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Article
Open AccessRetinal photoisomerization versus counterion protonation in light and dark-adapted bacteriorhodopsin and its primary photoproduct
Discovered over 50 years ago, bacteriorhodopsin is the first recognized and most widely studied microbial retinal protein. Serving as a light-activated proton pump, it represents the archetypal ion-pum** sys...
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Article
Open AccessThe carbonyl-lock mechanism underlying non-aromatic fluorescence in biological matter
Challenging the basis of our chemical intuition, recent experimental evidence reveals the presence of a new type of intrinsic fluorescence in biomolecules that exists even in the absence of aromatic or electro...
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Article
Open AccessAuthor Correction: Turning up the heat mimics allosteric signaling in imidazole-glycerol phosphate synthase
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Article
Open AccessTurning up the heat mimics allosteric signaling in imidazole-glycerol phosphate synthase
Allosteric drugs have the potential to revolutionize biomedicine due to their enhanced selectivity and protection against overdosage. However, we need to better understand allosteric mechanisms in order to ful...
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Article
Open AccessTracking excited state decay mechanisms of pyrimidine nucleosides in real time
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 ...
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Chapter
Photo-Active Biological Molecular Materials: From Photoinduced Dynamics to Transient Electronic Spectroscopies
We present an overview of a methodology for the simulation of the photo-response of biological (macro)molecules, designed around a Mechanics / Molecular Mechanics (QM/MM) subtractive . The resulting simulat...
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Protocol
Community Network Analysis of Allosteric Proteins
Community network analysis (CNA) of correlated protein motions allows modeling of signals propagation in allosteric proteic systems. From standard classical molecular dynamics (MD) simulations, protein motions...
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Chapter
Towards Accurate Simulation of Two-Dimensional Electronic Spectroscopy
We introduce the basic concepts of two-dimensional electronic spectroscopy (2DES) and a general theoretical framework adopted to calculate, from first principles, the nonlinear response of multi-chromophoric s...
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Article
COBRAMM 2.0 — A software interface for tailoring molecular electronic structure calculations and running nanoscale (QM/MM) simulations
We present a new version of the simulation software COBRAMM, a program package interfacing widely known commercial and academic software for molecular modeling. It allows a problem-driven tailoring of computat...
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Article
Towards Accurate Simulation of Two-Dimensional Electronic Spectroscopy
We introduce the basic concepts of two-dimensional electronic spectroscopy (2DES) and a general theoretical framework adopted to calculate, from first principles, the nonlinear response of multi-chromophoric s...
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Article
The highly excited-state manifold of guanine: calibration for nonlinear electronic spectroscopy simulations
A computational protocol based on the complete and restricted active space self-consistent field (CASSCF/RASSCF) methods and their second-order perturbation theory extensions (CASPT2/RASPT2) is employed to ben...
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Article
The effect of solvent relaxation in the ultrafast time-resolved spectroscopy of solvated benzophenone
Benzophenone (BP) despite its relatively simple molecular structure is a paradigmatic sensitizer, featuring both photocatalytic and photobiological effects due to its rather complex photophysical properties. I...
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Article
Spectroscopic fingerprints of DNA/RNA pyrimidine nucleobases in third-order nonlinear electronic spectra
Accurate ab initio modeling of spectroscopic signals in nonlinear electronic spectra, such as bidimensional (2D) spectra, requires the computation of the electronic transitions induced by the incoming pump/pro...
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Article
Ultraviolet vision: photophysical properties of the unprotonated retinyl Schiff base in the Siberian hamster cone pigment
The Siberian hamster ultraviolet (SHUV) visual pigment has an unprotonated Schiff-base (SB) retinyl chromophore in the dark state, which becomes protonated after photoexcitation during the early stages of the...
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Article
Open AccessAllosteric Pathways in the PPARγ-RXRα nuclear receptor complex
Understanding the nature of allostery in DNA-nuclear receptor (NR) complexes is of fundamental importance for drug development since NRs regulate the transcription of a myriad of genes in humans and other meta...
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Article
The role of quantum chemistry in the elucidation of the elementary mechanisms of catalytic processes: from atoms, to surfaces, to enzymes
The recent activity of the laboratory of quantum and computational chemistry of the University of Calabria in the field of catalysis is shortly reviewed. Theoretical determinations of the potential energy prof...
