4.6 Article

A State-Specific PCM-DFT method to include dynamic solvent effects in the calculation of ionization energies: Application to DNA bases

期刊

CHEMICAL PHYSICS LETTERS
卷 634, 期 -, 页码 20-24

出版社

ELSEVIER SCIENCE BV
DOI: 10.1016/j.cplett.2015.05.045

关键词

-

资金

  1. CNR/CNRS PICS project
  2. French Agency for Research [ANR-10-BLAN-0809-01, ANR-12-BS08-0001-01]
  3. Regione Campania

向作者/读者索取更多资源

A State-Specific PCM-DFT method taking into account dynamical solvent effects in the calculation of ionization energies (IEs) is reported. Mono-methylated nucleobases, representative of DNA blocks, are used as a test case. The accuracy of several functionals is tested, the M05-2X functional providing the most consistent performance. The inclusion of some molecules of the first hydration shell does not significantly affect the computed IE. The obtained vertical and adiabatic IEs are in good agreement with the available experimental and computational results, supporting the reliability of our method, enabling the calculation of first and upper ionization energies by using a single approach. (C) 2015 Published by Elsevier B.V.

作者

我是这篇论文的作者
点击您的名字以认领此论文并将其添加到您的个人资料中。

评论

主要评分

4.6
评分不足

次要评分

新颖性
-
重要性
-
科学严谨性
-
评价这篇论文

推荐

Article Biochemistry & Molecular Biology

Early steps of oxidative damage in DNA quadruplexes are position-dependent: Quantum mechanical and molecular dynamics analysis of human telomeric sequence containing ionized guanine

Haritha Asha, Petr Stadlbauer, Lara Martinez-Fernandez, Pavel Banas, Jiri Sponer, Roberto Improta, Luciana Esposito

Summary: The study investigates the structural behavior of a quadruplex helix sequence in human telomeres when one of the G bases is ionized to G(center dot+). It is found that the position of G(center dot+) influences structural rearrangements, electrostatic repulsion, and solvent exposure, providing new insights into guanine reactions. The research suggests structural determinants of reactivity and implications for understanding reactivity in other G-quadruplex topologies.

INTERNATIONAL JOURNAL OF BIOLOGICAL MACROMOLECULES (2022)

Article Chemistry, Physical

The Excited State Dynamics of a Mutagenic Cytidine Etheno Adduct Investigated by Combining Time-Resolved Spectroscopy and Quantum Mechanical Calculations

Paloma Lizondo-Aranda, Lara Martinez-Fernandez, Miguel A. Miranda, Roberto Improta, Thomas Gustavsson, Virginie Lhiaubet-Vallet

Summary: Joint femtosecond fluorescence upconversion experiments and theoretical calculations provide unprecedented characterization and understanding of the mutagenic etheno adduct εdC excited state relaxation. The fluorescence behavior of εdC is modified compared to dC, with increased lifetime and quantum yield. Quantum mechanical calculations reveal the involvement of a conical intersection in the nonradiative decay pathway, which explains the unique fluorescence properties of εdC and εdCH(+).

JOURNAL OF PHYSICAL CHEMISTRY LETTERS (2022)

Article Chemistry, Physical

Excited state absorption of DNA bases in the gas phase and in chloroform solution: a comparative quantum mechanical study

Daniil A. Fedotov, Alexander C. Paul, Henrik Koch, Fabrizio Santoro, Sonia Coriani, Roberto Improta

Summary: The excited state absorption (ESA) properties of four DNA bases were studied using different quantum mechanical methods. The calculated spectra were consistent with experimental results, supporting the accuracy of the computational approach.

PHYSICAL CHEMISTRY CHEMICAL PHYSICS (2022)

Article Biochemistry & Molecular Biology

High-Energy Long-Lived Emitting Mixed Excitons in Homopolymeric Adenine-Thymine DNA Duplexes

Ignacio Vaya, Thomas Gustavsson, Dimitra Markovitsi

Summary: This publication investigates the fluorescence properties of polymeric pA?pT and oligomeric A(20)?T-20 DNA duplexes using time-correlated single photon counting. It has been found that their emission on the nanosecond timescale is mainly determined by high-energy components peaking at a wavelength shorter than 305 nm. These components, attributed to mixed pi pi*/charge transfer excitons, are influenced by the duplex size and the ionic strength of the solution due to their anisotropy and sensitivity to base stacking. Identifying the impact of high-energy long-lived excited states on photochemical reactions through theoretical studies is a significant challenge.

MOLECULES (2022)

Article Chemistry, Analytical

Thienoguanosine brightness in DNA duplexes is governed by the localization of its ππ* excitation in the lowest energy absorption band

Stefano Ciaco, Krishna Gavvala, Vanille Greiner, Viola Mazzoleni, Pascal Didier, Marc Ruff, Lara Martinez-Fernandez, Roberto Improta, Yves Mely

Summary: This study investigates the fluorescence properties of Thienoguanosine (thG) in DNA duplexes and reveals a correlation between changes in fluorescence intensity and absorption properties under specific conditions.

METHODS AND APPLICATIONS IN FLUORESCENCE (2022)

Review Chemistry, Multidisciplinary

Nucleic Acids as a Playground for the Computational Study of the Photophysics and Photochemistry of Multichromophore Assemblies

Lara Martinez Fernandez, Fabrizio Santoro, Roberto Improta

Summary: This Account discusses the chemical physical effects of the interaction between light and multichromophoric assemblies (MCAs), aiming to control these processes based on our experience with nucleic acids. The article highlights the photophysics and photochemistry of DNA and its components, emphasizing the effects of nucleobases, reaction paths involving multiple bases, and factors such as backbone flexibility and solvent effect. The integration of complementary approaches, both computational and experimental, is stressed for a comprehensive understanding of the complex phenomena triggered by light absorption in MCAs.

ACCOUNTS OF CHEMICAL RESEARCH (2022)

Article Chemistry, Multidisciplinary

Solvent Effects on Ultrafast Charge Transfer Population: Insights from the Quantum Dynamics of Guanine-Cytosine in Chloroform

James A. Green, Sandra Gomez, Graham Worth, Fabrizio Santoro, Roberto Improta

Summary: The article discusses the charge transfer process from guanine to cytosine in solvent after light absorption. The research team members come from different research institutions.

CHEMISTRY-A EUROPEAN JOURNAL (2022)

Article Chemistry, Physical

Fluorescence of Bimolecular Guanine Quadruplexes: From Femtoseconds to Nanoseconds

Evangelos Balanikas, Thomas Gustavsson, Dimitra Markovitsi

Summary: This paper investigates the fluorescence characteristics of guanine quadruplexes (G4) formed by the association of two DNA strands in the presence of K+ cations. The maximum fluorescence spectrum is located at 334 nm with a quantum yield of 5.8 x 10-4. Ultrafast excitation transfer is found to be more efficient in this specific G4 structure due to the arrangement of peripheral thymines and their interaction with guanines. Additionally, a weak intensity excimer/exciplex emission band at 445 nm was observed, along with a long-lived fluorescence component at the blue side of the spectrum, which is uncommon for G4 structures.

JOURNAL OF PHYSICAL CHEMISTRY B (2023)

Article Chemistry, Medicinal

Computing the electronic circular dichroism spectrum of DNA quadruple helices of different topology: A critical test for a generalized excitonic model based on a fragment diabatization

Haritha Asha, James A. Green, Luciana Esposito, Fabrizio Santoro, Roberto Improta

Summary: This study uses the FrDEx model to simulate the ECD spectra of guanine-rich DNA sequences in quadruple helices with different topologies. The parameters of the FrDEx Hamiltonian are obtained from TD-DFT calculations with the M052X functional. The FrDEx spectra are in good agreement with the TD-DFT ones and show improvement compared to a standard excitonic Hamiltonian. The inclusion of the inner K+ cation in the calculation affects the ECD spectra.

CHIRALITY (2023)

Article Chemistry, Physical

The Ubiquity of High-Energy Nanosecond Fluorescence in DNA Duplexes

Thomas Gustavsson, Dimitra Markovitsi

Summary: Several studies have found that a significant part of DNA duplexes' intrinsic fluorescence decays with surprisingly long lifetimes at shorter wavelengths. This high-energy nanosecond emission (HENE) is hardly detectable in the fluorescence spectra of most duplexes, but it contrasts with the expected low-energy excimers/exciplexes. The excited states responsible for HENE remain unknown, and this Perspective provides a critical summary of experimental observations and theoretical approaches to foster future studies.

JOURNAL OF PHYSICAL CHEMISTRY LETTERS (2023)

Article Biochemistry & Molecular Biology

The Resonance Raman Spectrum of Cytosine in Water: Analysis of the Effect of Specific Solute-Solvent Interactions and Non-Adiabatic Couplings

Qiushuang Xu, Yanli Liu, Meishan Wang, Javier Cerezo, Roberto Improta, Fabrizio Santoro

Summary: In this study, the vibrational Resonance Raman (vRR) spectra of cytosine in water were computationally investigated using potential energy surfaces (PES) calculated by time-dependent density functional theory (TD-DFT) and CAM-B3LYP and PBE0 functionals. The close-lying and coupled electronic states of cytosine posed a challenge for the commonly used approach to compute vRR spectra. Two recently developed time-dependent approaches, based on either quantum dynamical numerical propagations or analytical correlation functions, were adopted to compute the vRR spectra. The inclusion of specific solute-solvent interactions remarkably improved the agreement with experiments by altering the composition of the normal modes.

MOLECULES (2023)

Article Biochemistry & Molecular Biology

Shedding Light on the Photophysics and Photochemistry of I-Motifs Using Quantum Mechanical Calculations

Roberto Improta

Summary: I-motifs are non-canonical DNA structures composed of intercalated hemiprotonated (CH.C)+ pairs. This study characterizes the photoactivated behavior of the (CH.C)+ core of I-motifs using time-dependent DFT calculations, providing a comprehensive understanding of their absorption, emission, and possible photochemical reactions. The results reproduced and assigned the spectral signatures of I-motifs, including infrared, absorption, fluorescence, and circular dichroism spectra, and proposed potential photoproducts through a photodimerization reaction with strong C?CH+ charge transfer character.

INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES (2023)

Article Chemistry, Physical

Effect of the DNA Polarity on the Relaxation of Its Electronic Excited States

Vasilis Petropoulos, Lorenzo Uboldi, Margherita Maiuri, Giulio Cerullo, Lara Martinez-Fernandez, Evangelos Balanikas, Dimitra Markovitsi

Summary: The polarity of DNA has been found to have an impact on the relaxation of DNA electronic excited states, with different nucleotide sequences leading to different optical properties.

JOURNAL OF PHYSICAL CHEMISTRY LETTERS (2023)

Article Biochemistry & Molecular Biology

The photophysics of protonated cytidine and hemiprotonated cytidine base pair: A computational study

Lara Martinez-Fernandez, Roberto Improta

Summary: In this study, the effect of pH reduction on the excited state processes of cytidine and a cytidine/cytidine pair in solution was investigated. Time-dependent density functional theory and CASSCF/CASPT2 calculations were used, along with a mixed discrete/continuum model to account for solvent effects. The results revealed the influence of N3 protonation on the steady-state infrared and absorption spectra of protonated cytidine, and predicted the presence of a non-radiative deactivation route for its spectroscopic state.

PHOTOCHEMISTRY AND PHOTOBIOLOGY (2023)

Review Biochemistry & Molecular Biology

Processes triggered in guanine quadruplexes by direct absorption of UV radiation: From fundamental studies toward optoelectronic biosensors

Dimitra Markovitsi

Summary: Guanine quadruplexes (GQs) are four-stranded DNA/RNA structures that show important polymorphism. Recent studies have explored the utilization of GQs in label-free and dye-free biosensors. This review discusses the fundamental studies on GQs and their potential in the design of optoelectronic biosensors using fluorescence or charge carriers directly from GQs. It explains how the excited state relaxation influences the fluorescence intensity and photoionization efficiency.

PHOTOCHEMISTRY AND PHOTOBIOLOGY (2023)

Correction Chemistry, Physical

Preparation and application of high performance PVDF/ PS electrospinning film-based triboelectric nanogenerator (vol 813, 140276, 2023)

Chen Luo, Yan Shao, Hua Yu, Hong-zhi Ma, Yu-hao Zhang, Long Gu, Bo Yin, Ming-bo Yang

CHEMICAL PHYSICS LETTERS (2024)

Article Chemistry, Physical

Complexes of the noble-gas atoms with borazine: Theoretical insights into structure, stability, and bonding character

Stefano Borocci, Armando Camerlingo, Felice Grandinetti, Maria Rutigliano, Nico Sanna

Summary: The complexes of He, Ne, Ar, Kr, and Xe with B3N3H6 were investigated using MP2, CCSD(T), and SAPT ab initio methods. The complexes can be described as mono-, di-, and tri-coordinated to the N atoms, with stability following the order N-mono < N-di < N-tri. The interactions are dominated by dispersion and the binding energies are within the range of 1 or 2 kcal mol(-1). The results were compared with a recent DFT study on larger BN sheets complexes [Phys. Chem. Chem. Phys. 24 (2022) 2554-2566.].

CHEMICAL PHYSICS LETTERS (2024)

Article Chemistry, Physical

Phosphoborane nanosheets as a sensing element for liquefied petroleum gas - A first-principles study

V. Nagarajan, R. Bhuvaneswari, R. Chandiramouli

Summary: In this study, stable phosphoborane was used as a sensor to detect isobutane and n-propane in Liquefied Petroleum Gas (LPG). Phosphoborane demonstrated structural stability and semiconducting nature, and exhibited promising adsorption properties for the LPG molecules.

CHEMICAL PHYSICS LETTERS (2024)

Article Chemistry, Physical

Analysis of Ca+(2S) + HD (v0=0, j0=0) → CaH plus /CaD plus plus D/H reaction dynamics using time-dependent wave packet method

Xiaoxi Xu, Zijiang Yang, Bayaer Buren, Maodu Chen

Summary: In this study, the time-dependent wave packet method was used to investigate the reaction channels and mechanisms of Ca+ + HD. The results show that the CaH+ + D reaction channel plays a primary role, which is consistent with experimental results. Complex forming and direct-abstraction reaction mechanisms exist in this reaction process.

CHEMICAL PHYSICS LETTERS (2024)

Article Chemistry, Physical

Silicon-Carbon nanofiber composite film for supercapacitor applications

Keshab Pandey, Hae Kyung Jeong

Summary: A free-standing silicon-carbon nanofiber composite film was synthesized and investigated for supercapacitor applications. It exhibited high specific capacitance, energy density, and power density. After 5000 cycles, the film showed excellent specific capacitance retention and Coulombic efficiency.

CHEMICAL PHYSICS LETTERS (2024)

Article Chemistry, Physical

Effects of surface polar unit densities on evaporation of nanosized water aggregation

Xinyu Zhang, Haosong Li, Xiaoyu Cao, Jing Gao, Yong Wei, Jianzhuo Zhu

Summary: The evaporation behavior of nanosized water aggregations on two-dimensional electroneutral solid surfaces with different surface polar unit densities was investigated. The results showed that the evaporation rate changes non-monotonically with the surface polar unit density, and the minimum evaporation rate is obtained when the surface has a modest surface polar unit ratio of 66.7%.

CHEMICAL PHYSICS LETTERS (2024)

Article Chemistry, Physical

High-performance triphylite-NaFePO4 synthesized by solvothermal sodium insertion process for sodium-ion batteries

Yanyan Xu, Rui Dai, Xiaojie Wang, Zhijun Qiao, Haowei Wen, Dianbo Ruan, Yuzuo Wang

Summary: This article presents an innovative solvothermal sodium insertion method for synthesizing Triphylite-NaFePO4, which demonstrates optimal electrochemical performance in sodium-ion batteries.

CHEMICAL PHYSICS LETTERS (2024)

Article Chemistry, Physical

Density functional theory of NO2 and N2O adsorption on the transition metal modified TiO2 surface

Meiyi Jiang, Kun Yang, Yancheng Liu, Li Yao

Summary: The geometric structure and electronic properties of transition metal M (M = Cu, Fe, Mn)-TiO2 (101) surface adsorbed by NO2 and N2O were calculated by density functional theory (DFT) and DFT + U theory. The results showed that the adsorption of NO2 and N2O on Mn and Fe atoms is more stable, and a large number of active electrons are formed around these atoms, facilitating the catalytic reactions.

CHEMICAL PHYSICS LETTERS (2024)

Article Chemistry, Physical

Carbon nanobracelets

Sergey A. Vyrko, Yulia G. Polynskaya, Nikita A. Matsokin, Andrey M. Popov, Andrey A. Knizhnik, Nikolai A. Poklonski, Yurii E. Lozovik

Summary: In this study, carbon nanobracelets, which are cyclic molecules composed of alternating polycyclic regions and double carbon chains, were investigated using spin-polarized density functional theory. The results show that carbon nanobracelets with odd number of monomers exhibit distinct electronic energy levels, band gaps, and carbon chain deformation compared to those with even number of monomers.

CHEMICAL PHYSICS LETTERS (2024)

Article Chemistry, Physical

Investigation of Ce-based buffer layers on electrochemical performance of YSZ-based symmetric solid oxide fuel cells

Chanchan Wang, Quan Yang, Yanzhi Ding, Xiaoyong Lu, Dong Tian

Summary: It has been found that the introduction of buffer layers improves the electrical performance of solid oxide fuel cells (SSOFCs). In this study, varying ratios of Gd-doped CeO2 were used as buffer layers in YSZ-based SSOFCs. The results demonstrate that the performance of SSOFCs is enhanced when a buffer layer is added, with the highest performance achieved using Ce0.8Gd0.2O2-delta (GDC20) as the buffer layer. This suggests that the use of GDC series buffer layers is an attractive strategy to optimize performance loss due to electrolyte-electrode interactions.

CHEMICAL PHYSICS LETTERS (2024)

Article Chemistry, Physical

A VUV photoionization study on the gas-phase synthesis of the first five-membered carbon ring-C7H6 isomers

Wang Li, Yi-Fan Zhang, Jia-Bin Huang, Chang-Yang Wang, Feng Zhang, Jiu-Zhong Yang, Long Zhao

Summary: The gas-phase reaction of propargyl with vinylacetylene was investigated using synchrotron photoionization and molecular-beam mass spectrometry methodologies. The formation mechanisms of the resulting cyclic structures were examined using quantum computations. Two previously unidentified isomers were detected and identified for the first time.

CHEMICAL PHYSICS LETTERS (2024)

Article Chemistry, Physical

Aspect ratio and quantum confinement tunable giant Two-Photon absorption from 1D CsPbI3 perovskite nanorods

Avijit Pramanik, Sanchita Kundu, Olorunsola Praise Kolawole, Kaelin Gates, Paresh Chandra Ray

Summary: This study investigates the influence of aspect ratio and quantum confinement on the single-photon and two-photon absorption cross-section of perovskite CsPbI3 nanorods. Experimental data shows that CsPbI3 nanorods have an extremely high two-photon absorption cross-section, significantly surpassing organic chromophores and other CsPbBr3 nanocrystals. Moreover, adjusting the aspect ratio can significantly enhance the absorption ability. Additionally, the study also reveals a moderate quantum confinement effect on the single-photon and two-photon absorption cross-section of the nanorods.

CHEMICAL PHYSICS LETTERS (2024)

Article Chemistry, Physical

Novel method for the prediction of distribution and elution characteristic of several drugs in cellulose diacetate-water system: Interaction between mixed solvent and cellulose diacetate

Hyon-Tae Pak, Jin-A Choe, Kyong-Sik Ju, Yong -Son Rim

Summary: Drug-loaded cellulose diacetate (CDA) membranes were prepared using different compositions of mixed solvent. The microstructure and performance of the membranes were investigated, and a method to predict drug release properties was proposed. The results showed that the composition of the mixed solvent significantly affected the overall performance of CDA membranes, and the release rates of drugs were related to Δdelta and the intrinsic viscosity of CDA.

CHEMICAL PHYSICS LETTERS (2024)

Article Chemistry, Physical

A potential energy surface of spectroscopic accuracy for a lithium clusters

Gabriella E. Ravin, E. Curotto

Summary: We have developed a systematic approach to optimize the training set sizes for neural networks in fitting ab initio potential energy surfaces. Using this approach, we have constructed several spectroscopic quality potential energy surfaces for [Li(H2)n]+, n = 1 - 9. The ground state properties have been computed for all the systems and selected states.

CHEMICAL PHYSICS LETTERS (2024)

Article Chemistry, Physical

Facile synthesis of NiS1.03@Ni7S6/carbon composites with the assistance of biomass resource for supercapacitors with superior electrochemical performance

Guohua Xu, Lei Xu, Feng Zhang, Chunling Yu, Yu Song

Summary: NiS1.03@Ni7S6/carbon composite was successfully prepared using corn stalk as a carbon source via a simple adsorption-sulphurization process. The composite exhibited a specific capacitance of 1554.6 F/g at 1 A/g as a supercapacitor electrode, with a capacitance retention rate of 80.4% after 5000 cycles. Furthermore, the NiS1.03@Ni7S6/carbon//AC asymmetric supercapacitor showed a high energy density of 41.2 Wh kg-1 at a power density of 750 W kg-1, and excellent cycling stability with 86.8% capacitance retention after 10,000 cycles.

CHEMICAL PHYSICS LETTERS (2024)