1
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Xu P, Wang D, Li D, Long J, Zhang S, Zhang B. UV wavelength-dependent photoionization quantum yields for the dark 1nπ* state of aqueous thymidine. Phys Chem Chem Phys 2024. [PMID: 39229763 DOI: 10.1039/d4cp02594f] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/05/2024]
Abstract
Despite the important role of the dark 1nπ* state in the photostability of thymidine in aqueous solution, no detailed ultraviolet (UV) wavelength-dependent investigation of the 1nπ* quantum yield (QY) in aqueous thymidine has been experimentally performed. Here, we investigate the wavelength-dependent photoemission spectra of aqueous thymidine from 266.7 to 240 nm using liquid-microjet photoelectron spectroscopy. Two observed ionization channels are assigned to resonant ionizations from 1ππ* to the cationic ground state D0 (π-1) and 1nπ* to the cationic excited state D1 (n-1). The weak 1nπ* → D1 ionization channel appears due to ultrafast 1ππ* → 1nπ* internal conversion within the pulse duration of ∼180 fs. The obtained 1nπ* quantum yields exhibit a strong wavelength dependence, ranging from 0 to 0.27 ± 0.01, suggesting a hitherto uncharacterized 1nπ* feature. The corresponding vertical ionization energies (VIEs) of D0 and D1 of aqueous thymidine are experimentally determined to be 8.47 ± 0.12 eV and 9.22 ± 0.29 eV, respectively. Our UV wavelength-dependent QYs might indicate that different structural critical points to connect the multidimensional 1ππ*/1nπ* conical intersection seam onto the multidimensional potential energy surface of the 1ππ* state might exist and determine the relaxation processes of aqueous thymidine upon UV excitation.
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Affiliation(s)
- Piao Xu
- State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics, Innovation Academy for Precision Measurement Science and Technology, Chinese Academy of Sciences, Wuhan 430071, China.
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Dongdong Wang
- State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics, Innovation Academy for Precision Measurement Science and Technology, Chinese Academy of Sciences, Wuhan 430071, China.
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Duoduo Li
- State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics, Innovation Academy for Precision Measurement Science and Technology, Chinese Academy of Sciences, Wuhan 430071, China.
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Jinyou Long
- State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics, Innovation Academy for Precision Measurement Science and Technology, Chinese Academy of Sciences, Wuhan 430071, China.
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Song Zhang
- State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics, Innovation Academy for Precision Measurement Science and Technology, Chinese Academy of Sciences, Wuhan 430071, China.
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Bing Zhang
- State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics, Innovation Academy for Precision Measurement Science and Technology, Chinese Academy of Sciences, Wuhan 430071, China.
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2
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Lizondo-Aranda P, Gustavsson T, Martínez-Fernández L, Improta R, Lhiaubet-Vallet V. The Excited State Dynamics of a Mutagenic Guanosine Etheno Adduct Investigated by Femtosecond Fluorescence Spectroscopy and Quantum Mechanical Calculations. Chemistry 2024; 30:e202401835. [PMID: 38869969 DOI: 10.1002/chem.202401835] [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: 05/10/2024] [Revised: 06/13/2024] [Accepted: 06/13/2024] [Indexed: 06/15/2024]
Abstract
Femtosecond fluorescence upconversion experiments were combined with CASPT2 and time dependent DFT calculations to characterize the excited state dynamics of the mutagenic etheno adduct 1,N2-etheno-2'-deoxyguanosine (ϵdG). This endogenously formed lesion is attracting great interest because of its ubiquity in human tissues and its highly mutagenic properties. The ϵdG fluorescence is strongly modified with respect to that of the canonical nucleoside dG, notably by an about 6-fold increase in fluorescence lifetime and quantum yield at neutral pH. In addition, femtosecond fluorescence upconversion experiments reveal the presence of two emission bands with maxima at 335 nm for the shorter-lived and 425 nm for the longer-lived. Quantum mechanical calculations rationalize these findings and provide absorption and fluorescence spectral shapes similar to the experimental ones. Two different bright minima are located on the potential energy surface of the lowest energy singlet excited state. One planar minimum, slightly more stable, is associated with the emission at 335 nm, whereas the other one, with a bent etheno ring, is associated with the red-shifted emission.
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Affiliation(s)
- Paloma Lizondo-Aranda
- Instituto Universitario Mixto de Tecnología Química (UPV-CSIC), Universitat Politècnica de Valencia, Consejo Superior de Investigaciones Científicas, Avda de los Naranjos s/n, Valencia, 46022, Spain
| | | | - Lara Martínez-Fernández
- Departamento de Química Física de Materiales, Instituto de Química Física Blas Cabrera, IQF-CSIC, Calle Serrano 119, 28006, Madrid, Spain
| | - Roberto Improta
- Istituto di Biostrutture e Bioimmagini, Consiglio Nazionale delle Ricerche, Via De Amicis 95, I-80145, Napoli, Italy
| | - Virginie Lhiaubet-Vallet
- Instituto Universitario Mixto de Tecnología Química (UPV-CSIC), Universitat Politècnica de Valencia, Consejo Superior de Investigaciones Científicas, Avda de los Naranjos s/n, Valencia, 46022, Spain
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3
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Ferreras KN, Gordon MS. A Merger of the Spin-Flip ORMAS Approach and the MC-PDFT Method. J Chem Theory Comput 2024; 20:5487-5496. [PMID: 38916956 DOI: 10.1021/acs.jctc.4c00322] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/27/2024]
Abstract
The SF-ORMAS-PDFT (spin-flip occupation restricted multiple active space-pair density functional theory) approach combines the SF-ORMAS-CI method with the MC-PDFT method to treat both static and dynamic correlation in multiconfigurational systems. The static correlation description is generated via the spin-flip approach, which uses a high-spin single reference determinant to treat excited states with multiconfigurational characters. The on-top pair density functional theory uses a translation scheme applied to GGA density functionals. The SF-ORMAS-PDFT scheme has also been combined with virtual valence orbitals (VVO), a well-defined subspace of the virtual molecular orbitals, giving rise to significant speedups relative to the use of the full virtual space. The accuracy of the SF-ORMAS-PDFT method is tested by calculating 65 vertical excitation energies of 12 small- and medium-sized organic molecules. The SF-ORMAS-PDFT vertical excitation energies calculated with VVOs are comparable to those calculated with the full virtual space. The SF-ORMAS-PDFT/6-31G(d) level of theory predicts the rotational barrier of ethylene to be 65.5 and 65.9 kcal/mol, with full virtual space and VVOs, respectively. These predicted barrier heights compare well with the experimental value of 65 kcal/mol.
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Affiliation(s)
- Katherine N Ferreras
- Department of Chemistry, Iowa State University and Ames National Laboratory, Ames, Iowa 50011, United States
| | - Mark S Gordon
- Department of Chemistry, Iowa State University and Ames National Laboratory, Ames, Iowa 50011, United States
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4
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Stolar T, Pearce BK, Etter M, Truong KN, Ostojić T, Krajnc A, Mali G, Rossi B, Molčanov K, Lončarić I, Meštrović E, Užarević K, Grisanti L. Base-pairing of uracil and 2,6-diaminopurine: from cocrystals to photoreactivity. iScience 2024; 27:109894. [PMID: 38783999 PMCID: PMC11112615 DOI: 10.1016/j.isci.2024.109894] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2023] [Revised: 12/18/2023] [Accepted: 05/01/2024] [Indexed: 05/25/2024] Open
Abstract
We show that the non-canonical nucleobase 2,6-diaminopurine (D) spontaneously base pairs with uracil (U) in water and the solid state without the need to be attached to the ribose-phosphate backbone. Depending on the reaction conditions, D and U assemble in thermodynamically stable hydrated and anhydrated D-U base-paired cocrystals. Under UV irradiation, an aqueous solution of D-U base-pair undergoes photochemical degradation, while a pure aqueous solution of U does not. Our simulations suggest that D may trigger the U photodimerization and show that complementary base-pairing modifies the photochemical properties of nucleobases, which might have implications for prebiotic chemistry.
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Affiliation(s)
- Tomislav Stolar
- Ruđer Bošković Institute, Bijenička c. 54, 10000 Zagreb, Croatia
- Federal Institute for Materials Research and Testing (BAM), Richard-Willstätter-Straße 11, 12489 Berlin, Germany
| | - Ben K.D. Pearce
- Johns Hopkins University, 3400 N. Charles Street, Baltimore, MD 21218, USA
| | - Martin Etter
- Deutsches Elektronen-Synchrotron (DESY), Notkestraße 85, 22607 Hamburg, Germany
| | - Khai-Nghi Truong
- Rigaku Europe SE, Hugenottenallee 167, 63263 Neu-Isenburg, Germany
| | - Tea Ostojić
- Ruđer Bošković Institute, Bijenička c. 54, 10000 Zagreb, Croatia
| | - Andraž Krajnc
- National Institute of Chemistry, Hajdrihova 19, 1000 Ljubljana, Slovenia
| | - Gregor Mali
- National Institute of Chemistry, Hajdrihova 19, 1000 Ljubljana, Slovenia
| | - Barbara Rossi
- Elettra Sincrotrone Trieste, Strada Statale 14 km 163.5, 34149 Trieste, Italy
| | | | - Ivor Lončarić
- Ruđer Bošković Institute, Bijenička c. 54, 10000 Zagreb, Croatia
| | - Ernest Meštrović
- Faculty of Chemical Engineering and Technology, University of Zagreb, Trg Marka Marulića 19, 10000 Zagreb, Croatia
| | | | - Luca Grisanti
- Ruđer Bošković Institute, Bijenička c. 54, 10000 Zagreb, Croatia
- National Research Council - Materials Foundry Institute (CNR-IOM) c/o SISSA (International School for Advanced Studies), Via Bonomea 265, 34136 Trieste, Italy
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5
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Riera Aroche R, Ortiz García YM, Martínez Arellano MA, Riera Leal A. DNA as a perfect quantum computer based on the quantum physics principles. Sci Rep 2024; 14:11636. [PMID: 38773193 PMCID: PMC11109248 DOI: 10.1038/s41598-024-62539-5] [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: 02/01/2024] [Accepted: 05/17/2024] [Indexed: 05/23/2024] Open
Abstract
DNA is a complex multi-resolution molecule whose theoretical study is a challenge. Its intrinsic multiscale nature requires chemistry and quantum physics to understand the structure and quantum informatics to explain its operation as a perfect quantum computer. Here, we present theoretical results of DNA that allow a better description of its structure and the operation process in the transmission, coding, and decoding of genetic information. Aromaticity is explained by the oscillatory resonant quantum state of correlated electron and hole pairs due to the quantized molecular vibrational energy acting as an attractive force. The correlated pairs form a supercurrent in the nitrogenous bases in a single band π -molecular orbital ( π -MO). The MO wave function ( Φ ) is assumed to be the linear combination of the n constituent atomic orbitals. The central Hydrogen bond between Adenine (A) and Thymine (T) or Guanine (G) and Cytosine (C) functions like an ideal Josephson Junction. The approach of a Josephson Effect between two superconductors is correctly described, as well as the condensation of the nitrogenous bases to obtain the two entangled quantum states that form the qubit. Combining the quantum state of the composite system with the classical information, RNA polymerase teleports one of the four Bell states. DNA is a perfect quantum computer.
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Affiliation(s)
- R Riera Aroche
- Department of Research in Physics, University of Sonora, Hermosillo, Sonora, Mexico
- Research and Higher Education Center of UNEPROP, Hermosillo, Sonora, Mexico
| | - Y M Ortiz García
- Research Institute of Dentistry, University of Guadalajara, Guadalajara Jalisco, Mexico
- Research and Higher Education Center of UNEPROP, Hermosillo, Sonora, Mexico
| | - M A Martínez Arellano
- General Hospital of the State of Sonora, Boulevar José María Escrivá de Balaguer 157, Colonia Villa del Palmar, C.P. 83105, Hermosillo, Sonora, Mexico
- Research and Higher Education Center of UNEPROP, Hermosillo, Sonora, Mexico
| | - A Riera Leal
- General Hospital of the State of Sonora, Boulevar José María Escrivá de Balaguer 157, Colonia Villa del Palmar, C.P. 83105, Hermosillo, Sonora, Mexico.
- Research and Higher Education Center of UNEPROP, Hermosillo, Sonora, Mexico.
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6
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Ishida K, Onoda Y, Kadomura-Ishikawa Y, Nagahashi M, Yamashita M, Fukushima S, Aizawa T, Yamauchi S, Fujikawa Y, Tanaka T, Uebanso T, Akutagawa M, Mawatari K, Takahashi A. Development of a standard evaluation method for microbial UV sensitivity using light-emitting diodes. Heliyon 2024; 10:e27456. [PMID: 38509990 PMCID: PMC10951525 DOI: 10.1016/j.heliyon.2024.e27456] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2023] [Revised: 01/17/2024] [Accepted: 02/29/2024] [Indexed: 03/22/2024] Open
Abstract
Ultraviolet (UV) light is an effective disinfection method. In particular, UV light-emitting diodes (UV-LEDs) are expected to have many applications as light sources owing to their compact form factor and wide range of choices of wavelengths. However, the UV sensitivity of microorganisms for each UV wavelength has not been evaluated comprehensively because standard experimental conditions based on LED characteristics have not been established. Therefore, it is necessary to establish a standard evaluation method based on LED characteristics. Here, we developed a new UV-LED device based on strictly controlled irradiation conditions using LEDs for each wavelength (250-365 nm), checked the validity of the device characteristics and evaluated the UV sensitivity of Escherichia coli using this new evaluation method. For this new device, we considered accurate irradiance, accurate spectra, irradiance uniformity, accurate dose, beam angle, surrounding material reflections, and sample condition. From our results, the following UV irradiation conditions were established as standard: 1 mW/cm2 irradiance, bacterial solution with absorbance value of A600 = 0.5 diluted 10 times solution, solution volume of 1 mL, working distance (WD) of 100 mm. In order to compare the effects of irradiation under uniform conditions on inactivation of microorganisms, we assessed inactivation effect of E. coli by LED irradiation at each wavelength using the U280 LED as a standard wavelength. The inactivation effect for U280 LED irradiation was -0.95 ± 0.21 log at a dose of 4 mJ/cm2. Under this condition of dose, our results showed a high wavelength dependence of the inactivation effect at each UV wavelength peaking at 267 nm. Our study showed that this irradiation system was validated for the standard UV irradiation system and could be contributed to the establishment of food and water hygiene control methods and the development of equipment for the prevention of infectious diseases.
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Affiliation(s)
- Kai Ishida
- Department of Microbial Control, Institute of Biomedical Sciences, Tokushima University Graduate School, Tokushima, Japan
| | - Yushi Onoda
- Department of Microbial Control, Institute of Biomedical Sciences, Tokushima University Graduate School, Tokushima, Japan
- Nichia Corporation, Tokushima, Japan
| | - Yasuko Kadomura-Ishikawa
- Department of Microbial Control, Institute of Biomedical Sciences, Tokushima University Graduate School, Tokushima, Japan
| | - Miharu Nagahashi
- Department of Preventive Environment and Nutrition, Institute of Biomedical Sciences, Tokushima University Graduate School, Tokushima, Japan
| | - Michiyo Yamashita
- Department of Preventive Environment and Nutrition, Institute of Biomedical Sciences, Tokushima University Graduate School, Tokushima, Japan
| | - Shiho Fukushima
- Department of Preventive Environment and Nutrition, Institute of Biomedical Sciences, Tokushima University Graduate School, Tokushima, Japan
| | | | | | | | | | - Takashi Uebanso
- Department of Microbial Control, Institute of Biomedical Sciences, Tokushima University Graduate School, Tokushima, Japan
- Department of Preventive Environment and Nutrition, Institute of Biomedical Sciences, Tokushima University Graduate School, Tokushima, Japan
| | - Masatake Akutagawa
- Department of Electrical and Electronic Engineering, Graduate School of Technology, Industrial and Social Sciences, University of Tokushima, Tokushima, Japan
| | - Kazuaki Mawatari
- Department of Microbial Control, Institute of Biomedical Sciences, Tokushima University Graduate School, Tokushima, Japan
- Department of Preventive Environment and Nutrition, Institute of Biomedical Sciences, Tokushima University Graduate School, Tokushima, Japan
| | - Akira Takahashi
- Department of Microbial Control, Institute of Biomedical Sciences, Tokushima University Graduate School, Tokushima, Japan
- Department of Preventive Environment and Nutrition, Institute of Biomedical Sciences, Tokushima University Graduate School, Tokushima, Japan
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7
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Cui E, Liu H, Wang Z, Chen H, Weng YX. Femtosecond fluorescence conical optical parametric amplification spectroscopy. THE REVIEW OF SCIENTIFIC INSTRUMENTS 2024; 95:033008. [PMID: 38517256 DOI: 10.1063/5.0197254] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/12/2024] [Accepted: 02/29/2024] [Indexed: 03/23/2024]
Abstract
Parametric superfluorescence (PSF), which originated from the optical amplification of vacuum quantum noise, is the primary noise source of femtosecond fluorescence non-collinear optical parametric amplification spectroscopy (FNOPAS). It severely affects the detection limit of FNOPAS to collect the femtosecond time-resolved spectra of extremely weak fluorescence. Here, we report the development of femtosecond fluorescence conical optical parametric amplification spectroscopy (FCOPAS), aimed at effectively suppressing the noise fluctuation from the PSF background. In contrast to traditional FNOPAS configurations utilizing lateral fluorescence collection and dot-like parametric amplification, FCOPAS employs an innovative conical fluorescence collection and ring-like amplification setup. This design enables effective cancellation of noise fluctuation across the entire PSF ring, resulting in an approximate order of magnitude reduction in PSF noise compared to prior FNOPAS outcomes. This advancement enables the resolution of transient fluorescence spectra of 4-dicyanomethylene-2-methyl-6-p-dimethylaminostyryl-4H-pyran (DCM) dye molecules in ethanol, even at an optically dilute concentration of 10-6 mol/l, with significantly enhanced signal-to-noise ratios. This improvement will be significant for extremely weak fluorescence detection on the femtosecond time scale.
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Affiliation(s)
- Ennan Cui
- The Laboratory of Soft Matter Physics, Beijing National Laboratory for Condensed Matter Physics, Institute of Physics, Chinese Academy of Sciences, Beijing 100190, China
- School of Physical Science, University of the Chinese Academy of Sciences, Beijing 100049, China
| | - Heyuan Liu
- The Laboratory of Soft Matter Physics, Beijing National Laboratory for Condensed Matter Physics, Institute of Physics, Chinese Academy of Sciences, Beijing 100190, China
- School of Physical Science, University of the Chinese Academy of Sciences, Beijing 100049, China
| | - Zhuan Wang
- The Laboratory of Soft Matter Physics, Beijing National Laboratory for Condensed Matter Physics, Institute of Physics, Chinese Academy of Sciences, Beijing 100190, China
| | - Hailong Chen
- The Laboratory of Soft Matter Physics, Beijing National Laboratory for Condensed Matter Physics, Institute of Physics, Chinese Academy of Sciences, Beijing 100190, China
- School of Physical Science, University of the Chinese Academy of Sciences, Beijing 100049, China
- Songshan Lake Materials Laboratory, Dongguan, Guangdong 523808, China
| | - Yu-Xiang Weng
- The Laboratory of Soft Matter Physics, Beijing National Laboratory for Condensed Matter Physics, Institute of Physics, Chinese Academy of Sciences, Beijing 100190, China
- School of Physical Science, University of the Chinese Academy of Sciences, Beijing 100049, China
- Songshan Lake Materials Laboratory, Dongguan, Guangdong 523808, China
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8
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Mayer D, Lever F, Gühr M. Time-resolved x-ray spectroscopy of nucleobases and their thionated analogs. Photochem Photobiol 2024; 100:275-290. [PMID: 38174615 DOI: 10.1111/php.13903] [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: 11/06/2023] [Revised: 12/20/2023] [Accepted: 12/21/2023] [Indexed: 01/05/2024]
Abstract
The photoinduced relaxation dynamics of nucleobases and their thionated analogs have been investigated extensively over the past decades motivated by their crucial role in organisms and their application in medical and biochemical research and treatment. Most of these studies focused on the spectroscopy of valence electrons and fragmentation. The advent of ultrashort x-ray laser sources such as free-electron lasers, however, opens new opportunities for studying the ultrafast molecular relaxation dynamics utilizing the site- and element-selectivity of x-rays. In this review, we want to summarize ultrafast experiments on thymine and 2-thiouracil performed at free-electron lasers. We performed time-resolved x-ray absorption spectroscopy at the oxygen K-edge after UV excitation of thymine. In addition, we investigated the excited state dynamics of 2-tUra via x-ray photoelectron spectroscopy at sulfur. For these methods, we show a strong sensitivity to the electronic state or charge distribution, respectively. We also performed time-resolved Auger-Meitner spectroscopy, which shows spectral shifts associated with internuclear distances close to the probed site. We discuss the complementary aspects of time-resolved x-ray spectroscopy techniques compared to optical and UV spectroscopy for the investigation of ultrafast relaxation processes.
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Affiliation(s)
- Dennis Mayer
- Deutsches Elektronen-Synchrotron DESY, Hamburg, Germany
| | - Fabiano Lever
- Deutsches Elektronen-Synchrotron DESY, Hamburg, Germany
| | - Markus Gühr
- Deutsches Elektronen-Synchrotron DESY, Hamburg, Germany
- Institute of Physical Chemistry, University of Hamburg, Hamburg, Germany
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9
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Ma C, Xiong Q, Lin J, Zeng X, Wang M, Kwok WM. Is 1-methylcytosine a faithful model compound for ultrafast deactivation dynamics of cytosine nucleosides in solution? Phys Chem Chem Phys 2024; 26:2963-2972. [PMID: 38214513 DOI: 10.1039/d3cp05509d] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2024]
Abstract
1-Methylcytosine (1mCyt) is the base for nucleoside N1-methylpseudodeoxycytidine of Hachimoji nucleic acids and a frequently used model compound for theoretical studies on excited states of cytosine nucleosides. However, there is little experimental characterization of spectra and photo-dynamic properties of 1mCyt. Herein, we report a comprehensive investigation into excited state dynamics and effects of solvents on fluorescence dynamics of 1mCyt in both water and acetonitrile. The study employed femtosecond broadband time-resolved fluorescence, transient absorption, and steady-state spectroscopy, along with density functional theory and time-dependent density functional theory calculations. The results obtained provide the first experimental evidence for identifying a dark-natured ∼5.7 ps lifetime nπ* state in the ultrafast non-radiative deactivation with 1mCyt in aqueous solution. This study also demonstrates a significant effect of the solvent on 1mCyt's fluorescence emission, which highlights the crucial role of solute-solvent hydrogen bonding in altering structures and reshaping the radiative as well as nonradiative dynamics of the 1mCyt's ππ* state in the aprotic solvent compared to the protic solvent. The solvent effect exhibited by 1mCyt is distinctive from that known for deoxycytidine, indicating the need for caution in using 1mCyt for modelling the ultrafast dynamics of Cyt nucleosides in solvents with varying properties. Overall, our study unveils a deactivation mechanism that confers a high degree of photo-stability for 1mCyt in solution, shedding light on the molecular basis for solvent-induced effects on the excited state dynamics of nucleobases and derivatives.
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Affiliation(s)
- Chensheng Ma
- College of Chemistry and Environmental Engineering, Shenzhen University, Shenzhen, Guangdong, 518071, P. R. China.
| | - Qingwu Xiong
- College of Chemistry and Environmental Engineering, Shenzhen University, Shenzhen, Guangdong, 518071, P. R. China.
- College of Physics and optoelectronic Engineering, Shenzhen University, Shenzhen, Guangdong, P. R. China
| | - Jingdong Lin
- College of Chemistry and Environmental Engineering, Shenzhen University, Shenzhen, Guangdong, 518071, P. R. China.
| | - Xiaoyan Zeng
- College of Chemistry and Environmental Engineering, Shenzhen University, Shenzhen, Guangdong, 518071, P. R. China.
| | - Mingliang Wang
- College of Chemistry and Environmental Engineering, Shenzhen University, Shenzhen, Guangdong, 518071, P. R. China.
| | - Wai-Ming Kwok
- Department of Applied Biology and Chemical Technology, The Hong Kong Polytechnic University, Hung Hom, Kowloon, Hong Kong, 999077, P. R. China.
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10
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Bezabih MS, Kaliakin DS, Blanco-González A, Barneschi L, Tarnovsky AN, Olivucci M. Comparative Study of Uracil Excited-State Photophysics in Water and Acetonitrile via RMS-CASPT2-Driven Quantum-Classical Trajectories. J Phys Chem B 2023; 127:10871-10879. [PMID: 38055701 DOI: 10.1021/acs.jpcb.3c06433] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/08/2023]
Abstract
We present a nonadiabatic molecular dynamics study of the ultrafast processes occurring in uracil upon UV light absorption, leading to electronic excitation and subsequent nonradiative decay. Previous studies have indicated that the mechanistic details of this process are drastically different depending on whether the process takes place in the gas phase, acetonitrile, or water. However, such results have been produced using quantum chemical methods that did not incorporate both static and dynamic electron correlation. In order to assess the previously proposed mechanisms, we simulate the photodynamics of uracil in the three environments mentioned above using quantum-classical trajectories and, for solvated uracil, hybrid quantum mechanics/molecular mechanics (QM/MM) models driven by the rotated multistate complete active space second-order perturbation (RMS-CASPT2) method. To do so, we exploit the gradient recently made available in OpenMolcas and compare the results to those obtained using the complete active space self-consistent field (CASSCF) method only accounting for static electron correlation. We show that RMS-CASPT2 produces, in general, a mechanistic picture different from the one obtained at the CASSCF level but confirms the hypothesis advanced on the basis of previous ROKS and TDDFT studies thus highlighting the importance of incorporating dynamic electron correlation in the investigation of ultrafast electronic deactivation processes.
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Affiliation(s)
- Meseret Simachew Bezabih
- Department of Chemistry, Bowling Green State University, Bowling Green, Ohio 43403, United States
| | - Danil S Kaliakin
- Department of Chemistry, Bowling Green State University, Bowling Green, Ohio 43403, United States
| | | | - Leonardo Barneschi
- Dipartimento di Biotechnologie, Chimica e Farmacia, Università di Siena, I-53100 Siena, Italy
| | - Alexander N Tarnovsky
- Department of Chemistry, Bowling Green State University, Bowling Green, Ohio 43403, United States
| | - Massimo Olivucci
- Department of Chemistry, Bowling Green State University, Bowling Green, Ohio 43403, United States
- Dipartimento di Biotechnologie, Chimica e Farmacia, Università di Siena, I-53100 Siena, Italy
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11
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Gustin I, Kim CW, McCamant DW, Franco I. Mapping electronic decoherence pathways in molecules. Proc Natl Acad Sci U S A 2023; 120:e2309987120. [PMID: 38015846 PMCID: PMC10710033 DOI: 10.1073/pnas.2309987120] [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: 06/13/2023] [Accepted: 10/25/2023] [Indexed: 11/30/2023] Open
Abstract
Establishing the fundamental chemical principles that govern molecular electronic quantum decoherence has remained an outstanding challenge. Fundamental questions such as how solvent and intramolecular vibrations or chemical functionalization contribute to the decoherence remain unanswered and are beyond the reach of state-of-the-art theoretical and experimental approaches. Here we address this challenge by developing a strategy to isolate electronic decoherence pathways for molecular chromophores immersed in condensed phase environments that enables elucidating how electronic quantum coherence is lost. For this, we first identify resonance Raman spectroscopy as a general experimental method to reconstruct molecular spectral densities with full chemical complexity at room temperature, in solvent, and for fluorescent and non-fluorescent molecules. We then show how to quantitatively capture the decoherence dynamics from the spectral density and identify decoherence pathways by decomposing the overall coherence loss into contributions due to individual molecular vibrations and solvent modes. We illustrate the utility of the strategy by analyzing the electronic decoherence pathways of the DNA base thymine in water. Its electronic coherences decay in [Formula: see text]30 fs. The early-time decoherence is determined by intramolecular vibrations while the overall decay by solvent. Chemical substitution of thymine modulates the decoherence with hydrogen-bond interactions of the thymine ring with water leading to the fastest decoherence. Increasing temperature leads to faster decoherence as it enhances the importance of solvent contributions but leaves the early-time decoherence dynamics intact. The developed strategy opens key opportunities to establish the connection between molecular structure and quantum decoherence as needed to develop chemical strategies to rationally modulate it.
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Affiliation(s)
- Ignacio Gustin
- Department of Chemistry, University of Rochester, Rochester, NY14627
| | - Chang Woo Kim
- Department of Chemistry, Chonnam National University, Gwangju61186, South Korea
| | - David W. McCamant
- Department of Chemistry, University of Rochester, Rochester, NY14627
| | - Ignacio Franco
- Department of Chemistry, University of Rochester, Rochester, NY14627
- Department of Physics, University of Rochester, Rochester, NY14627
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12
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Zhao L, Geng X, Han G, Guo Y, Liu R, Chen J. Revealing the excited-state dynamics of cytidine and the role of excited-state proton transfer process. Phys Chem Chem Phys 2023; 25:32002-32009. [PMID: 37975722 DOI: 10.1039/d3cp03683a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2023]
Abstract
The high photostability of DNAs and RNAs is inextricably related to the photochemical and photophysical properties of their building blocks, nucleobases and nucleosides, which can dissipate the absorbed UV light energy in a harmless manner. The deactivation mechanism of the nucleosides, especially the decay pathways of cytidine (Cyd), has been a matter of intense debate. In the current study, we employ high-level electronic structure calculations combined with excited state non-adiabatic dynamic simulations to provide a clear picture of the excited state deactivation of Cyd in both gas phase and aqueous solution. In both environments, a barrierless decay path driven by the ring-puckering motion and a relaxation channel with a small energy barrier driven by the elongation motion of CO bond are assigned to <200 fs and sub-picosecond decay time component, respectively. The presence of ribose group has a subtle effect on the dynamic behavior of Cyd in gas phase as the ribose-to-base hydrogen/proton transfer process is energetically inaccessible with a sizable energy barrier of about 1.4 eV. However, this energy barrier is significantly reduced in water, especially when an explicit water molecule is present. Therefore, we argue that the long-lived decay channel found in aqueous solution could be assigned to the Cyd-water intermolecular hydrogen/proton transfer process. The present study postulates a novel scenario toward deep understanding the intrinsic photostability of DNAs and RNAs and provides solid evidence to disclose the long history debate of cytidine excited-state decay mechanism, especially for the assignment of experimentally observed time components.
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Affiliation(s)
- Li Zhao
- College of Science, China University of Petroleum (East China), Qingdao 266580, Shandong, China.
| | - Xuehui Geng
- College of Science, China University of Petroleum (East China), Qingdao 266580, Shandong, China.
| | - Guoxia Han
- College of Science, China University of Petroleum (East China), Qingdao 266580, Shandong, China.
| | - Yahui Guo
- College of Science, China University of Petroleum (East China), Qingdao 266580, Shandong, China.
| | - Runze Liu
- Institute of Molecular Sciences and Engineering, Shandong University, Qingdao 266235, P. R. China
| | - Junsheng Chen
- Nano-Science Center & Department of Chemistry, University of Copenhagen, Universitetsparken 5, 2100 KøbenhavnØ, Denmark.
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13
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Martins da Silva AY, Arouche TDS, Siqueira MRS, Ramalho TC, de Faria LJG, Gester RDM, Carvalho Junior RND, Santana de Oliveira M, Neto AMDJC. SARS-CoV-2 external structures interacting with nanospheres using docking and molecular dynamics. J Biomol Struct Dyn 2023:1-16. [PMID: 37712854 DOI: 10.1080/07391102.2023.2252930] [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: 12/27/2022] [Accepted: 08/22/2023] [Indexed: 09/16/2023]
Abstract
Coronavirus is caused by the SARS-CoV-2 virus has shown rapid proliferation and scarcity of treatments with proven effectiveness. In this way, we simulated the hospitalization of carbon nanospheres, with external active sites of the SARS-CoV-2 virus (M-Pro, S-Gly and E-Pro), which can be adsorbed or inactivated when interacting with the nanospheres. The computational procedures performed in this work were developed with the SwissDock server for molecular docking and the GROMACS software for molecular dynamics, making it possible to extract relevant data on affinity energy, distance between molecules, free Gibbs energy and mean square deviation of atomic positions, surface area accessible to solvents. Molecular docking indicates that all ligands have an affinity for the receptor's active sites. The nanospheres interact favorably with all proteins, showing promising results, especially C60, which presented the best affinity energy and RMSD values for all protein macromolecules investigated. The C60 with E-Pro exhibited the highest affinity energy of -9.361 kcal/mol, demonstrating stability in both molecular docking and molecular dynamics simulations. Our RMSD calculations indicated that the nanospheres remained predominantly stable, fluctuating within a range of 2 to 3 Å. Additionally, the analysis of other structures yielded promising results that hold potential for application in other proteases.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Anderson Yuri Martins da Silva
- Laboratory for the Preparation and Computation of Nanomaterials (LPCN), Federal University of Pará, Belem, Brazil
- Graduated in Chemical Engineering, ITEC, Federal University of Pará, Belém, Brazil
- Postgraduate Program in Chemical Engineering, ITEC, Federal University of Pará, Belém, Brazil
| | - Tiago da Silva Arouche
- Laboratory for the Preparation and Computation of Nanomaterials (LPCN), Federal University of Pará, Belem, Brazil
- Graduated in Chemical Engineering, ITEC, Federal University of Pará, Belém, Brazil
| | | | - Teodorico Castro Ramalho
- Postgraduate Program in Engineering of Natural Resources of the Amazon, ITEC, Federal University of Pará, Belém, Brazil
| | | | - Rodrigo do Monte Gester
- Institute of Exact Sciences (ICE), Federal University of the South and Southeast of Pará, Maraba, Brazil
| | - Raul Nunes de Carvalho Junior
- Postgraduate Program in Chemical Engineering, ITEC, Federal University of Pará, Belém, Brazil
- Postgraduate Program in Engineering of Natural Resources of the Amazon, ITEC, Federal University of Pará, Belém, Brazil
- Faculty of Food Engineering ITEC, Federal University of Pará, Belém, Brazil
| | | | - Antonio Maia de Jesus Chaves Neto
- Laboratory for the Preparation and Computation of Nanomaterials (LPCN), Federal University of Pará, Belem, Brazil
- Graduated in Chemical Engineering, ITEC, Federal University of Pará, Belém, Brazil
- Postgraduate Program in Chemical Engineering, ITEC, Federal University of Pará, Belém, Brazil
- National Professional Master's in Physics Teaching, Federal University of Pará, Belém, Brazil
- Museu Paraense Emílio Goeldi, Diretoria, Coordenação de Botânica, Rua Augusto Corrêa, Belém, Brazil
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14
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Luppi E, Coccia E. Role of Inner Molecular Orbitals in High-Harmonic Generation Spectra of Aligned Uracil. J Phys Chem A 2023; 127:7335-7343. [PMID: 37640677 DOI: 10.1021/acs.jpca.3c03990] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/31/2023]
Abstract
In this work, we decompose the high-harmonic generation (HHG) signal of aligned gas-phase uracil into single molecular-orbital (MO) contributions. We compute HHG spectra for a pulse linearly polarized perpendicular to the molecular plane, with an intensity of 0.6 and 0.85 × 1014 W/cm2 and a wavelength of 800 nm. We use the real-time time-dependent Configuration Interaction with singles method, coupled to a Gaussian-based representation of the time-dependent wavefunction. The strong-field dynamics is affected by the energy of the ionization/recombination channels and by the coupling between the orbital symmetry and laser polarization. In the configuration studied here, we expect that π-type MOs favorably couple with the incoming pulse and play a substantial role in generating the HHG spectrum. Indeed, we show that HOMO, HOMO - 1, and HOMO - 4, which all are π-like, determine the intensity of harmonic peaks at different energies, while HOMO - 2 and HOMO - 3 provide a smaller contribution. It is worth mentioning that HOMO - 4 produces a stronger signal than that from HOMO - 1, even though the corresponding ionization energy, in an one-electron picture, is around 2.5 eV larger and more than 4 eV larger than the HOMO one.
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Affiliation(s)
- Eleonora Luppi
- Laboratoire de Chimie Théorique, Sorbonne Université, CNRS, Paris F-75005, France
| | - Emanuele Coccia
- Department of Chemical and Pharmaceutical Sciences, University of Trieste, via L. Giorgieri 1, Trieste 34127, Italy
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15
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Abou El-Nour KM, El-Sherbiny IM, Khairy GM, Abbas AM, Salem EH. Investigation of thymine as a potential cancer biomarker employing tryptophan with nanomaterials as a biosensor. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2023; 301:122928. [PMID: 37311362 DOI: 10.1016/j.saa.2023.122928] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/05/2023] [Revised: 05/02/2023] [Accepted: 05/26/2023] [Indexed: 06/15/2023]
Abstract
Tryptophan and tryptophan-based nanomaterials sensors in a solution have been developed to directly evaluate thymine. The determination of thymine has been done via quenching of the fluorescence of tryptophan and tryptophan-based nanomaterials such as graphene (Gr), graphene oxide (GO), gold nanoparticles (AuNPs), gold-silver nanocomposite (Au-Ag NC) in a physiological buffer. As the concentration of thymine rises, the fluorescence of tryptophan and tryptophan/nanomaterials becomes less intense. Trp, Trp/Gr, and tryptophan/(Au-Ag) NC systems' quenching mechanisms were dynamic, but tryptophan /GO and tryptophan/AuNPs' quenching mechanisms were static. The linear dynamic range for the determination of thy by tryptophan and tryptophan /nanomaterials is 10 to 200 μM. The detection limits for tryptophan, tryptophan /Gr, tryptophan /GO, tryptophan /AuNPs, and tryptophan/Au-Ag NC were 3.21, 14.20, 6.35, 4.67and 7.79 Μm, respectively. Thermodynamic parameters for the interaction of the Probes with Thy include the enthalpy (H°) and entropy (S°) change values, were assessed, as well as the binding constant (Ka) of Thy with Trp and Trp-based nanomaterials. A recovery study was conducted utilizing a human serum sample after the addition of the required quantity of the investigational thymine.
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Affiliation(s)
- Kholoud M Abou El-Nour
- Department of Chemistry, Suez Canal University, Faculty of Science, Ismailia 41522, Egypt.
| | - Ibrahim M El-Sherbiny
- Nanomedicine Research Labs, Center for Materials Sciences, Zewail City of Science and Technology, 6(th) October City, 12578 Giza, Egypt
| | - Gasser M Khairy
- Department of Chemistry, Suez Canal University, Faculty of Science, Ismailia 41522, Egypt
| | - Abbas M Abbas
- Department of Chemistry, Suez Canal University, Faculty of Science, Ismailia 41522, Egypt
| | - Eman H Salem
- Department of Chemistry, Suez Canal University, Faculty of Science, Ismailia 41522, Egypt
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16
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Orimo N, Yamamoto YI, Karashima S, Boyer A, Suzuki T. Ultrafast Electronic Relaxation in 6-Methyluracil and 5-Fluorouracil in Isolated and Aqueous Conditions: Substituent and Solvent Effects. J Phys Chem Lett 2023; 14:2758-2763. [PMID: 36897645 DOI: 10.1021/acs.jpclett.3c00195] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/18/2023]
Abstract
We report ultrafast extreme ultraviolet photoelectron spectroscopy of 6-methyluracil (6mUra) and 5-fluorouracil (5FUra) in the gas phase and 6mUra and 5-fluorouridine in an aqueous environment. In the gas phase, internal conversion (IC) occurs from 1ππ* to 1nπ* states in tens of femtoseconds, followed by intersystem crossing to the 3ππ* state in several picoseconds. In an aqueous solution, 6mUra undergoes IC almost exclusively to the ground state (S0) in about 100 fs, which is essentially the same process as that for unsubstituted uracil, but much faster than that for thymine (5-methyluracil). The different dynamics for C5 and C6 methylation suggest that IC from 1ππ* to S0 is facilitated by out-of-plane (OOP) motion of the C5 substituent. The slow IC for C5-substituted molecules in an aqueous environment is ascribed to the solvent reorganization that is required for this OOP motion to occur. The slow rate for 5FUrd may arise in part from an increased barrier height due to C5 fluorination.
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Affiliation(s)
- Natsumi Orimo
- Department of Chemistry, Graduate School of Science, Kyoto University, Kitashirakawa-Oiwakecho, Sakyo-Ku, Kyoto 606-8502, Japan
| | - Yo-Ichi Yamamoto
- Department of Chemistry, Graduate School of Science, Kyoto University, Kitashirakawa-Oiwakecho, Sakyo-Ku, Kyoto 606-8502, Japan
| | - Shutaro Karashima
- Department of Chemistry, Graduate School of Science, Kyoto University, Kitashirakawa-Oiwakecho, Sakyo-Ku, Kyoto 606-8502, Japan
| | - Alexie Boyer
- Department of Chemistry, Graduate School of Science, Kyoto University, Kitashirakawa-Oiwakecho, Sakyo-Ku, Kyoto 606-8502, Japan
| | - Toshinori Suzuki
- Department of Chemistry, Graduate School of Science, Kyoto University, Kitashirakawa-Oiwakecho, Sakyo-Ku, Kyoto 606-8502, Japan
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17
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Karak P, Moitra T, Ruud K, Chakrabarti S. Photophysics of uracil: an explicit time-dependent generating function-based method combining both nonadiabatic and spin-orbit coupling effects. Phys Chem Chem Phys 2023; 25:8209-8219. [PMID: 36881024 DOI: 10.1039/d2cp05955j] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/16/2023]
Abstract
We present a composite framework for calculating the rates of non-radiative deactivation processes, namely internal conversion (IC) and intersystem crossing (ISC), on an equal footing by explicitly computing the non-adiabatic coupling (NAC) and spin-orbit coupling (SOC) constants, respectively. The stationary-state approach uses a time-dependent generating function based on Fermi's golden rule. We validate the applicability of the framework by computing the rate of IC for azulene, obtaining comparable rates to experimental and previous theoretical results. Next, we investigate the photophysics associated with the complex photodynamics of the uracil molecule. Interestingly, our simulated rates corroborate experimental observations. Detailed analyses using Duschinsky rotation matrices, displacement vectors and NAC matrix elements are presented to interpret the findings alongside testing the suitability of the approach for such molecular systems. The suitability of the Fermi's golden rule based method is explained qualitatively in terms of single-mode potential energy surfaces.
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Affiliation(s)
- Pijush Karak
- Department of Chemistry, University of Calcutta, 92 A.P.C Road, Kolkata-700009, West Bengal, India.
| | - Torsha Moitra
- Hylleraas Centre for Quantum Molecular Sciences, Department of Chemistry, University of Tromsø-The Arctic University of Norway, 9037 Tromsø, Norway.
| | - Kenneth Ruud
- Hylleraas Centre for Quantum Molecular Sciences, Department of Chemistry, University of Tromsø-The Arctic University of Norway, 9037 Tromsø, Norway. .,Norwegian Defence Research Establishment, P.O.Box 25, 2027 Kjeller, Norway
| | - Swapan Chakrabarti
- Department of Chemistry, University of Calcutta, 92 A.P.C Road, Kolkata-700009, West Bengal, India.
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18
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Miura Y, Yamamoto YI, Karashima S, Orimo N, Hara A, Fukuoka K, Ishiyama T, Suzuki T. Formation of Long-Lived Dark States during Electronic Relaxation of Pyrimidine Nucleobases Studied Using Extreme Ultraviolet Time-Resolved Photoelectron Spectroscopy. J Am Chem Soc 2023; 145:3369-3381. [PMID: 36724068 DOI: 10.1021/jacs.2c09803] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
Ultrafast electronic relaxation of nucleobases from 1ππ* states to the ground state (S0) is considered essential for the photostability of DNA. However, transient absorption spectroscopy (TAS) has indicated that some nucleobases in aqueous solutions create long-lived 1nπ*/3ππ* dark states from the 1ππ* states with a high quantum yield of 0.4-0.5. We investigated electronic relaxation in pyrimidine nucleobases in both aqueous solutions and the gas phase using extreme ultraviolet (EUV) time-resolved photoelectron spectroscopy. Femtosecond EUV probe pulses cause ionization from all electronic states involved in the relaxation process, providing a clear overview of the electronic dynamics. The 1nπ* quantum yields for aqueous cytidine and uracil (Ura) derivatives were found to be considerably lower (<0.07) than previous estimates reported by TAS. On the other hand, aqueous thymine (Thy) and thymidine exhibited a longer 1ππ* lifetime and a higher quantum yield (0.12-0.22) for the 1nπ* state. A similar trend was found for isolated Thy and Ura in the gas phase: the 1ππ* lifetimes are 39 and 17 fs and the quantum yield for 1nπ* are 1.0 and 0.45 for Thy and Ura, respectively. The result indicates that single methylation to the C5 position hinders the out-of-plane deformation that drives the system to the conical intersection region between 1ππ* and S0, providing a large impact on the photophysics/photochemistry of a pyrimidine nucleobase. The significant reduction of 1nπ* yield in aqueous solution is ascribed to the destabilization of the 1nπ* state induced by hydrogen bonding.
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Affiliation(s)
- Yuta Miura
- Department of Chemistry, Graduate School of Science, Kyoto University, Kitashirakawa-Oiwakecho, Sakyo-Ku, Kyoto606-8502, Japan
| | - Yo-Ichi Yamamoto
- Department of Chemistry, Graduate School of Science, Kyoto University, Kitashirakawa-Oiwakecho, Sakyo-Ku, Kyoto606-8502, Japan
| | - Shutaro Karashima
- Department of Chemistry, Graduate School of Science, Kyoto University, Kitashirakawa-Oiwakecho, Sakyo-Ku, Kyoto606-8502, Japan
| | - Natsumi Orimo
- Department of Chemistry, Graduate School of Science, Kyoto University, Kitashirakawa-Oiwakecho, Sakyo-Ku, Kyoto606-8502, Japan
| | - Ayano Hara
- Department of Chemistry, Graduate School of Science, Kyoto University, Kitashirakawa-Oiwakecho, Sakyo-Ku, Kyoto606-8502, Japan
| | - Kanae Fukuoka
- Department of Chemistry, Graduate School of Science, Kyoto University, Kitashirakawa-Oiwakecho, Sakyo-Ku, Kyoto606-8502, Japan
| | - Tatsuya Ishiyama
- Department of Applied Chemistry, Graduate School of Science and Engineering, University of Toyama, Toyama930-8555, Japan
| | - Toshinori Suzuki
- Department of Chemistry, Graduate School of Science, Kyoto University, Kitashirakawa-Oiwakecho, Sakyo-Ku, Kyoto606-8502, Japan
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19
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Ostakhov SS, Kayumova RR, Akhiyarov AA, Ivanov SP, Khursan SL. Spectral-Luminescent Study of the Acid–Base Equilibrium of 5-Aminouracil and 6-Aminouracil in Aqueous Solutions. HIGH ENERGY CHEMISTRY 2023. [DOI: 10.1134/s0018143923010101] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/03/2023]
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20
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Huang X, Pei Z, Liang W. Analytical derivative couplings within the framework of time-dependent density functional theory coupled with conductor-like polarizable continuum model: Formalism, implementation, and applications. J Chem Phys 2023; 158:044122. [PMID: 36725492 DOI: 10.1063/5.0130617] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023] Open
Abstract
The nonadiabatic phenomena, which are characterized by a strong coupling between electronic and nuclear motions, are ubiquitous. The nonadiabatic effect of the studied system can be significantly affected by the surrounding environment, such as solvents, in which such nonadiabatic process takes place. It is essential to develop the theoretical models to simulate these processes while accurately modeling the solvent environment. The time-dependent density functional theory (TDDFT) is currently the most efficient approach to describe the electronic structures and dynamics of complex systems, while the polarizable continuum model (PCM) represents one of the most successful examples among continuum solvation models. Here, we formulate the first-order derivative couplings (DCs) between the ground and excited states as well as between two excited states by utilizing time-independent equation of motion formalism within the framework of both linear response and spin flip formulations of TDDFT/CPCM (the conductor-like PCM), and implement the analytical DCs into the Q-CHEM electronic structure software package. The analytic implementation is validated by the comparison of the analytical and finite-difference results, and reproducing geometric phase effect in the protonated formaldimine test case. Taking 4-(N,N-dimethylamino)benzonitrile and uracil in the gas phase and solution as an example, we demonstrate that the solvent effect is essential not only for the excitation energies of the low-lying excited-states but also for the DCs between these states. Finally, we calculate the internal conversion rate of benzophenone in a solvent with DC being used. The current implementation of analytical DCs together with the existing analytical gradient and Hessian of TDDFT/PCM excited states allows one to study the nonadiabatic effects of relatively large systems in solutions with low computational cost.
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Affiliation(s)
- Xunkun Huang
- State Key Laboratory of Physical Chemistry of Solid Surfaces, Collaborative Innovation Center of Chemistry for Energy Materials, Fujian Provincial Key Laboratory of Theoretical and Computational Chemistry, and Department of Chemistry, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, People's Republic of China
| | - Zheng Pei
- State Key Laboratory of Physical Chemistry of Solid Surfaces, Collaborative Innovation Center of Chemistry for Energy Materials, Fujian Provincial Key Laboratory of Theoretical and Computational Chemistry, and Department of Chemistry, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, People's Republic of China
| | - WanZhen Liang
- State Key Laboratory of Physical Chemistry of Solid Surfaces, Collaborative Innovation Center of Chemistry for Energy Materials, Fujian Provincial Key Laboratory of Theoretical and Computational Chemistry, and Department of Chemistry, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, People's Republic of China
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21
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Terao Y, Kumagai Y, Suzuki I, Tsuchiya T, Ukai M, Yokoya A, Fujii K, Fukuda Y, Saitoh Y. X-ray induced luminescence spectroscopy for DNA damaging intermediates aided by a monochromatic synchrotron radiation. Int J Radiat Biol 2023; 99:89-94. [PMID: 34402379 DOI: 10.1080/09553002.2021.1967506] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
PURPOSE To identify the bonding sites of initial radiation interaction with DNA and to trace the following chemical reaction sequences on the pathway of damage induction, we carry out a spectroscopy XIL (X-ray induced luminescence) using soft X-ray synchrotron radiation. This is a nondestructive analysis of the excited intermediate species produced in a molecular mechanism on the damage induction pathway. MATERIALS AND METHODS We introduce aqueous samples of UMP (uridine-5'-monophosphate) in the vacuum by the use of a liquid micro-jet technique. The luminescence in the region of UV-VIS (from visible to ultraviolet) radiation induced after the absorption of monochromatic soft X-ray by aqueous UMP is measured with sweeping the soft X-ray energy in the region of 370-560 eV. RESULTS The enhanced XIL intensities for aqueous UMP in the region of soft X-ray of 410-530 eV (in "water window" region) are obtained. The enhancement of XIL intensities in the UV-VIS region, relative to the water control, is explained by the excitation and ionization of a K-shell electron of nitrogen atoms in the uracil moiety. The enhanced XIL intensities do not match the structure of XANES (X-ray absorption near-edge structure) of the aqueous UMP. This suggests that the XIL intensities reflect the quantum yields of luminescence, or the quantum yields for conversion by UMP of an absorbed X-ray into UV-VIS radiation. In this paper, spectra of luminescence are shown to be resolved by combining low pass filters. The filtered luminescence spectra are obtained at the center of gravity (λc) of the band pass wavelength regions at λc = 270nm, 295 nm, 340 nm, 385 nm, 450 nm, and 525 nm., which show a trend similar to the fluorescence of nucleobases induced by ultraviolet radiation. CONCLUSION It is concluded that the origin of the observed XIL is the hydrated uracil moiety in aqueous UMP, decomposition of which is suppressed by the migration of excess charge and internal energy after the double ionization due to Auger decay.
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Affiliation(s)
- Yusaku Terao
- Department of Applied Physics, Tokyo University of Agriculture and Technology, Tokyo, Japan
| | - Yoshiaki Kumagai
- Department of Applied Physics, Tokyo University of Agriculture and Technology, Tokyo, Japan.,Institute of Engineering, Tokyo University of Agriculture and Technology, Tokyo, Japan
| | - Issei Suzuki
- Department of Applied Physics, Tokyo University of Agriculture and Technology, Tokyo, Japan
| | - Takahiro Tsuchiya
- Department of Applied Physics, Tokyo University of Agriculture and Technology, Tokyo, Japan
| | - Masatoshi Ukai
- Department of Applied Physics, Tokyo University of Agriculture and Technology, Tokyo, Japan.,Institute of Engineering, Tokyo University of Agriculture and Technology, Tokyo, Japan
| | - Akinari Yokoya
- Institute of Quantum Life Science, National Institute for Quantum and Radiological Science, Ibaraki, Japan
| | - Kentaro Fujii
- Institute of Quantum Life Science, National Institute for Quantum and Radiological Science, Ibaraki, Japan.,Quantum beam Science Research Directorate, National Institute for Quantum and Radiological Science, Hyogo, Japan
| | - Yoshihiro Fukuda
- Synchrotron Radiation Research Center, Japan Atomic Energy Agency, Hyogo, Japan
| | - Yuji Saitoh
- Synchrotron Radiation Research Center, Japan Atomic Energy Agency, Hyogo, Japan
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22
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Authentication of Covid-19 Vaccines Using Synchronous Fluorescence Spectroscopy. J Fluoresc 2023; 33:1165-1174. [PMID: 36609659 PMCID: PMC9825072 DOI: 10.1007/s10895-022-03136-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2022] [Accepted: 12/24/2022] [Indexed: 01/09/2023]
Abstract
The present study demonstrates the potential of synchronous fluorescence spectroscopy and multivariate data analysis for authentication of COVID-19 vaccines from various manufacturers. Synchronous scanning fluorescence spectra were recorded for DNA-based and mRNA-based vaccines obtained through the NHS Central Liverpool Primary Care Network. Fluorescence spectra of DNA and DNA-based vaccines as well as RNA and RNA-based vaccines were identical to one another. The application of principal component analysis (PCA), PCA-Gaussian Mixture Models (PCA-GMM)) and Self-Organising Maps (SOM) methods to the fluorescence spectra of vaccines is discussed. The PCA is applied to extract the characteristic variables of fluorescence spectra by analysing the major attributes. The results indicated that the first three principal components (PCs) can account for 99.5% of the total variance in the data. The PC scores plot showed two distinct clusters corresponding to the DNA-based vaccines and mRNA-based vaccines respectively. PCA-GMM clustering complemented the PCA clusters by further classifying the mRNA-based vaccines and the GMM clusters revealed three mRNA-based vaccines that were not clustered with the other vaccines. SOM complemented both PCA and PCA-GMM and proved effective with multivariate data without the need for dimensions reduction. The findings showed that fluorescence spectroscopy combined with machine learning algorithms (PCA, PCA-GMM and SOM) is a useful technique for vaccination verification and has the benefits of simplicity, speed and reliability.
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23
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Xu Q, Aranda D, Yaghoubi Jouybari M, Liu Y, Wang M, Cerezo J, Improta R, Santoro F. Nonadiabatic Vibrational Resonance Raman Spectra from Quantum Dynamics Propagations with LVC Models. Application to Thymine. J Phys Chem A 2022; 126:7468-7479. [PMID: 36099554 PMCID: PMC9596142 DOI: 10.1021/acs.jpca.2c05271] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2022] [Revised: 08/31/2022] [Indexed: 11/29/2022]
Abstract
We present a viable protocol to compute vibrational resonance Raman (vRR) spectra for systems with several close-lying and potentially coupled electronic states. It is based on the parametrization of linear vibronic coupling (LVC) models from time-dependent density functional theory (TD-DFT) calculations and quantum dynamics propagations of vibronic wavepackets with the multilayer version of the multiconfiguration time-dependent Hartree (ML-MCTDH) method. Our approach is applied to thymine considering seven coupled electronic states, comprising the three lowest bright states, and all vibrational coordinates. Computed vRR at different excitation wavelengths are in good agreement with the available experimental data. Up to 250 nm the signal is dominated by the lowest HOMO → LUMO transition, whereas at 233 nm, in the valley between the two lowest energy absorption bands, the contributions of all the three bright states, and their interferences and couplings, are important. Inclusion of solvent (water) effects improves the agreement with experiment, reproducing the coalescence of vibrational bands due to CC and C═O stretchings. With our approach we disentangle and assess the effect of interferences between the contribution of different quasi-resonant states to the transition polarizability and the effect of interstate couplings. Our findings strongly suggest that in cases of close-lying and potentially coupled states a simple inclusion of interference effects is not sufficient, and a fully nonadiabatic computation should instead be performed. We also document that for systems with strong couplings and quasi-degenerate states, the use of HT perturbative approach, not designed for these cases, may lead to large artifacts.
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Affiliation(s)
- Qiushuang Xu
- School
of Physics and Optoelectronics Engineering, Ludong University, 264025 Yantai, Shandong, PR China
- School
of Physics Engineering, Qufu Normal University, 2673100 Qufu, Shandong, PR China
- Consiglio
Nazionale delle Ricerche, Istituto di Chimica
dei Composti Organo Metallici (ICCOM-CNR), SS di Pisa, Area della Ricerca, via G. Moruzzi 1, I-56124 Pisa, Italy
| | - Daniel Aranda
- Instituto
de Ciencia Molecular (ICMol)., Universidad de Valencia, c/Catedrático José
Beltrán, 2, 46980 Paterna, Spain
| | - Martha Yaghoubi Jouybari
- Consiglio
Nazionale delle Ricerche, Istituto di Chimica
dei Composti Organo Metallici (ICCOM-CNR), SS di Pisa, Area della Ricerca, via G. Moruzzi 1, I-56124 Pisa, Italy
| | - Yanli Liu
- School
of Physics and Optoelectronics Engineering, Ludong University, 264025 Yantai, Shandong, PR China
| | - Meishan Wang
- School
of Physics and Optoelectronics Engineering, Ludong University, 264025 Yantai, Shandong, PR China
| | - Javier Cerezo
- Consiglio
Nazionale delle Ricerche, Istituto di Chimica
dei Composti Organo Metallici (ICCOM-CNR), SS di Pisa, Area della Ricerca, via G. Moruzzi 1, I-56124 Pisa, Italy
- Departamento
de Química, Universidad Autónoma
de Madrid, 28049 Madrid, Spain
| | - Roberto Improta
- Consiglio
Nazionale delle Ricerche, Istituto di Biostrutture
e Bioimmagini (IBB-CNR), Via De Amicis 95, I-80145 Napoli, Italy
- DTU Chemistry, Technical University of Denmark, Kemitorvet Bldg 207, DK-2800 Kongens Lyngby, Denmark
| | - Fabrizio Santoro
- Consiglio
Nazionale delle Ricerche, Istituto di Chimica
dei Composti Organo Metallici (ICCOM-CNR), SS di Pisa, Area della Ricerca, via G. Moruzzi 1, I-56124 Pisa, Italy
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24
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Milovanović B, Novak J, Etinski M, Domcke W, Došlić N. On the propensity of formation of cyclobutane dimers in face-to-face and face-to-back uracil stacks in solution. Phys Chem Chem Phys 2022; 24:14836-14845. [PMID: 35697028 DOI: 10.1039/d2cp00495j] [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
UV irradiation of RNA leads to the formation of intra- and inter-strand crosslinks of cyclobutane type. Despite the importance of this reaction, relatively little is known about how the mutual orientation of the two bases affects the outcome of the reaction. Here we report a comparative nonadiabatic molecular dynamics study of face-to-back (F2B) and face-to-face (F2F) stacked uracil-water clusters. The computations were performed using the second-order algebraic-diagrammatic-construction (ADC(2)) method. We found that F2B stacked uracil-water clusters either relax non-reactively to the ground state by an ethylenic twist around the CC bond or remain in the lowest nπ* state in which the two bases gradually move away from each other. This finding is consistent with the low propensity for the formation of intra-strand cyclobutane dimers between adjacent RNA bases. On the contrary, in F2F stacked uracil-water clusters, in addition to non-reactive deactivation, we found a pro-reactive deactivation pathway, which may lead to the formation of cyclobutane uracil dimers in the electronic ground state. On a qualitative level, the observed photodynamics of F2F stacked uracil-water clusters explains the greater propensity of RNA to form inter-strand cyclobutane-type crosslinks.
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Affiliation(s)
| | - Jurica Novak
- Department of Biotechnology, University of Rijeka, HR-51000 Rijeka, Croatia.,Scientific and Educational Center "Biomedical Technologies" School of Medical Biology, South Ural State University, RU-454080, Chelyabinsk, Russia.,Center for Artificial Intelligence and Cybersecurity, University of Rijeka, 51000 Rijeka, Croatia
| | - Mihajlo Etinski
- University of Belgrade, Faculty of Physical Chemistry, Belgrade, Serbia
| | - Wolfgang Domcke
- Department of Chemistry, Technical University of Munich, Garching, Germany
| | - Nađa Došlić
- Department of Physical Chemistry, Ruđer Bošković Institute, Zagreb, Croatia.
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25
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Ostakhov SS, Abdrakhimova GS, Kayumova RR, Ivanov SP, Khursan SL. Spectral–Luminescent and Spectrophotometric Study of Molecular and Anionic Forms of N-Methyl Derivatives of 5-Fluorouracil in Aqueous Solutions. HIGH ENERGY CHEMISTRY 2022. [DOI: 10.1134/s0018143922030080] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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26
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Kumar C, Luber S. Robust ΔSCF calculations with direct energy functional minimization methods and STEP for molecules and materials. J Chem Phys 2022; 156:154104. [PMID: 35459303 DOI: 10.1063/5.0075927] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
The direct energy functional minimization method using the orbital transformation (OT) scheme in the program package CP2K has been employed for Δ self-consistent field (ΔSCF) calculations. The OT method for non-uniform molecular orbitals occupations allows us to apply the ΔSCF method for various kinds of molecules and periodic systems. Vertical excitation energies of heteroaromatic molecules and condensed phase systems, such as solvated ethylene and solvated uracil obeying periodic boundary conditions, are reported using the ΔSCF method. In addition, a Re-phosphate molecule attached to the surface of anatase (TiO2) has been investigated. Additionally, we have implemented a recently proposed state-targeted energy projection ΔSCF algorithm [K. Carter-Fenk and J. M. Herbert, J. Chem. Theory Comput. 16(8), 5067-5082 (2020)] for diagonalization based SCF in CP2K. It is found that the OT scheme provides a smooth and robust SCF convergence for all investigated excitation energies and (non-)periodic systems.
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Affiliation(s)
- Chandan Kumar
- Department of Chemistry, University of Zurich, Zurich, Switzerland
| | - Sandra Luber
- Department of Chemistry, University of Zurich, Zurich, Switzerland
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27
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Hazrati H, Kudsk P, Ding L, Uthe H, Fomsgaard IS. Integrated LC-MS and GC-MS-Based Metabolomics Reveal the Effects of Plant Competition on the Rye Metabolome. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2022; 70:3056-3066. [PMID: 35227064 DOI: 10.1021/acs.jafc.1c06306] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Plants compete with their neighbors about the limited resources available to them. Plants under induced stress resulting from competition may alter their metabolome to increase their resilience or enhance their defense mechanisms. In the present study, rye (Secale cereale) plants were cocultivated with different densities (3, 12, and 18 plants per pot) of Austrian pea (Pisum sativum subsp. arvense), hairy vetch (Vicia villosa), and Alexandrian clover (Trifolium alexandrinum L.) to elucidate the changes in the rye metabolome in response to the different levels of competition. Global metabolic profiling by liquid chromatography triple quadrupole tandem mass spectrometry (LC-QqQ-MS), liquid chromatography quadrupole time-of-flight mass spectrometry (LC-QTOF-MS), and gas chromatography time-of-flight mass spectrometry (GC-TOF-MS) was performed on rye plants, and the acquired data were analyzed using uni- and multivariate statistics. Targeted analysis showed that a high level of competition reduced the concentration of aglycone benzoxazinoids (BXs) and increased glycoside BXs in rye roots. Untargeted metabolomics analysis indicated an increase in the rye root content of the allelopathic compounds 4-hydroxybenzoic acid and uracil in response to competition. Untargeted analysis of rye shoots revealed that the plant competition increased the d-pyroglutamic acid, which is an elicitor of reactive oxygen species (ROS). Our results have enhanced the knowledge of the biochemical response of plant species to cocultivation.
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Affiliation(s)
- Hossein Hazrati
- Department of Agroecology, Aarhus University, Forsøgsvej 1, 4200 Slagelse, Denmark
- Department of Biomedicine, Aarhus University, 8200 Aarhus, Denmark
| | - Per Kudsk
- Department of Agroecology, Aarhus University, Forsøgsvej 1, 4200 Slagelse, Denmark
| | - Ling Ding
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Søltofts Plads, Building 221, 2800 Kgs. Lyngby, Denmark
| | - Henriette Uthe
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Puschstrasse 4, 04103 Leipzig, Germany
| | - Inge S Fomsgaard
- Department of Agroecology, Aarhus University, Forsøgsvej 1, 4200 Slagelse, Denmark
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28
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Ortín-Fernández J, González-Vázquez J, Martínez-Fernández L, Corral I. Molecular Identification of the Transient Species Mediating the Deactivation Dynamics of Solvated Guanosine and Deazaguanosine. Molecules 2022; 27:989. [PMID: 35164254 PMCID: PMC8839017 DOI: 10.3390/molecules27030989] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2021] [Revised: 01/24/2022] [Accepted: 01/27/2022] [Indexed: 11/16/2022] Open
Abstract
Small structural alterations of the purine/pyrimidine core have been related to important photophysical changes, such as the loss of photostability. Similarly to canonical nucleobases, solute-solvent interactions can lead to a change in the excited state lifetimes and/or to the interplay of different states in the photophysics of these modified nucleobases. To shed light on both effects, we here report a complete picture of the absorption spectra and excited state deactivation of deoxyguanosine and its closely related derivative, deoxydeazaguanosine, in water and methanol through the mapping of the excited state potential energy surfaces and molecular dynamics simulations at the TD-DFT level of theory. We show that the N by CH exchange in the imidazole ring of deoxyguanosine translates into a small red-shift of the bright states and slightly faster dynamics. In contrast, changing solvent from water to methanol implies the opposite, i.e., that the deactivation of both systems to the ground state is significantly hindered.
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Affiliation(s)
- Javier Ortín-Fernández
- Departamento de Química, Módulo 13, Universidad Autónoma de Madrid, 28049 Madrid, Spain; (J.O.-F.); (J.G.-V.)
| | - Jesús González-Vázquez
- Departamento de Química, Módulo 13, Universidad Autónoma de Madrid, 28049 Madrid, Spain; (J.O.-F.); (J.G.-V.)
- Institute for Advanced Research in Chemistry (IAdChem), Universidad Autónoma de Madrid, 28049 Madrid, Spain
| | - Lara Martínez-Fernández
- Departamento de Química, Módulo 13, Universidad Autónoma de Madrid, 28049 Madrid, Spain; (J.O.-F.); (J.G.-V.)
- Institute for Advanced Research in Chemistry (IAdChem), Universidad Autónoma de Madrid, 28049 Madrid, Spain
| | - Inés Corral
- Departamento de Química, Módulo 13, Universidad Autónoma de Madrid, 28049 Madrid, Spain; (J.O.-F.); (J.G.-V.)
- Institute for Advanced Research in Chemistry (IAdChem), Universidad Autónoma de Madrid, 28049 Madrid, Spain
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29
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Tichý O, Burda JV. Estimation of electron absorption spectra and lifetime of the two lowest singlet excited states of pyrimidine nucleobases and their derivatives. J Mol Struct 2022. [DOI: 10.1016/j.molstruc.2021.131863] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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30
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Hoehn SJ, Krul SE, Skory BJ, Crespo-Hernández CE. Increased Photostability of the Integral mRNA Vaccine Component N 1 -Methylpseudouridine Compared to Uridine. Chemistry 2022; 28:e202103667. [PMID: 34875113 DOI: 10.1002/chem.202103667] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2021] [Indexed: 01/26/2023]
Abstract
N1 -Methylation of pseudouridine (m1 ψ) replaces uridine (Urd) in several therapeutics, including the Moderna and BioNTech-Pfizer COVID-19 vaccines. Importantly, however, it is currently unknown if exposure to electromagnetic radiation can affect the chemical integrity and intrinsic stability of m1 ψ. In this study, the photochemistry of m1 ψ is compared to that of uridine by using photoirradiation at 267 nm, steady-state spectroscopy, and quantum-chemical calculations. Furthermore, femtosecond transient absorption measurements are collected to delineate the electronic relaxation mechanisms for both nucleosides under physiologically relevant conditions. It is shown that m1 ψ exhibits a 12-fold longer 1 ππ* decay lifetime than uridine and a 5-fold higher fluorescence yield. Notably, however, the experimental results also demonstrate that most of the excited state population in both molecules decays back to the ground state in an ultrafast time scale and that m1 ψ is 6.7-fold more photostable than Urd following irradiation at 267 nm.
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Affiliation(s)
- Sean J Hoehn
- Department of Chemistry, Case Western Reserve University, 44106, Cleveland, Ohio, United States
| | - Sarah E Krul
- Department of Chemistry, Case Western Reserve University, 44106, Cleveland, Ohio, United States
| | - Brandon J Skory
- Department of Chemistry, Case Western Reserve University, 44106, Cleveland, Ohio, United States
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31
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Borrego-Varillas R, Nenov A, Kabaciński P, Conti I, Ganzer L, Oriana A, Jaiswal VK, Delfino I, Weingart O, Manzoni C, Rivalta I, Garavelli M, Cerullo G. Tracking excited state decay mechanisms of pyrimidine nucleosides in real time. Nat Commun 2021; 12:7285. [PMID: 34907186 PMCID: PMC8671501 DOI: 10.1038/s41467-021-27535-7] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2021] [Accepted: 11/24/2021] [Indexed: 11/18/2022] Open
Abstract
DNA owes its remarkable photostability to its building blocks-the nucleosides-that efficiently dissipate the energy acquired upon ultraviolet light absorption. The mechanism occurring on a sub-picosecond time scale has been a matter of intense debate. Here we combine sub-30-fs transient absorption spectroscopy experiments with broad spectral coverage and state-of-the-art mixed quantum-classical dynamics with spectral signal simulations to resolve the early steps of the deactivation mechanisms of uridine (Urd) and 5-methyluridine (5mUrd) in aqueous solution. We track the wave packet motion from the Franck-Condon region to the conical intersections (CIs) with the ground state and observe spectral signatures of excited-state vibrational modes. 5mUrd exhibits an order of magnitude longer lifetime with respect to Urd due to the solvent reorganization needed to facilitate bulky methyl group motions leading to the CI. This activates potentially lesion-inducing dynamics such as ring opening. Involvement of the 1nπ* state is found to be negligible.
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Affiliation(s)
| | - Artur Nenov
- Dipartimento di Chimica Industriale, Università degli Studi di Bologna, Viale del Risorgimento 4, Bologna, Italy
| | - Piotr Kabaciński
- Dipartimento di Fisica, Politecnico di Milano, Piazza Leonardo da Vinci 32, Milano, Italy
| | - Irene Conti
- Dipartimento di Chimica Industriale, Università degli Studi di Bologna, Viale del Risorgimento 4, Bologna, Italy
| | - Lucia Ganzer
- Dipartimento di Fisica, Politecnico di Milano, Piazza Leonardo da Vinci 32, Milano, Italy
| | - Aurelio Oriana
- Dipartimento di Fisica, Politecnico di Milano, Piazza Leonardo da Vinci 32, Milano, Italy
| | - Vishal Kumar Jaiswal
- Dipartimento di Chimica Industriale, Università degli Studi di Bologna, Viale del Risorgimento 4, Bologna, Italy
| | - Ines Delfino
- Dipartimento di Scienze Ecologiche e Biologiche, Università della Tuscia, Via San Camillo de Lellis, snc, Viterbo, Italy
| | - Oliver Weingart
- Institut für Theoretische Chemie und Computerchemie, Heinrich Heine Universität Düsseldorf, Universitätsstrasse 1, Düsseldorf, Germany
| | | | - Ivan Rivalta
- Dipartimento di Chimica Industriale, Università degli Studi di Bologna, Viale del Risorgimento 4, Bologna, Italy
- Université de Lyon, École Normale Supérieure de Lyon, CNRS UMR 5182, Laboratoire de Chimie, 46 allée d'Italie, F69364, Lyon, France
| | - Marco Garavelli
- Dipartimento di Chimica Industriale, Università degli Studi di Bologna, Viale del Risorgimento 4, Bologna, Italy.
| | - Giulio Cerullo
- IFN-CNR, Piazza Leonardo da Vinci 32, Milano, Italy.
- Dipartimento di Fisica, Politecnico di Milano, Piazza Leonardo da Vinci 32, Milano, Italy.
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32
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Kabaciński P, Romanelli M, Ponkkonen E, Jaiswal VK, Carell T, Garavelli M, Cerullo G, Conti I. Unified Description of Ultrafast Excited State Decay Processes in Epigenetic Deoxycytidine Derivatives. J Phys Chem Lett 2021; 12:11070-11077. [PMID: 34748341 PMCID: PMC8607503 DOI: 10.1021/acs.jpclett.1c02909] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2021] [Accepted: 11/01/2021] [Indexed: 06/13/2023]
Abstract
Epigenetic DNA modifications play a fundamental role in modulating gene expression and regulating cellular and developmental biological processes, thereby forming a second layer of information in DNA. The epigenetic 2'-deoxycytidine modification 5-methyl-2'-deoxycytidine, together with its enzymatic oxidation products (5-hydroxymethyl-2'-deoxycytidine, 5-formyl-2'-deoxycytidine, and 5-carboxyl-2'-deoxycytidine), are closely related to deactivation and reactivation of DNA transcription. Here, we combine sub-30-fs transient absorption spectroscopy with high-level correlated multiconfigurational CASPT2/MM computational methods, explicitly including the solvent, to obtain a unified picture of the photophysics of deoxycytidine-derived epigenetic DNA nucleosides. We assign all the observed time constants and identify the excited state relaxation pathways, including the competition of intersystem crossing and internal conversion for 5-formyl-2'-deoxycytidine and ballistic decay to the ground state for 5-carboxy-2'-deoxycytidine. Our work contributes to shed light on the role of epigenetic derivatives in DNA photodamage as well as on their possible therapeutic use.
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Affiliation(s)
- Piotr Kabaciński
- IFN-CNR,
Dipartimento di Fisica, Politecnico di Milano, Piazza Leonardo da Vinci 32, I-20133 Milano, Italy
| | - Marco Romanelli
- Dipartimento
di Chimica Industriale, Università
degli Studi di Bologna, Viale del Risorgimento 4, I-40136 Bologna, Italy
| | - Eveliina Ponkkonen
- Department
of Chemistry, Ludwig-Maximilians-Universität
München, Butenandtstrasse 5-13, Munich 81377, Germany
| | - Vishal Kumar Jaiswal
- Dipartimento
di Chimica Industriale, Università
degli Studi di Bologna, Viale del Risorgimento 4, I-40136 Bologna, Italy
| | - Thomas Carell
- Department
of Chemistry, Ludwig-Maximilians-Universität
München, Butenandtstrasse 5-13, Munich 81377, Germany
| | - Marco Garavelli
- Dipartimento
di Chimica Industriale, Università
degli Studi di Bologna, Viale del Risorgimento 4, I-40136 Bologna, Italy
| | - Giulio Cerullo
- IFN-CNR,
Dipartimento di Fisica, Politecnico di Milano, Piazza Leonardo da Vinci 32, I-20133 Milano, Italy
| | - Irene Conti
- Dipartimento
di Chimica Industriale, Università
degli Studi di Bologna, Viale del Risorgimento 4, I-40136 Bologna, Italy
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33
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Photochemistry of Thymine in Protic Polar Nanomeric Droplets Using Electrostatic Embeding TD-DFT/MM. Molecules 2021; 26:molecules26196021. [PMID: 34641565 PMCID: PMC8513085 DOI: 10.3390/molecules26196021] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2021] [Revised: 09/29/2021] [Accepted: 10/01/2021] [Indexed: 11/17/2022] Open
Abstract
Thymine photochemistry is important for understanding DNA photodamage. In the gas phase, thymine undergoes a fast non-radiative decay from S2 to S1. In the S1 state, it gets trapped for several picoseconds until returning to the ground-state S0. Here, we explore the electrostatic effects of nanomeric droplets of methanol and water on the excited states of thymine. For this purpose, we develop and implement an electrostatic embedding TD-DFT/MM method based on a QM/MM coupling defined through electrostatic potential fitting charges. We show that both in methanol and water, the mechanism is similar to the gas phase. The solvent molecules participate in defining the branching plane of S0/S1 intersection and have a negligible effect on the S1/S2 intersection. Despite the wrong topology of the ground/excited state intersections, electrostatic embedding TD-DFT/MM allows for a fast exploration of the potential energy surfaces and a qualitative picture of the photophysics of thymine in solvent droplets.
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34
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Valverde D, de Araújo AVS, Borin AC. Photophysical Deactivation Mechanisms of the Pyrimidine Analogue 1-Cyclohexyluracil. Molecules 2021; 26:5191. [PMID: 34500625 PMCID: PMC8434193 DOI: 10.3390/molecules26175191] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2021] [Revised: 08/21/2021] [Accepted: 08/23/2021] [Indexed: 11/17/2022] Open
Abstract
The photophysical relaxation mechanisms of 1-cyclohexyluracil, in vacuum and water, were investigated by employing the Multi-State CASPT2 (MS-CASPT2, Multi-State Complete Active-Space Second-Order Perturbation Theory) quantum chemical method and Dunning's cc-pVDZ basis sets. In both environments, our results suggest that the primary photophysical event is the population of the S11(ππ*) bright state. Afterwards, two likely deactivation pathways can take place, which is sustained by linear interpolation in internal coordinates defined via Z-Matrix scans connecting the most important characteristic points. The first one (Route 1) is the same relaxation mechanism observed for uracil, its canonical analogue, i.e., internal conversion to the ground state through an ethylenic-like conical intersection. The other route (Route 2) is the direct population transfer from the S11(ππ*) bright state to the T23(nπ*) triplet state via an intersystem crossing process involving the (S11(ππ*)/T23(nπ*))STCP singlet-triplet crossing point. As the spin-orbit coupling is not too large in either environment, we propose that most of the electronic population initially on the S11(ππ*) state returns to the ground following the same ultrafast deactivation mechanism observed in uracil (Route 1), while a smaller percentage goes to the triplet manifold. The presence of a minimum on the S11(ππ*) potential energy hypersurface in water can help to understand why experimentally it is noticed suppression of the triplet states population in polar protic solvent.
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Affiliation(s)
- Danillo Valverde
- Department of Fundamental Chemistry, Institute of Chemistry, University of São Paulo, Avenida Professor Lineu Prestes, 748, São Paulo 05508-000, SP, Brazil;
| | | | - Antonio Carlos Borin
- Department of Fundamental Chemistry, Institute of Chemistry, University of São Paulo, Avenida Professor Lineu Prestes, 748, São Paulo 05508-000, SP, Brazil;
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35
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Dziuba D, Didier P, Ciaco S, Barth A, Seidel CAM, Mély Y. Fundamental photophysics of isomorphic and expanded fluorescent nucleoside analogues. Chem Soc Rev 2021; 50:7062-7107. [PMID: 33956014 DOI: 10.1039/d1cs00194a] [Citation(s) in RCA: 29] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Fluorescent nucleoside analogues (FNAs) are structurally diverse mimics of the natural essentially non-fluorescent nucleosides which have found numerous applications in probing the structure and dynamics of nucleic acids as well as their interactions with various biomolecules. In order to minimize disturbance in the labelled nucleic acid sequences, the FNA chromophoric groups should resemble the natural nucleobases in size and hydrogen-bonding patterns. Isomorphic and expanded FNAs are the two groups that best meet the criteria of non-perturbing fluorescent labels for DNA and RNA. Significant progress has been made over the past decades in understanding the fundamental photophysics that governs the spectroscopic and environmentally sensitive properties of these FNAs. Herein, we review recent advances in the spectroscopic and computational studies of selected isomorphic and expanded FNAs. We also show how this information can be used as a rational basis to design new FNAs, select appropriate sequences for optimal spectroscopic response and interpret fluorescence data in FNA applications.
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Affiliation(s)
- Dmytro Dziuba
- Laboratoire de Bioimagerie et Pathologies, UMR 7021, Université de Strasbourg, 74 route du Rhin, 67401 Illkirch, France.
| | - Pascal Didier
- Laboratoire de Bioimagerie et Pathologies, UMR 7021, Université de Strasbourg, 74 route du Rhin, 67401 Illkirch, France.
| | - Stefano Ciaco
- Laboratoire de Bioimagerie et Pathologies, UMR 7021, Université de Strasbourg, 74 route du Rhin, 67401 Illkirch, France. and Department of Biotechnology, Chemistry and Pharmacy, University of Siena, via Aldo Moro 2, 53100 Siena, Italy
| | - Anders Barth
- Institut für Physikalische Chemie, Lehrstuhl für Molekulare Physikalische Chemie, Heinrich-Heine-Universität, 40225 Düsseldorf, Germany
| | - Claus A M Seidel
- Institut für Physikalische Chemie, Lehrstuhl für Molekulare Physikalische Chemie, Heinrich-Heine-Universität, 40225 Düsseldorf, Germany
| | - Yves Mély
- Laboratoire de Bioimagerie et Pathologies, UMR 7021, Université de Strasbourg, 74 route du Rhin, 67401 Illkirch, France.
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36
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Chakraborty P, Liu Y, McClung S, Weinacht T, Matsika S. Time Resolved Photoelectron Spectroscopy as a Test of Electronic Structure and Nonadiabatic Dynamics. J Phys Chem Lett 2021; 12:5099-5104. [PMID: 34028278 DOI: 10.1021/acs.jpclett.1c00926] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
We compare different levels of theory for simulating excited state molecular dynamics and use time-resolved photoelectron spectroscopy measurements to benchmark the theory. We perform trajectory surface hopping simulations for uracil excited to the first bright state (ππ*) using three different levels of theory (CASSCF, MRCIS, and XMS-CASPT2) in order to understand the role of dynamical correlation in determining the excited state dynamics, with a focus on the coupling between different electronic states and internal conversion back to the ground state. These dynamics calculations are used to simulate the time-resolved photoelectron spectra. The comparison of the calculated and measured spectra allows us to draw conclusions regarding the relative insights and quantitative accuracy of the calculations at the three different levels of theory, demonstrating that detailed quantitative comparisons of time-resolved photoelectron spectra can be used to benchmark methodology.
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Affiliation(s)
- Pratip Chakraborty
- Department of Chemistry, Temple University, Philadelphia, Pennsylvania 19122, United States
| | - Yusong Liu
- Department of Physics and Astronomy, Stony Brook University, Stony Brook, New York 11794, United States
| | - Samuel McClung
- Department of Physics and Astronomy, Stony Brook University, Stony Brook, New York 11794, United States
| | - Thomas Weinacht
- Department of Physics and Astronomy, Stony Brook University, Stony Brook, New York 11794, United States
| | - Spiridoula Matsika
- Department of Chemistry, Temple University, Philadelphia, Pennsylvania 19122, United States
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37
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Milovanović B, Novak J, Etinski M, Domcke W, Došlić N. Simulation of UV absorption spectra and relaxation dynamics of uracil and uracil-water clusters. Phys Chem Chem Phys 2021; 23:2594-2604. [PMID: 33475644 DOI: 10.1039/d0cp05618a] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Despite many studies, the mechanisms of nonradiative relaxation of uracil in the gas phase and in aqueous solution are still not fully resolved. Here we combine theoretical UV absorption spectroscopy with nonadiabatic dynamics simulations to identify the photophysical mechanisms that can give rise to experimentally observed decay time constants. We first compute and theoretically assign the electronic spectra of uracil using the second-order algebraic-diagrammatic-construction (ADC(2)) method. The obtained electronic states, their energy differences and state-specific solvation effects are the prerequisites for understanding the photodynamics. We then use nonadiabatic trajectory-surface-hopping dynamics simulations to investigate the photoinduced dynamics of uracil and uracil-water clusters. In contrast to previous studies, we found that a single mechanism - the ethylenic twist around the C[double bond, length as m-dash]C bond - is responsible for the ultrafast component of the nonradiative decay, both in the gas phase and in solution. Very good agreement with the experimentally determined ultrashort decay time constants is obtained.
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Affiliation(s)
| | - Jurica Novak
- Department of Physical Chemistry, Ruđer Bošković Institute, Zagreb, Croatia. and Higher Medical and Biological School, South Ural State University, Chelyabinsk, Russia
| | - Mihajlo Etinski
- University of Belgrade, Faculty of Physical Chemistry, Belgrade, Serbia
| | - Wolfgang Domcke
- Department of Chemistry, Technical University of Munich, Garching, Germany
| | - Nađa Došlić
- Department of Physical Chemistry, Ruđer Bošković Institute, Zagreb, Croatia.
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38
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Green JA, Jouybari MY, Aranda D, Improta R, Santoro F. Nonadiabatic Absorption Spectra and Ultrafast Dynamics of DNA and RNA Photoexcited Nucleobases. Molecules 2021; 26:1743. [PMID: 33804640 PMCID: PMC8003674 DOI: 10.3390/molecules26061743] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2021] [Revised: 03/12/2021] [Accepted: 03/14/2021] [Indexed: 11/16/2022] Open
Abstract
We have recently proposed a protocol for Quantum Dynamics (QD) calculations, which is based on a parameterisation of Linear Vibronic Coupling (LVC) Hamiltonians with Time Dependent (TD) Density Functional Theory (TD-DFT), and exploits the latest developments in multiconfigurational TD-Hartree methods for an effective wave packet propagation. In this contribution we explore the potentialities of this approach to compute nonadiabatic vibronic spectra and ultrafast dynamics, by applying it to the five nucleobases present in DNA and RNA. For all of them we computed the absorption spectra and the dynamics of ultrafast internal conversion (100 fs timescale), fully coupling the first 2-3 bright states and all the close by dark states, for a total of 6-9 states, and including all the normal coordinates. We adopted two different functionals, CAM-B3LYP and PBE0, and tested the effect of the basis set. Computed spectra are in good agreement with the available experimental data, remarkably improving over pure electronic computations, but also with respect to vibronic spectra obtained neglecting inter-state couplings. Our QD simulations indicate an effective population transfer from the lowest energy bright excited states to the close-lying dark excited states for uracil, thymine and adenine. Dynamics from higher-energy states show an ultrafast depopulation toward the more stable ones. The proposed protocol is sufficiently general and automatic to promise to become useful for widespread applications.
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Affiliation(s)
- James A. Green
- CNR—Consiglio Nazionale delle Ricerche, Istituto di Biostrutture e Bioimmagini (IBB-CNR), Via Mezzocannone 16, I-80136 Napoli, Italy;
| | - Martha Yaghoubi Jouybari
- CNR—Consiglio Nazionale Delle Ricerche, Istituto di Chimica dei Composti Organo Metallici (ICCOM-CNR), SS di Pisa, Area Della Ricerca, Via G. Moruzzi 1, I-56124 Pisa, Italy; (M.Y.J.); (D.A.)
| | - Daniel Aranda
- CNR—Consiglio Nazionale Delle Ricerche, Istituto di Chimica dei Composti Organo Metallici (ICCOM-CNR), SS di Pisa, Area Della Ricerca, Via G. Moruzzi 1, I-56124 Pisa, Italy; (M.Y.J.); (D.A.)
| | - Roberto Improta
- CNR—Consiglio Nazionale delle Ricerche, Istituto di Biostrutture e Bioimmagini (IBB-CNR), Via Mezzocannone 16, I-80136 Napoli, Italy;
| | - Fabrizio Santoro
- CNR—Consiglio Nazionale Delle Ricerche, Istituto di Chimica dei Composti Organo Metallici (ICCOM-CNR), SS di Pisa, Area Della Ricerca, Via G. Moruzzi 1, I-56124 Pisa, Italy; (M.Y.J.); (D.A.)
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39
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Valverde D, Mai S, Sanches de Araújo AV, Canuto S, González L, Borin AC. On the population of triplet states of 2-seleno-thymine. Phys Chem Chem Phys 2021; 23:5447-5454. [PMID: 33650609 DOI: 10.1039/d1cp00041a] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
The population and depopulation mechanisms leading to the lowest-lying triplet states of 2-Se-Thymine were studied at the MS-CASPT2/cc-pVDZ level of theory. Several critical points on different potential energy hypersurfaces were optimized, including minima, conical intersections, and singlet-triplet crossings. The accessibility of all relevant regions on the potential energy hypersurfaces was investigated by means of minimum energy paths and linear interpolation in internal coordinates techniques. Our analysis indicates that, after the population of the bright S2 state in the Franck-Condon region, the first photochemical event is a barrierless evolution towards one of its two minima. After that, three viable photophysical deactivation paths can take place. In one of them, the population in the S2 state is transferred to the T2 state via intersystem crossing and subsequently to the T1 state by internal conversion. Alternatively, the S1 state could be accessed by internal conversion through two distinct conical intersections with S2 state followed by singlet-triplet crossing with the T2 state. The absence of a second minimum on the T1 state and a small energy barrier on pathway along the potential energy surface towards the ground state from the lowest triplet state are attributed as potential reasons to explain why the lifetime of the triplet state of 2-Se-Thymine might be reduced in comparison with its thio-analogue.
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Affiliation(s)
- Danillo Valverde
- Institute of Physics, University of São Paulo, Rua do Matão 1371. 05508-090, São Paulo, SP, Brazil
| | - Sebastian Mai
- Photonics Institute, Vienna University of Technology, Gußhausstraße 27-29, 1040 Vienna, Austria and Institute of Theoretical Chemistry, Faculty of Chemistry, University of Vienna, Währinger Straße 17, 1090 Vienna, Austria.
| | | | - Sylvio Canuto
- Institute of Physics, University of São Paulo, Rua do Matão 1371. 05508-090, São Paulo, SP, Brazil
| | - Leticia González
- Institute of Theoretical Chemistry, Faculty of Chemistry, University of Vienna, Währinger Straße 17, 1090 Vienna, Austria.
| | - Antonio Carlos Borin
- Department of Fundamental Chemistry, Institute of Chemistry, University of São Paulo, Av. Prof. Lineu Prestes 748. 05508-000, São Paulo, SP, Brazil.
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40
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Fedotov DA, Paul AC, Posocco P, Santoro F, Garavelli M, Koch H, Coriani S, Improta R. Excited-State Absorption of Uracil in the Gas Phase: Mapping the Main Decay Paths by Different Electronic Structure Methods. J Chem Theory Comput 2021; 17:1638-1652. [PMID: 33529532 DOI: 10.1021/acs.jctc.0c01150] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
We present a computational study of the one-photon and excited-state absorption (ESA) from the two lowest energy excited states of uracil in the gas phase: an nπ* dark state (1n) and the lowest energy bright ππ* state (1π). The predictions of six different linear response electronic structure methods, namely, TD-CAM-B3LYP, EOM-CCSD, EOM-CC3, ADC(2), ADC(2)-x, and ADC(3) are critically compared. In general, the spectral shapes predicted by TD-CAM-B3LYP, EOM-CCSD, EOM-CC3, and ADC(3) are fairly similar, though the quality of TD-CAM-B3LYP slightly deteriorates in the high-energy region. By computing the spectra at some key structures on different potential energy surfaces (PES), that is, the Franck-Condon point, the 1n minimum, and structures representative of different regions of the 1π PES, we obtain important insights into the shift of the ESA spectra, following the motion of the wavepacket on the excited-state PES. Though 1π has larger ESA than 1n, some spectral regions are dominated by these latter signals. Aside from its methodological interest, we thus obtain interesting indications to interpret transient absorption spectra to disentangle the photoactivated dynamics of nucleobases.
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Affiliation(s)
- Daniil A Fedotov
- DTU Chemistry, Technical University of Denmark, Kemitorvet Bldg 207, DK-2800 Kongens Lyngby, Denmark
| | - Alexander C Paul
- Department of Chemistry, NTNU-Norwegian University of Science and Technology, N-7491 Trondheim, Norway
| | - Paolo Posocco
- Dipartimento di Scienze Chimiche e Farmaceutiche, Università degli Studi di Trieste, via L. Giorgieri 1, I-34127 Trieste, Italy
| | - Fabrizio Santoro
- Istituto di Chimica dei Composti Organometallici (ICCOM-CNR), Area della Ricerca del CNR, Via Moruzzi 1, I-56124 Pisa, Italy
| | - Marco Garavelli
- Department of Industrial Chemistry "Toso Montanari", Università degli Studi di Bologna, I-40126 Bologna, Italy
| | - Henrik Koch
- Department of Chemistry, NTNU-Norwegian University of Science and Technology, N-7491 Trondheim, Norway.,Scuola Normale Superiore, Piazza dei Cavalieri 7, I-56100 Pisa, Italy
| | - Sonia Coriani
- DTU Chemistry, Technical University of Denmark, Kemitorvet Bldg 207, DK-2800 Kongens Lyngby, Denmark.,Department of Chemistry, NTNU-Norwegian University of Science and Technology, N-7491 Trondheim, Norway
| | - Roberto Improta
- Istituto di Biostrutture e Bioimmagini-CNR, Via Mezzocannone 6, I-80134 Napoli, Italy
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41
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Chakraborty P, Liu Y, Weinacht T, Matsika S. Effect of dynamic correlation on the ultrafast relaxation of uracil in the gas phase. Faraday Discuss 2021; 228:266-285. [DOI: 10.1039/d0fd00110d] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
High level multi-reference non-adiabatic dynamics simulations reveal that uracil’s photoexcited S2 state decays very quickly without any significant trapping.
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Affiliation(s)
| | - Yusong Liu
- Department of Physics and Astronomy
- Stony Brook University
- New York 11794
- USA
| | - Thomas Weinacht
- Department of Physics and Astronomy
- Stony Brook University
- New York 11794
- USA
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42
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Ivanov SP, Ostakhov SS, Abdrakhimova GS, Akhiyarov AA, Khursan SL. On the use of the spectral luminescent method for studying acid-base equilibria of uracil derivatives in aqueous solutions. Biophys Chem 2020; 266:106432. [PMID: 32771804 DOI: 10.1016/j.bpc.2020.106432] [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: 05/19/2020] [Revised: 07/07/2020] [Accepted: 07/11/2020] [Indexed: 11/20/2022]
Abstract
The effect of pH on fluorescence parameters (spectral composition, intensity Ifl, and quantum yield φ) of thymine (T), 5-fluorouracil (FU) and 6-aminouracil (AU) have been investigated in aqueous solutions. As found, there is the regularity of the changes in the spectral composition, intensity, and quantum yields of uracil fluorescence depending on pH. The constants of the acid-base equilibria of uracils (pKa) determined by the fluorescence titration method are: 9.9 (T), 8.0 (FU), and 9.1 (AU) at 298 K. These pKa1 values satisfactorily agree with the previous estimates obtained by independent experimental or quantum chemical methods. The possibilities of the spectral fluorescence method for the quantitative description of the acid-base equilibria of uracils depending on the fluorescent features of the pyrimidinedione and its conjugate base are discussed.
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Affiliation(s)
- Sergey P Ivanov
- Ufa Institute of Chemistry, Ufa Federal Research Center of the Russian Academy of Sciences, 71 Prospekt Oktyabrya, 450054 Ufa, Russian Federation.
| | - Sergei S Ostakhov
- Ufa Institute of Chemistry, Ufa Federal Research Center of the Russian Academy of Sciences, 71 Prospekt Oktyabrya, 450054 Ufa, Russian Federation
| | - Gulnaz S Abdrakhimova
- Ufa Institute of Chemistry, Ufa Federal Research Center of the Russian Academy of Sciences, 71 Prospekt Oktyabrya, 450054 Ufa, Russian Federation
| | - Aidar A Akhiyarov
- Ufa Institute of Chemistry, Ufa Federal Research Center of the Russian Academy of Sciences, 71 Prospekt Oktyabrya, 450054 Ufa, Russian Federation
| | - Sergey L Khursan
- Ufa Institute of Chemistry, Ufa Federal Research Center of the Russian Academy of Sciences, 71 Prospekt Oktyabrya, 450054 Ufa, Russian Federation
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43
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Mancini G, Del Galdo S, Chandramouli B, Pagliai M, Barone V. Computational Spectroscopy in Solution by Integration of Variational and Perturbative Approaches on Top of Clusterized Molecular Dynamics. J Chem Theory Comput 2020; 16:5747-5761. [PMID: 32697580 PMCID: PMC8009517 DOI: 10.1021/acs.jctc.0c00454] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Abstract
![]()
Multiscale QM/MM approaches have
become the most suitable and effective
methods for the investigation of spectroscopic properties of medium-
or large-size chromophores in condensed phases. On these grounds,
we are developing a novel workflow aimed at improving the generality,
reliability, and ease of use of the available tools. In the present
paper, we report the latest developments of such an approach with
specific reference to a general workplan starting with the addition
of acetonitrile to the panel of solvents already available in the
General Liquid Optimized Boundary (GLOB) model enforcing nonperiodic
boundary conditions (NPBC). Next, the solvatochromic shifts induced
by acetonitrile on both rigid (uracil and thymine) and flexible (thyrosine)
chromophores have been studied introducing in our software a number
of new features ranging from rigid-geometry NPBC molecular dynamics
based on the quaternion formalism to a full integration of variational
(ONIOM) and perturbative (perturbed matrix method (PMM)) approaches
for describing different solute–solvent topologies and local
fluctuations, respectively. Finally, thymine and uracil have been
studied also in methanol to point out the generality of the computational
strategy. While further developments are surely needed, the strengths
of our integrated approach even in its present version are demonstrated
by the accuracy of the results obtained by an unsupervised approach
and coupled to a computational cost strongly reduced with respect
to that of conventional QM/MM models without any appreciable accuracy
deterioration.
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Affiliation(s)
- Giordano Mancini
- Scuola Normale Superiore di Pisa, Piazza dei Cavalieri 7, I-56126 Pisa, Italy.,Istituto Nazionale di Fisica Nucleare (INFN) sezione di Pisa, Largo Bruno Pontecorvo 3, 56127 Pisa, Italy
| | - Sara Del Galdo
- Scuola Normale Superiore di Pisa, Piazza dei Cavalieri 7, I-56126 Pisa, Italy
| | | | - Marco Pagliai
- Dipartimento di Chimica "Ugo Schiff", Università degli Studi di Firenze, Via della Lastruccia 3, 50019 Sesto Fiorentino, Italy
| | - Vincenzo Barone
- Scuola Normale Superiore di Pisa, Piazza dei Cavalieri 7, I-56126 Pisa, Italy.,Istituto Nazionale di Fisica Nucleare (INFN) sezione di Pisa, Largo Bruno Pontecorvo 3, 56127 Pisa, Italy
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44
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Omidyan R, Abedini F, Shahrokh L, Azimi G. Excited State Deactivation Mechanism in Protonated Uracil: New Insights from Theoretical Studies. J Phys Chem A 2020; 124:5089-5097. [PMID: 32469520 DOI: 10.1021/acs.jpca.0c02284] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
We have conducted here a theoretical exploration, discussing the distinct excited state lifetimes reported experimentally for the two lowest lying protonated isomers of uracil. In this regard, the first-principal computational levels as well as the nonadiabatic surface hopping dynamics have been employed. It has been revealed that relaxation of the 1ππ* state of enol-enol form (EE+) to the ground is barrier-free via out-of-plane coordinates, resulting in an ultrashort S1 lifetime of this species. For the second most stable isomer (EK+), however, a significant barrier predicted in the CASPT2 S1 potential energy profile along the twisting coordinate has been proposed to explain the relevant long lifetime reported experimentally.
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Affiliation(s)
- Reza Omidyan
- Department of Chemistry, University of Isfahan, 81746-73441 Isfahan, Iran
| | - Fatemeh Abedini
- Department of Chemistry, University of Isfahan, 81746-73441 Isfahan, Iran
| | - Leila Shahrokh
- Department of Chemistry, University of Isfahan, 81746-73441 Isfahan, Iran
| | - Gholamhassan Azimi
- Department of Chemistry, University of Isfahan, 81746-73441 Isfahan, Iran
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45
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Peng Q, Zhu YH, Zhang TS, Liu XY, Fang WH, Cui G. Selenium substitution effects on excited-state properties and photophysics of uracil: a MS-CASPT2 study. Phys Chem Chem Phys 2020; 22:12120-12128. [PMID: 32440669 DOI: 10.1039/d0cp01369b] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
The photophysics of selenium-substituted nucleobases has attracted recent experimental attention because they could serve as potential photosensitizers in photodynamic therapy. Herein, we present a comprehensive MS-CASPT2 study on the spectroscopic and excited-state properties, and photophysics of 2-selenouracil (2SeU), 4-selenouracil (4SeU), and 2,4-selenouracil (24SeU). Relevant minima, conical intersections, crossing points, and excited-state relaxation paths in the lowest five electronic states (i.e., S0, S1, S2, T2, and T1) are explored. On the basis of these results, their photophysical mechanisms are proposed. Upon photoirradiation to the bright S2 state, 2SeU quickly relaxes to its S2 minimum and then moves in an essentially barrierless way to a nearby S2/S1 conical intersection near which the S1 state is populated. Next, the S1 system arrives at an S1/T2/T1 intersection where a large S1/T1 spin-orbit coupling of 430.8 cm-1 makes the T1 state populated. In this state, a barrier of 6.8 kcal mol-1 will trap 2SeU for a while. In parallel, for 4SeU or 24SeU, the system first relaxes to the S2 minimum and then overcomes a small barrier to approach an S2/S1 conical intersection. Once hopping to the S1 state, there exists an extended region with very close S1, T2, and T1 energies. Similarly, a large S1/T1 spin-orbit coupling of 426.8 cm-1 drives the S1→ T1 intersystem crossing process thereby making the T1 state populated. Similarly, an energy barrier heavily suppresses electronic transition to the S0 state. The present work manifests that different selenium substitutions on uracil can lead to a certain extent of different vertical and adiabatic excitation energies, excited-state properties, and relaxation pathways. These insights could help understand the photophysics of selenium-substituted nucleobases.
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Affiliation(s)
- Qin Peng
- Key Laboratory of Theoretical and Computational Photochemistry, Ministry of Education, College of Chemistry, Beijing Normal University, Beijing 100875, China.
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46
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Shi Y, Zhao X, Wang C, Wang Y, Zhang S, Li P, Feng X, Jin B, Yuan M, Cui S, Sun Y, Zhang B, Sun S, Jin X, Wang H, Zhao G. Ultrafast Nonadiabatic Photoisomerization Dynamics Mechanism for the UV Photoprotection of Stilbenoids in Grape Skin. Chem Asian J 2020; 15:1478-1483. [PMID: 32196972 DOI: 10.1002/asia.202000219] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2020] [Revised: 03/18/2020] [Indexed: 12/12/2022]
Abstract
Natural UV photoprotection plays a vital role in physiological protection. It has been reported that UVC radiation can make resveratrol (RSV) and piceatannol (PIC) accumulate in grape skin. In this work, we demonstrated that RSV and PIC could significantly absorb UVA and UVB, and confirmed their satisfactory photostability. Furthermore, we clarified the UV photoprotection mechanism of typical stilbenoids of RSV and PIC for the first time by using combined femtosecond transient absorption (FTA) spectroscopy and time-dependent density functional theory (TD-DFT) calculations. RSV and PIC can be photoexcited to the excited state after UVA and UVB absorption. Subsequently, the photoisomerized RSV and PIC quickly relax to the ground state via nonadiabatic transition from the S1 state at a conical intersection (CI) position between potential energy surfaces (PESs) of S1 and S0 states. This ultrafast trans-cis photoisomerization will take place within a few tens of picoseconds. As a result, the UV energy absorbed by RSV and PIC could be dissipated by an ultrafast nonadiabatic photoisomerization process.
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Affiliation(s)
- Yanan Shi
- Tianjin Key Laboratory of Molecular Optoelectronic Sciences National Demonstration Center for Experimental Chemistry & Chemical engineering Education National Virtual Simulation Experimental Teaching Center for Chemistry & Chemical Engineering Education Department of Chemistry, School of Science Tianjin University, Tianjin, 300354, P. R. China
| | - Xiaoying Zhao
- Tianjin Key Laboratory of Molecular Optoelectronic Sciences National Demonstration Center for Experimental Chemistry & Chemical engineering Education National Virtual Simulation Experimental Teaching Center for Chemistry & Chemical Engineering Education Department of Chemistry, School of Science Tianjin University, Tianjin, 300354, P. R. China
| | - Chao Wang
- Tianjin Key Laboratory of Molecular Optoelectronic Sciences National Demonstration Center for Experimental Chemistry & Chemical engineering Education National Virtual Simulation Experimental Teaching Center for Chemistry & Chemical Engineering Education Department of Chemistry, School of Science Tianjin University, Tianjin, 300354, P. R. China
| | - Ye Wang
- State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics Wuhan Institute of Physics and Mathematics, Chinese Academy of Sciences, Wuhan, 430071, China
| | - Song Zhang
- State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics Wuhan Institute of Physics and Mathematics, Chinese Academy of Sciences, Wuhan, 430071, China
| | - Peng Li
- Institute of Molecular Sciences and Engineering, Shandong University, Qingdao, 266235, P. R. China
| | - Xia Feng
- Tianjin Key Laboratory of Molecular Optoelectronic Sciences National Demonstration Center for Experimental Chemistry & Chemical engineering Education National Virtual Simulation Experimental Teaching Center for Chemistry & Chemical Engineering Education Department of Chemistry, School of Science Tianjin University, Tianjin, 300354, P. R. China
| | - Bing Jin
- State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics Wuhan Institute of Physics and Mathematics, Chinese Academy of Sciences, Wuhan, 430071, China
| | - Minghu Yuan
- State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics Wuhan Institute of Physics and Mathematics, Chinese Academy of Sciences, Wuhan, 430071, China
| | - Shen Cui
- Tianjin Key Laboratory of Molecular Optoelectronic Sciences National Demonstration Center for Experimental Chemistry & Chemical engineering Education National Virtual Simulation Experimental Teaching Center for Chemistry & Chemical Engineering Education Department of Chemistry, School of Science Tianjin University, Tianjin, 300354, P. R. China
| | - Yan Sun
- Tianjin Key Laboratory of Molecular Optoelectronic Sciences National Demonstration Center for Experimental Chemistry & Chemical engineering Education National Virtual Simulation Experimental Teaching Center for Chemistry & Chemical Engineering Education Department of Chemistry, School of Science Tianjin University, Tianjin, 300354, P. R. China
| | - Bing Zhang
- State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics Wuhan Institute of Physics and Mathematics, Chinese Academy of Sciences, Wuhan, 430071, China
| | - Shuqing Sun
- Tianjin Key Laboratory of Molecular Optoelectronic Sciences National Demonstration Center for Experimental Chemistry & Chemical engineering Education National Virtual Simulation Experimental Teaching Center for Chemistry & Chemical Engineering Education Department of Chemistry, School of Science Tianjin University, Tianjin, 300354, P. R. China
| | - Xiaoning Jin
- Tianjin Key Laboratory of Molecular Optoelectronic Sciences National Demonstration Center for Experimental Chemistry & Chemical engineering Education National Virtual Simulation Experimental Teaching Center for Chemistry & Chemical Engineering Education Department of Chemistry, School of Science Tianjin University, Tianjin, 300354, P. R. China
| | - Haiyuan Wang
- Tianjin Key Laboratory of Molecular Optoelectronic Sciences National Demonstration Center for Experimental Chemistry & Chemical engineering Education National Virtual Simulation Experimental Teaching Center for Chemistry & Chemical Engineering Education Department of Chemistry, School of Science Tianjin University, Tianjin, 300354, P. R. China
| | - Guangjiu Zhao
- Tianjin Key Laboratory of Molecular Optoelectronic Sciences National Demonstration Center for Experimental Chemistry & Chemical engineering Education National Virtual Simulation Experimental Teaching Center for Chemistry & Chemical Engineering Education Department of Chemistry, School of Science Tianjin University, Tianjin, 300354, P. R. China
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47
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Banerjee P, Mondal D, Ghosh M, Mukherjee D, Nandi PK, Maiti TK, Sarkar N. Selective Self-Assembly of 5-Fluorouracil through Nonlinear Solvent Response Modulates Membrane Dynamics. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2020; 36:2707-2719. [PMID: 32097563 DOI: 10.1021/acs.langmuir.9b03544] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Controllable self-assembly and understanding of the interaction between single metabolite fibrils and live-cell membranes have paramount importance in providing minimal treatment in several neurodegenerative disorders. Here, utilizing the nonlinear nature and peculiar hydrogen bonding behavior of the dimethyl sulfoxide (DMSO)-water mixture, the selective self-assembly of a single metabolite 5-fluorouracil (5-FU) is achieved. A direct correlation between water availability and selective self-assembly of 5-FU is ratified from the excited-state dynamics. The specific fibrillar structures of 5-FU exhibit a great potential to modulate live cell membrane fluidity and model membrane lipid distribution. After 5-FU fibril addition, a disorder of H-bonded water molecules arises several layers beyond the first hydration shell of the polar headgroups, which essentially modifies interfacial water structure and dynamics. Overall, our results shed light on the role of solvent to govern specific self-assembly and also lay the foundation accounting for the earlier stage of several diseases and multidrug resistance.
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Affiliation(s)
- Pavel Banerjee
- Department of Chemistry, Indian Institute of Technology Kharagpur, Kharagpur 721302, West Bengal, India
| | - Dipankar Mondal
- Department of Chemistry, Indian Institute of Technology Kharagpur, Kharagpur 721302, West Bengal, India
| | - Meghna Ghosh
- Department of Chemistry, Indian Institute of Technology Kharagpur, Kharagpur 721302, West Bengal, India
| | - Devdeep Mukherjee
- Department of Biotechnology, Indian Institute of Technology Kharagpur, Kharagpur 721302, West Bengal, India
| | - Pratyush Kiran Nandi
- Department of Chemistry, Indian Institute of Technology Kharagpur, Kharagpur 721302, West Bengal, India
| | - Tapas Kumar Maiti
- Department of Biotechnology, Indian Institute of Technology Kharagpur, Kharagpur 721302, West Bengal, India
| | - Nilmoni Sarkar
- Department of Chemistry, Indian Institute of Technology Kharagpur, Kharagpur 721302, West Bengal, India
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48
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Xu R, Hu Z, Wang X, Liu Y, Zhou Z, Xu J, Sun Z, Sun H, Chen J. Intramolecular Charge Transfer in 5-Halogen Cytidines Revealed by Femtosecond Time-Resolved Spectroscopy. J Phys Chem B 2020; 124:2560-2567. [DOI: 10.1021/acs.jpcb.0c00455] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Affiliation(s)
- Rui Xu
- State Key Laboratory of Precision Spectroscopy, East China Normal University, Shanghai 200062, China
| | - Zhubin Hu
- State Key Laboratory of Precision Spectroscopy, East China Normal University, Shanghai 200062, China
| | - Xueli Wang
- State Key Laboratory of Precision Spectroscopy, East China Normal University, Shanghai 200062, China
| | - Yufeng Liu
- State Key Laboratory of Precision Spectroscopy, East China Normal University, Shanghai 200062, China
| | - Zhongneng Zhou
- State Key Laboratory of Precision Spectroscopy, East China Normal University, Shanghai 200062, China
| | - Jianhua Xu
- State Key Laboratory of Precision Spectroscopy, East China Normal University, Shanghai 200062, China
- Collaborative Innovation Center of Extreme Optics, Shanxi University, Taiyuan, Shanxi 030006, China
| | - Zhenrong Sun
- State Key Laboratory of Precision Spectroscopy, East China Normal University, Shanghai 200062, China
| | - Haitao Sun
- State Key Laboratory of Precision Spectroscopy, East China Normal University, Shanghai 200062, China
- NYU-ECNU Center for Computational Chemistry at NYU Shanghai, Shanghai 200062, China
| | - Jinquan Chen
- State Key Laboratory of Precision Spectroscopy, East China Normal University, Shanghai 200062, China
- Collaborative Innovation Center of Extreme Optics, Shanxi University, Taiyuan, Shanxi 030006, China
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Banerjee P, Pyne A, Sarkar N. Understanding the Self-Assembling Behavior of Biological Building Block Molecules: A Spectroscopic and Microscopic Approach. J Phys Chem B 2020; 124:2065-2080. [PMID: 32081003 DOI: 10.1021/acs.jpcb.9b09123] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
"Mother nature" utilizes molecular self-assembly as an efficient tool to design several fascinating supramolecular architectures from simple building blocks like amino acids, peptides, and nucleobases. The self-assembling behavior of various biologically important molecules, morphological outcomes, molecular mechanism of association, and finally their applications in the real world draw broad interest from chemical and biological point of views. In this present Feature Article, the amyloid hypothesis is extended to include nonproteinaceous single metabolites that invoke a new paradigm for the pathology of inborn metabolic disorders. In this scenario, we dedicate this paper to understanding the morphological consequences and mechanistic insight of the self-assembly of some important amino acids (e.g., l-phenylalanine, l-tyrosine, glycine, etc.) and nucleobases (adenine and eight uracil moiety derivatives). Using proper spectroscopic and microscopic tools, distinct assembling mechanisms of different amino acids and nucleobases have been established. Again, lanthanides, polyphenolic compounds such as crown ethers, and a worldwide drink, beer, are elegantly employed as inhibitors of the resulting fibrillar aggregated structures. As a consequence, this study will cover literally a vast region in the self-assembling outcomes of single biologically important molecules, and therefore, we expect that a detailed understanding of such morphological outcomes using spectroscopic and microscopic approaches may open a new paradigm in this burgeoning field.
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Affiliation(s)
- Pavel Banerjee
- Department of Chemistry, Indian Institute of Technology Kharagpur, Kharagpur 721302 WB, India
| | - Arghajit Pyne
- Department of Chemistry, Indian Institute of Technology Kharagpur, Kharagpur 721302 WB, India
| | - Nilmoni Sarkar
- Department of Chemistry, Indian Institute of Technology Kharagpur, Kharagpur 721302 WB, India
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Martinez-Fernandez L, Gustavsson T, Diederichsen U, Improta R. Excited State Dynamics of 8-Vinyldeoxyguanosine In Aqueous Solution Studied by Time-Resolved Fluorescence Spectroscopy and Quantum Mechanical Calculations. Molecules 2020; 25:E824. [PMID: 32070032 PMCID: PMC7071107 DOI: 10.3390/molecules25040824] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2020] [Revised: 02/10/2020] [Accepted: 02/10/2020] [Indexed: 02/08/2023] Open
Abstract
The fluorescent base guanine analog, 8-vinyl-deoxyguanosine (8vdG), is studied in solution using a combination of optical spectroscopies, notably femtosecond fluorescence upconversion and quantum chemical calculations, based on time-dependent density functional theory (TD-DFT) and including solvent effect by using a mixed discrete-continuum model. In all investigated solvents, the fluorescence is very long lived (3-4 ns), emanating from a stable excited state minimum with pronounced intramolecular charge-transfer character. The main non-radiative decay channel features a sizeable energy barrier and it is affected by the polarity and the H-bonding properties of the solvent. Calculations provide a picture of dynamical solvation effects fully consistent with the experimental results and show that the photophysical properties of 8vdG are modulated by the orientation of the vinyl group with respect to the purine ring, which in turn depends on the solvent. These findings may have importance for the understanding of the fluorescence properties of 8vdG when incorporated in a DNA helix.
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Affiliation(s)
- Lara Martinez-Fernandez
- Departamento de Química, Facultad de Ciencias and IADCHEM (Institute for Advanced Research in Chemistry) Universidad Autónoma de Madrid, Cantoblanco, 28049 Madrid, Spain;
| | - Thomas Gustavsson
- Université Paris-Saclay, CEA, CNRS, LIDYL, 91191 Gif-sur-Yvette, France
| | - Ulf Diederichsen
- Univ Goettingen, Inst Organ & Biomol Chem, Tammannstr 2, D-37077 Goettingen, Germany;
| | - Roberto Improta
- Istituto di Biostrutture e Bioimmagini, CNR, Via Mezzocannone 16, I-80134 Napoli, Italy
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