MegaLTR: a web server and standalone pipeline for detecting and annotating LTR-retrotransposons in plant genomes.

LTR-retrotransposons (LTR-RTs) are a class of RNA-replicating transposon elements (TEs) that can alter genome structure and function by moving positions, repositioning genes, shifting exons, and causing chromosomal rearrangements. LTR-RTs are widespread in many plant genomes and constitute a significant portion of the genome. Their movement and activity in eukaryotic genomes can provide insight into genome evolution and gene function, especially when LTR-RTs are located near or within genes. Building the redundant and non-redundant LTR-RTs libraries and their annotations for species lacking this resource requires extensive bioinformatics pipelines and expensive computing power to analyze large amounts of genomic data. This increases the need for online services that provide computational resources with minimal overhead and maximum efficiency. Here, we present MegaLTR as a web server and standalone pipeline that detects intact LTR-RTs at the whole-genome level and integrates multiple tools for structure-based, homologybased, and de novo identification, classification, annotation, insertion time determination, and LTR-RT gene chimera analysis. MegaLTR also provides statistical analysis and visualization with multiple tools and can be used to accelerate plant species discovery and assist breeding programs in their efforts to improve genomic resources. We hope that the development of online services such as MegaLTR, which can analyze large amounts of genomic data, will become increasingly important for the automated detection and annotation of LTR-RT elements.

AlignStatPlot: An R package and online tool for robust sequence alignment statistics and innovative visualization of big data.

Multiple sequence alignment (MSA) is essential for understanding genetic variations controlling phenotypic traits in all living organisms. The post-analysis of MSA results is a difficult step for researchers who do not have programming skills. Especially those working with large scale data and looking for potential variations or variable sample groups. Generating bi-allelic data and the comparison of wild and alternative gene forms are important steps in population genetics. Customising MSA visualisation for a single page view is difficult, making viewing potential indels and variations challenging. There are currently no bioinformatics tools that permit post-MSA analysis, in which data on gene and single nucleotide scales could be combined with gene annotations and used for cluster analysis. We introduce "AlignStatPlot," a new R package and online tool that is well-documented and easy-to use for MSA and post-MSA analysis. This tool performs both traditional and cutting-edge analyses on sequencing data and generates new visualisation methods for MSA results. When compared to currently available tools, AlignStatPlot provides a robust ability to handle and visualise diversity data, while the online version will save time and encourage researchers to focus on explaining their findings. It is a simple tool that can be used in conjunction with population genetics software.

TEMM: A Curated Data Resource for Transposon Element-Based Molecular Markers in Plants.

Transposon elements (TEs) are mobile genetic elements that can insert themselves into new locations and modify the plant genome. In recent years, they have been used as molecular markers in plant breeding programs. TE-based molecular markers (TE-markers) are divided into two categories depending on the transcription mechanism of the TEs. The first category is retrotransposon-based molecular markers, which include RBIP, IRAP, REMAP, and iPBS. The second group is DNA-based-TE-markers, which include MITE, TE-junction, and CACTA TE-markers. These markers are a good tool for studying genetic diversity and can provide information on plants' phylogenetic and evolutionary history. They can help improve breeding programs to increase agronomic traits and develop new varieties. Overall, TE-markers play an important role in plant genetics and plant breeding and contribute to a better understanding of plant biology. Here, we present TEMM, a curated data resource for TE-markers in plants. Relevant research articles were screened to collect primer sequences and related information. Only articles containing primer sequences are added to the present data resource. TEMM contains 784 primers with their associated PCR reaction programs and their applications in various crops. These include 203 IPBS, 191 RBIP, 140 IRAP, 78 TE-junction, 76 IRAPS, 47 RBIP-IRAP, 16 IRAP-REMAP, 12 REMAP, 12 REMA-IRAP, 6 REMA, and 3 ISBP primers. The data resource is freely available at https://bioinformatics.um6p.ma/TEMM .

CicerSpTEdb2.0: An Upgrade of Cicer Species Transposable Elements Database.

To meet the critical demand of LTR-RTs data-driven research, we updated the CicerSpTEdb database to version 2.0, which includes more accurate intact LTR-RT elements with annotation of internal domains. We also added the ability to BLAST against TEs of Cicer species. As a result, 3701 intact LTR-RTs were detected in the studied genomes, including 2840 Copia and 861 Gypsy elements. Of the 3701 intact LTR-RTs, 588 were in C. arietinum, including 475 Copia and 113 Gypsy. While 1373 were detected in C. reticulatum, including 1041 Copia and 332 Gypsy. Furthermore, 1740 were found in C. echinospermum, including 1324 Copia and 416 Gypsy. Based on LTR-RT clades, the analysis classified the 3701 identified intact LTR-RTs in the studied genomes as Ale (850), SIRE (740), unknown (455), Ikeros (323), Reina (290), Tork (290), Ivana (282), Tekay (197), Athila (128), TAR (99), CRM (31), and Ogre (16) elements. The newly updated CicerSpTEdb2.0 will be a valuable resource for TEs of Cicer species and their comparative genomics.Database URL: http://cicersptedb.easyomics.org/index.php.

Identification, characterization, and validation of NBS-encoding genes in grass pea.

Grass pea is a promising crop with the potential to provide food and fodder, but its genomics has not been adequately explored. Identifying genes for desirable traits, such as drought tolerance and disease resistance, is critical for improving the plant. Grass pea currently lacks known R-genes, including the nucleotide-binding site-leucine-rich repeat (NBS-LRR) gene family, which plays a key role in protecting the plant from biotic and abiotic stresses. In our study, we used the recently published grass pea genome and available transcriptomic data to identify 274 NBS-LRR genes. The evolutionary relationships between the classified genes on the reported plants and LsNBS revealed that 124 genes have TNL domains, while 150 genes have CNL domains. All genes contained exons, ranging from 1 to 7. Ten conserved motifs with lengths ranging from 16 to 30 amino acids were identified. We found TIR-domain-containing genes in 132 LsNBSs, with 63 TIR-1 and 69 TIR-2, and RX-CCLike in 84 LsNBSs. We also identified several popular motifs, including P-loop, Uup, kinase-GTPase, ABC, ChvD, CDC6, Rnase_H, Smc, CDC48, and SpoVK. According to the gene enrichment analysis, the identified genes undergo several biological processes such as plant defense, innate immunity, hydrolase activity, and DNA binding. In the upstream regions, 103 transcription factors were identified that govern the transcription of nearby genes affecting the plant excretion of salicylic acid, methyl jasmonate, ethylene, and abscisic acid. According to RNA-Seq expression analysis, 85% of the encoded genes have high expression levels. Nine LsNBS genes were selected for qPCR under salt stress conditions. The majority of the genes showed upregulation at 50 and 200 µM NaCl. However, LsNBS-D18, LsNBS-D204, and LsNBS-D180 showed reduced or drastic downregulation compared to their respective expression levels, providing further insights into the potential functions of LsNBSs under salt stress conditions. They provide valuable insights into the potential functions of LsNBSs under salt stress conditions. Our findings also shed light on the evolution and classification of NBS-LRR genes in legumes, highlighting the potential of grass pea. Further research could focus on the functional analysis of these genes, and their potential use in breeding programs to improve the salinity, drought, and disease resistance of this important crop.

A large-scale assessment of the quality of plant genome assemblies using the LTR assembly index.

Recent advances in genome sequencing have led to an increase in the number of sequenced genomes. However, the presence of repetitive sequences complicates the assembly of plant genomes. The LTR assembly index (LAI) has recently been widely used to assess the quality of genome assembly, as a higher LAI is associated with a higher quality of assembly. Here, we assessed the quality of assembled genomes of 1664 plant and algal genomes using LAI and reported the results as data repository called PlantLAI (https://bioinformatics.um6p.ma/PlantLAI). A number of 55 117 586 pseudomolecules/scaffolds with a total length of 988.11 gigabase-pairs were examined using the LAI workflow. A total of 46 583 551 accurate LTR-RTs were discovered, including 2 263 188 Copia, 2 933 052 Gypsy, and 1 387 311 unknown superfamilies. Consequently, only 1136 plant genomes are suitable for LAI calculation, with values ranging from 0 to 31.59. Based on the quality classification system, 476 diploid genomes were classified as draft, 472 as reference, and 135 as gold genomes. We also provide a free webtool to calculate the LAI of newly assembled genomes and the ability to save the result in the repository. The data repository is designed to fill in the gaps in the reported LAI of existing genomes, while the webtool is designed to help researchers calculate the LAI of their newly sequenced genomes.

Genome-wide identification, characterization, and validation of the bHLH transcription factors in grass pea.

Background: The basic helix-loop-helix (bHLH) transcription factor is a vital component in plant biology, with a significant impact on various aspects of plant growth, cell development, and physiological processes. Grass pea is a vital agricultural crop that plays a crucial role in food security. However, the lack of genomic information presents a major challenge to its improvement and development. This highlights the urgency for deeper investigation into the function of bHLH genes in grass pea to improve our understanding of this important crop. Results: The identification of bHLH genes in grass pea was performed on a genome-wide scale using genomic and transcriptomic screening. A total of 122 genes were identified as having conserved bHLH domains and were functionally and fully annotated. The LsbHLH proteins could be classified into 18 subfamilies. There were variations in intron-exon distribution, with some genes lacking introns. The cis-element and gene enrichment analyses showed that the LsbHLHs were involved in various plant functions, including response to phytohormones, flower and fruit development, and anthocyanin synthesis. A total of 28 LsbHLHs were found to have cis-elements associated with light response and endosperm expression biosynthesis. Ten conserved motifs were identified across the LsbHLH proteins. The protein-protein interaction analysis showed that all LsbHLH proteins interacted with each other, and nine of them displayed high levels of interaction. RNA-seq analysis of four Sequence Read Archive (SRA) experiments showed high expression levels of LsbHLHs across a range of environmental conditions. Seven highly expressed genes were selected for qPCR validation, and their expression patterns in response to salt stress showed that LsbHLHD4, LsbHLHD5, LsbHLHR6, LsbHLHD8, LsbHLHR14, LsbHLHR68, and LsbHLHR86 were all expressed in response to salt stress. Conclusion: The study provides an overview of the bHLH family in the grass pea genome and sheds light on the molecular mechanisms underlying the growth and evolution of this crop. The report covers the diversity in gene structure, expression patterns, and potential roles in regulating plant growth and response to environmental stress factors in grass pea. The identified candidate LsbHLHs could be utilized as a tool to enhance the resilience and adaptation of grass pea to environmental stress.

The inhibitive action of 2-mercaptobenzothiazole on the porosity of corrosion film formed on aluminum and aluminum-titanium alloys in hydrochloric acid solution.

2-Mercaptobenzothiazole (2-MBT) in a solution of 0.5 M HCl is an effective corrosion inhibitor for aluminum and aluminum-titanium alloys. Tafel polarization and electrochemical impedance spectroscopy (EIS) were employed to assess this heterocyclic compound's anticorrosive potential and complementary by scanning electron microscope (SEM) and calculating porosity percentage in the absence and presence of various inhibitor concentrations. Inhibition efficiency (IE%) was strongly related to concentration (10-6-10-3 M). Temperature's effect on corrosion behavior was investigated. The data exhibited that the IE% decreases as the temperature increases. An increase in activation energy (Ea) with increasing the inhibitor concentration and the decrease in the IE% value of the mentioned compound with raising the temperature indicates that the inhibitor molecules are adsorbed physically on the surface. Thermodynamic activation parameters for Al and Al-Ti alloy dissolution in both 0.5 M HCl and the inhibited solution were calculated and discussed. According to Langmuir's adsorption isotherm, the inhibitor molecules were adsorbed. The evaluated standard values of the enthalpy ([Formula: see text], entropy ([Formula: see text] and free energy changes ([Formula: see text] showed that [Formula: see text] and [Formula: see text] are negative, while [Formula: see text] was positive. The formation of a protective layer adsorbed on the surfaces of the substrates was confirmed with the surface analysis (SEM). The porosity percentage is significantly reduced in the inhibitor presence and gradually decreased with increasing concentration. Furthermore, the density functional theory (DFT) and Monte Carlo (MC) simulations were employed to explain the variance in protecting the Al surface from corrosion. Interestingly, the theoretical findings align with their experimental counterparts. The planarity of 2-MBT and the presence of heteroatoms are the playmakers in the adsorption process.

PlantLTRdb: An interactive database for 195 plant species LTR-retrotransposons.

LTR-retrotransposons (LTR-RTs) are a large group of transposable elements that replicate through an RNA intermediate and alter genome structure. The activities of LTR-RTs in plant genomes provide helpful information about genome evolution and gene function. LTR-RTs near or within genes can directly alter gene function. This work introduces PlantLTRdb, an intact LTR-RT database for 195 plant species. Using homology- and de novo structure-based methods, a total of 150.18 Gbp representing 3,079,469 pseudomolecules/scaffolds were analyzed to identify, characterize, annotate LTR-RTs, estimate insertion ages, detect LTR-RT-gene chimeras, and determine nearby genes. Accordingly, 520,194 intact LTR-RTs were discovered, including 29,462 autonomous and 490,732 nonautonomous LTR-RTs. The autonomous LTR-RTs included 10,286 Gypsy and 19,176 Copia, while the nonautonomous were divided into 224,906 Gypsy, 218,414 Copia, 1,768 BARE-2, 3,147 TR-GAG and 4,2497 unknown. Analysis of the identified LTR-RTs located within genes showed that a total of 36,236 LTR-RTs were LTR-RT-gene chimeras and 11,619 LTR-RTs were within pseudo-genes. In addition, 50,026 genes are within 1 kbp of LTR-RTs, and 250,587 had a distance of 1 to 10 kbp from LTR-RTs. PlantLTRdb allows researchers to search, visualize, BLAST and analyze plant LTR-RTs. PlantLTRdb can contribute to the understanding of structural variations, genome organization, functional genomics, and the development of LTR-RT target markers for molecular plant breeding. PlantLTRdb is available at https://bioinformatics.um6p.ma/PlantLTRdb.

Pyridinium-Inspired Organocatalysts for Carbon Dioxide Fixation: A Density Functional Theory Inspection.

The current project aims to apply the virtues of minimalism to examine the catalytic ability of commercially organic compounds of small chemical structures to catalyze the coupling reaction between carbon dioxide and propylene oxide (PO) under mild conditions. The proposed catalysts are pyridinium iodide (A), 2-hydroxypyridinium iodide (B), and piperidinium iodide (C), where their structure is based on cooperative acidic and nucleophilic motifs. The quantum chemistry model, M062X-D3/def2-TZVP//M062X-D3/def2-SVPP, was used to understand the reaction mechanism and the catalytic performance. Since the coupling reaction was performed under excess PO, we proposed that PO serves as a reactant and solvent. Therefore, calculations were performed in gas and liquid phases for comparison. The findings indicated that the rate-determining step depends on the chemical structure of the catalyst and whether the phase is a gas or liquid phase. In general, modeling in the liquid phase produces potential energy surfaces of lower energy barriers. The noncovalent interactions reflect the role of hydrogen bonding in controlling the kinetic behavior of the coupling reaction. Based on the finding, catalyst A is the best candidate for transforming CO2 into cyclic carbonates.

MegaSSR: a web server for large scale microsatellite identification, classification, and marker development.

Next-generation sequencing technologies have opened new avenues for using genomic data to study and develop molecular markers and improve genetic resources. Simple Sequence Repeats (SSRs) as genetic markers are increasingly used in molecular diversity and molecular breeding programs that require bioinformatics pipelines to analyze the large amounts of data. Therefore, there is an ongoing need for online tools that provide computational resources with minimal effort and maximum efficiency, including automated development of SSR markers. These tools should be flexible, customizable, and able to handle the ever-increasing amount of genomic data. Here we introduce MegaSSR (https://bioinformatics.um6p.ma/MegaSSR), a web server and a standalone pipeline that enables the design of SSR markers in any target genome. MegaSSR allows users to design targeted PCR-based primers for their selected SSR repeats and includes multiple tools that initiate computational pipelines for SSR mining, classification, comparisons, PCR primer design, in silico PCR validation, and statistical visualization. MegaSSR results can be accessed, searched, downloaded, and visualized with user-friendly web-based tools. These tools provide graphs and tables showing various aspects of SSR markers and corresponding PCR primers. MegaSSR will accelerate ongoing research in plant species and assist breeding programs in their efforts to improve current genomic resources.

Transposable elements: multifunctional players in the plant genome.

Transposable elements (TEs) are indispensable components of eukaryotic genomes that play diverse roles in gene regulation, recombination, and environmental adaptation. Their ability to mobilize within the genome leads to gene expression and DNA structure changes. TEs serve as valuable markers for genetic and evolutionary studies and facilitate genetic mapping and phylogenetic analysis. They also provide insight into how organisms adapt to a changing environment by promoting gene rearrangements that lead to new gene combinations. These repetitive sequences significantly impact genome structure, function and evolution. This review takes a comprehensive look at TEs and their applications in biotechnology, particularly in the context of plant biology, where they are now considered "genomic gold" due to their extensive functionalities. The article addresses various aspects of TEs in plant development, including their structure, epigenetic regulation, evolutionary patterns, and their use in gene editing and plant molecular markers. The goal is to systematically understand TEs and shed light on their diverse roles in plant biology.

Synthesis of Cyano-Benzylidene Xanthene Synthons Using a Diprotic Brønsted Acid Catalyst, and Their Application as Efficient Inhibitors of Aluminum Corrosion in Alkaline Solutions.

Novel cyano-benzylidene xanthene derivatives were synthesized using one-pot and condensation reactions. A diprotic Brønsted acid (i.e., oxalic acid) was used as an effective catalyst for the promotion of the synthesis process of the new starting xanthene-aldehyde compound. Different xanthene concentrations (ca. 0.1-2.0 mM) were applied as corrosion inhibitors to control the alkaline uniform corrosion of aluminum. Measurements were conducted in 1.0 M NaOH solution using Tafel extrapolation and linear polarization resistance (LPR) methods. The investigated xanthenes acted as mixed-type inhibitors that primarily affect the anodic process. Their inhibition efficiency values were enhanced with inhibitor concentration, and varied according to their chemical structures. At a concentration of 2.0 mM, the best-performing studied xanthene derivative recorded maximum inhibition efficiency values of 98.9% (calculated via the Tafel extrapolation method) and 98.4% (estimated via the LPR method). Scanning electron microscopy (SEM) was used to examine the morphology of the corroded and inhibited aluminum surfaces, revealing strong inhibitory action of each studied compound. High-resolution X-ray photoelectron spectroscopy (XPS) profiles validated the inhibitor compounds' adsorption on the Al surface. Density functional theory (DFT) and Monte Carlo simulations were applied to investigate the distinction of the anticorrosive behavior among the studied xanthenes toward the Al (111) surface. The non-planarity of xanthenes and the presence of the nitrile group were the key players in the adsorption process. A match between the experimental and theoretical findings was evidenced.

Appraisal of synthetic cationic Gemini surfactants as highly efficient inhibitors for carbon steel in the acidization of oil and gas wells: an experimental and computational approach.

New cationic Gemini surfactant (CGS) molecules were synthesized and investigated as anticorrosive materials for carbon steel (CS) in 1 M HCl solution by chemical, electrochemical and theoretical studies such as DFT and MDS approaches. The anticorrosion efficacy increased with the increase in the CGS concentration. It reached 95.66% at 5 × 10-3 M of the CGS molecule using PDP measurements. PDP studies confirm that the CGS molecule acts as a mixed inhibitor. The EIS outcomes were explained by an equivalent circuit in which a constant phase element (CPE) rather than a double-layer capacitance (C dl) was exploited to donate a more precise fit of the experimental outcomes. The CGS molecule follows the Langmuir isotherm as it is chemically adsorbed onto the surface of CS. To explore the kinetic and adsorption mechanisms, the thermodynamic characteristics of the activation and adsorption processes were assessed under the impact of temperature. Frontier molecular orbitals (FMOs) were achieved by the density functional theory (DFT) method. The study of interatomic interactions at the [CS (Fe(110))]/CGS level was discussed using molecular dynamics (MD) simulation.

PltRNAdb: Plant transfer RNA database.

Transfer RNAs (tRNAs) are intermediate-sized non-coding RNAs found in all organisms that help translate messenger RNA into protein. Recently, the number of sequenced plant genomes has increased dramatically. The availability of this extensive data greatly accelerates the study of tRNAs on a large scale. Here, 8,768,261 scaffolds/chromosomes containing 229,093 giga-base pairs representing whole-genome sequences of 256 plant species were analyzed to identify tRNA genes. As a result, 331,242 nuclear, 3,216 chloroplast, and 1,467 mitochondrial tRNA genes were identified. The nuclear tRNA genes include 275,134 tRNAs decoding 20 standard amino acids, 1,325 suppressor tRNAs, 6,273 tRNAs with unknown isotypes, 48,475 predicted pseudogenes, and 37,873 tRNAs with introns. Efforts also extended to the creation of PltRNAdb (https://bioinformatics.um6p.ma/PltRNAdb/index.php), a data source for tRNA genes from 256 plant species. PltRNAdb website allows researchers to search, browse, visualize, BLAST, and download predicted tRNA genes. PltRNAdb will help improve our understanding of plant tRNAs and open the door to discovering the unknown regulatory roles of tRNAs in plant genomes.

Utilizing biomass energy for improving summer squash greenhouse productivity during the winter season.

The objective of this present research is to use agricultural residues as a source of energy for heating greenhouses during winter seasons and sequestrating soil carbon dioxide through adding biochar to the soil media. To fulfill the objective of the research work, summer squash was transplanted in a constructed greenhouse and heated using an attached biomass-burning system. The performance of the attached biomass-burning system was experimentally studied under different agricultural residues (corn stalks, cotton stalks and okra stalks), heating fluids (water and oil) and air fan operating periods (10, 15 and 20 min/h). Results indicated that the biomass-burning system allowed increasing temperature and relative humidity inside the greenhouse up to 27.2 and 80 %, respectively. The maximum biomass-burning system efficiency of 81 % was achieved with the use of okra stalks as a source of energy and oil as a heating fluid side by side with adjusting the suction fan operating period at 15 min/h. Adding bio-charcoal to the soil media, enhanced the soil carbon, resulting in a total fresh yield of 3.7 and 2.9 kg/pot with a total number of leaves per plant of 55 and 47 leaves under conditions of with and without charcoal addition, respectively.

The anti-corrosive behavior of benzo-fused N-heterocycles: an in silico study toward developing organic corrosion inhibitors.

The work provides a computational protocol to predict the anti-corrosive performance of organic molecules through three successive phases of calculations; electron propagator theory (EPT), Monte Carlo (MC) simulations, and the density functional based tight-binding (DFTB) method. The protocol was applied to investigate the influence of two structural factors on the anti-corrosive performance of benzo fused-N-heterocycles (BFNHs) against the Fe(110) surface in an acidic medium; positional isomerism and the gradual insertion of nitrogen atoms in the heterocycle ring. The choice of BFNHs is attributed to their anti-corrosion activity and their use as building blocks in the molecular structure of many organic inhibitors. The findings indicate that EPT is a safe method for calculating the quantum chemical descriptors of the isolated molecules. Besides, the current work recommends using MC simulations and the DFTB method to describe the physical and chemical adsorption, respectively. Unexpected results were observed, as the gradual insertion of nitrogen atoms is not a specific factor for improving the inhibition efficiency of BFNHs. The findings were crystallized in equations linking the physical and chemical adsorption energies with the quantum chemical descriptors with a correlation exceeding 0.75. Besides, the peri steric hindrance plays an influential role in chemical adsorption. Intriguingly, the continuous introduction of nitrogen atoms does not increase the efficiency of the inhibitor along the way. For example, phthalazine exhibited better efficiency than benzotetrazine. In light of the above, the present protocol helps understand the anti-corrosive behavior of organic inhibitors and provides a feasible method to develop novel corrosion inhibitors.

CicerSpTEdb: A web-based database for high-resolution genome-wide identification of transposable elements in Cicer species.

Recently, Cicer species have experienced increased research interest due to their economic importance, especially in genetics, genomics, and crop improvement. The Cicer arietinum, Cicer reticulatum, and Cicer echinospermum genomes have been sequenced and provide valuable resources for trait improvement. Since the publication of the chickpea draft genome, progress has been made in genome assembly, functional annotation, and identification of polymorphic markers. However, work is still needed to identify transposable elements (TEs) and make them available for researchers. In this paper, we present CicerSpTEdb, a comprehensive TE database for Cicer species that aims to improve our understanding of the organization and structural variations of the chickpea genome. Using structure and homology-based methods, 3942 C. echinospermum, 3579 C. reticulatum, and 2240 C. arietinum TEs were identified. Comparisons between Cicer species indicate that C. echinospermum has the highest number of LTR-RT and hAT TEs. C. reticulatum has more Mutator, PIF Harbinger, Tc1 Mariner, and CACTA TEs, while C. arietinum has the highest number of Helitron. CicerSpTEdb enables users to search and visualize TEs by location and download their results. The database will provide a powerful resource that can assist in developing TE target markers for molecular breeding and answer related biological questions. Database URL: http://cicersptedb.easyomics.org/index.php.

A DFT-design of single component bifunctional organocatalysts for the carbon dioxide/propylene oxide coupling reaction.

The aim of this work is to develop single-component bifunctional organic catalysts capable of effective coupling reactions between CO2 and propylene epoxide (PO) under mild conditions using density functional theory (DFT) calculations. The dual functionalities of the target catalysts come from their inclusion of a hydroxyl-containing electrophile and the nucleophilicity of iodide ion. In this respect, a series of hydroxyl-functionalized quaternary onium-based ionic liquids were studied using M062X-D3/def2-TZVP//M062X-D3/def2-SVPP model chemistry. The design of catalysts was based on tailoring two structural factors; the first one is the onium center of pnictogens (N, P, As, Sb and Bi), and the second one is the number of hydrogen bond donor groups (n = 1-3). The proposed catalysts were examined by investigation of their catalytic mechanisms to afford the cyclic carbonate. Additionally, the highest active transition state, along with the potential energy difference, was examined using non-covalent interaction (NCI) analysis. Also, the activation strain model (ASM) was used to explain the kinetic behavior of PO activation. The findings showed that the ring-opening step of PO is always the critical step of the reaction. Among the suggested catalysts, the results indicated that the dihydroxyl ammonium-based catalyst (2OH-NI) is a good choice for this catalysis under mild and solvent-free conditions.

Diaryl Sulfide Derivatives as Potential Iron Corrosion Inhibitors: A Computational Study.

The present work aimed to assess six diaryl sulfide derivatives as potential corrosion inhibitors. These derivatives were compared with dapsone (4,4'-diaminodiphenyl sulfone), a common leprosy antibiotic that has been shown to resist the corrosion of mild steel in acidic media with a corrosion efficiency exceeding 90%. Since all the studied compounds possess a common molecular backbone (diphenyl sulfide), dapsone was taken as the reference compound to evaluate the efficiency of the remainder. In this respect, two structural factors were examined, namely, (i) the effect of replacement of the S-atom of diaryl sulfide by SO or SO2 group, (ii) the effect of the introduction of an electron-withdrawing or an electron-donating group in the aryl moiety. Two computational chemical approaches were used to achieve the objectives: the density functional theory (DFT) and the Monto Carlo (MC) simulation. First, B3LYP/6-311+G(d,p) model chemistry was employed to calculate quantum chemical descriptors of the studied molecules and their geometric and electronic structures. Additionally, the mode of adsorption of the tested molecules was investigated using MC simulation. In general, the adsorption process was favorable for molecules with a lower dipole moment. Based on the adsorption energy results, five diaryl sulfide derivatives are expected to act as better corrosion inhibitors than dapsone.