Retinal 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-pumping system. Here we compare the photochemical dynamics of bacteriorhodopsin light and dark-adapted forms with that of the first metastable photocycle intermediate known as "K". We observe that following thermal double isomerization of retinal in the dark from bio-active all-trans 15-anti to 13-cis, 15-syn, photochemistry proceeds even faster than the ~0.5 ps decay of the former, exhibiting ballistic wave packet curve crossing to the ground state. In contrast, photoexcitation of K containing a 13-cis, 15-anti chromophore leads to markedly multi-exponential excited state decay including much slower stages. QM/MM calculations, aimed to interpret these results, highlight the crucial role of protonation, showing that the classic quadrupole counterion model poorly reproduces spectral data and dynamics. Single protonation of ASP212 rectifies discrepancies and predicts triple ground state structural heterogeneity aligning with experimental observations. These findings prompt a reevaluation of counter ion protonation in bacteriorhodopsin and contribute to the broader understanding of its photochemical dynamics.

Theoretical Insights into Bifurcated Intramolecular Dihydrogen Bonds.

Two-ring intramolecular π-electron delocalization assisted dihydrogen bonds existing in (1Z,4Z)-1,4-dipentene-3-bora-1,5-diol and its symmetrically substituted derivatives have been analysed here since the MP2/6-311++G(d,p) calculations on these systems were performed. The influence of the coexistence of two intramolecular dihydrogen bonded rings in these molecular structures on properties of intramolecular dihydrogen bonds as well as on the π-electron delocalization within these rings was investigated. The comparison with corresponding structures of typical two-ring, so-called resonance-assisted, RAHB, systems was performed. The results of calculations show that such rings' coexistence leads to the weakening of dihydrogen bonds, similarly as for the typical two-ring RAHB systems. The Quantum Theory of ''Atoms in Molecules'' (QTAIM) was also applied here to get more details about the nature of dihydrogen bonds. Correlations between dihydrogen bond strength measures and other energetic, geometrical and topological parameters were also analysed. It was found that characteristics of bond critical points as well as of ring critical points are useful to estimate the strength of intramolecular dihydrogen bonds in two-ring dihydrogen bonded systems discussed here. The Natural Bond Orbital, NBO, approach parameters are also discussed as useful ones to describe properties of dihydrogen bonded systems.

Double Centrosymmetric Si···π Tetrel Bonds as New Synthons─Evidence from Crystal Structures and DFT Calculations.

The crystal structure of bis((µ2-ethynylsilyloxo)-dichloro-aluminum), BEDCA, and a few related structures are characterized by the occurrence of tetrel bonds that link molecules. Particularly, centosymmetric dimers in such structures occur that are connected by two equivalent Si···π tetrel bonds. The dimer of BEDCA and dimers of other model species that similarly are linked by two equivalent Si···π tetrel bonds are analyzed theoretically. Some of the complexes calculated here are also characterized by the occurrence of triel bonds. Thus, ωB97XD/aug-cc-pVTZ calculations are performed and these DFT results are further supported by calculations with the use of other theoretical approaches: the quantum theory of atoms in molecules, QTAIM; the natural bond orbital, NBO; the energy decomposition analysis, EDA; and the noncovalent interactions method, NCI. The results show that the tetrel bonds analyzed here are rather weak, and they are not detected by the QTAIM approach; however, they are detected by other approaches, like NBO, for example. On the other hand, the triel bonds that occur in a few complexes discussed here are very strong and possess characteristics of covalent bonds.

Quantum-Classical Protocol for Efficient Characterization of Absorption Lineshape and Fluorescence Quenching upon Aggregation: The Case of Zinc Phthalocyanine Dyes.

A quantum-classical protocol that incorporates Jahn-Teller vibronic coupling effects and cluster analysis of molecular dynamics simulations is reported, providing a tool for simulations of absorption spectra and ultrafast nonadiabatic dynamics in large molecular photosystems undergoing aggregation in solution. Employing zinc phthalocyanine dyes as target systems, we demonstrated that the proposed protocol provided fundamental information on vibronic, electronic couplings and thermal dynamical effects that mostly contribute to the absorption spectra lineshape and the fluorescence quenching processes upon dye aggregation. Decomposing the various effects arising upon dimer formation, the structure-property relations associated with their optical responses have been deciphered at atomistic resolution.

Comparison of polyacrylate polyalcohol copolymer (PPC) and dextranomer/hyaluronic acid (Dx/HA) for treatment of vesicoureteral reflux. A systematic review and meta-analysis.

PURPOSE: Our study aimed to compare the efficacy of polyacrylate polyalcohol copolymer and Dextranomer-Hyaluronic Acid for endoscopic treatment of vesicoureteral reflux. MATERIAL AND METHODS: MEDLINE, EMBASE, Scopus, Web of science, Ovid, Cochrane databases, Google scholar have been searched for studies published until January 2022 in any language. Studies that compared the success rate for endoscopic treatment of vesicoureteral reflux in children with two bulking agents, namely, "polyacrylate polyalcohol copolymer." and "Dextranomer-Hyaluronic Acid" were included for this analysis. RESULTS: Nine studies were included in data synthesis for this meta-analysis. Pooled data with a total of 763 ureters in PPC group and 718 ureters in Dx/HA group indicated that ureters in PPC group were more likely to undergo complete reflux resolution than Dx/HA (OR 3.80, 95% CI: 2.71; 5.31). Among subgroup of patients with high grade reflux, PPC injection had more resolution rate compared to Dx/HA patients (OR: 2.92, 95% CI: 1.19-7.16). In total, 95.81% of the PPC group and 86.52% of the Dx/HA group experienced success after the third injection. However a concerning complication of endoscopic treatment which is ureterovesical junction obstruction (UVJO) was more prevalent in PPC group. So the possible benefits arising from endoscopic treatment with PPC could be offset by the costs of re-implantation surgery or stenting in the case of UVJO. CONCLUSION: These data indicate that PPC injection for vesicoureteral reflux treatment was associated with a higher success rate, but concerningly, UVJO incidence was higher in the PPC group which might negate the possible benefits of PPC injection However, due to the lack of studies with long-term follow-up, we couldn't reach a definitive conclusion about the superiority of one of the bulking agents over the other.

Fenofibrate in primary sclerosing cholangitis; a randomized, double-blind, placebo-controlled trial.

Primary sclerosing cholangitis (PSC) is a chronic cholestatic liver disease with no medical treatment proven to improve survival and postpone liver transplantation. Previous studies have shown the effectiveness of fibrates in primary biliary cholangitis. The current study prospectively evaluated the effect of fenofibrate on PSC patients. We administered 200 mg of fenofibrate to PSC patients in the intervention arm and a placebo in the control arm once per day for 6 months and evaluated liver biochemistries (alkaline phosphatase, aspartate aminotransferase, alanine aminotransferase, bilirubin, and albumin) and the Mayo Risk Score at the start and end of the study. The primary endpoint was defined as a reduction greater than 50% or normalization of ALP levels. Secondary endpoints were an improvement in the Mayo Risk Score and serum bilirubin levels. Thirty patients were included (19 female, 11 male, 40.2 ± 9.2 years old), all under treatment with Ursodeoxycholic acid prior to this study. ALP and ALT levels significantly decreased in the fenofibrate group, by 64.7% (mean difference = 557, p = 0.004, 95% CI = 208.72, 905.27) and 52.78%, (p = 0.006), respectively. The primary endpoint was achieved in 66.7% of patients (10 in 15) in the fenofibrate group versus 20% of patients (3 in 15) in the placebo group (p = 0.009). Other endpoints were not met. As studies have demonstrated lower levels of ALP may improve outcomes for PSC, our study resulted in significantly lower levels of ALP in the fenofibrate group, which could translate into better disease prognosis in PSC.

Proton and Lithium Cations Linked to π-Electron and σ-Electron Systems: Are Such Interactions beyond or within the Definition of Hydrogen/Lithium Bond?

MP2/aug-cc-pVTZ calculations were performed on systems containing a proton or a lithium cation located between two π-electron systems or between π-electron and σ-electron units. The proton or the lithium cation attached to the acetylene or its derivative may be treated as the Lewis acid unit while the remaining part of the complex, the π-electron species or the dihydrogen, act as the Lewis base through their π-electrons or σ-electrons, respectively. The complexes analysed here are linked by the π⋅⋅⋅H+ /Li+ ⋅⋅⋅π and π⋅⋅⋅H+ /Li+ ⋅⋅⋅σ interactions. It is discussed whether these interactions are classified as hydrogen and lithium bonds. Therefore, different definitions of the latter interactions are presented. The Electron Localization Function (ELF) and the Natural Bond Orbital (NBO) approaches were applied to analyse the above-mentioned complexes. The unique properties of interactions with the proton and with the lithium cation that occur in complexes analysed here are described.

Dietary Blueberry Ameliorates Vascular Complications in Diabetic Mice Possibly through NOX4 and Modulates Composition and Functional Diversity of Gut Microbes.

SCOPE: In diabetes, endothelial inflammation and dysfunction play a pivotal role in the development of vascular disease. This study investigates the effect of dietary blueberries on vascular complications and gut microbiome in diabetic mice. METHODS AND RESULTS: Seven-week-old diabetic db/db mice consume a standard diet (db/db) or a diet supplemented with 3.8% freeze-dried blueberry (db/db+BB) for 10 weeks. Control db/+ mice are fed a standard diet (db/+). Vascular inflammation is assessed by measuring monocyte binding to vasculature and inflammatory markers. Isometric tension procedures are used to assess mesenteric artery function. db/db mice exhibit enhanced vascular inflammation and reduced endothelial-dependent vasorelaxation as compared to db/+ mice, but these are improved in db/db+BB mice. Blueberry supplementation reduces the expression of NOX4 and IκKß in the aortic vessel and vascular endothelial cells (ECs) isolated from db/db+BB compared to db/db mice. The blueberry metabolites serum reduces glucose and palmitate induced endothelial inflammation in mouse aortic ECs. Further, blueberry supplementation increases commensal microbes and modulates the functional potential of gut microbes in diabetic mice. CONCLUSION: Dietary blueberry suppresses vascular inflammation, attenuates arterial endothelial dysfunction, and supports the growth of commensal microbes in diabetic mice. The endothelial-specific vascular benefits of blueberries are mediated through NOX4 signaling.

Hydrogen and Lithium Bonds-Lewis Acid Units Possessing Multi-Center Covalent Bonds.

MP2/aug-cc-pVTZ calculations were carried out on complexes wherein the proton or the lithium cation is located between π-electron systems, or between π-electron and σ-electron units. The acetylene or its fluorine and lithium derivatives act as the Lewis base π-electron species similarly to molecular hydrogen, which acts as the electron donor via its σ-electrons. These complexes may be classified as linked by π-H∙∙∙π/σ hydrogen bonds and π-Li∙∙∙π/σ lithium bonds. The properties of these interactions are discussed, and particularly the Lewis acid units are analyzed, because multi-center π-H or π-Li covalent bonds may occur in these systems. Various theoretical approaches were applied here to analyze the above-mentioned interactions-the Quantum Theory of Atoms in Molecules (QTAIM), the Symmetry-Adapted Perturbation Theory (SAPT) and the Non-Covalent Interaction (NCI) method.

Separation of CH4, H2S, N2 and CO2 gases using four types of nanoporous graphene cluster model: a quantum chemical investigation.

Nanoporous graphene is being regarded as a promising candidate for reliable gas separation and purification applications. In the present research, the permeation barrier, selectivity and all thermodynamic functions for passing of four different molecules including CH4, H2S, N2 and CO2 gases on four types of porous graphene which is doped by two, three and six nitrogen atoms using quantum mechanical modelling, based on the density functional theory, B97D, and cc-pVTZ basis set have been evaluated. We find that the permeation barrier of all studied gases especially carbon dioxide decreased by considering the functionalized porous graphene by two, three and six nitrogens-doped, respectively. The results of our study propose using a porous graphene sheet as highly efficient and highly selective membranes for gas separations.

Clinical and Laboratory Predictors of Severity, Criticality, and Mortality in COVID-19: A Multisystem Disease.

Coronavirus disease 2019 (COVID-19) pandemic continues devastating effects on healthcare systems. Such a crisis calls for an urgent need to develop a risk stratification tool. The present chapter aimed to identify laboratory and clinical correlates of adverse outcomes in patients with COVID-19. To this end, we conducted a systematic evaluation of studies that investigated laboratory abnormalities in patients with COVID-19 and compared i. patients with a severe form of disease and patients with a non-severe form of the disease, ii. patients who were in critical condition and patients who were not in critical condition, and iii. patients who survived and patients who died. We included 54 studies in the data synthesis. Compared to patients with a non-severe form of COVID-19, patients who had a severe form of disease revealed higher values for white blood cells (WBC), polymorphonuclear leukocytes (PMN), total bilirubin, alanine aminotransferase (ALT), creatinine, troponin, procalcitonin, lactate dehydrogenase (LDH), and D-dimer. By contrast, platelet count, lymphocyte count, and albumin levels were decreased in patients with a severe form of COVID-19. Also, patients with a severe phenotype of disease were more likely to have diabetes, chronic heart disease, chronic obstructive pulmonary disease (COPD), cerebrovascular disease, hypertension, chronic kidney disease (CKD), and malignancy. Compared to patients who survived, patients who died had higher WBC, PMN, total bilirubin, ALT, procalcitonin, IL-6, creatinine, PT, lymphocyte count, platelet count, and albumin. Also, non-survivors revealed a higher prevalence of diabetes, chronic heart disease, COPD, cerebrovascular disease, and CKD. Meta-analyses identified several laboratory parameters that might help the prediction of severe, critical, and lethal phenotypes of COVID-19. These parameters correlate with the immune system function, inflammation, coagulation, and liver and kidney function.

Coexistence of Intra- and Intermolecular Hydrogen Bonds: Salicylic Acid and Salicylamide and Their Thiol Counterparts.

The ωB97-XD/6-311++G(d,p) calculations were carried out on dimers and monomers of salicylic acid and salicylamide as well as on their thiol counterparts; different conformations of these species were considered. The searches through the Cambridge Structural Database were performed to find related structures; thus the analysis of results of these searches is presented. Various approaches were applied to analyze inter- and intramolecular hydrogen bonds occurring in the above-mentioned species: natural bond orbital (NBO) method, symmetry-adapted perturbation theory (SAPT) approach, the quantum theory of atoms in molecules (QTAIM), and the electron localization function (ELF) method. The results of calculations indicate a slight mutual influence of inter- and intramolecular hydrogen bonds. However, the frequent occurrence of both interactions in crystal structures indicates the importance of their coexistence. The occurrence of intramolecular chalcogen bonds for trans conformations of species analyzed is also discussed.

Apamin administration impact on miR-219 and miR-155-3p expression in cuprizone induced multiple sclerosis model.

Multiple sclerosis (MS) is a chronic debilitating disease that attacks the central nervous system. This study aims to investigate miR-219 and miR-155-3p expression levels involved in the myelination process following the administration of apamin peptide in the model of multiple sclerosis disease. Forty-four 8 week C57BL/6 male mice (22 ± 5 g) randomly divided into six groups. Apamin (100 µg/kg/BW) was administered intraperitoneally as a co-treatment during phase I (demyelination) or post-treatment phase II (remyelination) twice a week in cuprizone induced MS model. At the end of study myelin content and microRNA expression levels were measured with LFB staining and quantitative Real-Time PCR method, respectively. It was observed that the intended microRNAs were dysregulated during the different phases of disease induction. After 6 weeks of cuprizone exposure, miR-219 downregulated in phase I in comparison with the negative control. On the other hand, the apamin co-treatment significantly inhibit the miR-155-3p upregulation during the phase I as compared with the cuprizone group (p < 0.0001). Apamin has more impact on the miR155-3p reduction in phase I than miR-219 elevation in phase II. It could be considered as a therapeutic option for decreasing plaque formation during the exacerbation phase of the MS disease. Apamin has more impact on the miR155-3p reduction in phase I than miR-219 elevation in phase II. It could be considered as a therapeutic option for decreasing plaque formation during the exacerbation phase of the MS disease.

S-H O and O-H O Hydrogen Bonds-Comparison of Dimers of Thiocarboxylic and Carboxylic Acids.

ωB97-XD/aug-cc-pVTZ calculations were performed on dimers of selected thiocarboxylic acids and on analogous carboxylic acids. The sample of calculated thiocarboxylic acids is an extension of the Cambridge Structural Database search that contains only a few such structures. The Natural Bond Orbital (NBO) method, Symmetry-Adapted Perturbation Theory (SAPT) approach, Non-Covalent Interaction (NCI) method and Quantum Theory of Atoms in Molecules (QTAIM) were applied additionally to analyse interactions in dimers of thiocarboxylic and carboxylic acids. The insights into crystal structures as well as into results of calculations show that the formation of S-H…O hydrogen bonds between molecules of thiocarboxylic acids is steered by the same mechanisms as the formation of much stronger O-H…O hydrogen bonds in carboxylic acids. The intramolecular O-H…O and C-H…S hydrogen bonds occurring in few considered structures are also analysed.

Multistate Multiconfiguration Quantum Chemical Computation of the Two-Photon Absorption Spectra of Bovine Rhodopsin.

Recently, progress in IR sources has led to the discovery that humans can detect infrared (IR) light. This is hypothesized to be due to the 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 and extended multiconfiguration quasi-degenerate perturbation theory calculations to simulate the TPA spectrum of bovine rhodopsin (Rh) as a model for the human photoreceptor. The results show that the TPA spectrum of Rh has an intense S0 → S1 band but shows also S0 → S2 and S0 → S3 transitions whose intensities, relative to the S0 → S1 band, are significantly increased when compared to the corresponding bands of the OPA spectrum. In conclusion, we show that IR light in the 950 nm region can be perceived by rod photoreceptors, thus supporting the two-photon origin of the IR perception. We also found that the same photoreceptor can perceive red (i.e., close to 680 nm) light provided that TPA induces population of S2.

Ternary Complex Formation and Photoactivation of a Photoenzyme Results in Altered Protein Dynamics.

The interplay between protein dynamics and catalysis remains a fundamental question in enzymology. We here investigate the ns-timescale dynamics of a light-dependent NADPH:protochlorophyllide oxidoreductase (LPOR), a photoenzyme crucial for chlorophyll synthesis. LPORs catalyze the light-triggered trans addition of a hydride and a proton across the C17═C18 double bond of the chlorophyll precursor protochlorophyllide (Pchlide). Because of the lack of an LPOR structure, the global structural and dynamic consequences of LPOR/Pchlide/NADPH ternary complex formation remain elusive. Moreover, photoactivation of LPORs by low-light preillumination is controversially discussed as unequivocal proof for this phenomenon is lacking. By employing quasielastic neutron spectroscopy (QENS), we show that the formation of the ternary holoprotein complex as well as photoactivation lead to progressive rigidification of the protein. These findings are supported by thermostability measurements, which reveal different melting behavior and thermostabilities for the apo- and holoprotein ternary complexes. Molecular dynamics simulations in good agreement with the experimental QENS results suggest that the increased flexibility observed for the apoprotein stems from structural fluctuations of the NADPH and Pchlide substrate binding sites of the enzyme. On the basis of our results, in conjunction with activity and stability measurements, we provide independent proof for LPOR photoactivation, defined as a process that modifies the protein structure and dynamics, resulting in an increased substrate turnover. Our findings advance the structural and dynamic understanding of LPORs and provide a first link between protein dynamics and catalysis for this enzyme class.

Fabrication of microporous inorganic microneedles by centrifugal casting method for transdermal extraction and delivery.

Microneedle patches have been widely used as transdermal transport systems because of their painless and easy application. Marked rigidity, strength, biocompatibility, and physiological stability are unique features of microneedles fabricated from ceramic materials to be used as microneedle patches. However, the conventional ceramic microneedles are typically dense structures with limited free space for biomolecule loading. A facile method is required for fabrication of biocompatible ceramic microneedles with interconnected porosity. Herein, the simple method of centrifugal casting was developed for fabrication of microporous microneedles from alumina suspensions. The slurry or resin-based alumina suspensions were casted into micromolds under centrifugal force, followed by sintering at high temperatures. The effects of particle size, solvent type, binder amount, resin content and sintering temperature on the microstructure and mechanical properties of microneedles were investigated. By optimizing the process parameters, highly porous (up to 60%) microneedles with interconnected micropores (of diameter ∼1-1.5 µm) were produced. The microporous microneedles were biocompatible and mechanically strong for skin penetration. The potential use of the microneedles for transdermal transportation of biomolecules was shown by fast and accurate extraction of glucose from a skin model and efficient loading and fast release of insulin under physiological conditions. The results suggested that the microporous alumina microneedles may serve as molecular transport systems in transdermal biosensing and drug delivery.

Theoretical Model of the Protochlorophyllide Oxidoreductase from a Hierarchy of Protocols.

The enzyme protochlorophyllide oxidoreductase (LPOR) catalyzes the light-driven reduction of protochlorophyllide (Pchlide), a crucial step in chlorophyll biosynthesis. Molecular understanding of the photocatalytic mechanism of LPOR is essential for harnessing light energy to mediate enzymatic reactions. The absence of X-ray crystal structure has promoted the development of LPOR homology models that lack a catalytically competent active site and could not explain the variously reported spectroscopic evidence, including time-resolved optical spectroscopy data. We have refined previous structural models to account for the catalytic active site and the characteristic experimental spectral features of Pchlide binding, including the 26 cm-1 red shift of the C13(1) carbonyl stretch vibration in the mid-infrared (IR) and the 12 nm red shift of the Q x electronic band. A hierarchy of theoretical methods, including homology modeling, molecular dynamics simulations, hybrid quantum mechanics [(TD-)DFT]/molecular mechanics [AMBER] calculations, and computational vibrational and electronic spectroscopies, have been combined in an iterative protocol to reproduce experimental evidence and to predict ultrafast transient IR spectroscopic fingerprints associated with the catalytic process. The successful application to the LPOR enzyme indicates that the presented hierarchical protocol provides a general workflow to protein structure refinement.