method
is promising for calculating the low-lying excitonic states of molecular
systems. However, so far it has only been applied to rather small
molecules and in the commonly implemented diagonal approximations
to the electronic self-energy, it depends on a mean-field starting
point. We describe here an implementation of the self-consistent and
starting-point-independent quasiparticle self-consistent (qsGW)-BSE approach, which is suitable for calculations on
large molecules. We herein show that eigenvalue-only self-consistency
can lead to an unfaithful description of some excitonic states for
chlorophyll dimers while the qsGW-BSE vertical excitation
energies (VEEs) are in excellent agreement with spectroscopic experiments
for chlorophyll monomers and dimers measured in the gas phase. Furthermore,
VEEs from time-dependent density functional theory calculations tend
to disagree with experimental values and using different range-separated
hybrid (RSH) kernels does change the VEEs by up to 0.5 eV. We use
the new qsGW-BSE implementation to calculate the
lowest excitation energies of the six chromophores of the photosystem
II (PSII) reaction center (RC) with nearly 2000 correlated electrons.
Using more than 11,000 (6000) basis functions, the calculation could
be completed in less than 5 (2) days on a single modern compute node.
In agreement with previous TD-DFT calculations using RSH kernels on
models that also do not include environmental effects, our qsGW-BSE calculations only yield states with local characters
in the low-energy spectrum of the hexameric complex. Earlier works
with RSH kernels have demonstrated that the protein environment facilitates
the experimentally observed interchromophoric charge transfer. Therefore,
future research will need to combine correlation effects beyond TD-DFT
with an explicit treatment of environmental electrostatics.
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Affiliation(s)
- Arno Förster
- Theoretical Chemistry, Vrije Universiteit, De Boelelaan 1083, NL-1081 HVAmsterdam, The Netherlands
| | - Lucas Visscher
- Theoretical Chemistry, Vrije Universiteit, De Boelelaan 1083, NL-1081 HVAmsterdam, The Netherlands
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21
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Coppola F, Cimino P, Perrella F, Crisci L, Petrone A, Rega N. Electronic and Vibrational Manifold of Tetracyanoethylene-Chloronaphthalene Charge Transfer Complex in Solution: Insights from TD-DFT and Ab Initio Molecular Dynamics. J Phys Chem A 2022; 126:7179-7192. [PMID: 36174118 PMCID: PMC9574931 DOI: 10.1021/acs.jpca.2c05001] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2022] [Revised: 09/17/2022] [Indexed: 11/29/2022]
Abstract
The interplay between light absorption and the molecular environment has a central role in the observed photophysics of a wide range of photoinduced chemical and biological phenomena. The understanding of the interplay between vibrational and electronic transitions is the focus of this work, since it can provide a rationale to tune the optical properties of charge transfer (CT) materials used for technological applications. A clear description of these processes poses a nontrivial challenge from both the theoretical and experimental points of view, where the main issue is how to accurately describe and probe drastic changes in the electronic structure and the ultrafast molecular relaxation and dynamics. In this work we focused on the intermolecular CT reaction that occurs upon photon absorption in a π-stacked model system in dichloromethane solution, in which the 1-chloronaphthalene (1ClN) acts as the electron donor and tetracyanoethylene (TCNE) is the electron acceptor. Density functional theory calculations have been carried out to characterize both the ground-state properties and more importantly the low-lying CT electronic transition, and excellent agreement with recently available experimental results [Mathies, R. A.; et al. J. Phys. Chem. A 2018, 122 (14), 3594] was obtained. The minima of the ground state and first singlet excited state have been accurately characterized in terms of spatial arrangements and vibrational Raman frequencies, and the CT natures of the first two low-lying electronic transitions in the absorption spectra have been addressed and clarified too. Finally, by modeling the possible coordination sites of the TCNE electron acceptor with respect to monovalent ions (Na+, K+) in an implicit solution of acetonitrile, we find that TCNE can accommodate a counterion in two different arrangements, parallel and orthogonal to the C═C axis, leading to the formation of a contact ion pair. The nature of the counterion and its relative position entail structural modifications of the TCNE radical anion, mainly the central C═C and C≡N bonds, compared to the isolated case. An important red shift of the C═C stretching frequency was observed when the counterion is orthogonal to the double bond, to a greater extent for Na+. On the contrary, in the second case, where the counterion ion lies along the internuclear C═C axis, we find that K+ polarizes the electron density of the double bond more, resulting in a greater red shift than with Na+.
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Affiliation(s)
- Federico Coppola
- Department
of Chemical Sciences, University of Napoli
Federico II, Complesso Universitario di M.S. Angelo, 80126 Napoli, Italy
- Scuola
Superiore Meridionale, Largo San Marcellino 10, 80138 Napoli, Italy
| | - Paola Cimino
- Department
of Pharmaceutical Sciences, University of
Salerno, 84084 Fisciano, Italy
| | - Fulvio Perrella
- Department
of Chemical Sciences, University of Napoli
Federico II, Complesso Universitario di M.S. Angelo, 80126 Napoli, Italy
- Scuola
Superiore Meridionale, Largo San Marcellino 10, 80138 Napoli, Italy
| | - Luigi Crisci
- Department
of Chemical Sciences, University of Napoli
Federico II, Complesso Universitario di M.S. Angelo, 80126 Napoli, Italy
| | - Alessio Petrone
- Department
of Chemical Sciences, University of Napoli
Federico II, Complesso Universitario di M.S. Angelo, 80126 Napoli, Italy
- Scuola
Superiore Meridionale, Largo San Marcellino 10, 80138 Napoli, Italy
- Istituto
Nazionale di Fisica Nucleare, Sezione di Napoli, Complesso Universitario di Monte S. Angelo ed. 6, 80126 Napoli, Italy
| | - Nadia Rega
- Department
of Chemical Sciences, University of Napoli
Federico II, Complesso Universitario di M.S. Angelo, 80126 Napoli, Italy
- Scuola
Superiore Meridionale, Largo San Marcellino 10, 80138 Napoli, Italy
- Istituto
Nazionale di Fisica Nucleare, Sezione di Napoli, Complesso Universitario di Monte S. Angelo ed. 6, 80126 Napoli, Italy
- Centro
Interdipartimentale di Ricerca sui Biomateriali (CRIB), Piazzale Tecchio, 80125 Napoli, Italy
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22
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Zhu X, Chen Z, Ai H. Mechanistic insight into the tautomerization of histidine initiated by water-catalyzed N-H and C-H cleavages. J Mol Model 2022; 28:325. [PMID: 36136156 DOI: 10.1007/s00894-022-05222-8] [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: 05/24/2022] [Accepted: 07/12/2022] [Indexed: 10/14/2022]
Abstract
The N-H and C-H activation is of great significance in organic chemistry and chemical industry fields, especially, in the utilization of petroleum raw materials. High NδH (tautomer of natural histidine) content would increase Alzheimer's disease risk. To inhibit this and improve the activation of N-H and C-H bonds, the isomerization mechanism from NδH to NεH of histidine-containing dipeptide catalyzed by water cluster was explored. The results discovered that water cluster assists this reaction by reducing the activation energies from 68.20 to 9.60 kcal mol-1, and its size not only affects the reaction rate but also determines the reaction pathway in a degree. Moreover, water cluster, taken as a potential green catalyst, is more effective on the reactions involving N-H and C-H bond cleavages than reported common toxic organometallic compounds and has different catalytic mechanisms. This work also provides some theoretical guidance for the modulation of Alzheimer's disease induced by histidine isomerization.
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Affiliation(s)
- Xueying Zhu
- School of Chemistry and Chemical Engineering, University of Jinan, Jinan, 250022, People's Republic of China.
| | - Zijiao Chen
- Institute of Science and Technology, Xinjiang University, Aksu, 843100, People's Republic of China
| | - Hongqi Ai
- School of Chemistry and Chemical Engineering, University of Jinan, Jinan, 250022, People's Republic of China.
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23
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Mikalčiūtė A, Gelzinis A, Mačernis M, Büchel C, Robert B, Valkunas L, Chmeliov J. Structure-based model of fucoxanthin-chlorophyll protein complex: Calculations of chlorophyll electronic couplings. J Chem Phys 2022; 156:234101. [PMID: 35732526 DOI: 10.1063/5.0092154] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023] Open
Abstract
Diatoms are a group of marine algae that are responsible for a significant part of global oxygen production. Adapted to life in an aqueous environment dominated by the blue-green light, their major light-harvesting antennae-fucoxanthin-chlorophyll protein complexes (FCPs)-exhibit different pigment compositions than of plants. Despite extensive experimental studies, until recently the theoretical description of excitation energy dynamics in these complexes was limited by the lack of high-resolution structural data. In this work, we use the recently resolved crystallographic information of the FCP complex from Phaeodactylum tricornutum diatom [Wang et al., Science 363, 6427 (2019)] and quantum chemistry-based calculations to evaluate the chlorophyll transition dipole moments, atomic transition charges from electrostatic potential, and the inter-chlorophyll couplings in this complex. The obtained structure-based excitonic couplings form the foundation for any modeling of stationary or time-resolved spectroscopic data. We also calculate the inter-pigment Förster energy transfer rates and identify two quickly equilibrating chlorophyll clusters.
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Affiliation(s)
- Austėja Mikalčiūtė
- Institute of Chemical Physics, Faculty of Physics, Vilnius University, Saulėtekio Avenue 9, LT-10222 Vilnius, Lithuania
| | - Andrius Gelzinis
- Institute of Chemical Physics, Faculty of Physics, Vilnius University, Saulėtekio Avenue 9, LT-10222 Vilnius, Lithuania
| | - Mindaugas Mačernis
- Institute of Chemical Physics, Faculty of Physics, Vilnius University, Saulėtekio Avenue 9, LT-10222 Vilnius, Lithuania
| | - Claudia Büchel
- Institute of Molecular Biosciences, Goethe University Frankfurt, Max-von-Laue Straße 9, 60438 Frankfurt, Germany
| | - Bruno Robert
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), Gif-sur-Yvette, France
| | - Leonas Valkunas
- Institute of Chemical Physics, Faculty of Physics, Vilnius University, Saulėtekio Avenue 9, LT-10222 Vilnius, Lithuania
| | - Jevgenij Chmeliov
- Institute of Chemical Physics, Faculty of Physics, Vilnius University, Saulėtekio Avenue 9, LT-10222 Vilnius, Lithuania
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24
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Quantum chemical study of the defect laden monolayer boron nitride nanosheets for adsorption of pesticides from wastewater. Colloids Surf A Physicochem Eng Asp 2022. [DOI: 10.1016/j.colsurfa.2022.128795] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
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25
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Dindorkar SS, Yadav A. Comparative study on adsorption behaviour of the monolayer graphene, boron nitride and silicon carbide hetero-sheets towards carbon monoxide: Insights from first-principle studies. COMPUT THEOR CHEM 2022. [DOI: 10.1016/j.comptc.2022.113676] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
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26
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Samanta B, Morales-García Á, Illas F, Goga N, Anta JA, Calero S, Bieberle-Hütter A, Libisch F, Muñoz-García AB, Pavone M, Caspary Toroker M. Challenges of modeling nanostructured materials for photocatalytic water splitting. Chem Soc Rev 2022; 51:3794-3818. [PMID: 35439803 DOI: 10.1039/d1cs00648g] [Citation(s) in RCA: 25] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Understanding the water splitting mechanism in photocatalysis is a rewarding goal as it will allow producing clean fuel for a sustainable life in the future. However, identifying the photocatalytic mechanisms by modeling photoactive nanoparticles requires sophisticated computational techniques based on multiscale modeling. In this review, we will survey the strengths and drawbacks of currently available theoretical methods at different length and accuracy scales. Understanding the surface-active site through Density Functional Theory (DFT) using new, more accurate exchange-correlation functionals plays a key role for surface engineering. Larger scale dynamics of the catalyst/electrolyte interface can be treated with Molecular Dynamics albeit there is a need for more generalizations of force fields. Monte Carlo and Continuum Modeling techniques are so far not the prominent path for modeling water splitting but interest is growing due to the lower computational cost and the feasibility to compare the modeling outcome directly to experimental data. The future challenges in modeling complex nano-photocatalysts involve combining different methods in a hierarchical way so that resources are spent wisely at each length scale, as well as accounting for excited states chemistry that is important for photocatalysis, a path that will bring devices closer to the theoretical limit of photocatalytic efficiency.
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Affiliation(s)
- Bipasa Samanta
- Department of Materials Science and Engineering, Technion - Israel Institute of Technology, Haifa 3600003, Israel
| | - Ángel Morales-García
- Departament de Ciència de Materials i Química Física & Institut de Química Teòrica i Computacional (IQTCUB), Universitat de Barcelona, c/Martí i Franquès 1-11, 08028 Barcelona, Spain.
| | - Francesc Illas
- Departament de Ciència de Materials i Química Física & Institut de Química Teòrica i Computacional (IQTCUB), Universitat de Barcelona, c/Martí i Franquès 1-11, 08028 Barcelona, Spain.
| | - Nicolae Goga
- Faculty of Engineering in Foreign Languages, Universitatea Politehnica din Bucuresti, Bucuresti, Romania.
| | - Juan Antonio Anta
- Department of Physical, Chemical and Natural Systems, Universidad Pablo de Olavide, Crta. De Utrera km. 1, 41089 Sevilla, Spain.
| | - Sofia Calero
- Materials Simulation & Modeling, Department of Applied Physics, Eindhoven University of Technology, 5600 MB Eindhoven, The Netherlands
| | - Anja Bieberle-Hütter
- Electrochemical Materials and Interfaces, Dutch Institute for Fundamental Energy Research (DIFFER), 5600 HH Eindhoven, The Netherlands.
| | - Florian Libisch
- Institute for Theoretical Physics, TU Wien, 1040 Vienna, Austria.
| | - Ana B Muñoz-García
- Dipartimento di Fisica "Ettore Pancini", Università di Napoli Federico II, Via Cintia 21, Napoli 80126, Italy.
| | - Michele Pavone
- Dipartimento di Scienze Chimiche, Università di Napoli Federico II, Via Cintia 21, Napoli 80126, Italy.
| | - Maytal Caspary Toroker
- Department of Materials Science and Engineering, Technion - Israel Institute of Technology, Haifa 3600003, Israel.,The Nancy and Stephen Grand Technion Energy Program, Technion - Israel Institute of Technology, Haifa 3600003, Israel.
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27
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ZHU ZHE, Higashi M, Saito S. Excited states of chlorophyll a and b in solution by time-dependent density functional theory. J Chem Phys 2022; 156:124111. [DOI: 10.1063/5.0083395] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
The ground state and excited state electronic properties of chlorophyll (Chl) a and Chl b in diethyl ether, acetone, and ethanol solutions are investigated using quantum mechanical and molecular mechanical calculations with density functional theory (DFT) and time-dependent DFT (TDDFT). Although the DFT/TDDFT methods are widely used, the electronic structures of molecules, especially large molecules, calculated with these methods are known to be strongly dependent on the functionals and the parameters used in functionals. Here, we optimize the range-separated parameter, µ, of the CAM-B3LYP functional of Chl a and Chl b to reproduce the experimental excitation energy differences of these Chl molecules in solution. The optimal values of µ for Chl a and Chl b are smaller than the default value of µ and that for bacteriochlorophyll a, indicating the change in electronic distribution, i.e., an increase in electron delocalization, within the molecule. We find that the electronic distribution of Chl b with an extra formyl group is different from that of Chl a. We also find that the polarity of solution and hydrogen bond cause the decrease in the excitation energies and the increase in the widths of excitation energy distributions of Chl a and Chl b. The present results are expected to be useful for understanding the electronic properties of each pigment molecule in a local heterogeneous environment, which will play an important role in the excitation energy transfer in light-harvesting complex II.
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Affiliation(s)
| | - Masahiro Higashi
- Department of Molecular Engineering, Kyoto University - Katsura Campus, Japan
| | - Shinji Saito
- Department of Theoretical and Computational Molecular Science, Institute for Molecular Science, Japan
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Thiacalixarenes with Sulfur Functionalities at Lower Rim: Heavy Metal Ion Binding in Solution and 2D-Confined Space. Int J Mol Sci 2022; 23:ijms23042341. [PMID: 35216456 PMCID: PMC8875454 DOI: 10.3390/ijms23042341] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2021] [Revised: 02/07/2022] [Accepted: 02/18/2022] [Indexed: 02/04/2023] Open
Abstract
Sulfur-containing groups preorganized on macrocyclic scaffolds are well suited for liquid-phase complexation of soft metal ions; however, their binding potential was not extensively studied at the air-water interface, and the effect of thioether topology on metal ion binding mechanisms under various conditions was not considered. Herein, we report the interface receptor characteristics of topologically varied thiacalixarene thioethers (linear bis-(methylthio)ethoxy derivative L2, O2S2-thiacrown-ether L3, and O2S2-bridged thiacalixtube L4). The study was conducted in bulk liquid phase and Langmuir monolayers. For all compounds, the highest liquid-phase extraction selectivity was revealed for Ag+ and Hg2+ ions vs. other soft metal ions. In thioether L2 and thiacalixtube L4, metal ion binding was evidenced by a blue shift of the band at 303 nm (for Ag+ species) and the appearance of ligand-to-metal charge transfer bands at 330-340 nm (for Hg2+ species). Theoretical calculations for thioether L2 and its Ag and Hg complexes are consistent with experimental data of UV/Vis, nuclear magnetic resonance (NMR) spectroscopy, and single-crystal X-ray diffractometry of Ag-thioether L2 complexes and Hg-thiacalixtube L4 complex for the case of coordination around the metal center involving two alkyl sulfide groups (Hg2+) or sulfur atoms on the lower rim and bridging unit (Ag+). In thiacrown L3, Ag and Hg binding by alkyl sulfide groups was suggested from changes in NMR spectra upon the addition of corresponding salts. In spite of the low ability of the thioethers to form stable Langmuir monolayers on deionized water, one might argue that the monolayers significantly expand in the presence of Hg salts in the water subphase. Hg2+ ion uptake by the Langmuir-Blodgett (LB) films of ligand L3 was proved by X-ray photoelectron spectroscopy (XPS). Together, these results demonstrate the potential of sulfide groups on the calixarene platform as receptor unit towards Hg2+ ions, which could be useful in the development of Hg2+-selective water purification systems or thin-film sensor devices.
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Shang C, Cao Y, Shao Z, Sun C, Li Y. Tactfully unveiling the effect of solvent polarity on the ESIPT mechanism and photophysical property of the 3-hydroxylflavone derivative. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2022; 267:120496. [PMID: 34689094 DOI: 10.1016/j.saa.2021.120496] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/14/2021] [Revised: 09/24/2021] [Accepted: 10/09/2021] [Indexed: 06/13/2023]
Abstract
In this contribution, the solvent effects on the excited-state intramolecular proton transfer (ESIPT) and photophysical properties of 2-(4-(diphenylamine)phenyl)-3-hydroxy-4H-chromen-4-one (3HF-OH, Dyes Pigm. 2021, 184, 108865) in the dimethylsulfoxide (DMSO), acetonitrile (ACN), dichloromethane (DCM) and cyclohexane (CYH) phases have been comprehensively explored by using the density functional theory (DFT) and time-dependent density functional theory (TD-DFT) methods. The obtained bond lengths, bond angles and infrared (IR) vibration analysis related to the intramolecular hydrogen bond (IHB) reveal that the IHB intensity of 3HF-OH is weakened as the solvent polarity increased. Besides, the ESIPT process changes from the endothermic to the exothermic with the enlargement of solvent polarity, and the reaction barrier increases gradually. It is worth noting that the molecular configuration torsion of 3HF-OH is gradually intensified with the decline of solvent polarity, which aggravates the twisted intramolecular charge transfer (TICT) state and thereby partially attenuates the short-wavelength fluorescence of 3HF-OH in the CYH solvent. In addition to these, the structural torsion has restrained the occurrence of the ESIPT behavior by means of elevating the energy barrier. This theoretical research would provide valuable guidance for regulating and controlling the photophysical behavior of compounds via the strategy of changing solvent polarity.
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Affiliation(s)
- Changjiao Shang
- College of Science, Northeast Forestry University, Harbin 150040, Heilongjiang, China
| | - Yunjian Cao
- College of Science, Northeast Forestry University, Harbin 150040, Heilongjiang, China
| | - Zhuqi Shao
- College of Science, Northeast Forestry University, Harbin 150040, Heilongjiang, China
| | - Chaofan Sun
- College of Science, Northeast Forestry University, Harbin 150040, Heilongjiang, China.
| | - Yuanzuo Li
- College of Science, Northeast Forestry University, Harbin 150040, Heilongjiang, China.
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30
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Kupfer S, Wächtler M, Guthmuller J. Light‐Driven Multi‐Charge Separation in a Push‐Pull Ruthenium‐based Photosensitizer – Assessed by RASSCF and TDDFT Simulations. CHEMPHOTOCHEM 2022. [DOI: 10.1002/cptc.202200010] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Affiliation(s)
- Stephan Kupfer
- Friedrich Schiller Universitat Jena Chemisch Geowissenschaftliche Fakultat Institute of Physical Chemistry Helmholtzweg 1 07743 Jena GERMANY
| | - Maria Wächtler
- Leibniz Institute of Photonic Technology: Leibniz-Institut fur Photonische Technologien Functional Interfaces GERMANY
| | - Julien Guthmuller
- Gdansk University of Technology: Politechnika Gdanska Institute of Physics and Computer Science POLAND
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Li M, Kobayashi R, Amos RD, Ford MJ, Reimers JR. Density functionals with asymptotic-potential corrections are required for the simulation of spectroscopic properties of materials. Chem Sci 2022; 13:1492-1503. [PMID: 35222934 PMCID: PMC8809424 DOI: 10.1039/d1sc03738b] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2021] [Accepted: 12/31/2021] [Indexed: 11/21/2022] Open
Abstract
Five effects of correction of the asymptotic potential error in density functionals are identified that significantly improve calculated properties of molecular excited states involving charge-transfer character. Newly developed materials-science computational methods are used to demonstrate how these effects manifest in materials spectroscopy. Connection is made considering chlorophyll-a as a paradigm for molecular spectroscopy, 22 iconic materials as paradigms for 3D materials spectroscopy, and the VN - defect in hexagonal boron nitride as an example of the spectroscopy of defects in 2D materials pertaining to nanophotonics. Defects can equally be thought of as being "molecular" and "materials" in nature and hence bridge the relms of molecular and materials spectroscopies. It is concluded that the density functional HSE06, currently considered as the standard for accurate calculations of materials spectroscopy, should be replaced, in most instances, by the computationally similar but asymptotically corrected CAM-B3LYP functional, with some specific functionals for materials-use only providing further improvements.
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Affiliation(s)
- Musen Li
- International Centre for Quantum and Molecular Structures and Department of Physics, Shanghai University Shanghai 200444 China
| | - Rika Kobayashi
- ANU Supercomputer Facility Leonard Huxley Bldg. 56, Mills Rd Canberra ACT 2601 Australia
| | - Roger D Amos
- ANU Supercomputer Facility Leonard Huxley Bldg. 56, Mills Rd Canberra ACT 2601 Australia
| | - Michael J Ford
- University of Technology Sydney, School of Mathematical and Physical Sciences Ultimo New South Wales 2007 Australia
| | - Jeffrey R Reimers
- International Centre for Quantum and Molecular Structures and Department of Physics, Shanghai University Shanghai 200444 China
- University of Technology Sydney, School of Mathematical and Physical Sciences Ultimo New South Wales 2007 Australia
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Drzewiecka-Matuszek A, Rutkowska-Zbik D. Application of TD-DFT Theory to Studying Porphyrinoid-Based Photosensitizers for Photodynamic Therapy: A Review. Molecules 2021; 26:7176. [PMID: 34885763 PMCID: PMC8658767 DOI: 10.3390/molecules26237176] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2021] [Revised: 11/23/2021] [Accepted: 11/24/2021] [Indexed: 11/30/2022] Open
Abstract
An important focus for innovation in photodynamic therapy (PDT) is theoretical investigations. They employ mostly methods based on Time-Dependent Density Functional Theory (TD-DFT) to study the photochemical properties of photosensitizers. In the current article we review the existing state-of-the-art TD-DFT methods (and beyond) which are employed to study the properties of porphyrinoid-based systems. The review is organized in such a way that each paragraph is devoted to a separate aspect of the PDT mechanism, e.g., correct prediction of the absorption spectra, determination of the singlet-triplet intersystem crossing, and interaction with molecular oxygen. Aspects of the calculation schemes are discussed, such as the choice of the most suitable functional and inclusion of a solvent. Finally, quantitative structure-activity relationship (QSAR) methods used to explore the photochemistry of porphyrinoid-based systems are discussed.
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Affiliation(s)
| | - Dorota Rutkowska-Zbik
- Jerzy Haber Institute of Catalysis and Surface Chemistry Polish Academy of Sciences, Niezapominajek 8, 30-239 Krakow, Poland;
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Li S, Bodenstedt K, Kharma M, Burson CM, Alhmoud D, Moulder CA, Farvid S, Ghimire MM, Rawashdeh AMM, El Bouanani M, Omary MA. Can A Double-Doped Device Modification of A Standard Bilayer OLED Improve the Photo- And/or Electro-luminescence Efficiency? A Case Study of Architecture Design in Fluorescent Devices with A Potential Roadmap for High-Efficiency Phosphorescent Devices. COMMENT INORG CHEM 2021. [DOI: 10.1080/02603594.2021.1992399] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Affiliation(s)
- Shan Li
- Departments of Chemistry and Materials Science and Engineering, University of North Texas, Denton, Texas, USA
| | - Kurt Bodenstedt
- Departments of Chemistry and Materials Science and Engineering, University of North Texas, Denton, Texas, USA
| | - Mustafa Kharma
- Department of Chemistry, Yarmouk University, Irbid, Jordan
- Department of Chemistry, Jordan University, Amman, Jordan
| | - Claire M. Burson
- Departments of Chemistry and Materials Science and Engineering, University of North Texas, Denton, Texas, USA
- Department of Chemistry, Southern Methodist University, Dallas, Texas, USA
| | - Dieaa Alhmoud
- Department of Chemistry, Yarmouk University, Irbid, Jordan
- Department of Chemistry, University of Massachusetts, Amherst, Massachusetts, USA
| | - Catherine A. Moulder
- Departments of Chemistry and Materials Science and Engineering, University of North Texas, Denton, Texas, USA
- Department of Chemistry, Washington State University, Pullman, Washington, USA
| | - Seyedmajid Farvid
- Departments of Chemistry and Materials Science and Engineering, University of North Texas, Denton, Texas, USA
| | - Mukunda M. Ghimire
- Department of Chemistry, Lebanon Valley College, Annville, Pennsylvania, USA
| | | | - Mohamed El Bouanani
- Departments of Chemistry and Materials Science and Engineering, University of North Texas, Denton, Texas, USA
| | - Mohammad A. Omary
- Departments of Chemistry and Materials Science and Engineering, University of North Texas, Denton, Texas, USA
- Department of Chemistry, Yarmouk University, Irbid, Jordan
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Büchner R, Fondell M, Haverkamp R, Pietzsch A, Vaz da Cruz V, Föhlisch A. The porphyrin center as a regulator for metal-ligand covalency and π hybridization in the entire molecule. Phys Chem Chem Phys 2021; 23:24765-24772. [PMID: 34714305 PMCID: PMC8579471 DOI: 10.1039/d1cp03944j] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The central moiety of porphyrins is shown to control the charge state of the inner complex and links it by covalent interaction to the peripheral substituents. This link, which enables the versatile functions of porphyrins, is not picked up in the established, reduced four orbital picture [Gouterman, J. Mol. Spectrosc., 1961, 6, 138]. X-ray absorption spectroscopy at the N K-edge with density functional theory approaches gives access to the full electronic structure, in particular the π* manifold beyond the Gouterman orbitals. Systematic variation of the central moiety highlights two linked, governing trends: The ionicity of the porphyrin center increases from the aminic N-H to N-Cu to N-Zn to N-Mg to the iminic N:. At the same time covalency with peripheral substituents increases and compensates the buildup of high charge density at the coordinated nitrogen sites.
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Affiliation(s)
- Robby Büchner
- Institute of Physics and Astronomy, University of Potsdam, Karl-Liebknecht-Str. 24-25, 14476 Potsdam, Germany.
| | - Mattis Fondell
- Institute for Methods and Instrumentation for Synchrotron Radiation Research, Helmholtz-Zentrum Berlin für Materialien und Energie, Albert-Einstein-Str. 15, 12489 Berlin, Germany.
| | - Robert Haverkamp
- Institute for Methods and Instrumentation for Synchrotron Radiation Research, Helmholtz-Zentrum Berlin für Materialien und Energie, Albert-Einstein-Str. 15, 12489 Berlin, Germany.
| | - Annette Pietzsch
- Institute for Methods and Instrumentation for Synchrotron Radiation Research, Helmholtz-Zentrum Berlin für Materialien und Energie, Albert-Einstein-Str. 15, 12489 Berlin, Germany.
| | - Vinícius Vaz da Cruz
- Institute for Methods and Instrumentation for Synchrotron Radiation Research, Helmholtz-Zentrum Berlin für Materialien und Energie, Albert-Einstein-Str. 15, 12489 Berlin, Germany.
| | - Alexander Föhlisch
- Institute of Physics and Astronomy, University of Potsdam, Karl-Liebknecht-Str. 24-25, 14476 Potsdam, Germany. .,Institute for Methods and Instrumentation for Synchrotron Radiation Research, Helmholtz-Zentrum Berlin für Materialien und Energie, Albert-Einstein-Str. 15, 12489 Berlin, Germany.
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35
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Liu Y, Zhu C. Trajectory surface hopping molecular dynamics simulations for retinal protonated Schiff-base photoisomerization. Phys Chem Chem Phys 2021; 23:23861-23874. [PMID: 34651159 DOI: 10.1039/d1cp03401d] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Global switching trajectory surface hopping molecular dynamics simulations are performed using accurate on-the-fly (TD)CAM-B3LYP/6-31G potential energy surfaces to study retinal protonated Schiff-base photoisomerization up to S1 excitation. The simulations detected two-layer conical intersection networks: one is at an energy as high as 8 eV and the other is in the energy range around 3-4 eV. Six conical intersections within the low-layer energy region that correspond to active conical intersections under experimental conditions are found via the use of pairwise isomers, within which nonadiabatic molecular dynamics simulations are performed. Eight isomer products are populated with simulated sampling trajectories from which the simulated quantum yield in the gas phase is estimated to be 0.11 (0.08) moving from the all-trans isomer to the 11-cis (11-cis to all-trans) isomer in comparison with an experimental value of 0.09 (0.2) in the solution phase. Each conical intersection is related to one specific twist angle accompanying a related CC double bond motion during photoisomerization. Nonplanar distortion of the entire dynamic process has a significant role in the formation of the relevant photoisomerization products. The present simulation indicates that all hopping points show well-behaved potential energy surface topology, as calculated via the conventional TDDFT method, at conical intersections between S1 and S0 states. Therefore, the present nonadiabatic dynamics simulations with the TDDFT method are very encouraging for simulating various large systems related to retinal Schiff-base photoisomerization in the real world.
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Affiliation(s)
- Yuxiu Liu
- Department of Applied Chemistry and Institute of Molecular Science, National Chiao-Tung University, Hsinchu 30010, Taiwan.
| | - Chaoyuan Zhu
- Department of Applied Chemistry and Institute of Molecular Science, National Chiao-Tung University, Hsinchu 30010, Taiwan. .,Department of Applied Chemistry and Center for Emergent Functional Matter Science, National Yang Ming Chiao Tung University, Hsinchu 30010, Taiwan
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36
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Srivastava R. Physicochemical, antioxidant properties of carotenoids and its optoelectronic and interaction studies with chlorophyll pigments. Sci Rep 2021; 11:18365. [PMID: 34526535 PMCID: PMC8443628 DOI: 10.1038/s41598-021-97747-w] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2021] [Accepted: 07/28/2021] [Indexed: 11/13/2022] Open
Abstract
The physicochemical and antioxidant properties of seven carotenoids: antheraxanthin, β-carotene, neoxanthin, peridinin, violaxanthin, xanthrophyll and zeaxanthin were studied by theoretical means. Then the Optoelectronic properties and interaction of chlorophyll-carotenoid complexes are analysed by TDDFT and IGMPLOT. Global reactivity descriptors for carotenoids and chlorophyll (Chla, Chlb) are calculated via conceptual density functional theory (CDFT). The higher HOMO-LUMO (HL) gap indicated structural stability of carotenoid, chlorophyll and chlorophyll-carotenoid complexes. The chemical hardness for carotenoids and Chlorophyll is found to be lower in the solvent medium than in the gas phase. Results showed that carotenoids can be used as good reactive nucleophile due to lower µ and ω. As proton affinities (PAs) are much lower than the bond dissociation enthalpies (BDEs), it is anticipated that direct antioxidant activity in these carotenoids is mainly due to the sequential proton loss electron transfer (SPLET) mechanism with dominant solvent effects. Also lower PAs of carotenoid suggest that antioxidant activity by the SPLET mechanism should be a result of a balance between proclivities to transfer protons. Reaction rate constant with Transition-State Theory (TST) were estimated for carotenoid-Chlorophyll complexes in gas phase. Time dependent Density Functional Theory (TDDFT) showed that all the chlorophyll (Chla, Chlb)-carotenoid complexes show absorption wavelength in the visible region. The lower S1-T1 adiabatic energy gap indicated ISC transition from S1 to T1 state.
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Affiliation(s)
- Ruby Srivastava
- CSIR-Centre for Cellular and Molecular Biology, Hyderabad, India.
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37
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Pham NNT, Han SH, Park JS, Lee SG. Optical and Electronic Properties of Organic NIR-II Fluorophores by Time-Dependent Density Functional Theory and Many-Body Perturbation Theory: GW-BSE Approaches. NANOMATERIALS (BASEL, SWITZERLAND) 2021; 11:2293. [PMID: 34578610 PMCID: PMC8466807 DOI: 10.3390/nano11092293] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/02/2021] [Revised: 08/30/2021] [Accepted: 09/01/2021] [Indexed: 11/16/2022]
Abstract
Organic-molecule fluorophores with emission wavelengths in the second near-infrared window (NIR-II, 1000-1700 nm) have attracted substantial attention in the life sciences and in biomedical applications because of their excellent resolution and sensitivity. However, adequate theoretical levels to provide efficient and accurate estimations of the optical and electronic properties of organic NIR-II fluorophores are lacking. The standard approach for these calculations has been time-dependent density functional theory (TDDFT). However, the size and large excitonic energies of these compounds pose challenges with respect to computational cost and time. In this study, we used the GW approximation combined with the Bethe-Salpeter equation (GW-BSE) implemented in many-body perturbation theory approaches based on density functional theory. This method was used to perform calculations of the excited states of two NIR molecular fluorophores (BTC980 and BTC1070), going beyond TDDFT. In this study, the optical absorption spectra and frontier molecular orbitals of these compounds were compared using TDDFT and GW-BSE calculations. The GW-BSE estimates showed excellent agreement with previously reported experimental results.
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Affiliation(s)
- Nguyet N. T. Pham
- School of Chemical Engineering, Pusan National University, Busan 46241, Korea; (N.N.T.P.); (S.H.H.)
| | - Seong Hun Han
- School of Chemical Engineering, Pusan National University, Busan 46241, Korea; (N.N.T.P.); (S.H.H.)
| | - Jong S. Park
- School of Chemical Engineering, Pusan National University, Busan 46241, Korea; (N.N.T.P.); (S.H.H.)
- Department of Organic Material Science and Engineering, Pusan National University, Busan 46241, Korea
| | - Seung Geol Lee
- School of Chemical Engineering, Pusan National University, Busan 46241, Korea; (N.N.T.P.); (S.H.H.)
- Department of Organic Material Science and Engineering, Pusan National University, Busan 46241, Korea
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Komatsu Y, Takizawa K. A quantum chemical study on the effects of varying the central metal in extended photosynthetic pigments. Phys Chem Chem Phys 2021; 23:14404-14414. [PMID: 34180470 DOI: 10.1039/d1cp00760b] [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
In a certain period of Earth's history, chlorophylls with Mg as their central metal would have been selected as the major photosynthetic pigments, reflecting the radiation in habitats. Assuming evolution in different light and material environments, different photosynthetic pigments would occur. This study is the first attempt to evaluate the physical and chemical properties of model photosynthetic pigments and their potential to function in a variety of light environments using quantum chemistry calculations. Specifically, bacteriochlorophyll b (Bchl b), phthalocyanine (Pht) and meso-dibenzoporphycene (mDBPc) were selected as template molecules, while Be, Mg, Ca, Ni, Zn, Sr, Pd, Cd, Ba, Pt, Hg, Pb and H2 were examined as the central metals in each molecule in various solvents. The results showed that the light absorption by each of these compounds varied over a range of 100 nm depending on the central metal and the surrounding solvent, and Pb produced the largest red shift in the absorption bands of all three photosynthetic pigments. The Pht molecules showed similar redox properties to the chlorophylls, suggesting that these derivatives could be substituted for the special pairs in reaction centers, while the mDBPc molecules appear to be more suitable as accessory pigments due to their extraordinarily broad absorption ranges of approximately 500 nm depending on the conditions.
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Affiliation(s)
- Yu Komatsu
- AstroBiology Center, Osawa 2-21-1, Mitaka, Tokyo, Japan. and National Astronomical Observatory of Japan, Osawa 2-21-1, Mitaka, Tokyo, Japan
| | - Kenji Takizawa
- AstroBiology Center, Osawa 2-21-1, Mitaka, Tokyo, Japan. and National Institute for Basic Biology, Nishigonaka 38, Myodaiji, Okazaki, Aichi, Japan
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39
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Li M, Reimers JR, Ford MJ, Kobayashi R, Amos RD. Accurate prediction of the properties of materials using the CAM-B3LYP density functional. J Comput Chem 2021; 42:1486-1497. [PMID: 34013573 DOI: 10.1002/jcc.26558] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2021] [Revised: 04/21/2021] [Accepted: 04/26/2021] [Indexed: 12/25/2022]
Abstract
Density functionals with asymptotic corrections to the long-range potential provide entry-level methods for calculations on molecules that can sustain charge transfer, but similar applications in materials science are rare. We describe an implementation of the CAM-B3LYP range-separated functional within the Vienna Ab-initio Simulation Package (VASP) framework, together with its analytical functional derivatives. Results obtained for eight representative materials: aluminum, diamond, graphene, silicon, NaCl, MgO, 2D h-BN, and 3D h-BN, indicate that CAM-B3LYP predictions embody mean-absolute deviations (MAD) compared to HSE06 that are reduced by a factor of six for lattice parameters, four for quasiparticle band gaps, three for the lowest optical excitation energies, and six for exciton binding energies. Further, CAM-B3LYP appears competitive compared to ab initio G0 W0 and Bethe-Salpeter equation approaches. The CAM-B3LYP implementation in VASP was verified by comparison of optimized geometries and reaction energies for isolated molecules taken from the ACCDB database, evaluated in large periodic unit cells, to analogous results obtained using Gaussian basis sets. Using standard GW pseudopotentials and energy cutoffs for the plane-wave calculations and the aug-cc-pV5Z basis set for the atomic-basis ones, the MAD in energy for 1738 chemical reactions was 0.34 kcal mol-1 , while for 480 unique bond lengths this was 0.0036 Å; these values reduced to 0.28 kcal mol-1 (largest error 0.94 kcal mol-1 ) and 0.0009 Å by increasing the plane-wave cutoff energy to 850 eV.
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Affiliation(s)
- Musen Li
- International Centre for Quantum and Molecular Structures and Department of Physics, Shanghai University, Shanghai, China
| | - Jeffrey R Reimers
- International Centre for Quantum and Molecular Structures and Department of Physics, Shanghai University, Shanghai, China.,School of Mathematical and Physical Sciences, University of Technology Sydney, Ultimo, Australia
| | - Michael J Ford
- School of Mathematical and Physical Sciences, University of Technology Sydney, Ultimo, Australia
| | - Rika Kobayashi
- ANU Supercomputer Facility, Leonard Huxley Building 56, Mills Rd, Acton, ACT, 2601, Australia
| | - Roger D Amos
- ANU Supercomputer Facility, Leonard Huxley Building 56, Mills Rd, Acton, ACT, 2601, Australia
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40
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Dunlop D, Večeřa M, Gyepes R, Kubát P, Lang K, Horáček M, Pinkas J, Šimková L, Liška A, Lamač M. Luminescent Cationic Group 4 Metallocene Complexes Stabilized by Pendant N-Donor Groups. Inorg Chem 2021; 60:7315-7328. [PMID: 33945274 DOI: 10.1021/acs.inorgchem.1c00461] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
Cationic group 4 metallocene complexes with pendant imine and pyridine donor groups were prepared as stable crystalline [B(C6F5)4]- salts either by protonation of the intramolecularly bound ketimide moiety in neutral complexes [(η5-C5Me5){η5-C5H4CMe2CMe2C(R)═N-κN}MCl] (M = Ti, Zr, Hf; R = t-Bu, Ph) by PhNMe2H+[B(C6F5)4]- to give [(η5-C5Me5){η5-C5H4CMe2CMe2C(R)═NH-κN}MCl]+[B(C6F5)4]- or by chloride ligand abstraction from the complexes [(η5-C5Me5)(η5-C5H4CMe2CH2C5H4N)MCl2] (M = Ti, Zr) by Li[B(C6F5)4]·2.5Et2O to give [(η5-C5Me5)(η5-C5H4CMe2CH2C5H4N-κN)MCl]+[B(C6F5)4]-. Solid state structures of the new compounds were established by X-ray diffraction analysis, and their electrochemical behavior was studied by cyclic voltammetry. The cationic complexes of Zr and Hf, compared to the corresponding neutral species, exhibited significantly enhanced luminescence predominantly from triplet ligand-to-metal (3LMCT) excited states with lifetimes up to 62 μs and quantum yields up to 58% in the solid state. DFT calculations were performed to explain the structural features and optical and electrochemical properties of the complexes.
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Affiliation(s)
- David Dunlop
- J. Heyrovský Institute of Physical Chemistry of the Czech Academy of Sciences, Dolejškova 2155/3, 182 23 Praha 8, Czech Republic.,Department of Inorganic Chemistry, Faculty of Science, Charles University in Prague, Hlavova 2030, 128 40 Praha 2, Czech Republic
| | - Miloš Večeřa
- J. Heyrovský Institute of Physical Chemistry of the Czech Academy of Sciences, Dolejškova 2155/3, 182 23 Praha 8, Czech Republic
| | - Róbert Gyepes
- J. Heyrovský Institute of Physical Chemistry of the Czech Academy of Sciences, Dolejškova 2155/3, 182 23 Praha 8, Czech Republic.,Department of Inorganic Chemistry, Faculty of Science, Charles University in Prague, Hlavova 2030, 128 40 Praha 2, Czech Republic
| | - Pavel Kubát
- J. Heyrovský Institute of Physical Chemistry of the Czech Academy of Sciences, Dolejškova 2155/3, 182 23 Praha 8, Czech Republic
| | - Kamil Lang
- Institute of Inorganic Chemistry of the Czech Academy of Sciences, 250 68 Husinec-Řež, Czech Republic
| | - Michal Horáček
- J. Heyrovský Institute of Physical Chemistry of the Czech Academy of Sciences, Dolejškova 2155/3, 182 23 Praha 8, Czech Republic
| | - Jiří Pinkas
- J. Heyrovský Institute of Physical Chemistry of the Czech Academy of Sciences, Dolejškova 2155/3, 182 23 Praha 8, Czech Republic
| | - Ludmila Šimková
- J. Heyrovský Institute of Physical Chemistry of the Czech Academy of Sciences, Dolejškova 2155/3, 182 23 Praha 8, Czech Republic
| | - Alan Liška
- J. Heyrovský Institute of Physical Chemistry of the Czech Academy of Sciences, Dolejškova 2155/3, 182 23 Praha 8, Czech Republic
| | - Martin Lamač
- J. Heyrovský Institute of Physical Chemistry of the Czech Academy of Sciences, Dolejškova 2155/3, 182 23 Praha 8, Czech Republic
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41
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Kang H, Ye J, Wang H, Zhang Y, Qiu Y. DFT study of effect of substituents on second-order NLO response of novel BODIPY dyes. Theor Chem Acc 2021. [DOI: 10.1007/s00214-021-02758-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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42
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Coppola F, Cimino P, Raucci U, Chiariello MG, Petrone A, Rega N. Exploring the Franck-Condon region of a photoexcited charge transfer complex in solution to interpret femtosecond stimulated Raman spectroscopy: excited state electronic structure methods to unveil non-radiative pathways. Chem Sci 2021; 12:8058-8072. [PMID: 34194695 PMCID: PMC8208128 DOI: 10.1039/d1sc01238j] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2021] [Accepted: 04/27/2021] [Indexed: 01/12/2023] Open
Abstract
We present electronic structure methods to unveil the non-radiative pathways of photoinduced charge transfer (CT) reactions that play a main role in photophysics and light harvesting technologies. A prototypical π-stacked molecular complex consisting of an electron donor (1-chloronaphthalene, 1ClN) and an electron acceptor (tetracyanoethylene, TCNE) was investigated in dichloromethane solution for this purpose. The characterization of TCNE:π:1ClN in both its equilibrium ground and photoinduced low-lying CT electronic states was performed by using a reliable and accurate theoretical-computational methodology exploiting ab initio molecular dynamics simulations. The structural and vibrational time evolution of key vibrational modes is found to be in excellent agreement with femtosecond stimulated Raman spectroscopy experiments [R. A. Mathies et al., J. Phys. Chem. A, 2018, 122, 14, 3594], unveiling a correlation between vibrational fingerprints and electronic properties. The evaluation of nonadiabatic coupling matrix elements along generalized normal modes has made possible the interpretation on the molecular scale of the activation of nonradiative relaxation pathways towards the ground electronic state. In particular, two low frequency vibrational modes such as the out of plane bending and dimer breathing and the TCNE central C[double bond, length as m-dash]C stretching play a prominent role in relaxation phenomena from the electronic CT state to the ground state one.
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Affiliation(s)
- Federico Coppola
- Department of Chemical Sciences, University of Napoli Federico II, Complesso Universitario di M.S. Angelo via Cintia Napoli 80126 Italy
| | - Paola Cimino
- Department of Pharmaceutical Sciences, University of Salerno Salerno 84084 Italy
| | - Umberto Raucci
- Department of Chemical Sciences, University of Napoli Federico II, Complesso Universitario di M.S. Angelo via Cintia Napoli 80126 Italy
| | - Maria Gabriella Chiariello
- Department of Chemical Sciences, University of Napoli Federico II, Complesso Universitario di M.S. Angelo via Cintia Napoli 80126 Italy
| | - Alessio Petrone
- Department of Chemical Sciences, University of Napoli Federico II, Complesso Universitario di M.S. Angelo via Cintia Napoli 80126 Italy
| | - Nadia Rega
- Department of Chemical Sciences, University of Napoli Federico II, Complesso Universitario di M.S. Angelo via Cintia Napoli 80126 Italy
- Centro Interdipartimentale di Ricerca sui Biomateriali (CRIB) Piazzale Tecchio Napoli I-80125 Italy
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43
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Muya JT, Donald KJ, Ceulemans A, Parish C. A comparison of the chemical bonding and reactivity of Si 8H 8O 12 and Ge 8H 8O 12: A theoretical study. J Chem Phys 2021; 154:164305. [PMID: 33940821 DOI: 10.1063/5.0046059] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
We have analyzed the chemical bonding and reactivity in the cubic molecule octahydridosilsesquioxane, Si8H8O12, and its counterpart Ge8H8O12 by means of ab initio quantum chemical methods and group theory. Density functional theory and MP2 methods combined with the basis sets 6-311+G(d) and 6-311++G(2d,p) were used for geometry optimization and vibrational frequency analysis. The geometries of Si8H8O12 and Ge8H8O12 are unstable under Oh symmetry and distort to the rare Th molecular symmetry. The energy gained from this pseudo-Jahn-Teller distortion ranges from 0.78 to 6.14 kcal mol-1 depending on methodological treatment. The Fukui functions and the molecular electrostatic potential were both used as DFT-based reactivity descriptors. Our study shows that Si8H8O12 and Ge8H8O12 are both hard amphoteric molecules. The cavity within each cage is acidic and able to encapsulate hard small bases such as F-. The exterior of the cages is basic and can form stable exohedral complexes with hard acids, as in the case of H+. The insertion of F- in Si8H8O12 and Ge8H8O12 cages gives the most stable endohedral complexes of the series studied, characterized by formation energies of -3.50 and -3.45 eV at CAM-B3LYP/6-311+G(d) and -3.61 and -3.68 eV at the MP2/6-311++G(d,p) level, respectively. The calculated formation energies of the exohedral and endohedral complexes align with the DFT reactivity descriptor analysis.
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Affiliation(s)
- Jules Tshishimbi Muya
- Department of Chemistry, Faculty of Sciences, University of Kinshasa, Kinshasa, DR Congo and Research Center for Theoretical Chemistry and Physics in Central Africa, Faculty of Science, University of Kinshasa, Kinshasa, DR Congo
| | - Kelling J Donald
- Department of Chemistry, University of Richmond, Richmond, Virginia 23173, USA
| | | | - Carol Parish
- Department of Chemistry, University of Richmond, Richmond, Virginia 23173, USA
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44
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Brütting M, Foerster JM, Kümmel S. Investigating Primary Charge Separation in the Reaction Center of Heliobacterium modesticaldum. J Phys Chem B 2021; 125:3468-3475. [PMID: 33788561 DOI: 10.1021/acs.jpcb.0c10283] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
We compute the primary charge separation step in the homodimeric reaction center (RC) of Heliobacterium modesticaldum from first principles. Using time-dependent density functional theory with the optimally tuned range-separated hybrid functional ωPBE, we calculate the excitations of a system comprising the special pair, the adjacent accessory bacteriochlorophylls, and the most relevant parts of the surrounding protein environment. The structure of the excitation spectrum can be rationalized from coupling of the individual bacteriochlorophyll pigments similar to molecular J- and H-aggregates. We find excited states corresponding to forward-charge transfer along the individual branches of the RC of H. modesticaldum. In the spectrum, these are located at an energy between the coupled Qy and Qx transitions. With ab initio Born-Oppenheimer molecular dynamics simulations, we reveal the influence of thermal vibrations on the excited states. The results show that the energy gap between the coupled Qy and the forward-charge transfer excitations is ∼0.4 eV, which we consider to conflict with the concept of a direct transfer mechanism. Our calculations, however, reveal a certain spectral overlap of the forward-charge transfer and the coupled Qx excitations. The reliability and robustness of the results are demonstrated by several numerical tests.
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45
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Tuning Single-Molecule Conductance by Controlled Electric Field-Induced trans-to-cis Isomerisation. APPLIED SCIENCES-BASEL 2021. [DOI: 10.3390/app11083317] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
External electric fields (EEFs) have proven to be very efficient in catalysing chemical reactions, even those inaccessible via wet-chemical synthesis. At the single-molecule level, oriented EEFs have been successfully used to promote in situ single-molecule reactions in the absence of chemical catalysts. Here, we elucidate the effect of an EEFs on the structure and conductance of a molecular junction. Employing scanning tunnelling microscopy break junction (STM-BJ) experiments, we form and electrically characterize single-molecule junctions of two tetramethyl carotene isomers. Two discrete conductance signatures show up more prominently at low and high applied voltages which are univocally ascribed to the trans and cis isomers of the carotenoid, respectively. The difference in conductance between both cis-/trans- isomers is in concordance with previous predictions considering π-quantum interference due to the presence of a single gauche defect in the trans isomer. Electronic structure calculations suggest that the electric field polarizes the molecule and mixes the excited states. The mixed states have a (spectroscopically) allowed transition and, therefore, can both promote the cis-isomerization of the molecule and participate in electron transport. Our work opens new routes for the in situ control of isomerisation reactions in single-molecule contacts.
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46
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Switching Ion Binding Selectivity of Thiacalix[4]arene Monocrowns at Liquid-Liquid and 2D-Confined Interfaces. Int J Mol Sci 2021; 22:ijms22073535. [PMID: 33805474 PMCID: PMC8038083 DOI: 10.3390/ijms22073535] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2021] [Revised: 03/23/2021] [Accepted: 03/25/2021] [Indexed: 11/23/2022] Open
Abstract
Understanding the interaction of ions with organic receptors in confined space is of fundamental importance and could advance nanoelectronics and sensor design. In this work, metal ion complexation of conformationally varied thiacalix[4]monocrowns bearing lower-rim hydroxy (type I), dodecyloxy (type II), or methoxy (type III) fragments was evaluated. At the liquid–liquid interface, alkylated thiacalixcrowns-5(6) selectively extract alkali metal ions according to the induced-fit concept, whereas crown-4 receptors were ineffective due to distortion of the crown-ether cavity, as predicted by quantum-chemical calculations. In type-I ligands, alkali-metal ion extraction by the solvent-accessible crown-ether cavity was prevented, which resulted in competitive Ag+ extraction by sulfide bridges. Surprisingly, amphiphilic type-I/II conjugates moderately extracted other metal ions, which was attributed to calixarene aggregation in salt aqueous phase and supported by dynamic light scattering measurements. Cation–monolayer interactions at the air–water interface were monitored by surface pressure/potential measurements and UV/visible reflection–absorption spectroscopy. Topology-varied selectivity was evidenced, towards Sr2+ (crown-4), K+ (crown-5), and Ag+ (crown-6) in type-I receptors and Na+ (crown-4), Ca2+ (crown-5), and Cs+ (crown-6) in type-II receptors. Nuclear magnetic resonance and electronic absorption spectroscopy revealed exocyclic coordination in type-I ligands and cation–π interactions in type-II ligands.
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47
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Lahav Y, Noy D, Schapiro I. Spectral tuning of chlorophylls in proteins - electrostatics vs. ring deformation. Phys Chem Chem Phys 2021; 23:6544-6551. [PMID: 33690760 DOI: 10.1039/d0cp06582j] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
In photosynthetic complexes, tuning of chlorophyll light-absorption spectra by the protein environment is crucial to their efficiency and robustness. Recombinant type II water soluble chlorophyll-binding proteins from Brassicaceae (WSCPs) are useful for studying spectral tuning mechanisms due to their symmetric homotetramer structure, and the ability to rigorously modify the chlorophyll's protein surroundings. Our previous comparison of the crystal structures of two WSCP homologues suggested that protein-induced chlorophyll ring deformation is the predominant spectral tuning mechanism. Here, we implement a more rigorous analysis based on hybrid quantum mechanics and molecular mechanics calculations to quantify the relative contributions of geometrical and electrostatic factors to the absorption spectra of WSCP-chlorophyll complexes. We show that when considering conformational dynamics, geometry distortions such as chlorophyll ring deformation accounts for about one-third of the spectral shift, whereas the direct polarization of the electron density accounts for the remaining two-thirds. From a practical perspective, protein electrostatics is easier to manipulate than chlorophyll conformations, thus, it may be more readily implemented in designing artificial protein-chlorophyll complexes.
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Affiliation(s)
- Yigal Lahav
- Fritz Haber Centre for Molecular Dynamics Research, Institute of Chemistry, Hebrew University of Jerusalem, Israel.
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48
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Non-conservative circular dichroism of photosystem II reaction centers: Is there an enhancement by a coupling with charge transfer states? J Photochem Photobiol A Chem 2021. [DOI: 10.1016/j.jphotochem.2020.112883] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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49
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Araújo JR, de Andrade RB, Batista HJ, Ventura E, do Monte SA. Can a gas phase contact ion pair containing a hydrocarbon carbocation be formed in the ground state? RSC Adv 2021; 11:4221-4230. [PMID: 35424376 PMCID: PMC8694316 DOI: 10.1039/d0ra10523f] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2020] [Accepted: 01/11/2021] [Indexed: 11/21/2022] Open
Abstract
So far, no conclusive evidence of a ground-state contact ion-pair containing a hydrocarbon carbocation has been given in the gas phase.
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Affiliation(s)
- José R. Araújo
- Departamento de Química
- CCEN
- Universidade Federal da Paraíba
- João Pessoa
- Brazil
| | | | - Hélcio J. Batista
- Departamento de Química
- Universidade Federal Rural de Pernambuco
- Recife
- Brazil
| | - Elizete Ventura
- Departamento de Química
- CCEN
- Universidade Federal da Paraíba
- João Pessoa
- Brazil
| | - Silmar A. do Monte
- Departamento de Química
- CCEN
- Universidade Federal da Paraíba
- João Pessoa
- Brazil
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50
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Reimers JR, Rätsep M, Freiberg A. Asymmetry in the Q y Fluorescence and Absorption Spectra of Chlorophyll a Pertaining to Exciton Dynamics. Front Chem 2020; 8:588289. [PMID: 33344415 PMCID: PMC7738624 DOI: 10.3389/fchem.2020.588289] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2020] [Accepted: 10/26/2020] [Indexed: 11/13/2022] Open
Abstract
Significant asymmetry found between the high-resolution Qy emission and absorption spectra of chlorophyll-a is herein explained, providing basic information needed to understand photosynthetic exciton transport and photochemical reactions. The Qy spectral asymmetry in chlorophyll has previously been masked by interference in absorption from the nearby Qx transition, but this effect has recently been removed using extensive quantum spectral simulations or else by analytical inversion of absorption and magnetic circular dichroism data, allowing high-resolution absorption information to be accurately determined from fluorescence-excitation spectra. To compliment this, here, we measure and thoroughly analyze the high-resolution differential fluorescence line narrowing spectra of chlorophyll-a in trimethylamine and in 1-propanol. The results show that vibrational frequencies often change little between absorption and emission, yet large changes in line intensities are found, this effect also being strongly solvent dependent. Among other effects, the analysis in terms of four basic patterns of Duschinsky-rotation matrix elements, obtained using CAM-B3LYP calculations, predicts that a chlorophyll-a molecule excited into a specific vibrational level, may, without phase loss or energy relaxation, reemit the light over a spectral bandwidth exceeding 1,000 cm−1 (0.13 eV) to influence exciton-transport dynamics.
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Affiliation(s)
- Jeffrey R Reimers
- School of Chemistry, The University of Sydney, Sydney, NSW, Australia
| | - Margus Rätsep
- Institute of Physics, University of Tartu, Tartu, Estonia
| | - Arvi Freiberg
- Institute of Physics, University of Tartu, Tartu, Estonia.,Institute of Molecular and Cell Biology, University of Tartu, Tartu, Estonia
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