Laura Milena Pedraza-González

• PhD
• Assistant Professor of Physical Chemistry at University of Pisa

We assess the performance of the recently developed Any-Particle Molecular-Orbital second- order proton propagator (APMO/PP2) scheme [M. Diaz-Tinoco, J. Romero, J. V. Ortiz, A. Reyes, R. Flores-Moreno, J. Chem. Phys., 2013, 138, 194108] on the calculation of gas phase proton affinities (PAs) of a set of 150 organic molecules comprising several func...

Higher plants Photosystem I absorbs near-infrared light through long-wavelength chlorophylls, enriched under vegetation canopies, to enhance photon capture. Far-red absorption originates from chlorophylls pairs within the Lhca3 and Lhca4 subunits of the LHCI antenna, known as the “red cluster” composed of chlorophylls a603 and a609. - We used rever...

In this study, we evaluate the performance of two cost-effective models, namely, TD-DFT and ΔSCF methods, combined withdifferent molecular mechanics models, to predict the photophysical andphotochemical properties of a set of fluorescent mutants of the microbialrhodopsin Archaerhodopsin-3. We investigate absorption energies andexcited-state isomeri...

In this study, we evaluate the performance of two cost-effective models, namely TD-DFT and ∆SCF methods, combined with different Molecular Mechanics models, to predict photophysical and photochemical properties of a set of fluorescent mutants of the microbial rhodopsin Archaerhodopsin3. We investigate absorption energies and excited state isomeriza...

Light-harvesting complexes (LHC) are known to regulate the flux of energy in different light conditions and activate quenching processes to prevent photodamage in case of high light. However, the molecular mechanisms behind these photoprotective processes remain unclear. A widely accepted model suggests an excitation-energy transfer from excited ch...

Melanopsin is a photopigment belonging to the G Protein-Coupled Receptor (GPCR) family expressed in a subset of intrinsically photosensitive retinal ganglion cells (ipRGCs) and responsible for a variety of processes. The bistability and, thus, the possibility to function under low retinal availability would make melanopsin a powerful optogenetic to...

Rhodopsins are light-responsive proteins forming two vast and evolutionary distinct superfamilies whose functions are invariably triggered by the photoisomerization of a single retinal chromophore. In 2018 a third widespread superfamily...

Carotenoid pigments are known to present a functional versatility when bound to light-harvesting complexes. This versatility originates from a strong correlation between a complex electronic structure and a flexible geometry that is easily tunable by the surrounding protein environment. Here, we investigated how the different L1 and L2 sites of the...

Melanopsin (MeOp) is a G protein-coupled Receptor (GPCR) family photopigment, expressed in intrinsically photosensitive retinal ganglion cells (ipRGCs) that display remarkable functional diversity. In addition to non-image-forming visual functions, MeOp also controls signaling underlying the retina development, circadian clock, mood, and behavior....

Carotenoid pigments are known to present a functional versatility when bound to light-harvesting complexes. This versatility originates from a strong correlation between a complex electronic structure and a flexible geometry which is easily tunable by the surrounding protein environment. Here, we investigated how the different L1 and L2 sites of th...

In response to varying light conditions, light-harvesting complexes (LHCs) switch from a light-harvesting state to a quenched state to protect the photosynthetic organism from excessive light irradiation in a strategy known as nonphotochemical quenching (NPQ). NPQ is activated by an acidification of the thylakoid lumen, which is sensed directly or...

The appearance of a new coronavirus, SARS-CoV-2, in 2019 kicked off an international public health emergency. Although rapid progress in vaccination has reduced the number of deaths, the development of alternative treatments to overcome the disease is still necessary. It is known that the infection begins with the interaction of the spike glycoprot...

In response to varying light conditions, light-harvesting complexes (LHCs) switch from a light-harvesting to a quenched state to protect the photosynthetic organism from excessive light irradiation, in a strategy known as nonphotochemical quenching (NPQ). NPQ is activated by an acidification of the thylakoid lumen which is sensed directly or indire...

We present a computational protocol for the fast and automated screening of excited-state hybrid quantum mechanics/molecular mechanics (QM/MM) models of rhodopsins to be used as fluorescent probes based on the automatic rhodopsin modeling protocol (a-ARM). Such "a-ARM fluorescence screening protocol" is implemented through a general Python-based dr...

The understanding of how the rhodopsin sequence can be modified to exactly modulate the spectroscopic properties of its retinal chromophore, is a prerequisite for the rational design of more effective optogenetic tools. One key problem is that of establishing the rules to be satisfied for achieving highly fluorescent rhodopsins with a near infrared...

The lack of a theory capable of connecting the amino acid sequence of a light-absorbing protein with its fluorescence brightness is hampering the development of tools for understanding neuronal communications. Here we demonstrate that a theory can be established by constructing quantum chemical models of a set of Archaerhodopsin reporters in their...

Computational studies have shown that one or more positrons can stabilize two repelling atomic anions through the formation of two-center positronic bonds. In the present work, we study the energetic stability of a system containing two positrons and three hydride anions, namely 2e+[H3 3-]. To this aim, we performed a preliminary scan of the potent...

Computational studies have shown that one or more positrons can stabilize two repelling atomic anions through the formation of two-center positronic bonds. In the present work, we study the energetic stability of a system containing two positrons and three hydride anions, namely 2\ce{e^+[H^{3-}_3]}. To this aim, we performed a preliminary scan of t...

In recent years, photoactive proteins such as rhodopsins have become a common target for cutting-edge research in the field of optogenetics. Alongside wet-lab research, computational methods are also developing rapidly to provide the necessary tools to analyze and rationalize experimental results and, most of all, drive the design of novel systems....

In recent years, photoactive proteins such as rhodopsins have become a common target for cutting-edge research in the field of optogenetics. Alongside wet-lab research, computational methods are also developing rapidly to provide the necessary tools to analyze and rationalize experimental results and, most of all, drive the design of novel systems....

Color tuning in animal and microbial rhodopsins has attracted the interest of many researchers, as the color of their common retinal chromophores is modulated by the amino acid residues forming the chromophore cavity. Critical cavity amino acid residues are often called “color switches”, as the rhodopsin color is effectively tuned through their sub...

This perspective article highlights the challenges in the theoretical description of photoreceptor proteins using multiscale modelling, as discussed at the CECAM workshop in Tel Aviv, Israel. The participants have identified grand challenges and discussed the development of new tools to address them. Recent progress in understanding representative...

The automatic building of quantum mechanical/molecular mechanical models (QM/MM) of rhodopsins has been recently proposed. This is a prototype of an approach that will be expanded to make possible the systematic computational investigation of biological photoreceptors. QM/MM models represent useful tools for biophysical studies and for protein engi...

MOLCAS/OpenMolcas is an ab initio electronic structure program providing a large set of computational methods from Hartree–Fock and density functional theory to various implementations of multiconfigurational theory. This article provides a comprehensive overview of the main features of the code, specifically reviewing the use of the code in previo...

This article introduces Web-ARM, a specialized, on-line available, tool designed to build quantum mechanical/molecular mechanical models of rhodopsins, a widely spread family of light-responsive proteins. Web-ARM allows to rapidly build models of rhodopsins with a documented quality and to predict trends in UV-Vis absorption maximum wavelengths, ba...

We report a computational study on homo- and heteronuclear e⁺[X⁻Y⁻] compounds formed by two halide anions (X⁻,Y⁻= F⁻,Cl⁻,Br⁻) and one positron. Our results indicate the formation of energetically stable positronic molecules in all cases. Analysis of the electron and positron densities points out that the formation of positron covalent bonds underli...

Recently, progress in IR sources, has led to the discovery that humans can detect infrared (IR) light. This is hypothesized due to two-photon absorption (TPA) events promoting the retina dim-light rod photoreceptor rhodopsin to the same excited state populated via one-photon absorption (OPA). Here, we combine quantum mechanics/molecular mechanics a...

The Automatic Rhodopsin Modeling (ARM) protocol, has recently been proposed as a tool for the fast and parallel generation of basic hybrid quantum mechanics/molecular mechanics (QM/MM) models of wild-type and mutant rhodopsins. However, in its present version, the input preparation requires a few hour long user's manipulation of the template protei...

In this work we propose schemes based on the extended Koopmans' theorem for quantum nuclei (eKT), in the framework of the any particle molecular orbital approach (APMO/KT), for the quantitative prediction of gas phase proton affinities (PAs). The performance of these schemes has been tested on a set of 300 organic molecules containing diverse funct...

Phys. Chem. Chem. Phys., 2017,19, 25324-25333

Recently, several groups have extended and implemented molecular orbital (MO) schemes to simultaneously obtain wave functions for electrons and selected nuclei. Many of these schemes employ an extended Hartree-Fock approach as a first step to find approximate electron-nuclear wave functions and energies. Numerous studies conducted with these extend...

The solvent effect on the nucleophile and leaving group atoms of the prototypical F- + CH3Cl → CH3F + Cl- backside bimolecular nucleophilic substitution reaction (SN2) is analyzed employing the reaction force and the atomic contributions methods on the intrinsic reaction coordinate (IRC). Solvent effects were accounted for using the polarizable con...

Abstract. We assess the performance of the recently developed Any-Particle Molecular Orbital second order proton propagator (APMO/PP2) scheme on the calculation of gas phase proton affinities (PAs) of a set of 150 organic molecules comprising several functional groups: amines, alcohols, aldehydes, amides, ketones, esters, ethers, carboxilic acids a...