Reactivity Dynamics

1-D MOF [Ag2(C10H10N3O3S)2(C4H8N)2]n: photocatalytic treatment, crystallographic evaluation, ADMET parameters, CT-DNA and anticancer activity

Newly synthesized dinuclear crystalline polymer, the silver complex of bidentate Sulfamethoxazole (Ag-SMX) in the presence of secondary ligand pyrrolidine has been characterized by elemental, spectral (1H-NMR spectra, FT-IR spectra, UV-Vis spectra.), powder XRD, and single-crystal X-ray diffraction (single-crystal) analysis. The synthesis molecular structure of the dinuclear [Ag2(C10H10N3O3S)2(C4H8N)2]n complex reveals a one-dimensional polymeric chain with seesaw geometry (τ4 = 0.71): two silvers interlink each other by argentophilic interaction with Ag1…Ag2 separation distance of 3.0047(6) Å. The Hirshfeld surfaces (HS) and 2D fingerprint plots were used to examine the interconnects in the crystal packing. Molecule properties including MEP, MPA, HOMO-LUMO energy, and global reactivity descriptor parameters were computed to understand the molecule's stability. From ADMET parameters, human Intestinal Absorbance data revealed that the compound has the potential to be well absorbed, and also Ag-smx complex cannot cross the blood-brain barrier (BBB). The capacity of the silver complex to interact with CtDNA was investigated using absorption spectroscopy and viscosity tests. The interaction between CT-DNA reveals that the Ag-SMX complex exhibits the strongest binding affinity among all known sulfonamide derivatives and their metal complexes. The silver complex has higher inhibitory action than the free SMX ligand, according to data from a panel of gram (+ve) and gram (-ve) organisms' minimum inhibitory concentrations. In vitro cytotoxicity investigation revealed that the IC50 value for Ag-SMX is 57.12 g/mL and for SMX is 100.90 g/mL against human lung cancer cell line (A549). This study revealed that, when compared to SMX free-ligand, Ag-SMX is the most effective in terms of cytotoxicity toward the human lung cancer cell line (A549 cell line). In under 120 min, the synthesized Ag-smx complex showed exceptional photo-degradation characteristics against methylene blue (MB) (10 ppm) in visible light radiation.Communicated by Ramaswamy H. Sarma.

Structural insights and cytotoxicity evaluation of benz[e]indole pyrazolyl-substituted amides

Five new compounds of benz[e]indole pyrazolyl-substituted amides (2a-e) were synthesised in low to good yields via the direct amide-coupling reaction between a pyrazolyl derivative containing a carboxylic acid and several amine substrates. The molecular structures were determined by various spectroscopic methods, such as NMR (1H, 13C and 19F), FT-IR and high-resolution mass spectrometry (HRMS). X-ray crystallographic analysis on the 4-fluorobenzyl derivative (2d) reveals the amide-O atom to reside to the opposite side of the molecule to the pyrazolyl-N and pyrrolyl-N atoms; in the molecular packing, helical chains feature amide-N‒H⋯N(pyrrolyl) hydrogen bonds. Density-functional theory (DFT) at the geometry-optimisation B3LYP/6-31G(d) level on the full series shows general agreement with the experimental structures. While the LUMO in each case is spread over the benz[e]indole pyrazolyl moiety, the HOMO spreads over the halogenated benzo-substituted amide moieties or is localised near the benz[e]indole pyrazolyl moieties. The MTT assay showed that 2e, exhibited the highest toxicity against a human colorectal carcinoma (HCT 116 cell line) without appreciable toxicity towards the normal human colon fibroblast (CCD-18Co cell line). Based on molecular docking calculations, the probable cytotoxic mechanism of 2e is through the DNA minor groove binding.

Directionality and additivity effects of molecular acidity and aromaticity for substituted benzoic acids under external electric fields

Our recent study [M. Li et al.Phys. Chem. Chem. Phys., 2023, 25, 2595-2605] unveiled that the impact of an external electric field on molecular acidity and aromaticity for benzoic acid is directional, which can be understood using changes in frontier orbitals and partial charges. However, it is unclear if the effect will disappear when substituting groups are present and whether new patterns of changes will show up. In this work, as a continuation of our efforts to appreciate the impact of external electric fields on physiochemical properties, we find that the directionality effect is still in place for substituted benzoic acid derivatives and that there exists the additivity effect with respect to the number of substituent groups, regardless of the direction of the applied field and the type of substituting groups. We confirm the findings using electron-donating and electron-accepting groups with the electric field applied either parallelly or perpendicularly to the carboxyl group along the benzene ring. The directionality and additivity effects uncovered from this work should enrich the body of our knowledge about the impact of external electric fields on physiochemical properties and could be applicable to other systems and properties as well.

DFT exchange: sharing perspectives on the workhorse of quantum chemistry and materials science

In this paper, the history, present status, and future of density-functional theory (DFT) is informally reviewed and discussed by 70 workers in the field, including molecular scientists, materials scientists, method developers and practitioners. The format of the paper is that of a roundtable discussion, in which the participants express and exchange views on DFT in the form of 302 individual contributions, formulated as responses to a preset list of 26 questions. Supported by a bibliography of 777 entries, the paper represents a broad snapshot of DFT, anno 2022.

A systematic computational study of acridine derivatives through conceptual density functional theory

A detailed computational analysis of acridine derivatives viz. acridone, 9-amino acridine hydrochloride hydrate, proflavin, acridine orange and acridine yellow is done in terms of conceptual density functional theory (CDFT). CDFT-based global descriptors-ionization potential, electron affinity, HOMO-LUMO gap, hardness, softness, electronegativity and electrophilicity index of acridine derivatives for ground state as well as excited state are estimated with the help of different hybrid functionals B3LYP/6-31G (d, p), B3LYP/6-311G (d, p), B3LYP/DGDZVP and B3LYP/LANL2DZ. Acridine derivatives show higher values of ionization potential and electron affinity in excited state as compared to ground state, indicating that these compounds are willing to accept electrons in excited state rather than donating electron. Acridone shows the maximum HOMO-LUMO energy gap in ground and excited state which implies that one-way electron transfer is most feasible with this compound. Our computed results emphasize the pronounced electron acceptor behaviour of the acridine derivatives in the excited state which has already been experimentally verified. It is observed that the trend in the computed values of the descriptors is not much improved on refinement of the basis set.

Chemical Reactivity and Optical and Pharmacokinetics Studies of 14 Multikinase Inhibitors and Their Docking Interactions Toward ACK1 for Precision Oncology

Activated Cdc42-associated kinase 1 (ACK1/TNK2) has a significant role in cell endocytosis, survival, proliferation, and migration. Mutations in ACK1 are closely associated with the occurrence and development of cancers. In this work, a conceptual density functional theory (CDFT)-based computational peptidology (CDFT-CP) method is used to study the chemical reactivity of 14 multikinase inhibitors. Optical properties of these inhibitors are studied by time-dependent density functional theory (TDDFT). Various biological and pharmacokinetic parameters are studied by Osiris, Molinspiration, and BOILED-Egg in SwissADME software tools. Physicochemical and biopharmaceutical (PCB), Salmonella typhimurium reverse mutation assay (AMES) mutagenicity, toxicity, and risk prediction are estimated by Simulations plus ADMET Predictor 10.2 software. MD simulations for an active model of ACK1 is carried out by the CABS-flex 2.0 web server, and potential binding pockets for ACK1 are searched using the PrankWeb server. SwissTargetPrediction is used to predict the potential targets for the multikinase inhibitors. Docking studies are carried out for ACK1–multikinase inhibitors using Autodock 4.2 software. Noncovalent interactions for ACK1–multikinase inhibitor complexes are studied using the Protein–Ligand Interaction Profiler (PLIP) server. Results indicated higher binding affinities and strong noncovalent interactions in ACK1–multikinase inhibitor complexes.

Theoretical Studies on the Molecular Properties, Toxicity, and Biological Efficacy of 21 New Chemical Entities

New chemical entities (NCEs) such as small molecules and antibody-drug conjugates have strong binding affinity for biological targets, which provide deep insights into structure-specific interactions for the design of future drugs. As structures of drugs increase in complexity, the importance of computational predictions comes into sharp focus. Knowledge of various computational tools enables us to predict the molecular properties, toxicity, and biological efficacy of the drugs and help the medicinal chemists to discover new drugs more efficiently. Newly approved drugs have higher affinities for proteins and nucleic acids and are applied for the treatment of human diseases. We have carried out the computational studies of 21 such NCEs, specifically small molecules and antibody-drug conjugates, and studied the biological efficacy of these drugs. Their bioactivity score and molecular and pharmacokinetic properties were evaluated using online computer software programs, viz., Molinspiration and Osiris Property Explorer. The SwissTargetPrediction tool was used for the efficient prediction of protein targets for the NCEs. The results indicated higher stability for the drug complexes due to a larger HOMO-LUMO gap. A high electrophilicity index reflects good electrophilic behavior and high reactivity of the drugs. Lipinski's ''rule of five'' indicated that most of the drug complexes are likely to be orally active. These drugs also showed non-mutagenic, non-tumorigenic, non-irritant, and non-effective reproductive behavior. We hope that these studies will provide an insight into molecular recognition and definitely help the medicinal chemists to design new drugs in future.

Characterization of Phytochemicals in Ulva intestinalis L. and Their Action Against SARS-CoV-2 Spike Glycoprotein Receptor-Binding Domain

Coronavirus disease-2019 (COVID-19) has caused a severe impact on almost all aspects of human life and economic development. Numerous studies are being conducted to find novel therapeutic strategies to overcome COVID-19 pandemic in a much effective way. Ulva intestinalis L. (Ui), a marine microalga, known for its antiviral property, was considered for this study to determine the antiviral efficacy against severe acute respiratory syndrome-associated Coronavirus-2 (SARS-CoV-2). The algal sample was dried and subjected to ethanolic extraction, followed by purification and analysis using gas chromatography-coupled mass spectrometry (GC-MS). Forty-three known compounds were identified and docked against the S1 receptor binding domain (RBD) of the spike (S) glycoprotein. The compounds that exhibited high binding affinity to the RBD of S1 protein were further analyzed for their chemical behaviour using conceptual density-functional theory (C-DFT). Finally, pharmacokinetic properties and drug-likeliness studies were carried out to test if the compounds qualified as potential leads. The results indicated that mainly phenols, polyenes, phytosteroids, and aliphatic compounds from the extract, such as 2,4-di-tert-butylphenol (2,4-DtBP), doconexent, 4,8,13-duvatriene-1,3-diol (DTD), retinoyl-β-glucuronide 6',3'-lactone (RBGUL), and retinal, showed better binding affinity to the target. Pharmacokinetic validation narrowed the list to 2,4-DtBP, retinal and RBGUL as the possible antiviral candidates that could inhibit the viral spike protein effectively.

Conceptual density functional theory based electronic structure principles

In this review article, we intend to highlight the basic electronic structure principles and various reactivity descriptors as defined within the premise of conceptual density functional theory (CDFT). Over the past several decades, CDFT has proven its worth in providing valuable insights into various static as well as time-dependent physicochemical problems. Herein, having briefly outlined the basics of CDFT, we describe various situations where CDFT based reactivity theory could be employed in order to gain insights into the underlying mechanism of several chemical processes.