Roberto Improta
YOU?
Author Swipe
View article: Decoding the base flipping mechanism of the SET- and RING-associated (SRA) domain of the epigenetic UHRF1 protein
Decoding the base flipping mechanism of the SET- and RING-associated (SRA) domain of the epigenetic UHRF1 protein Open
Ubiquitin-like, containing PHD and RING fingers domains 1 (UHRF1) plays a pivotal role in replicating DNA methylation patterns during cell division. Acting as a DNA reader, UHRF1, via its SET- and RING-associated (SRA) domain, recognizes h…
View article: Fluorescent Silver Nanoclusters Associated with Double-Stranded Poly(dGdC) DNA
Fluorescent Silver Nanoclusters Associated with Double-Stranded Poly(dGdC) DNA Open
Here, we demonstrate through AFM imaging and CD spectroscopy that the binding of silver ions (Ag+) to poly(dGdC), a double-stranded (ds) DNA composed of two identical repeating strands, at a stoichiometry of one Ag+ per GC base pair induce…
View article: Effect of A-DNA and B-DNA Conformation on the Interplay between Local Excitations and Charge-Transfer States in the Ultrafast Decay of Guanine–Cytosine Stacked Dimers: A Quantum Dynamical Investigation
Effect of A-DNA and B-DNA Conformation on the Interplay between Local Excitations and Charge-Transfer States in the Ultrafast Decay of Guanine–Cytosine Stacked Dimers: A Quantum Dynamical Investigation Open
We here simulate in the gas phase the population dynamics of guanine/cytosine (GC) and cytosine/guanine (CG) stacked dimers in B-DNA and A-DNA arrangement, following excitation in the lowest-energy band, and considering the four lowest-ene…
View article: Localized and Excimer Triplet Electronic States of Naphthalene Dimers: A Computational Study
Localized and Excimer Triplet Electronic States of Naphthalene Dimers: A Computational Study Open
We perform DFT calculations with different hybrid (ωB97X-D and M05-2X) and double hybrid (B2PLYP-D3 and ωB2PLYP) functionals to characterize the lowest energy triplet excited states of naphthalene monomer and dimers in different stacking a…
View article: On the nature of the triplet electronic states of naphthalene dimers
On the nature of the triplet electronic states of naphthalene dimers Open
Time-resolved spectra and calculations shed light on the nature of the long-living triplet states formed in high yield by exciting covalent stacked naphthalene dimers and on the effects modulating the equilibrium between localized and exci…
View article: Exploring excited-state proton transfer reactions in isothiazologuanosine, an isofunctional fluorescent analogue of guanosine
Exploring excited-state proton transfer reactions in isothiazologuanosine, an isofunctional fluorescent analogue of guanosine Open
Due to its complex photophysics, isothiazologuanosine ( tz G), an isomorphic and isofunctional fluorescent analogue of guanosine, is highly responsive over a wide range of acidic (0–5) and basic pH values (8–10).
View article: Experimental and Computational Evidence of a Stable RNA G‐Triplex Structure at Physiological Temperature in the SARS‐CoV‐2 Genome
Experimental and Computational Evidence of a Stable RNA G‐Triplex Structure at Physiological Temperature in the SARS‐CoV‐2 Genome Open
RG1 is a quadruplex‐forming sequence in the SARS‐CoV‐2 genome proposed as possible therapeutic target for COVID‐19. We demonstrate that the dominant conformation of RG1 under physiological conditions differs from the parallel quadruplex pr…
View article: Experimental and Computational Evidence of a Stable RNA G‐Triplex Structure at Physiological Temperature in the SARS‐CoV‐2 Genome
Experimental and Computational Evidence of a Stable RNA G‐Triplex Structure at Physiological Temperature in the SARS‐CoV‐2 Genome Open
RG1 is a quadruplex‐forming sequence in the SARS‐CoV‐2 genome proposed as possible therapeutic target for COVID‐19. We demonstrate that the dominant conformation of RG1 under physiological conditions differs from the parallel quadruplex pr…
View article: Cover Feature: The Excited State Dynamics of a Mutagenic Guanosine Etheno Adduct Investigated by Femtosecond Fluorescence Spectroscopy and Quantum Mechanical Calculations (Chem. Eur. J. 49/2024)
Cover Feature: The Excited State Dynamics of a Mutagenic Guanosine Etheno Adduct Investigated by Femtosecond Fluorescence Spectroscopy and Quantum Mechanical Calculations (Chem. Eur. J. 49/2024) Open
This article relates to: The Excited State Dynamics of a Mutagenic Guanosine Etheno Adduct Investigated by Femtosecond Fluorescence Spectroscopy and Quantum Mechanical Calculations
\nPaloma Lizondo-Aranda, Thomas Gustavsson, Lara Martínez-…
View article: The Excited State Dynamics of a Mutagenic Guanosine Etheno Adduct Investigated by Femtosecond Fluorescence Spectroscopy and Quantum Mechanical Calculations
The Excited State Dynamics of a Mutagenic Guanosine Etheno Adduct Investigated by Femtosecond Fluorescence Spectroscopy and Quantum Mechanical Calculations Open
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, N 2 ‐etheno‐2’‐deoxyguanosine (ϵdG). This endogeno…
View article: Non-adiabatic direct quantum dynamics using force fields: Toward solvation
Non-adiabatic direct quantum dynamics using force fields: Toward solvation Open
Quantum dynamics simulations are becoming a powerful tool for understanding photo-excited molecules. Their poor scaling, however, means that it is hard to study molecules with more than a few atoms accurately, and a major challenge at the …
View article: Ag+-Mediated Folding of Long Polyguanine Strands to Double and Quadruple Helixes
Ag+-Mediated Folding of Long Polyguanine Strands to Double and Quadruple Helixes Open
Metal-mediated base pairing of DNA has been a topic of extensive research spanning over more than four decades. Precise positioning of a single metal ion by predetermining the DNA sequence, as well as improved conductivity offered by the i…
View article: Ultrafast Formation of a Delocalized Triplet-Excited State in an Epigenetically Modified DNA Duplex under Direct UV Excitation
Ultrafast Formation of a Delocalized Triplet-Excited State in an Epigenetically Modified DNA Duplex under Direct UV Excitation Open
Epigenetic modifications impart important functionality to nucleic acids during gene expression but may increase the risk of photoinduced gene mutations. Thus, it is crucial to understand how these modifications affect the photostability o…
View article: The photoactivated dynamics of dGpdC and dCpdG sequences in DNA: a comprehensive quantum mechanical study
The photoactivated dynamics of dGpdC and dCpdG sequences in DNA: a comprehensive quantum mechanical study Open
We disentangle the photophysical processes triggered in a representative DNA sequence by absorption of UV light, giving new molecular insights on the sub picosecond component of phenomena with great biological importance.
View article: Shedding Light on the Photophysics and Photochemistry of I-Motifs Using Quantum Mechanical Calculations
Shedding Light on the Photophysics and Photochemistry of I-Motifs Using Quantum Mechanical Calculations Open
I-motifs are non-canonical DNA structures formed by intercalated hemiprotonated (CH·C)+ pairs, i.e., formed by a cytosine (C) and a protonated cytosine (CH+), which are currently drawing great attention due to their biological relevance an…
View article: The photophysics of protonated cytidine and hemiprotonated cytidine base pair: A computational study
The photophysics of protonated cytidine and hemiprotonated cytidine base pair: A computational study Open
We here study the effect that a lowering of the pH has on the excited state processes of cytidine and a cytidine/cytidine pair in solution, by integrating time‐dependent density functional theory and CASSCF/CASPT2 calculations, and includi…
View article: Issue Information
Issue Information Open
No abstract is available for this article.
View article: The Resonance Raman Spectrum of Cytosine in Water: Analysis of the Effect of Specific Solute–Solvent Interactions and Non-Adiabatic Couplings
The Resonance Raman Spectrum of Cytosine in Water: Analysis of the Effect of Specific Solute–Solvent Interactions and Non-Adiabatic Couplings Open
In this contribution, we report a computational study of the vibrational Resonance Raman (vRR) spectra of cytosine in water, on the grounds of potential energy surfaces (PES) computed by time-dependent density functional theory (TD-DFT) an…
View article: 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
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 Open
In this study, we exploit a recently developed fragment diabatization‐based excitonic model, FrDEx, to simulate the electronic circular dichroism (ECD) spectra of three guanine‐rich DNA sequences arranged in guanine quadruple helices with …
View article: Front Cover: Solvent Effects on Ultrafast Charge Transfer Population: Insights from the Quantum Dynamics of Guanine‐Cytosine in Chloroform (Chem. Eur. J. 57/2022)
Front Cover: Solvent Effects on Ultrafast Charge Transfer Population: Insights from the Quantum Dynamics of Guanine‐Cytosine in Chloroform (Chem. Eur. J. 57/2022) Open
Charge transfer in solvent: Guanine is illustrated transferring an electron to cytosine in chloroform after the absorption of light. This is the first step of a deactivation pathway observed previously in experiment, which could also be op…
View article: Solvent Effects on Ultrafast Charge Transfer Population: Insights from the Quantum Dynamics of Guanine‐Cytosine in Chloroform
Solvent Effects on Ultrafast Charge Transfer Population: Insights from the Quantum Dynamics of Guanine‐Cytosine in Chloroform Open
Invited for the cover of this issue is the group of G. A. Worth, F. Santoro and R. Improta at UCL, ICOOM‐CNR and IBB‐CNR. The image depicts charge transfer from guanine to cytosine in solvent after the absorption of light. Read the full te…
View article: Nonadiabatic Vibrational Resonance Raman Spectra from Quantum Dynamics Propagations with LVC Models. Application to Thymine
Nonadiabatic Vibrational Resonance Raman Spectra from Quantum Dynamics Propagations with LVC Models. Application to Thymine Open
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 f…
View article: Solvent Effects on Ultrafast Charge Transfer Population: Insights from the Quantum Dynamics of Guanine‐Cytosine in Chloroform
Solvent Effects on Ultrafast Charge Transfer Population: Insights from the Quantum Dynamics of Guanine‐Cytosine in Chloroform Open
We study the ultrafast photoactivated dynamics of the hydrogen bonded dimer Guanine‐Cytosine in chloroform solution, focusing on the population of the Guanine→Cytosine charge transfer state (GC‐CT), an important elementary process for the …
View article: An Excitonic Model Incorporating Charge Transfer States to Compute the Electronic Circular Dichroism Spectra of Guanine Quadruplexes
An Excitonic Model Incorporating Charge Transfer States to Compute the Electronic Circular Dichroism Spectra of Guanine Quadruplexes Open
Paper published in J. Chem. Theory Comput. 2021, 17, 1, 405–415
View article: Excited state absorption of DNA bases in the gas phase and in chloroform solution: a comparative quantum mechanical study
Excited state absorption of DNA bases in the gas phase and in chloroform solution: a comparative quantum mechanical study Open
We report a benchmark of excited state absorption of the four DNA bases using ab initio (EOM-CCSD, EOM-CC3) and TD-CAM-B3LYP methods, in the gas phase and in chloroform, a step towards the interpretation of time-resolved absorption spectra…
View article: The Excited State Dynamics of a Mutagenic Cytidine Etheno Adduct Investigated by Combining Time-Resolved Spectroscopy and Quantum Mechanical Calculations
The Excited State Dynamics of a Mutagenic Cytidine Etheno Adduct Investigated by Combining Time-Resolved Spectroscopy and Quantum Mechanical Calculations Open
Joint femtosecond fluorescence upconversion experiments and theoretical calculations provide a hitherto unattained degree of characterization and understanding of the mutagenic etheno adduct 3,N4-etheno-2'-deoxycytidine (εdC) excited state…
View article: Early steps of oxidative damage in DNA quadruplexes are position-dependent: quantum mechanical and molecular dynamics analysis of human telomeric sequence containing ionized Guanine.
Early steps of oxidative damage in DNA quadruplexes are position-dependent: quantum mechanical and molecular dynamics analysis of human telomeric sequence containing ionized Guanine. Open
Guanine radical cation (G+ ) is a key intermediate in many oxidative processes occurring in nucleic acids. Here, by combining mixed Quantum Mechanical/Molecular Mechanics calculations and Molecular Dynamics (MD) simulations, we study how …
View article: The Ultrafast Quantum Dynamics of Photoexcited Adenine–Thymine Basepair Investigated with a Fragment-based Diabatization and a Linear Vibronic Coupling Model
The Ultrafast Quantum Dynamics of Photoexcited Adenine–Thymine Basepair Investigated with a Fragment-based Diabatization and a Linear Vibronic Coupling Model Open
In this contribution we present a quantum dynamical study of the photoexcited hydrogen bonded base pair adenine-thymine (AT) in a Watson-Crick arrangement. To that end, we parametrize Linear Vibronic Coupling (LVC) models with Time-Depende…