Accurate Structures and Spectroscopic Parameters of Phenylalanine and Tyrosine in the Gas Phase: A Joint Venture of DFT and Composite Wave-Function Methods

A general strategy for the accurate computation of conformational and spectroscopic properties of flexible molecules in the gas phase is applied to two representative proteinogenic amino acids with aromatic side chains, namely, phenylalanine and tyrosine. The main features of all the most stable conformers predicted by this computational strategy closely match those of the species detected in microwave and infrared experiments. Together with their intrinsic interest, the accuracy of the results obtained with reasonable computer times paves the route for accurate investigations of other flexible bricks of life

Fast exploration of potential energy surfaces with a joint venture of quantum chemistry, evolutionary algorithms and unsupervised learning

Contemporary molecular spectroscopy allows the study of flexible molecules, whose conformational behavior is ruled by flat potential energy surfaces (PESs) involving a large number of energy minima with comparable stability. Under such circumstances assignment and interpretation of the spectral signatures can strongly benefit from quantum chemical computations, which face, however, several difficulties. In particular, the mandatory characterization of all the relevant energy minima leads to a huge increase in the number of accurate quantum chemical computations (which may even hamper the feasibility of a study) and the intricate couplings among several soft degrees of freedom can defy simple heuristic approaches and chemical intuition. From this point of view, the exploration of flat PESs is akin to other optimization problems and can be tackled with suitable metaheuristics, which can drive QC computations by reducing the number of necessary calculations and providing effective routes to sample the most relevant regions of the PES. Unfortunately, in spite of the significant reduction of the number of QC calculations, a brute-force approach based on state-of-the-art methods remains infeasible. This problem can be solved effectively by multi-level strategies combining methods of different accuracy in the first PES exploration, refinement of the structures of the most important stationary points and computation of spectroscopic parameters. Building on previous experience, in this contribution we introduce new improvements in an evolutionary algorithm based method using curvilinear coordinates for both intra- and inter-molecular interactions. Two test cases will be analyzed in detail, namely aspartic acid in the gas-phase and the silver cation in aqueous solution. Comparison between fully a priori computed spectroscopic parameters and the experimental counterparts will provide an unbiased validation of the proposed strategy

Integration of Quantum Chemistry, Statistical Mechanics, and Artificial Intelligence for Computational Spectroscopy: The UV-Vis Spectrum of TEMPO Radical in Different Solvents

The ongoing integration of quantum chemistry, statistical mechanics, and artificial intelligence is paving the route toward more effective and accurate strategies for the investigation of the spectroscopic properties of medium-to-large size chromo-phores in condensed phases. In this context we are developing a novel workflow aimed at improving the generality, reliability, and ease of use of the available computational tools. In this paper we report our latest developments with specific reference to unsupervised atomistic simulations employing non periodic boundary conditions (NPBC) followed by clustering of the trajectories employing optimized feature spaces. Next accurate variational computations are performed for a representative point of each cluster, whereas intracluster fluctuations are taken into account by a cheap yet reliable perturbative approach. A number of methodological improvements have been introduced including, e.g., more realistic reaction field effects at the outer boundary of the simulation sphere, automatic definition of the feature space by continuous perception of solute-sol v e n t interactions, full account of polarization and charge transfer in the first solvation shell, and inclusion of vibronic contributions. After its validation, this new approach has been applied to the challenging case of solvatochromic effects on the UV-vis spectra of a prototypical nitroxide radical (TEMPO) in different solvents. The reliability, effectiveness, and robustness of the new platform is demonstrated by the remarkable agreement with experiment of the results obtained through an unsupervised approach characterized by a strongly reduced computational cost as compared to that of conventional quantum mechanics and molecular mechanics models without any accuracy reduction

Circularly polarized luminescence of natural products lycorine and narciclasine: role of excited-state intramolecular proton-transfer and test of pH sensitivity

: Circularly polarized luminescence (CPL) is increasingly gaining interest not only for its applicative potentialities but also for providing an understanding of the excited state properties of chiral molecules. However, applications of CPL are mainly in the field of materials science: special organic molecules and polymers, metal (lanthanide) complexes, and organic dyes are actively and intensely studied. So far natural compounds have not been investigated much. We fill the gap here by measuring circular dichroism (CD) and CPL of lycorine and narciclasine, the most abundant known alkaloid and isocarbostyril from Amaryllidaceae, which exhibit a large spectrum of biological activities and are promising anticancer compounds. Dual fluorescence detection in narciclasine led us to unveil an occurring excited-state intramolecular proton transfer (ESIPT) process, this mechanism well accounts for the Stokes shift and CPL spectra observed in narciclasine. The same molecule is interesting also as a pH chiroptical switch. Both in absorption and emission, lycorine and narciclasine are also studied computationally via density functional theory (DFT) calculations further shedding light on their properties

Incidencia de los aditivos plastificantes y el agregado procesado de tres canteras para el concreto en la construcción de viviendas en el Pueblo Joven APIPA del distrito de Cerro Colorado de la ciudad de Arequipa 2021

El presente trabajo “Incidencia de los aditivos plastificantes y el agregado procesado de tres canteras para el concreto en la construcción de viviendas en el pueblo joven Apipa del distrito de Cerro Colorado de la ciudad de Arequipa 2021” tuvo como objetivo determinar la incidencia o influencias del uso de aditivos plastificantes y agregados procesados de tres canteras locales (Río Socabaya, Kilómetro 48, La Rinconada ) en la elaboración del concreto utilizado en la construcción de viviendas, corroborando los resultados obtenidos de las diversas mezclas experimentales con pruebas de laboratorio al concreto habitual, determinando la dosificación optima de los agregados de las tres canteras utilizando el aditivo plastificante Sikacem para demostrar la mejora de la trabajabilidad en el estado fresco y la resistencia a la compresión en el estado endurecido para un concreto f ́c= 280 kg/cm2. La metodología utilizada en la investigación es de tipo aplicada, método científico, nivel explicativo y diseño experimental puro. La población está conformada por tres canteras (Río Socabaya, Kilómetro 48, La Rinconada), canteras de agregados procesados en la ciudad de Arequipa. Como resultados de la investigación determinamos que los agregados de la cantera La Rinconada con la adición de 500 ml de aditivo plastificante Sikacem tiene una mejor trabajabilidad y resistencia a la compresión a los 28 días que utilizando agregados de las otras dos canteras con la misma cantidad de aditivo plastificante. Se concluye, según los resultados obtenidos en el laboratorio, que la mezcla de concreto más óptima fue la que utilizó agregados de la cantera La Rinconada y el aditivo plastificante Sikacem, los cuales arrojan mejores resultados que trabajando de una manera empírica o con un diseño de concreto convencional

NF-κB Mediates Tumor Necrosis Factor α-Induced Expression of Optineurin, a Negative Regulator of NF-κB

Optineurin is a ubiquitously expressed multifunctional cytoplasmic protein encoded by OPTN gene. The expression of optineurin is induced by various cytokines. Here we have investigated the molecular mechanisms which regulate optineurin gene expression and the relationship between optineurin and nuclear factor κB (NF-κB). We cloned and characterized human optineurin promoter. Optineurin promoter was activated upon treatment of HeLa and A549 cells with tumor necrosis factor α (TNFα). Mutation of a putative NF-κB-binding site present in the core promoter resulted in loss of basal as well as TNFα-induced activity. Overexpression of p65 subunit of NF-κB activated this promoter through NF-κB site. Oligonucleotides corresponding to this putative NF-κB-binding site showed binding to NF-κB. TNFα-induced optineurin promoter activity was inhibited by expression of inhibitor of NF-κB (IκBα) super-repressor. Blocking of NF-κB activation resulted in inhibition of TNFα-induced optineurin gene expression. Overexpressed optineurin partly inhibited TNFα-induced NF-κB activation in Hela cells. Downregulation of optineurin by shRNA resulted in an increase in TNFα-induced as well as basal NF-κB activity. These results show that optineurin promoter activity and gene expression are regulated by NF-κB pathway in response to TNFα. In addition these results suggest that there is a negative feedback loop in which TNFα-induced NF-κB activity mediates expression of optineurin, which itself functions as a negative regulator of NF-κB

Overexpression of optineurin E50K disrupts Rab8 interaction and leads to a progressive retinal degeneration in mice

Glaucoma is one of the leading causes of bilateral blindness affecting nearly 8 million people worldwide. Glaucoma is characterized by a progressive loss of retinal ganglion cells (RGCs) and is often associated with elevated intraocular pressure (IOP). However, patients with normal tension glaucoma (NTG), a subtype of primary open-angle glaucoma (POAG), develop the disease without IOP elevation. The molecular pathways leading to the pathology of NTG and POAG are still unclear. Here, we describe the phenotypic characteristics of transgenic mice overexpressing wild-type (Wt) or mutated optineurin (Optn). Mutations E50K, H486R and Optn with a deletion of the first (amino acids 153–174) or second (amino acids 426–461) leucine zipper were used for overexpression. After 16 months, histological abnormalities were exclusively observed in the retina of E50K mutant mice with loss of RGCs and connecting synapses in the peripheral retina leading to a thinning of the nerve fiber layer at the optic nerve head at normal IOP. E50K mice also showed massive apoptosis and degeneration of entire retina, leading to approximately a 28% reduction of the retina thickness. At the molecular level, introduction of the E50K mutation disrupts the interaction between Optn and Rab8 GTPase, a protein involved in the regulation of vesicle transport from Golgi to plasma membrane. Wt Optn and an active GTP-bound form of Rab8 complex were localized at the Golgi complex. These data suggest that alternation of the Optn sequence can initiate significant retinal degeneration in mice

Transcript levels of Toll-Like receptors 5, 8 and 9 correlate with inflammatory activity in Ulcerative Colitis

<p>Abstract</p> <p>Background</p> <p>Dysregulation of innate immune response by Toll-Like Receptors (TLRs) is a key feature in Ulcerative Colitis (UC). Most studies have focused on <it>TLR2, TLR3</it>, and <it>TLR4 </it>participation in UC. However, few studies have explored other TLRs. Therefore, the aim of this study was to evaluate the mRNA profiles of <it>TLR1 to 9 </it>in colonic mucosa of UC patients, according to disease activity.</p> <p>Methods</p> <p>Colonic biopsies were taken from colon during colonoscopy in 51 patients with Ulcerative Colitis and 36 healthy controls. mRNA levels of <it>TLR1 to 9, Tollip</it>, inflammatory cytokines <it>IL6 </it>and <it>TNF </it>were assessed by RT-qPCR with hydrolysis probes. Characterization of <it>TLR9 </it>protein expression was performed by Immunohistochemistry.</p> <p>Results</p> <p>Toll-like receptors <it>TLR8, TLR9</it>, and <it>IL6 </it>mRNA levels were significantly higher in the colonic mucosa from UC patients (both quiescent and active) as compared to healthy individuals (p < 0.04). In the UC patients group the <it>TLR2, TLR4, TLR8 </it>and <it>TLR9 </it>mRNA levels were found to be significantly lower in patients with quiescent disease, as compared to those with active disease (p < 0.05), whereas <it>TLR5 </it>showed a trend (p = 0.06). <it>IL6 </it>and <it>TNF </it>mRNA levels were significantly higher in the presence of active disease and help to discriminate between quiescent and active disease (p < 0.05). Also, <it>IL6 </it>and <it>TNF </it>mRNA positively correlate with TLRs mRNA with the exception for <it>TLR3</it>, with stronger correlations for <it>TLR5, TLR8</it>, and <it>TLR9 </it>(p < 0.0001). <it>TLR9 </it>protein expression was mainly in the lamina propria infiltrate.</p> <p>Conclusions</p> <p>This study demonstrates that <it>TLR2, TLR4, TLR8</it>, and <it>TLR9 </it>expression increases in active UC patients, and that the mRNA levels positively correlate with the severity of intestinal inflammation as well as with inflammatory cytokines.</p

Molecular Dynamics Simulations Enforcing Nonperiodic Boundary Conditions: New Developments and Application to the Solvent Shifts of Nitroxide Magnetic Parameters

Multiscale methods combining quantum mechanicsand molecular mechanics (QM/MM) have become the mostsuitable and effective strategies for the investigation of thespectroscopic properties of medium-to-large size chromophoresin condensed phases. In this context, we are developing a novelworkflow aimed at improving the generality, reliability, and ease ofuse of the available computational tools. In this paper, we reportour latest developments with specific reference to a generalprotocol based on atomistic simulations, carried out undernonperiodic boundary conditions (NPBC). In particular, we addto our in house MD engine a new efficient treatment of meanfieldelectrostatic contributions to energy and forces, together with the capability of performing the simulations either in the canonical(NVT) or in the isothermal-isobaric (NPT) ensemble. Next, we provide convincing evidence that the NBPC approach enhanced byspecific tweaks for rigid body propagation, allows for the simulation of solute-solvent systems with a minimum number of degrees offreedom and large integration time step. After its validation, this new approach is applied to the challenging case of solvatochromiceffects on the electron paramagnetic resonance (EPR) spectrum of a prototypical nitroxide radical. To this end, we propose andvalidate also an automated protocol to extract and weight simulation snapshots, making use of a continuous description of thestrength of solute-solvent hydrogen bridges. While further developments are being worked on, the effectiveness of our approach,even in its present form, is demonstrated by the accuracy of the results obtained through an unsupervised approach characterized bya strongly reduced computational cost as compared to that of conventional QM/MM models, without any appreciable deteriorationof accuracy