Conceptual density functional theory based electronic structure principles

Understanding the coupling of non-metallic heteroatoms to CO2 from a Conceptual DFT perspective

CONTEXT

A Conceptual DFT (CDFT) study has been carry out to analyse the coupling reactions of the simplest amine (CH3NH2), alcohol (CH3OH), and thiol (CH3SH) compounds with CO2 to form the corresponding adducts CH3NHCO2H, CH3OCO2H, and CH3SCO2H. The reaction mechanism takes place in a single step comprising two chemical events: nucleophilic attack of the non-metallic heteroatoms to CO2 followed by hydrogen atom transfer (HAT). According to our calculations, the participation of an additional nucleophilic molecule as HAT assistant entails important decreases in activation electronic energies. In such cases, the formation of a six-membered ring in the transition state (TS) reduces the angular stress with respect to the non-assisted paths, characterised by four-membered ring TSs. Through the analysis of the energy and reaction force profiles along the intrinsic reaction coordinate (IRC), the ratio of structural reorganisation and electronic rearrangement for both activation and relaxation energies has been computed. In addition, the analysis of the electronic chemical potential and reaction electronic flux profiles confirms that the highest electronic activity as well as their changes take place in the TS region. Finally, the distortion/interaction model using an energy decomposition scheme based on the electron density along the reaction coordinate has been carried out and the relative energy gradient (REG) method has been applied to identify the most important components associated to the barriers.

METHODS

The theoretical calculation were performed with Gaussian-16 scientific program. The B3LYP-D3(BJ)/aug-cc-pVDZ level was used for optimization of the minima and TSs. IRC calculations has also been carried out connecting the TS with the associated minima. Conceptual-DFT (CDFT) calculations have been carried out with the Eyringpy program and in-house code. The distortion/interaction model along the reaction coordinate have used the decomposition scheme of Mandado et al. and the analysis of the importance of each components have been done with the relative energy gradient (REG) method.

CO2 reduction using aluminum hydride: Generation of in-situ frustrated Lewis pairs and small molecule activation therein

CO2 reduction is appealing for the long-term production of high-value fuels and chemicals. Herein, using density functional theory (DFT) based calculations, we study the CO2 reduction pathway to formic acid using aluminum hydride and phosphine derivatives. Our primary focus is on aluminum hydride derivatives, aimed at improving the efficiency of the CO2 reduction process. Substituents with σ-donating properties at the aluminum center are discovered to lower the activation barriers. We demonstrate how di-tert-butylphosphine oxide (LB-O)/di-tert-butylphosphine sulfide (LB-S)/di-tert-butylphosphanimine (LB-N) work together with aluminum hydride to facilitate CO2 reduction process and generate in-situ frustrated Lewis pairs (FLPs), such as FLP-O, FLP-S, and FLP-N. The activation strain model (ASM) analysis reveals the significance of strain energy in determining activation barriers. EDA-NOCV and PIO analyses elucidate the orbital interactions at the corresponding transition states. Furthermore, the study delves into the activation of various small molecules, such as dihydrogen, acetylene, ethylene, carbon dioxide, nitrous oxide, and acetonitrile, using those in-situ generated FLPs. The study highlights the low activation barriers and emphasizes the potential for small molecule activation in this context.

Computational Organic Chemistry: The Frontier for Understanding and Designing Bioorthogonal Cycloadditions

Computational organic chemistry has become a valuable tool in the field of bioorthogonal chemistry, offering insights and aiding in the progression of this branch of chemistry. In this review, I present an overview of computational work in this field, including an exploration of both the primary computational analysis methods used and their application in the main areas of bioorthogonal chemistry: (3 + 2) and [4 + 2] cycloadditions. In the context of (3 + 2) cycloadditions, detailed studies of electronic effects have informed the evolution of cycloalkyne/1,3-dipole cycloadditions. Through computational techniques, researchers have found ways to adjust the electronic structure via hyperconjugation to enhance reactions without compromising stability. For [4 + 2] cycloadditions, methods such as distortion/interaction analysis and energy decomposition analysis have been beneficial, leading to the development of bioorthogonal reactants with improved reactivity and the creation of orthogonal reaction pairs. To conclude, I touch upon the emerging fields of cheminformatics and machine learning, which promise to play a role in future reaction discovery and optimization.

Unraveling Reactivity Pathways: Dihydrogen Activation and Hydrogenation of Multiple Bonds by Pyramidalized Boron-Based Frustrated Lewis Pairs

The activation of H2 by pyramidalized boron-based frustrated Lewis Pairs (FLPs) (B/E-FLP systems where "E" refers to N, P, As, Sb, and Bi) have been explored using density functional theory (DFT) based computational study. The activation pathway for the entire process is accurately characterized through the utilization of the activation strain model (ASM) of reactivity, shedding light on the underlying physical factors governing the process. The study also explores the hydrogenation process of multiple bonds with the help of B/N-FLP. The research findings demonstrate that the liberation of activated dihydrogen occurs in a synchronized, albeit noticeably asynchronous, fashion. The transformation is extensively elucidated using the activation strain model and the energy decomposition analysis. This approach suggests a co-operative double hydrogen-transfer mechanism, where the B-H hydride triggers a nucleophilic attack on the carbon atom of the multiple bonds, succeeded by the migration of the protic N-H.

Synthesis of eugenol derivative by the ring opening of epoxide eugenol and its analysis through chemical reactivity: a DFT approach

Eugenol, a plant bioactive component, is frequently found in a variety of medicinal plants with well-defined functional attributes. Essential oils containing eugenol were extracted from buds of Eugenia caryophyllata commonly named clove using hydrodistillation. Afterwards, the analysis of the essential oils using gas chromatography/mass spectrometry (GC/MS) shows that eugenol is the major constituent with 70.14% of it. The alkene group in eugenol was epoxidised using m-chloroperbenzoic acid leading to the synthesis of epoxide eugenol. The epoxide ring was cleaved to vanillyl glycol by mixed the epoxide eugenol with aluminum chloride hydrate in an ethanolic medium. A Density Functional Theory (DFT) study was investigated to understand the reactivity of the epoxide eugenol with the aluminum chloride hydrate. The results obtained from DFT based reactivity descriptors were in good agreement with the experiment results.

New modifications of PBAT by a small amount of oxalic acid: Fast crystallization and enhanced degradation in all natural environments

Biodegradable plastics are often mistakenly thought to be capable of degrading in any environment, but their slow degradation rate in the natural environment is still unsatisfactory. We synthetized a novel series of poly(butylene oxalate-co-adipate-co-terephthalate) (PBOAT) with unchanged melting point (135 °C), high elastic modulus (140 - 219 MPa) and elongation at break (478 - 769%). Fast isothermal crystallization with a semi-crystallization time < 20 s was demonstrated by the PBOAT. In N2 and air atmospheres, the PBOAT maintained the Td,5% higher than 329 °C. They also had good thermal stability at melt processing temperature for more than 20 min. PBOAT exhibited faster hydrolysis and seawater degradation, even under natural soil burial without light, but still kept stable under low humidity conditions during the storage and the shelf-life. Moreover, the hydrolysis mechanisms were clarified based on Fukui function analysis and DFT calculation, indicating that the hydrolysis of PBOAT would be more straightforward. The mechanism of soil burial is also elucidated through detailed characterization of the structure changes. The PBOAT offered a fresh approach to the development of high-performing, naturally degradable materials.

Enumeration, Nomenclature, and Stability Rules of Carbon Nanobelts

With recent breakthroughs and advances in synthetic chemistry, carbon nanobelts (CNBs) have become an emerging hot topic in chemistry and materials science. Owing to their unique molecular structures, CNBs have intriguing properties with applications in synthetic materials, host-guest chemistry, optoelectronics, and so on. Although a considerable number of CNBs with diverse forms have been synthesized, no systematic nomenclature is available yet for this important family of macrocycles. Moreover, little is known about the detailed isomerism of CNBs, which, in fact, exhibits greater complexity than that of carbon nanotubes. The copious variety of CNB isomers, along with the underlying structure-property relationships, bears fundamental relevance to the ongoing design and synthesis of novel nanobelts. In this paper, we propose an elegant approach to systematically enumerate, classify, and name all possible isomers of CNBs. Besides the simplest, standard CNBs defined by chiral indices (n, m), the nonstandard CNBs (n, m, l) involve an additional winding index l. Based on extensive quantum chemical calculations, we present a comprehensive study of the relative isomer stability of CNBs containing up to 30 rings. A simple Hückel-based model with a high predictive power reveals that the relative stability of standard CNBs is governed by the π stabilization and the strain destabilization induced by the cylindrical carbon framework, and the former effect prevails over the latter. For nonstandard CNBs, a third stability factor, the H···H repulsion in the benzo[c]phenanthrene-like motifs, is also shown to be important and can be incorporated into the simple quantitative model. In general, lower-energy CNB isomers have a larger HOMO-LUMO gap, suggesting that their thermodynamic stability coincides with kinetic stability. The most stable CNB isomers determined can be considered the optimal targets for future synthesis. These results lay an initial foundation and provide a useful theoretical tool for further research on CNBs and related analogues.

Thiophene Stability in Photodynamic Therapy: A Mathematical Model Approach

Thiophene-containing photosensitizers are gaining recognition for their role in photodynamic therapy (PDT). However, the inherent reactivity of the thiophene moiety toward singlet oxygen threatens the stability and efficiency of these photosensitizers. This study presents a novel mathematical model capable of predicting the reactivity of thiophene toward singlet oxygen in PDT, using Conceptual Density Functional Theory (CDFT) and genetic programming. The research combines advanced computational methods, including various DFT techniques and symbolic regression, and is validated with experimental data. The findings underscore the capacity of the model to classify photosensitizers based on their photodynamic efficiency and safety, particularly noting that photosensitizers with a constant rate 1000 times lower than that of unmodified thiophene retain their photodynamic performance without substantial singlet oxygen quenching. Additionally, the research offers insights into the impact of electronic effects on thiophene reactivity. Finally, this study significantly advances thiophene-based photosensitizer design, paving the way for therapeutic agents that achieve a desirable balance between efficiency and safety in PDT.

Investigating sulfonamides - Human serum albumin interactions: A comprehensive approach using multi-spectroscopy, DFT calculations, and molecular docking

The environmental and health risks associated with sulfonamide antibiotics (SAs) are receiving increasing attention. Through multi-spectroscopy, density functional theory (DFT), and molecular docking, this study investigated the interaction features and mechanisms between six representative SAs and human serum albumin (HSA). Multi-spectroscopy analysis showed that the six SAs had significant binding capabilities with HSA. The order of binding constants at 298 K was as follows: sulfadoxine (SDX): 7.18 × 105 L mol-1 > sulfamethizole (SMT): 6.28 × 105 L mol-1 > sulfamerazine (SMR): 2.70 × 104 L mol-1 > sulfamonomethoxine (SMM): 2.54 × 104 L mol-1 > sulfamethazine (SMZ): 3.06 × 104 L mol-1 > sulfadimethoxine (SDM): 2.50 × 104 L mol-1. During the molecular docking process of the six SAs with HSA, the binding affinity range is from -7.4 kcal mol-1 to -8.6 kcal mol-1. Notably, the docking result of HSA-SDX reached the maximum of -8.6 kcal mol-1, indicating that SDX may possess the highest binding capacity to HSA. HSA-SDX binding, identified as a static quenching and exothermic process, is primarily driven by hydrogen bonds (H bonds) or van der Waals (vdW) interactions. The quenching processes of SMR/SMZ/SMM/SDX/SMT to HSA are a combination of dynamic and static quenching, indicating an endothermic reaction. Hydrophobic interactions are primarily accountable for SMR/SMZ/SMM/SDX/SMT and HSA binding. Competition binding results revealed that the primary HSA-SAs binding sites are in the subdomain IB of the HAS structure, consistent with the results of molecule docking. The correlation analysis based on DFT calculations revealed an inherent relationship between the structural chemical features of SAs and the binding performance of HSA-SAs. The dual descriptor (DD) and the electrophilic Fukui function were found to have a significant relationship (0.71 and -0.71, respectively) with the binding constants of HSA-SAs, predicting the binding performance of SAs and HSA. These insights have substantial scientific value for evaluating the environmental risks of SAs as well as understanding their impact on biological life activities.

Evaluation of the Anticancer and Biological Activities of Istaroxime via Ex Vivo Analyses, Molecular Docking and Conceptual Density Functional Theory Computations

Cancer is a disease that occurs as a result of abnormal or uncontrolled growth of cells due to DNA damage, among many other causes. Certain cancer treatments aim to increase the excess of DNA breaks to such an extent that they cannot escape from the general mechanism of cell checkpoints, leading to the apoptosis of mutant cells. In this study, one of the Sarco-endoplasmic reticulum Ca2+ATPase (SERCA2a) inhibitors, Istaroxime, was investigated. There has been very limited number of articles so far reporting Istaroxime's anticancer activity; thus, we aimed to evaluate the anticancer effects of Istaroxime by cell proliferation assay and revealed the cytotoxic activity of the compound. We further determined the interaction of Istaroxime with topoisomerase enzymes through enzyme activity tests and detailed molecular modeling analysis. Istaroxime exhibited an antiproliferative effect on A549, MCF7, and PC3 cell lines and inhibited Topoisomerase I, suggesting that Istaroxime can act as a Topoisomerase I inhibitor under in vitro conditions. Molecular docking analysis supported the experimental observations. A chemical reactivity analysis of the Istaroxime molecule was made in the light of Density Functional Theory computations. For this aim, important chemical reactivity descriptors such as hardness, electronegativity, and electrophilicity were computed and discussed as detailed.

Spectroscopic characterization, molecular docking and machine learning studies of sulphur containing hydrazide derivatives

Machine learning applied in chemistry is a growing field of research. For assessing structure-property variations, this paper describes in silico studies of the hydrazide derivatives of thiosemicarbazide (TSCZ) and thiocarbohydrazide (TCHZ). The structures of TSCZ and TCHZ have been elucidated using modern spectroscopic techniques. The UV-vis spectra showed strong charge transfer transitions (π-π*) for TSCZ and TCHZ with high extinction coefficients. The NBO analysis showed orbital overlap between lp1 (N2) and σ* (C3-S4) in TSCZ and TCHZ due to intramolecular charge transfer. The first hyperpolarizabilities (β0) for TSCZ and TCHZ were found to be 0.7155 and 2.1615 × 10-30 esu, respectively, indicating their greater suitability for NLO applications as compared to standard reference urea. The strong electrophilic behaviour of TSCZ and TCHZ has been indicated by their global elecrophilicity index. The electrophilic reactivity descriptor analysis indicated that the investigated molecules could serve as precursors for the targeted synthesis of new heterocyclic derivatives. The docking studies showed appreciable binding energies with target proteins having PDB IDs 2WJE and 6CLU of Gram-positive bacteria, namely, Streptococcus pneumoniae phosphatase (PTP-CPS4B) and Staphylococcus aureus dihydropteroate synthase (saDHPS), respectively, for TSCZ and TCHZ, predicting good antimicrobial activity.

Talarolide A and Talaropeptides A-D: Potential Marine-Derived Therapeutic Peptides with Interesting Chemistry and Biological Activity Studied through Density Functional Theory (DFT) and Conceptual DFT

Molecules sourced from marine environments hold immense promise for the development of novel therapeutic drugs, owing to their distinctive chemical compositions and valuable medicinal attributes. Notably, Talarolide A and Talaropeptides A-D have gained recent attention as potential candidates for pharmaceutical applications. This study aims to explore the chemical reactivity of Talarolide A and Talaropeptides A-D through the application of molecular modeling and computational chemistry techniques, specifically employing Conceptual Density Functional Theory (CDFT). By investigating their chemical behaviors, the study seeks to contribute to the understanding of the potential pharmacological uses of these marine-derived compounds. The molecular geometry optimizations and frequency calculations were conducted using the Density Functional Tight Binding (DFTBA) method. This was followed by a subsequent round of geometry optimization, frequency analysis, and computation of electronic properties and chemical reactivity descriptors. We employed the MN12SX/Def2TZVP/H2O model chemistry, utilizing the Gaussian 16 program and the SMD solvation model. The analysis of the global reactivity descriptors arising from CDFT was achieved as well as the graphical comparison of the dual descriptor DD revealing the areas of the molecules with more propensity to suffer a nucleophilic or electrophilic attack. Additionally, Molinspiration and SwissTargetPrediction were considered for the calculation of molecular characteristics and predicted biological targets. These include enzymes, nuclear receptors, kinase inhibitors, GPCR ligands, and ion channel modulators. The graphical results show that Talarolide A and the Talaropeptides A-D are likely to behave as protease inhibitors.

Sensory-Guided Isolation, Identification, and Active Site Calculation of Novel Umami Peptides from Ethanol Precipitation Fractions of Fermented Grain Wine (Huangjiu)

Huangjiu is rich in low-molecular-weight peptides and has an umami taste. In order for its umami peptides to be discovered, huangjiu was subjected to ultrafiltration, ethanol precipitation, and macroporous resin purification processes. The target fractions were gathered according to sensory evaluation. Subsequently, we used peptidomics to identify the sum of 4158 peptides in most umami fractions. Finally, six novel umami peptides (DTYNPR, TYNPR, SYNPR, RFRQGD, NFHHGD, and FHHGD) and five umami-enhancing peptides (TYNPR, SYNPR, NFHHGD, FHHGD, and TVDGPSH) were filtered via virtual screening, molecular docking, and sensory verification. Moreover, the structure-activity relationship was discussed using computational approaches. Docking analysis showed that all umami peptides tend to bind with T1R1 through hydrogen bonds and hydrophobic forces, which involve key residues HIS71, ASP147, ARG151, TYR220, SER276, and ALA302. The active site calculation revealed that the positions of the key umami residues D and R in the terminal may cause taste differences in identified peptides.

Preliminary Evaluation of Lablab purpureus Phytochemicals for Anti-BoHV-1 Activity Using In Vitro and In Silico Approaches

Lablab purpureus from the Fabaceae family has been reported to have antiviral properties and used in traditional medical systems like ayurveda and Chinese medicine and has been employed to treat a variety of illnesses including cholera, food poisoning, diarrhea, and phlegmatic diseases. The bovine alphaherpesvirus-1 (BoHV-1) is notorious for causing significant harm to the veterinary and agriculture industries. The removal of the contagious BoHV-1 from host organs, particularly in those reservoir creatures, has required the use of antiviral drugs that target infected cells. This study developed LP-CuO NPs from methanolic crude extracts, and FTIR, SEM, and EDX analyses were used to confirm their formation. SEM analysis revealed that the LP-CuO NPs had a spherical shape with particle sizes between 22 and 30 nm. Energy-dispersive X-ray pattern analysis revealed the presence of only copper and oxide ions. By preventing viral cytopathic effects in the Madin-Darby bovine kidney cell line, the methanolic extract of Lablab purpureus and LP-CuO NPs demonstrated a remarkable dose-dependent anti-BoHV-1 action in vitro. Furthermore, molecular docking and molecular dynamics simulation studies of bio-actives from Lablab purpureus against the BoHV-1 viral envelope glycoprotein disclosed effective interactions between all phytochemicals and the protein, although kievitone was found to have the highest binding affinity, with the greatest number of interactions, which was also validated with molecular dynamics simulation studies. Understanding the chemical reactivity qualities of the four ligands was taken into consideration facilitated by the global and local descriptors, which aimed to predict the chemical reactivity descriptors of the studied molecules through the conceptual DFT methodology, which, along with ADMET finding, support the in vitro and in silico results.

First-Principles Calculations to Investigate the Stability and Thermodynamic Properties of a Newly Exposed Lithium-Gallium-Iridium-Based Full-Heusler Compound

The structural, optical, electrical, thermodynamic, superconducting, and mechanical characteristics of LiGa₂Ir full-Heusler alloys with the MnCu₂Al configuration were comprehensively examined in this work using the first-principles computation approach premised upon density functional analysis. This theoretical approach is the first to investigate the influence of pressure on the mechanical and optical characteristics of LiGa₂Ir. The structural and chemical bonding analysis shows that hydrostatic pressure caused a decrease in the lattice constant, volume, and bond length of each cell. According to the mechanical property calculations, the LiGa₂Ir cubic Heusler alloy exhibits mechanical stability. It also has ductility and anisotropic behavior. This metallic substance shows no band gap throughout the applied pressure range. The physical characteristics of the LiGa₂Ir full-Heusler alloy are analyzed in the operating pressure range of 0-10 GPa. The quasi-harmonic Debye model is employed to analyze thermodynamic properties. The Debye temperature (291.31 K at 0 Pa) increases with hydrostatic pressure. A newly invented structure attracted a lot of attention around the globe for its superior superconductivity (T_c ∼ 2.95 K). Optical functions have also been improved after applying stress to utilize it in optoelectronic/nanoelectric devices. The optical function analysis is supported strongly by the electronic properties. Due to these reasons, LiGa₂Ir imposed an essential guiding principle for relevant future research and could be a credible candidate substance for industrial settings.

Source toxicity characteristics of short- and medium-chain chlorinated paraffin in multi-environmental media: Product source toxicity, molecular source toxicity and food chain migration control through silica methods

Short and medium-chain chlorinated paraffin (SCCP/MCCP) have been widely studied because of their extensive environmental hazards. In this study, product source toxicity, molecular source toxicity and food chain migration of SCCP and MCCP in multi-environmental media were comprehensively considered. The additive combination of SCCP and MCCP in the air, water and soil environment was adjusted, and PVC, PU and rubber products with the lowest source toxicity were screened. The source toxicity of SCCP and MCCP in the water environment was inhibited by design of the feed additive addition scheme (highest inhibition was 16.29 %), and the source toxicity of SCCP and MCCP in the soil environment was affected by different field management measures (highest inhibition was 38.22 %). A forage fertilizer addition plan, a cattle feed addition plan and a special population healthy complementary food regulation plan were developed to prevent the migration step by step and absorption of SCCP and MCCP in the terrestrial food chain. In addition, by means of density functional theory and analysis of key amino acid residues, the mechanism of toxicity difference between SCCP and MCCP was analyzed from the level of chemical interaction, and rationality of the inhibition scheme designed in this study was verified.

Synthesis of Disubstituted Carboxonium Derivatives of Closo-Decaborate Anion [2,6-B10H8O2CC6H5]-: Theoretical and Experimental Study

A comprehensive study focused on the preparation of disubstituted carboxonium derivatives of closo-decaborate anion [2,6-B₁₀H₈O₂CC₆H₅]^- was carried out. The proposed synthesis of the target product was based on the interaction between the anion [B₁₀H₁₁]^- and benzoic acid C₆H₅COOH. It was shown that the formation of this product proceeds stepwise through the formation of a mono-substituted product [B₁₀H₉OC(OH)C₆H₅]^-. In addition, an alternative one-step approach for obtaining the target derivative is postulated. The structure of tetrabutylammonium salts of carboxonium derivative ((C₄H₉)₄N)[2,6-B₁₀H₈O₂CC₆H₅] was established with the help of X-ray structure analysis. The reaction pathway for the formation of [2,6-B₁₀H₈O₂CC₆H₅]^- was investigated with the help of density functional theory (DFT) calculations. This process has an electrophile induced nucleophilic substitution (EINS) mechanism, and intermediate anionic species play a key role. Such intermediates have a structure in which one boron atom coordinates two hydrogen atoms. The regioselectivity for the process of formation for the 2,6-isomer was also proved by theoretical calculations. Generally, in the experimental part, the simple and available approach for producing disubstituted carboxonium derivative was introduced, and the mechanism of this process was investigated with the help of theoretical calculations. The proposed approach can be applicable for the preparation of a wide range of disubstituted derivatives of closo-borate anions.

Structure and Bonding in Planar Hypercoordinate Carbon Compounds

The term hypercoordination refers to the extent of the coordination of an element by its normal value. In the hypercoordination sphere, the element can achieve planar and/or non-planar molecular shape. Hence, planar hypercoordinate carbon species violate two structural rules: (i) The highest coordination number of carbon is four and (ii) the tetrahedral orientation by the connected elements and/or groups. The unusual planar orientations are mostly stabilized by the electronic interactions of the central atom with the surrounding ligands. In this review article, we will talk about the current progress in the theoretical prediction of viable planar hypercoordinate carbon compounds. Primary knowledge of the planar hypercoordinate chemistry will lead to its forthcoming expansion. Experimental and theoretical interests in planar tetracoordinate carbon (ptC), planar pentacoordinate carbon (ppC), and planar hexacoordinate carbon (phC) are continued. The proposed electronic and mechanical strategies are helpful for the designing of the ptC compounds. Moreover, the 18-valence electron rule can guide the design of new ptC clusters computationally as well as experimentally. However, the counting of 18-valence electrons is not a requisite condition to contain a ptC in a cluster. Furthermore, this ptC idea is expanded to the probability of a greater coordination number of carbon in planar orientations. Unfortunately, until now, there are no such logical approaches to designing ppC, phC, or higher-coordinate carbon molecules/ions. There exist a few global minimum structures of phC clusters identified computationally, but none have been detected experimentally. All planar hypercoordinate carbon species in the global minima may be feasible in the gas phase.

OSCAR: an extensive repository of chemically and functionally diverse organocatalysts

The automated construction of datasets has become increasingly relevant in computational chemistry. While transition-metal catalysis has greatly benefitted from bottom-up or top-down strategies for the curation of organometallic complexes libraries, the field of organocatalysis is mostly dominated by case-by-case studies, with a lack of transferable data-driven tools that facilitate both the exploration of a wider range of catalyst space and the optimization of reaction properties. For these reasons, we introduce OSCAR, a repository of 4000 experimentally derived organocatalysts along with their corresponding building blocks and combinatorially enriched structures. We outline the fragment-based approach used for database generation and showcase the chemical diversity, in terms of functions and molecular properties, covered in OSCAR. The structures and corresponding stereoelectronic properties are publicly available (https://archive.materialscloud.org/record/2022.106) and constitute the starting point to build generative and predictive models for organocatalyst performance.

Exploration of Anti-HIV Phytocompounds against SARS-CoV-2 Main Protease: Structure-Based Screening, Molecular Simulation, ADME Analysis and Conceptual DFT Studies

The ever-expanding pandemic severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection has gained attention as COVID-19 and caused an emergency in public health to an unmatched level to date. However, the treatments used are the only options; currently, no effective and licensed medications are available to combat disease transmission, necessitating further research. In the present study, an in silico-based virtual screening of anti-HIV bioactive compounds from medicinal plants was carried out through molecular docking against the main protease (M^pro) (PDB: 6LU7) of SARS-CoV-2, which is a key enzyme responsible for virus replication. A total of 16 anti-HIV compounds were found to have a binding affinity greater than -8.9 kcal/mol out of 150 compounds screened. Pseudohypericin had a high affinity with the energy of -10.2 kcal/mol, demonstrating amino acid residual interactions with LEU141, GLU166, ARG188, and GLN192, followed by Hypericin (-10.1 kcal/mol). Moreover, the ADME (Absorption, Distribution, Metabolism and Excretion) analysis of Pseudohypericin and Hypericin recorded a low bioavailability (BA) score of 0.17 and violated Lipinski's rule of drug-likeness. The docking and molecular simulations indicated that the quinone compound, Pseudohypericin, could be tested in vitro and in vivo as potent molecules against COVID-19 disease prior to clinical trials.This was also supported by the theoretical and computational studies conducted. The global and local descriptors, which are the underpinnings of Conceptual Density FunctionalTheory (CDFT) have beenpredicted through successful model chemistry, hoping that they could be of help in the comprehension of the chemical reactivity properties of the molecular systems considered in this study.

Theoretical designing of non-fullerene derived organic heterocyclic compounds with enhanced nonlinear optical amplitude: a DFT based prediction

In current era, non-fullerene (NF) chromophores have been reported as significant NLO materials due to promising optoelectronic properties. Therefore, a series of NF based chromophores abbreviated as TPBD2-TPBD6 with D–π–A architecture was designed from the reference compound (TPBR1) by its structural tailoring with an efficient donor and various acceptor groups for the first time. First, the structures of said compounds were optimized at M06-2X/6-311G (d,p) level. Further, the optimized structures were utilized to execute frontier molecular orbitals (FMOs), UV–Visible (UV–Vis) absorption, density of states (DOS) and transition density matrix (TDM) analyses at the same level to understand the non-linear (NLO) response of TPBR1 and TPBD2-TPBD6. Promising NLO results were achieved for all derivatives i.e., the highest amplitude of linear polarizability ⟨α⟩, first (βtotal) and second ($$\gamma$$ γ total) hyperpolarizabilities than their parent molecule. The compound TPBD3 was noted with the most significant NLO properties as compared to the standard molecule. The structural modeling approach by utilizing the acceptor molecules has played a prominent role in attaining favorable NLO responses in the molecules. Thus, our study has tempted the experimentalists to synthesize the proposed NLO materials for the modern optoelectronic high-tech applications.

Phytoconstituents of Withania somnifera unveiled Ashwagandhanolide as a potential drug targeting breast cancer: Investigations through computational, molecular docking and conceptual DFT studies

Breast cancer is the second most common malignancy in females worldwide and poses a great challenge that necessitates the identification of novel therapeutic agents from several sources. This research aimed to study the molecular docking and molecular dynamics simulations of four proteins (such as PDB: 6CBZ, 1FDW, 5GWK and 2WTT) with the selected phytochemicals from Withania somnifera to identify the potential inhibitors for breast cancer. The molecular docking result showed that among 44 compounds, two of them, Ashwagandhanolide and Withanolide sulfoxide have the potential to inhibit estrogen receptor alpha (ERα), 17-beta-hydroxysteroid -dehydrogenase type 1 (17β-HSD1), topoisomerase II alpha (TOP2A) and p73 tetramerization domain that are expressed during breast cancer. The molecular dynamics (MD) simulations results suggested that Ashwagandhanolide remained inside the binding cavity of four targeted proteins and contributed favorably towards forming a stable protein-ligand complex throughout the simulation. Absorption, Distribution, Metabolism, Excretion and Toxicity (ADMET) properties confirmed that Ashwagandhanolide is hydrophobic and has moderate intestinal permeability, good intestinal absorption, and poor skin permeability. The compound has a relatively low VDss value (-1.652) and can be transported across ABC transporter and good central nervous system (CNS) permeability but did not easily cross the blood-brain barrier (BBB). This compound does not possess any mutagenicity, hepatotoxicity and skin sensitization. Based on the results obtained, the present study highlights the anticancer potential of Ashwagandhanolide, a compound from W. somnifera. Furthermore, in vitro and in vivo studies are necessary to perform before clinical trials to prove the potentiality of Ashwagandhanolide.

On the Periodicity of the Information Theory and Conceptual DFT-Based Reactivity Descriptors

The periodic trends in conceptual density functional and information theory-based reactivity descriptors are reported for the atoms H to Ba (Z = 1 to 56). Ionization potential, electron affinity, electronegativity, and hardness show periodic behavior following the Aufbau principle and popular electronic structure principles. They are in agreement with those reported in standard chemistry textbooks. The trend in the electrophilicity index, however, shows an interesting behavior, where it contradicts earlier reports. Our calculation reveals that the noble gas elements correspond to minimum ω values in each period which obey the minimum electrophilicity principle as well as reflect their low reactivity. Periodic trends in electroaccepting and electrodonating powers, along with that of net electrophilicity, are as expected. The behavior of information theory-based Shannon and GBP entropies, along with the Shannon entropy of shape function are also explored across the periodic table.

In Vitro Anticancer Screening, Molecular Docking and Antimicrobial Studies of Triazole-Based Nickel(II) Metal Complexes

Herein we describe the synthesis of a series of nickel(II) complexes (C1–C3) with Schiff bases (HL1–HL3) derived from 4-amino-5-mercapto-3-methyl-1,2,4-triazole and ortho/meta/para-nitrobenzaldehyde having composition [Ni(L)₂(H₂O)₂]. The obtained ligands and their complexes were characterized using physico-chemical techniques viz., elemental analysis, magnetic moment study, spectral (electronic, FT-IR, 1H-NMR) and thermal analysis. The elemental analysis and spectral analysis revealed that Schiff bases behave as monoanionic bidentate ligands towards the Ni(II) ion. Whereas, the magnetic moment study suggested the octahedral geometry of all the Ni(II) complexes. The thermal behavior of the complexes has been studied by thermogravimetric analysis and agrees well with the composition of complexes. Further, the biological activities such as antimicrobial and antifungal studies of the Schiff bases and Ni(II) complexes have been screened against bacterial species (Staphylococcus aureus and Pseudomonas aeruginosa) and fungal species (Aspergillus niger and Candida albicans) activity by MIC method, the results of which revealed that metal complexes exhibited significant antimicrobial activities than their respective ligands against the tested microbial species. Furthermore, the molecular docking technique was employed to investigate the active sites of the selected protein, which indeed helped us to screen the potential anticancer agents among the synthesized ligand and complexes. Further, these compounds have been screened for their in vitro anticancer activity using OVCAR-3 cell line. The results revealed that the complexes are more active than the ligands.

Rationalizing the Substituent Effects in Diels-Alder Reactions of Triazolinediones with Anthracene

In this work we tackle the problem of the substituent effects in the Diels-Alder cycloadditions between triazolinediones (TADs) and anthracene. Experiments showed that aryl TADs substituted with electron-withdrawing groups (EWG) are more reactive than those substituted with electron-donating (EDG) or alkyl groups. However, the molecular origin of this preference is not yet understood. By a combination of methods including the activation strain model (ASM), energy decomposition analysis (EDA), molecular orbital (MO) theory, and conceptual density functional theory (CDFT), we disclosed the substituent effects of TADs. First, ASM/EDA analysis revealed that the reactivity of alkyl and aryl-substituted TADs is controlled by interaction energies, ΔE_int, which are ultimately defined by orbital interactions between frontier molecular orbitals. Moreover, alkyl-TADs are also controlled by the extent of strain at the transition state. The MO analysis suggested that the rate acceleration for EWG-substituted TADs is due to a more favorable orbital interaction between the HOMO of anthracene and the LUMO of the TADs, which is corroborated by calculations of charge transfer at the transition states. From CDFT, the chemical potential of anthracene is higher than those of TADs, indicating a flow of electron density from anthracene to TADs, in agreement with the results from the electrophilicity index.

Effect of Structural Variation on Spectral, NLO Properties, and Biological Activity of Pyrrole Hydrazones

This paper describes spectral, non-linear optical (NLO), and biological activity variation of pyrrole hydrazones as a result of structural variation. In order to study structure-property variation, pyrrole hydrazones (3A, 3B, and 3C) were synthesized in both solid and solution phases. The grinding solvent-free method becomes rapid, easy, convenient, useful, sustainable, and eco-friendly green synthesis as compared to the classical solution phase reactions. The structure of pyrrole hydrazones has been elucidated by microanalysis and quantum chemical calculations. The intense emission at λ_em 521 nm (3A and 3B) and 617 nm (3C) in the visible (green and orange) region with Stokes shifts at 195, 160, and 282 nm reveals that the studied compounds work as good photoluminescent materials. All compounds show strong n-π* and charge transfer (π-π*) transitions in the UV-vis region with high extinction coefficients. In the studied systems (3A, 3B, and 3C), the orbital overlap between σ(NH-O) → σ*(NH-O) is found due to intra-molecular charge transfer. The first hyperpolarizabilities were found to be 48.83 × 10^-30 esu for 3B and 63.89 × 10^-30 esu for 3C, showing variation with structure. Their high values indicate more suitability for NLO application. Incorporation and/or change in position of electron-withdrawing groups increase the β₀ values of 3B and 3C compared to 3A. The β value also increases monotonically as the polarity of the solvents increases. The red shift in N-H and C=O stretching Fourier-transform infrared bonds is due to the formation of dimers. The synthesized 3A, 3B, and 3C show good antimicrobial activity and are predicted to be potential antibacterial and antifungal drugs. The 3B has more molar refractivity (122.16 esu) than 3A and 3C and correlates well with the calculated binding affinity and experimental antimicrobial data.

Molecular Electrides: An In Silico Perspective

Electrides are defined as the ionic compounds where the electron(s) serves as an anion. These electron(s) is (are) not bound to any atoms, bonds, or molecules rather than they are localized into the space, crystal voids, or interlayer between two molecular slabs. There are three major categories of electrides, known as organic electriades, inorganic electrides, and molecular electrides. The computational techniques have proven as a great tool to provide emphasis on the electride materials. In this review, we have focused on the computational methodologies and criteria that help to characterize molecular electrides. A detailed account of the computational methods and basis sets applicable for molecular electrides have been discussed along with their limitation(s) in this field. The main criterion for the identification of the electrides has also been discussed thoroughly with proper examples. The molecular electrides presented here have been justified with all the required criteria that support and proved their electride characteristics. We have also presented a few systems which have similar properties but are not considered as molecular electrides. Moreover, the applicability of the electrides in catalytic processes has also been presented.

Theoretical Study of the Structural, Optoelectronic, and Reactivity Properties of N-[5′-Methyl-3′-Isoxasolyl]-N-[(E)-1-(-2-)]Methylidene] Amine and Some of Its Fe2+, Co2+, Ni2+, Cu2+, and Zn2+ Complexes for OLED and OFET Applications

Herein, we report the structural, electronic, and charge transfer properties of N-[5′-methyl-3′-isoxasolyl]-N-[(E)-1-(-2-thiophene)] methylidene] amine (L) and its Fe2+, Co2+, Ni2+, Cu2+, and Zn2+ complexes (dubbed A, B, C, D, and E, respectively) using the density functional theory (DFT). All molecules investigated were optimized at the BP86/def2-TZVP/RI level of theory. Single point energy calculations were carried out at the M06-D3ZERO/def2-TZVP/RIJCOSX level of theory. Reorganization energies of the hole and electron (λh and λe) and the charge transfer mobilities of the electron and hole (μe and μh) have been computed and reported. The λe and λh values vary in the order D > E > A > B > C > L and E > A > D > L > C > B, respectively, while μe and μh vary in the order B > C > L > A > E > D and C > B > A > L > E > D, respectively. μh of B (39.5401 cm2·V−1S−1) and C (366.4740 cm2·V−1s−1) is remarkably large, suggesting their application in organic light-emitting diode (OLED) and organic field-effect transistor (OFET) technologies. Electron excitation analysis based on time-dependent (TD)-DFT calculations revealed that charge transfer excitations may significantly affect charge transfer mobilities. Based on charge transfer mobility results, B and C are outstanding and are promising molecules for the manufacture of electron and hole-transport precursor materials for the construction of OLED and OFET devices as compared to L. The results also show that L and all its complexes interestingly have higher third-order NLO activity than those of para-nitroaniline, a prototypical NLO molecule.

An insight into reactivity and bioactivity properties of quorum sensing peptides against PDE10A: a computational peptidology approach

Peptides are currently the most promising lead molecules. Quorum sensing peptides have a variety of structural features and are regularly exposed to post-translational modifications. Antiparkinsonian drugs lose their efficacy after a long period of use, and patients develop motor problems such as drug-induced dyskinesia (DIDs). The interaction between PDE10A and cAMP is necessary for dopamine neurotransmission and may play a role in Parkinson's disease pathogenesis. cAMP and cGMP are cyclic nucleotides that act as secondary messengers in the signal transduction pathway, influencing a range of CNS activities. PDE enzymes hydrolyze phosphodiester bonds to break down cAMP and cGMP, allowing them to control intracellular levels of these second messengers effectively. PDE expression, and hence cyclic nucleotide levels and their downstream targets, may change with age and in numerous age-related illnesses, including Parkinson's disease, according to mounting evidence. At the peak of dyskinesias, cyclic nucleotide levels were lower, and using phosphodiesterase inhibitors before antiparkinsonian medicines reduced the severity of dyskinesias. In a recent study, PapRIV was found to have the ability to activate BV-2 microglia cells, indicating that this quorum sensing peptide may play a role in gut-brain contact. As a result of the current in silico work, mainly focused on QSPs as a lead molecule for inhibiting PDE10A, the SRNAT QSP sequence has been a potent molecule in molecular docking and molecular dynamics simulations. Furthermore, we can test the efficiency of therapeutic components in vitro and in vivo utilizing this computational approach against PDE10A.

Adiabatic models for the quantum dynamics of surface scattering with lattice effects

In this contribution, we review models for the lattice effects in quantum dynamics calculations on surface scattering, which is important to modeling heterogeneous catalysis for achieving an interpretation of experimental measurements. Unlike dynamics models for reactions in the gas phase, those for heterogeneous reactions have to include the effects of the surface. For manageable computational costs in calculations, the effects of static surface (SS) are firstly modeled as this is simply and easily implemented. Then, the SS model has to be improved to include the effects of the flexible surface, that is the lattice effects. To do this, various surface models have been designed where the coordinates of the surface atoms are introduced in the Hamiltonian operator, especially those of the top surface atom. Based on this model Hamiltonian operator, extensive multi-dimension quantum dynamics calculations can be performed to recover the lattice effects. Here, we first review an overview of the techniques in constructing the Hamiltonian operator, which is a sum of the kinetic energy operator (KEO) and potential energy surface (PES). Since the PES containing the coordinates of the surface atoms in a cell is still expensive, the SS model is often accepted. We consider a mathematical model, called the coupled harmonic oscillator (CHO) model, to introduce the concepts of adiabatic and diabatic representations for separating the molecule and surface. Under the adiabatic model, we further introduce the expansion model where the potential function is Taylor expanded around the optimized geometry of the surface. By an expansion model truncated at the first and second order, various coupling surface models between the molecule and surface are derived. Moreover, by further and deeply understanding the adiabatic representation, an effective Hamiltonian operator is obtained by optimizing the total wave function in factorized form. By this factorized form of wave function and effective Hamiltonian operator, the geometry phase of the surface wave function is theoretically found. This theoretical prediction may be measured by carefully designing experiments. Finally, discussions on the adiabatic representation, the PES construction, and possibility of the classical-dynamics solutions are given. Based on these discussions, a simple outlook on the dynamics of photocatalytics is finally given.

Virtual Prospection of Marine Cyclopeptides as Therapeutics by Means of Conceptual DFT and Computational ADMET

Bioactive peptides are chemical compounds created through the covalent bonding of amino acids, known as amide or peptide bonds. Due to their unusual chemistry and various biological effects, marine bioactive peptides have garnered considerable research. The effectiveness of a bioactive marine peptide is attributed to its structural features, such as amino acid content and sequence, which vary depending on the degree of action. Cyclic peptides combine several favorable properties such as good binding affinity, target selectivity and low toxicity that render them an attractive modality for the development of therapeutics. The apratoxins are a class of molecules formed by a series of cyclic depsipeptides with potent cytotoxic activities. The objective of this research is to pursue a computational prospection of the molecular structures and properties of several cylopeptides of marine origin with potential therapeutic applications. The methodology will be based on the determination of the chemical reactivity descriptors of the studied molecules through the consideration of the Conceptual DFT model and validation of a particular model chemistry, MN12SX/Def2TZVP/H₂O. These studies will be complemented by a determination of the pharmacokinetics and ADMET parameters by resorting to certain cheminformatics tools.

From the Electron Density Gradient to the Quantitative Reactivity Indicators: Local Softness and the Fukui Function

Important reactivity measures such as the local softness, the Fukui function, and the global hardness have been calculated directly from first principles with the use of the electron density function, beyond the finite difference approximation. Our recently derived density gradient theorem and the principle of nearsightedness of the electronic matter have been instrumental in obtaining the original, albeit approximate, result on the local softness of an atom. By integration of the local softness s(r), we obtain the global softness S and the Fukui function f(r) = s(r)/S. Local and global softness values have also been calculated analytically for the basic hydrogenic orbitals; the general relation to the atomic number S = σZ ^-2 has been demonstrated, with constants σ characteristic for each orbital type. Global hardness η = 1/S calculated for atoms and ions has been favorably tested against its conventional measure given by the finite difference approximation: (I - A). Calculated test results for atoms and ions in rows 1-4 of the periodic table have been presented.

N-((1H-Pyrrol-2-yl)methylene)-6-methoxypyridin-3-amine and Its Co(II) and Cu(II) Complexes as Antimicrobial Agents: Chemical Preparation, In Vitro Antimicrobial Evaluation, In Silico Analysis and Computational and Theoretical Chemistry Investigations

Researchers are interested in Schiff bases and their metal complexes because they offer a wide range of applications. The chemistry of Schiff bases of heterocompounds has got a lot of attention because of the metal's ability to coordinate with Schiff base ligands. In the current study, a new bidentate Schiff base ligand, N-((1H-pyrrol-2-yl)methylene)-6-methoxypyridin-3-amine (MPM) has been synthesized by condensing 6-methoxypyridine-3-amine with pyrrole-2-carbaldehyde. Further, MPM is used to prepare Cu(II) and Co(II) metal complexes. Analytical and spectroscopic techniques are used for the structural elucidation of the synthesized compounds. Both MPM and its metal complexes were screened against Escherichia coli, Bacillus subtilis, Staphylococcus aureus and Klebsiella pneumoniae species for antimicrobial studies. Furthermore, these compounds were subjected to in silico studies against bacterial proteins to comprehend their best non-bonded interactions. The results confirmed that the Schiff base ligand show considerably higher binding affinity with good hydrogen bonding and hydrophobic interactions against various tested microbial species. These results were complemented with a report of the Conceptual DFT global reactivity descriptors of the studied compounds together with their biological scores and their ADMET computed parameters.

Phenylamine/Amide Grafted in Silica as Sensing Nanocomposites for the Removal of Carbamazepine: A DFT Approach

This study aimed to remove carbamazepine from aqueous solutions, using functional silica phenylamine (SiBN), which is characterized and showed excellent chemical and thermal stability. Adsorbents based on silica were developed due to their unusually large surface area, homogenous pore structure, and well-modified surface properties, as silica sparked tremendous interest. It was determined to develop a novel silica adsorbent including phenylamine and amide (SiBCON). The adsorbents obtained were analyzed by various spectroscopy devices, including SEM, FT-IR and TGA analysis. The maximum removal rates for carbamazepine were 98.37% and 98.22% for SiBN and SiBCON, respectively, when optimized at room temperature, pH 9.0, initial concentration of 10 mg·L−1 and contact time of 15 min. Theoretical tools are widely used in the prediction of the power of interactions between chemical systems. The computed data showed that new amine modified silica is quite effective in terms of the removal of carbamazepine from aqueous solution. Calculation binding energies and DFT data showed that there is a powerful interaction between amine-modified silica and carbamazepine.

Harvesting the fragment-based nature of bifunctional organocatalysts to enhance their activity

Enhancing the activity of bifunctional organocatalysts: a fragment-based approach coupled with activity maps helps identifying better-performing catalytic motifs.

A straightforward method to quantify the electron-delocalizing ability of pi-conjugated molecules

Electronic delocalization is essential to the properties of pi-conjugated molecules. We introduce the inter-fragment delocalization index (IFDI) as an easy-to-use computational method for quantifying the electronic delocalization in pi-conjugated oligomers...

XNgNSi (X = HCC, F; Ng = Kr, Xe, Rn): A New Class of Metastable Insertion Compounds Containing Ng-C/F and Ng-N Bonds and Possible Isomerization therein

Recently, astronomically important silaisocyanoacetylene (HCCNSi) possessing a large dipole moment has been detected for the first time with the help of crossed molecular beam experiments. Quantum chemical computations at higher levels of theory have also been performed to characterize the transient species. In this study, we have analyzed the equilibrium geometry, stability, reactivity, and energetics as well as the nature of bonding in the noble gas (Ng) inserted HCCNSi compound. We have also considered its F analogue to understand the influence of the most electronegative atom in the compound. Metastable behavior of the XNgNSi compounds (X = HCC, F; Ng = Kr-Rn) is examined by calculating thermochemical parameters like free energy change (ΔG) and zero-point-energy-corrected dissociation energy (D₀) at 298 K for all possible two-body (2B) and three-body (3B) (both neutral as well as ionic) dissociation channels using coupled-cluster theory [CCSD(T)] in addition to density functional theory (DFT) as well as second order Møller-Plesset perturbation theory (MP2). The set of predicted compounds is found to be endergonic in nature, having high positive free energy change suggesting the thermochemical stability of the compounds except for the 2B Ng-release paths. Though thermodynamically feasible, they are kinetically protected with very high activation free energy barriers. Interestingly, the release of Ng from the parent moiety XNgNSi produces the XSiN isomer, by 180° flipping of the NSi moiety. This can also be seen in the dynamical simulation carried out with the help of atom-centered density matrix propagation (ADMP) technique at 2000K for 1 ps. The bonding in Ng-C, Ng-F, and Ng-N bonds of the studied compounds is analyzed and described with the aid of natural bond orbital (NBO), topological parameters computed using atoms-in-molecules theory (AIM), energy decomposition analysis (EDA), and adaptive natural density partitioning (AdNDP) methods. The natural charge distribution on the constituent atoms suggests that the compounds can be partitioned into both ways of representations, viz., neutral radical as well as ionic fragments. Lastly, the reactivity of the compounds is scrutinized using certain reactivity descriptors calculated within the domain of conceptual density functional theory (CDFT).