Anti-mutagenic agent targeting LexA to combat antimicrobial resistance in mycobacteria.

Antimicrobial resistance (AMR) is a serious global threat demanding innovations for effective control of pathogens. The bacterial SOS response, regulated by the master regulators, LexA and RecA, contributes to AMR through advantageous mutations. Targeting the LexA/RecA system with a novel inhibitor could suppress the SOS response and potentially reduce the occurrence of AMR. RecA presents a challenge as a therapeutic target due to its conserved structure and function across species, including humans. Conversely, LexA which is absent in eukaryotes, can be potentially targeted, due to its involvement in SOS response which is majorly responsible for adaptive mutagenesis and AMR. Our studies combining bioinformatic, biochemical, biophysical, molecular, and cell-based assays present a unique inhibitor of mycobacterial LexA, wherein we show that the inhibitor interacts directly with the catalytic site residues of LexA of Mycobacterium tuberculosis (Mtb), consequently hindering its cleavage, suppressing SOS response thereby reducing mutation frequency and AMR.

Decoding the plant clock: a review of mathematical models for the circadian regulatory network.

Most organisms have evolved specific mechanisms to respond to changes in environmental conditions such as light and temperature over the course of day. These periodic changes in the physiology and behaviour of organisms, referred to as circadian rhythms, are a consequence of intricate molecular mechanisms in the form of transcription and translational feedback loops. The plant circadian regulatory network is a complex web of interconnected feedback loops involving various transcription factors such as CCA1, LHY, PRRs, TOC1, LUX, ELF3, ELF4, RVE8, and more. This network enables plants to adapt and thrive in diverse environmental conditions. It responds to entrainment signals, including light, temperature, and nutrient concentrations and interacts with most of the physiological functions such as flowering, growth and stress response. Mathematical modelling of these gene regulatory networks enables a deeper understanding of not only the function but also the perturbations that may affect the plant growth and function with changing climate. Over the years, numerous mathematical models have been developed to understand the diverse aspects of plant circadian regulation. In this review, we have delved into the systematic development of these models, outlining the model components and refinements over time. We have also highlighted strengths and limitations of each of the models developed so far. Finally, we conclude the review by describing the prospects for investigation and advancement of these models for better understanding of plant circadian regulation.

Addressing the Challenge of a Simultaneous Destructive Assay of Plutonium and Uranium: Highly Precise, Robust, Universal, and Reagent-Free Differential Pulse Voltametric Method Development in Biodegradable Methanesulfonic Acid Medium.

The destructive assay of bulk uranium and plutonium, a cornerstone for chemical quality control and nuclear material accounting of fuel matrices, mandates robust and precise methodologies. Despite ongoing research, simultaneous, matrix independent determination of U and Pu has eluded solution owing to inherent limitations in aqueous acid medium, viz., coexistence of multiple oxidation states, coupled electrochemical reactions, smaller potential window, and requirement for multistep sample preconditioning and tedious electrode modification. The present study addresses this challenge wherein non-aqueous methanesulfonic acid (MSA) served the dual role of solvent and analyte media with a bare glassy carbon (GC) electrode. Fuel matrices, viz., (U, Pu)C, (U, Pu)O2, PuO2, UO3, UO2, and U3O8, were quantitatively dissolved in biodegradable MSA, without using any additives. Redox speciation of the analytes, U and Pu, in MSA was probed by ultraviolet-visible spectrophotometry and electrometry, revealing the absence of electrocatalytic regeneration and stabilization of single oxidation state, viz., U(VI) and Pu(IV), along with relevant redox-energetic (electron transfer and reversibility) and kinetic data. Bidentate coordination of MSA with the U analyte was indicated by X-ray absorption spectroscopy studies and was corroborated by density functional theory-based investigations, providing the optimized structure, viz., [UO2(MSA)2] and [Pu(MSA)4], binding modes and energy, partial charges, and molecular orbital diagrams. Based on these insights, the feasibility of differential pulse voltammetry (DPV)-based assay method development for U and Pu separately and in different U/Pu ratios, representing assorted fuel matrices, was probed. Analytical figures of merit for both U and Pu (detection limit of ∼10-5 M, precision of ∼0.2%, accuracy of ∼0.2%, high sensitivity, repeatability, and non-influence of relevant interferences) were determined, method validated employing actual fuel samples, and compared with the established, multi-step biamperometry method. Hence, a universal, simultaneous U and Pu destructive assay method in non-aqueous MSA media based on DPV with a commercial GC electrode was demonstrated.

In-Situ-Generated Fluoride-Assisted Rapid Dissolution of Uranium Oxides by Ionic Liquids.

A quantitative, rapid, endothermic dissolution of U3O8 in C4mim·PF6 (1-alkyl-3-methyl imidazolium hexafluorophosphate) has been achieved within 2 h at 65 °C by in situ generated fluoride ions by pre-equilibrating the ionic liquid with suitable concentrations of nitric acid. The efficiency of the dissolution followed the trend: UO3 > UO2 > U3O8. The fluoride generation was found to increase with the concentration of nitric acid being equilibrated, the water content of the ionic liquid, and also the time of equilibration. The rate of dissolution of U3O8 followed the trend: C4mim·PF6> C6mim·PF6 > C8mim·PF6. The maximum loading observed for the present case was 200 mg mL-1 which is considered to be quite high with an ionic liquid. The effects of different acid pre-equilibration (HClO4, HCl) on F- generation and subsequent dissolution characteristics have also been investigated. The in situ F- generation, as well as U3O8 dissolution, were found to predominantly follow a pseudo-second-order rate kinetics, while the rate constants for U3O8 dissolution were found to be higher than that of F- generation. The dissolved uranium was successfully electrodeposited on a Cu plate, as confirmed by EDXRF, while the formation of UO2 was revealed from the XRD pattern of the deposit.

A Remarkable Strategy to Hijack U(VI) from Mixed Metal Ion Solutions Using 1-Hydroxy-2-pyridone.

The present work envisages a chelation driven, facile, selective, and rapid method for uranium(VI) separation from a (U, Th) mixture using 1-hydroxy-2-pyridone (1,2-HOPO). Herein, U(VI) was selectively precipitated as the neutral [UO2(HOPO)2(H2O)]·nH2O (orange colored) complex while Th(IV) and other metal ions remained in the solution. The pH of the medium played a key role in facilitating the separation process.

Experimental and Theoretical Insight into the Ionic Liquid-Mediated Complexation of Trivalent Lanthanides with ß-Diketone and Its Fluorinated Analogue.

A multitechnique approach with theoretical insights has been employed to understand the complexation of trivalent lanthanides with two ß-diketones, viz. 1-phenyl-1,3-butanedione (L1) and 4,4,4-trifluoro-1-phenyl-1,3-butanedione (L2), in an ionic liquid (C6mim·NTf2). UV-vis spectral analysis of complexation using Nd3+ revealed the predominance of ML2+ and ML4- species. The stability constants for the PB complexes were higher (ß2 ∼ 10.45 ± 0.05, ß4 ∼ 15.51 ± 0.05) than those for the TPB (ß2 ∼ 7.56 ± 0.05, ß4 ∼ 13.19 ± 0.06). The photoluminescence titration using Eu3+ corroborated the same observations with slightly higher stability constants, probably due to the higher ionic potential of Eu3+. The more asymmetric (AL2ML4 ∼ 5.2) Eu-L2 complex was found to contain one water molecule in the primary coordination sphere of Eu3+ with more covalency of the Eu3+-O bond (Ω2L1 = 8.5 × 10-20, Ω4L1 = 1.3 × 10-20) compared to the less asymmetric Eu-L1 complex (AL1ML4 ∼ 3.5) with two water molecules having less Eu-O covalency (Judd-Offelt parameters: Ω2L1 = 7.3 × 10-20, Ω4L1 = 1.0 × 10-20). Liquid-liquid extraction studies involving Nd3+ and Eu3+ revealed the formation of the ML4- complex following an 'anion exchange' mechanism. The shift of the enol peak from 1176 to 1138 cm-1 on the complexation of the ß-diketones with Eu3+ was confirmed from the FTIR spectra. 1H NMR titration of the ß-diketones with La(NTf2)3 evidenced the participation of α-H of the ß-diketones and protons at C2, C4, and C5 positions of the methylimidazolium ring. For the ML2 complex, 4 donor O atoms are suggested to coordinate to the trivalent lanthanides with bond distances of 2.3297-2.411 Å for La-O, 2.206-2.236 Å for Eu-O, and 2.217-2.268 Å for Nd-O, respectively, while for the ML4 complex, 8 donor O atoms were coordinated with bond lengths of 2.506-2.559 Å for La-O, 2.367-2.447 Å for Eu-O, and 2.408-2.476 Å for Nd-O. The Nd3+ ion was higher by 9.7 kcal·mol-1 than that of the La3+ ion for the 1:4 complex. The complexation energy with L1 was quite higher than that with L2 for both 1:2 and 1:4 complexes. Using cyclic voltammetry, the redox behavior of trivalent lanthanides Eu and Gd with ß-diketonate in ionic liquid medium was probed and their redox energetic and kinetic parameters were determined.

Structural differences in the FAD-binding pockets and lid loops of mammalian CRY1 and CRY2 for isoform-selective regulation.

The circadian clock is a biological timekeeper that operates through transcription-translation feedback loops in mammals. Cryptochrome 1 (CRY1) and Cryptochrome 2 (CRY2) are highly conserved core clock components having redundant and distinct functions. We recently identified the CRY1- and CRY2-selective compounds KL101 and TH301, respectively, which provide useful tools for the exploration of isoform-selective CRY regulation. However, intrinsic differences in the compound-binding FAD (flavin adenine dinucleotide) pockets between CRY1 and CRY2 are not well understood, partly because of nonoptimal properties of previously reported apo form structures in this particular region constituted by almost identical sequences. Here, we show unliganded CRY1 and CRY2 crystal structures with well-defined electron densities that are largely free of crystal contacts at the FAD pocket and nearby lid loop. We revealed conformational isomerism in key residues. In particular, CRY1 W399 and corresponding CRY2 W417 in the FAD pocket had distinct conformations ("out" for CRY1 and "in" for CRY2) by interacting with the lid loop residues CRY1 Q407 and CRY2 F424, respectively, resulting in different overall lid loop structures. Molecular dynamics simulations supported that these conformations were energetically favorable to each isoform. Isoform-selective compounds KL101 and TH301 preferred intrinsic "out" and "in" conformations of the tryptophan residue in CRY1 and CRY2, respectively, while the nonselective compound KL001 fit to both conformations. Mutations of lid loop residues designed to perturb their isoform-specific interaction with the tryptophan resulted in reversed responses of CRY1 and CRY2 to KL101 and TH301. We propose that these intrinsic structural differences of CRY1 and CRY2 can be targeted for isoform-selective regulation.

Isoform-selective regulation of mammalian cryptochromes.

CRY1 and CRY2 are essential components of the circadian clock controlling daily physiological rhythms. Accumulating evidences indicate distinct roles of these highly homologous proteins, in addition to redundant functions. Therefore, the development of isoform-selective compounds represents an effective approach towards understanding the similarities and differences of CRY1 and CRY2 by controlling each isoform individually. We conducted phenotypic screenings of circadian clock modulators, and identified KL101 and TH301 that selectively stabilize CRY1 and CRY2, respectively. Crystal structures of CRY-compound complexes revealed conservation of compound-binding sites between CRY1 and CRY2. We further discovered a unique mechanism underlying compound selectivity in which the disordered C-terminal region outside the pocket was required for the differential effects of KL101 and TH301 against CRY isoforms. By using these compounds, we found a new role of CRY1 and CRY2 as enhancers of brown adipocyte differentiation, providing the basis of CRY-mediated regulation of energy expenditure.

Marine biological macromolecules as matrix material for biosensor fabrication.

The ocean covers two-third of our planet and has great biological heterogeneity. Marine organisms like algae, vertebrates, invertebrates, and microbes are known to provide many natural products with biological activities as well as potential sources of biomaterials for therapeutic, biomedical, biosensors, and climate stabilization. Over the years, the field of biosensors has gained huge attention due to their extraordinary ability to provide early disease diagnosis, rapid detection of various molecules and substances along with long-term monitoring. This review aims to focus on the properties and employment of various biomaterials (carbohydrate polymers, proteins, polyacids, etc.) of marine origins such as alginate, chitin, chitosan, fucoidan, carrageenan, chondroitin sulfate, hyaluronic acid, collagen, marine pigments, marine nanoparticles, hydroxyapatite, biosilica, lectins, and marine whole cell in the design and development of biosensors. Furthermore, this review also covers the source of such marine biomaterials and their promising evolution in the fabrication of biosensors that are potent to be employed in the biomedical, environmental science, and agricultural sciences domains. The use of such fabricated biosensors harnesses the system with excellent specificity, selectivity, biocompatibility, thermal stability, and minimal cost advantages.

Chemical and Redox Speciation of Uranyl with Three Environmentally Relevant Bifunctional Chelates: Multi-Technique Approach Combined with Theoretical Estimations.

Carbon and phosphorous are two primary elements common to the bio-geosphere and are omnipresent in both biotic and abiotic arenas. Phosphonate and carboxylate are considered as building blocks of glyphosate and humic substances and constituents of the cellular wall of bacteria and are the driving functionalities for most of the chemical interactions involving these two elements. Phosphonocarboxylates, a combination of both the functionalities in one moiety, are ideal models to dig deep into for understanding the chemical interactions of the two functional groups with metal ions. Phosphorous and carbon majorly exist as inorganic/organic phosphate and carboxylate, respectively, in the bio-geosphere. Aquatic contamination is a major concern for uranium, and the presence of complexing agents would alter the uranium concentrations in aquifers. Determination of solution thermodynamic parameters, speciation plots, redox patterns, Eh-pH diagrams, coordination structures, and molecular-level understanding by density functional theory calculations was carried out to interpret the uranyl (UO22+) interaction with three environmentally relevant phosphonocarboxylates, namely, phosphono-formic acid (PFA), phosphono-acetic acid (PAA), and phosphono-propanoic acid (PPA). UO22+ forms 1:1 complexes with the three phosphonocarboxylates in the monoprotonated form, having nearly the same stability, and the complexes [UO2(PFAH)], [UO2(PAAH)], and [UO2(PPAH)] involve chelate formation of five, six, and seven membered rings, respectively, through the participation of an oxygen each from the carboxylate and phosphonate, strengthened by an intra-molecular hydrogen bonding through the proton of the phosphonate moiety with uranyl oxygen. The complex formations are favored both enthalpically and entropically, with the latter being more contributive to the overall free energy of formation. The redox speciation showed an aqueous soluble complex formation over a wide pH range of 1-8. Electrospray ionization mass spectrometry and extended X-ray absorption fine structure established the coordination modes, which are further corroborated by density functional calculations. The knowledge gained from the present studies provide potential inputs in framing the cleanup, sequestering, microbial, and bio-remediation strategies for uranyl from aquatic environments.

Light-Control over Casein Kinase 1δ Activity with Photopharmacology: A Clear Case for Arylazopyrazole-Based Inhibitors.

Protein kinases are responsible for healthy cellular processes and signalling pathways, and their dysfunction is the basis of many pathologies. There are numerous small molecule inhibitors of protein kinases that systemically regulate dysfunctional signalling processes. However, attaining selectivity in kinase inhibition within the complex human kinome is still a challenge that inspires unconventional approaches. One of those approaches is photopharmacology, which uses light-controlled bioactive molecules to selectively activate drugs only at the intended space and time, thereby avoiding side effects outside of the irradiated area. Still, in the context of kinase inhibition, photopharmacology has thus far been rather unsuccessful in providing light-controlled drugs. Here, we present the discovery and optimisation of a photoswitchable inhibitor of casein kinase 1δ (CK1δ), important for the control of cell differentiation, circadian rhythm, DNA repair, apoptosis, and numerous other signalling processes. Varying the position at which the light-responsive azobenzene moiety has been introduced into a known CK1δ inhibitor, LH846, revealed the preferred regioisomer for efficient photo-modulation of inhibitory activity, but the photoswitchable inhibitor suffered from sub-optimal (photo)chemical properties. Replacement of the bis-phenyl azobenzene group with the arylazopyrazole moiety yielded a superior photoswitch with very high photostationary state distributions, increased solubility and a 10-fold difference in activity between irradiated and thermally adapted samples. The reasons behind those findings are explored with molecular docking and molecular dynamics simulations. Results described here show how the evaluation of privileged molecular architecture, followed by the optimisation of the photoswitchable unit, is a valuable strategy for the challenging design of the photoswitchable kinase inhibitors.

Strong Anharmonicity-Induced Low Thermal Conductivity and High n-type Mobility in the Topological Insulator Bi1.1 Sb0.9 Te2 S.

Intrinsically low lattice thermal conductivity (κlat ) while maintaining the high carrier mobility (µ) is of the utmost importance for thermoelectrics. Topological insulators (TI) can possess high µ due to the metallic surface states. TIs with heavy constituents and layered structure can give rise to high anharmonicity and are expected to show low κlat . Here, we demonstrate that Bi1.1 Sb0.9 Te2 S (BSTS), which is a 3D bulk TI, exhibits ultra-low κlat of 0.46 Wm-1 K-1 along with high µ of ≈401 cm2  V-1 s-1 . Sound velocity measurements and theoretical calculations suggest that chemical bonding hierarchy and high anharmonicity play a crucial role behind such ultra-low κlat . BSTS possesses low energy optical phonons which strongly couple with the heat carrying acoustic phonons leading to ultra-low κlat . Further, Cl has been doped at the S site of BSTS which increases the electron concentration and reduces the κlat resulting in a promising n-type thermoelectric figure of merit (zT) of ≈0.6 at 573 K.

Photopharmacological Manipulation of Mammalian CRY1 for Regulation of the Circadian Clock.

CRY1 and CRY2 proteins are highly conserved components of the circadian clock that controls daily physiological rhythms. Disruption of CRY functions are related to many diseases, including circadian sleep phase disorder. Development of isoform-selective and spatiotemporally controllable tools will facilitate the understanding of shared and distinct functions of CRY1 and CRY2. Here, we developed CRY1-selective compounds that enable light-dependent manipulation of the circadian clock. From phenotypic chemical screening in human cells, we identified benzophenone derivatives that lengthened the circadian period. These compounds selectively interacted with the CRY1 photolyase homology region, resulting in activation of CRY1 but not CRY2. The benzophenone moiety rearranged a CRY1 region called the "lid loop" located outside of the compound-binding pocket and formed a unique interaction with Phe409 in the lid loop. Manipulation of this key interaction was achieved by rationally designed replacement of the benzophenone with a switchable azobenzene moiety whose cis-trans isomerization can be controlled by light. The metastable cis form exhibited sufficiently high half-life in aqueous solutions and structurally mimicked the benzophenone unit, enabling reversible period regulation over days by cellular irradiation with visible light. This study revealed an unprecedented role of the lid loop in CRY-compound interaction and paves the way for spatiotemporal regulation of CRY1 activity by photopharmacology for molecular understanding of CRY1-dependent functions in health and disease.

Small Conformational Changes Underlie Evolution of Resistance to NNRTI in HIV Reverse Transcriptase.

Despite achieving considerable success in reducing the number of fatalities due to acquired immunodeficiency syndrome, emergence of resistance against the reverse transcriptase (RT) inhibitor drugs remains one of the biggest challenges of the human immunodeficiency virus antiretroviral therapy (ART). Non-nucleoside reverse transcriptase inhibitors (NNRTIs) form a large class of drugs and a crucial component of ART. In NNRTIs, even a single resistance mutation is known to make the drugs completely ineffective. Additionally, several inhibitor-bound RTs with single resistance mutations do not exhibit any significant variations in their three-dimensional structures compared with the inhibitor-bound RT but completely nullify their inhibitory functions. This makes understanding the structural mechanism of these resistance mutations crucial for drug development. Here, we study several single resistance mutations in the allosteric inhibitor (nevirapine)-bound RT to analyze the mechanism of small structural changes leading to these large functional effects. In this study, we have shown that in absence of significant conformational variations in the inhibitor-bound wild-type RT and RT with single resistance mutations, the protein contact network analysis of their static structures, along with molecular dynamics simulations, can be a useful approach to understand the functional effect of small local conformational variations. The simple network analysis exposes the localized contact changes that lead to global rearrangement in the communication pattern within RT. Furthermore, these conformational changes have implications on the overall dynamics of RT. Using various measures, we show that a single resistance mutation can change the network structure and dynamics of RT to behave more like unbound RT, even in the presence of the inhibitor. This combined coarse-grained contact network and molecular dynamics approach promises to be a useful tool to analyze structure-function studies of proteins that show large functional changes with negligible variations in their overall conformation.

Conformational dynamics of human protein kinase CK2α and its effect on function and inhibition.

Protein kinase, casein kinase II (CK2), is ubiquitously expressed and highly conserved protein kinase that shows constitutive activity. It phosphorylates a diverse set of proteins and plays crucial role in several cellular processes. The catalytic subunit of this enzyme (CK2α) shows remarkable flexibility as evidenced in numerous crystal structures determined till now. Here, using analysis of multiple crystal structures and long timescale molecular dynamics simulations, we explore the conformational flexibility of CK2α. The enzyme shows considerably higher flexibility in the solution as compared to that observed in crystal structure ensemble. Multiple conformations of hinge region, located near the active site, were observed during the dynamics. We further observed that among these multiple conformations, the most populated conformational state was inadequately represented in the crystal structure ensemble. The catalytic spine, was found to be less dismantled in this state as compared to the "open" hinge/αD state crystal structures. The comparison of dynamics in unbound (Apo) state and inhibitor (CX4945) bound state exhibits inhibitor induced suppression in the overall dynamics of the enzyme. This is especially true for functionally important glycine-rich loop above the active site. Together, this work gives novel insights into the dynamics of CK2α in solution and relates it to the function. This work also explains the effect of inhibitor on the dynamics of CK2α and paves way for development of better inhibitors.

Role of Computational Methods in Going beyond X-ray Crystallography to Explore Protein Structure and Dynamics.

Protein structural biology came a long way since the determination of the first three-dimensional structure of myoglobin about six decades ago. Across this period, X-ray crystallography was the most important experimental method for gaining atomic-resolution insight into protein structures. However, as the role of dynamics gained importance in the function of proteins, the limitations of X-ray crystallography in not being able to capture dynamics came to the forefront. Computational methods proved to be immensely successful in understanding protein dynamics in solution, and they continue to improve in terms of both the scale and the types of systems that can be studied. In this review, we briefly discuss the limitations of X-ray crystallography in studying protein dynamics, and then provide an overview of different computational methods that are instrumental in understanding the dynamics of proteins and biomacromolecular complexes.

Performance analysis of un-doped and doped titania (TiO 2 ) as an electron transport layer (ETL) for perovskite solar cells.

CONTEXT: Density functional theory (DFT) calculations are carried out on pure and doped rutile TiO 2 . The bandgap (E g ) for pristine, S-doped, Fe-doped, and Fe/S co-doped materials is direct, with values of 2.98 eV, 2.18 eV, 1.58 eV, and 1.40 eV. The effective mass of charge carriers (m*) and ratio of effective masses of holes to effective masses of electrons (R) are also investigated, and it is discovered that Fe/S co-doped materials have the lowest charge carrier recombination rate. The Fe/S co-doped material has the highest ε ( ω ) . α ( ω ) of doped materials shifted into the visible range. Due to the high dopant concentration in Fe and Fe/S-doped cases, the E g is lowered to a relatively small value; hence, only pristine and S-doped materials are verified as electron transport layer (ETL). A solar cell device analysis employing pure and S-doped rutile TiO 2 as ETL is completed using DFT-derived parameters in SCAPS-1D modeling software for the first time. For the optimized solar cells, current-voltage (IV) characteristics, quantum efficiency (QE), capacitance-voltage (CV) characteristics, and capacitance-frequency (Cf) characteristics are provided. The aim of the present study is to improve efficiency of perovskite solar cell by doping as well as to improve accuracy of simulation by applying DFT extracted parameters as input. From the analysis, improvement is found in efficiency of doped TiO 2 compared to un-doped TiO 2 . The efficiency of the PSC with S-doped ETL is 1.418% higher than the PSC with un-doped ETL. METHOD: Quantumwise Automistic Tool Kit (ATK) is used to extract DFT parameters. Using these DFT parameters as input in SCAPS-1D (Solar Cell Capacitance Simulator), solar cells for doped and un-doped material are simulated. The density functional theory (DFT)-based orthogonalized linear combination of atomic orbital (OLCAO) technique is used. Structural optimization is done using the LBFGS (Limited-memory Broyden-Fletcher-Goldfarb-Shanno). PBESol-GGA (Perdew-Burke-Ernzerhof solid-generalized gradient approximation) is applied as exchange correlation for calculating structural parameters, while MGGA-TB09 (meta-generalized gradient approximation-Tran and Blaha) is applied as exchange correlation for calculating optical and electronic properties.

Role of phonon scattering and bonding in resolving lattice thermal conductivity ambiguities of ß-Ga2O3.

Understanding the lattice thermal conductivity (κl) of ß-Ga2O3 is very intriguing owing to its advantages in high-voltage and high-temperature applications. Despite several attempts, the underlying mechanism and causes of the notable discrepancies found in the κl values of ß-Ga2O3 along [100] and [001] directions calculated using first principles remained unresolved. We demonstrate that the understanding of the nature of chemical bonding is crucial to overcome the inconsistency in theoretically reported κl values. In low-symmetry structures such as ß-Ga2O3, the nature of the interactions is primarily long-range; therefore, a sufficiently large supercell inclusive of various bonding characteristics is required to capture relevant phonon wavelengths. Bonding nature-aware structure modeling allows precise estimation of acoustic and optical mode contributions towards κl. Additionally, phonon mean free path analysis confirms that considering only third-order interaction terms is adequate to determine the κl of ß-Ga2O3. The calculated κl values are in excellent agreement with experimentally reported values in all three directions. Our results establish that the bonding nature and its influence on phonon scattering are essential to consider in calculating κl accurately.

Low depth sequencing reveals the critically endangered Batagur kachuga (Red-crowned roofed turtle) mitochondrial genome and its evolutionary implications.

The Batagur kachuga (B. kachuga), commonly known as the Red-crowned roofed turtle, is a critically endangered species native to India and its neighboring countries like Bangladesh, and Nepal. The present study is the first report of the complete mitochondrial genome of B. kachuga (16,517 bp) construed via the next-generation sequencing (NGS) approach from eggshell DNA. There are 22 transfer RNAs (tRNAs), 2 ribosomal RNAs (rRNAs), 13 protein-coding genes (PCGs), and one putative control region (CR/D-loop) in the mitogenome. The CR region from the current study reveals conserved TAS, CD, and CSB domains and two AT-rich tandem repeat regions. Most genes are encoded in the heavy strand except the NADH dehydrogenase subunit 6 (ND6) gene and seven tRNA genes. Most PCGs start with the initiation codon ATG, except the COI (Cytochrome Oxidase Subunit-I) gene, which starts with the GTG codon. The present investigation also predicts the distinctive cloverleaf structures of tRNAs except for tRNA-Ser1 and tRNA-Ser-2, which lack a DHU arm. The comparative analysis of Ka/Ks with other 33 species from Order Testudines, in relation to B. kachuga, revealed negative selection in most PCGs, indicating a process of preservation and purification that aids in eliminating undesirable or detrimental substitutes. Phylogenetic analysis of this species has been analysed using the complete mitogenome of 33 turtle species. The maximum likelihood phylogenetic tree strongly supports each family in different clades and also reveals a close relationship between the Pangashura and Batagur genera. Our study suggests the generation of genome-wide molecular data, in terms of mitogenomes, SNPs, and SSRs, is needed to improve the understanding of this species and their phylogenetics and evolutionary relationships, which will help to improve the conservation efforts of this species.

Unusual redox stability of pentavalent uranium with hetero-bifunctional phosphonocarboxylate: insight into aqueous speciation.

The +5 state is an unusual oxidation state of uranium due to its instability in the aqueous phase. As a result, gaining information about its aqueous speciation is extremely difficult. The present work is an attempt in that direction and it provides insight into the existence of a new pentavalent species in the presence of hetero-bifunctional phosphonocarboxylate (PC) chelators, other than the carbonate ion, in the aqueous medium. The aqueous chemistry of pentavalent uranium species with three environmentally relevant PCs was probed using electrochemical and DFT methods to understand the redox energy and kinetics of conversion of the U(VI)/U(V) couple, stability, structure, stoichiometry, binding modes, etc. Interestingly, pentavalent uranium complexes with PCs are quite persistent over a wide range of pH starting from acidic to alkaline conditions. The PC chelators block the cation-cation interaction (CCI) of U(V) through strong hetero-bidentate chelation and intermolecular hydrogen bonding (IMHB) interactions which stabilize the pentavalent metal ion against disproportionation. For uranyl species in the presence of PCs, acting as chelators, CV plots were obtained at varying pH values from 2 to 8. The obtained results indicate an irreversible single redox peak involving U(VI) to U(V) conversion and association of a coupled chemical reaction with the electron transfer step. ESI-MS studies were performed to understand the speciation effect on the U(VI)/U(V) redox couple with varying pH. Speciation modelling of U(V) with the PC ligands was carried out, which indicated that the U(V) is redox stable in nearly 47% of the pH region in the presence of the PCs as compared to the carboxylate-based chelators. The free energy and reduction potential of the U(V) complexes and the reduction free energy and disproportionation free energy for the U(VI)/U(V) couple were determined by DFT computations in the presence of the PCs. In situ spectroelectrochemical spectra were recorded to provide evidence for the existence of U(V) species with PCs in the aqueous medium and to acquire its absorption spectra. The present study is highly significant for understanding the coordination chemistry of pentavalent uranium species, accurate modelling of uranium, and isolation of U(V).