Explicit Solutions for Real-time Reversible Inhibition Kinetics using Lambert W Function: Towards Progress Curve Analysis

Accurate estimation of kinetic parameters is challenging due to the dynamics and mathematical nature of the chemical systems. This paper presents simple, yet efficient closed-form solutions for the enzymatic conversion of the substrate to the product in real-time derived using the Lambert W function. The real values of the Lambert W function were calculated from the Lambert package as implemented in MATLAB. The expressions exhibit remarkable robustness in estimating the parameters for randomized data at 1% to 4% variation in noise levels. Furthermore, unlike the initial rates method, the expressions estimate chemical kinetic parameters utilizing a full range of experimental data, thus minimizing the risk of missing information that would be detected at an extended time-span. Thus, the implementation of closed-form solutions presented in this paper for the estimation of kinetic parameters eliminates common pitfalls imposed by the initial rates and double reciprocal methods. Keywords:          Enzyme, Lambert W function, Reversible inhibition, Closed-form solution

Novel Xanthate Complexes for the Size Controlled Synthesis of Copper Sulfide Nanorods

We present a simple, easily scalable route to monodisperse copper sulfide nanocrystals by the hot injection of a series of novel copper­(I) xanthate single-source precursors [(PPh₃)₂Cu­(S₂COR)] (R = isobutyl, 2-methoxyethyl, 2-ethoxyethyl, 1-methoxy-2-propyl, 3-methoxy-1-butyl, and 3-methoxy-3-methyl-1-butyl), whose crystal structures are also reported. We show that the width of the obtained rods is dependent on the length of the xanthate chain, which we rationalize through a computational study, where we show that there is a relationship between the ground-state energy of the precursor and the copper sulfide rod width

Investigation of optoelectronic properties of triphenylamine-based dyes featuring heterocyclic anchoring groups for DSSCs’ applications: a theoretical study

This research article published by Springer Nature Switzerland AG., 2020Design and synthesis of new potent sensitizers are of interest for realization of high-efficiency Dye Sensitized Solar Cells (DSSCs). Modification of the triphenylamine-based dyes by introducing suitable anchoring groups aimed at improvement of optoelectronic properties is attempted in our work. The molecular structure, molecular orbitals and energies, electronic absorption spectra, free energies of electron injection and dye regeneration, chemical reactivity parameters and adsorption to TiO2 semiconductor have been reported. Density functional theory (DFT) and time-dependent DFT (TD-DFT) were used to obtain the reported properties. The results reveal superior optical, electronic properties, chemical reactivity parameters and adsorption energies for the investigated dyes. The findings evince that the dyes featuring heterocyclic anchoring groups could be potential candidates for DSSCs’ applications; the new materials are worthy of being investigated experimentally

A Molecular Investigation of the Solvent Influence on Inter- and Intra-Molecular Hydrogen Bond Interaction of Linamarin

This research article published by MDPI, 2022Linamarin has been reported to have anticancer activities; however, its extraction and isolation using different solvents yield a low amount. Therefore, understanding the physical prop‐ erties, such as solvents’ solubility, membrane permeability and lipophilicity and how they are asso‐ ciated with different solvents, is a paramount topic for discussion, especially for its potential as a drug. Linamarin has a sugar moiety with many polar groups responsible for its physical properties. Following current trends, a molecular dynamics simulation is performed to investigate its physical properties and how different solvents, such as water, methanol (MeOH), dimethyl sulfoxide (DMSO) and dichloromethane (DCM), affect such properties. In this work, we have investigated the influence of intermolecular and intramolecular hydrogen bonding and the influence of polar and non‐polar solvents on the physical properties of linamarin. Furthermore, solvation free‐energy and electronic structure analysis are performed. The structural analysis results show that the polar groups of linamarin have strong interactions with all solvents except the etheric oxygen groups. A detailed analysis shows intermolecular hydrogen bonding between polar solvents (water, MeOH and DMSO) and the hydroxyl oxygens of linamarin. Water exhibits the strongest interaction with linamarin’s functional groups among the investigated solvents. The findings show that within the first solvation shell, the number of water molecules is greatest, while MeOH has the fewest. Cen‐ trally to the structural analysis, solvation free energy confirms DMSO to be the best solvent since it prefers to interact with linamarin over itself, while water prefers to interact with itself. While the solute–solvent interactions are strongest between linamarin and water, the solvent–solvent interac‐ tions are strongest in water. As a result, the solvation free‐energy calculations reveal that linamarin solvation is most favourable in DMSO

Molecular modification of dye constituents through grafting anchoring groups and pi-spacers: towards DSSCs application

A Dissertation Submitted in Partial Fulfillment of the Requirements for the Degree of Doctor of Philosophy in Materials Science and Engineering of the Nelson Mandela African Institution of Science and TechnologyTriphenylamine based dyes molecular modification by grafting anchoring groups and spacers was performed within computational framework aimed at potential materials for dye- sensitized solar cells (DSSCs) application. For the modification, benzothiadiazole-like spacers, heterocyclic anchoring groups and heteroatom doping have been taken into account. The reported structural and optoelectronic properties of the dyes were realized through density functional theory and time-dependent density functional theory using B3LYP and CAM-B3LYP functionals coupled with 6-31G(d,p) and 6-31G+(d,p) basis sets. The findings show that presence of atoms of nitrogen and sulphur in the -spacers has a beneficial impact on the material‟s properties, whereas the branched -spacer impairs the electronic light absorption characteristics of the sensitizers. The heterocyclic anchoring units result in a bathochromic shift with maximum absorption within 450 − 600 nm. The computed light harvesting efficiencies, excited-state lifetimes, electron injection and regeneration abilities prove that dyes with heterocyclic anchoring groups to be potential candidates for DSSC applications. The heteroatom doping demonstrates that the chalcogens enhance the absorption and fluorescent emission spectra of the isolated dyes in the visible and near infra-red regions with maximum wavelength 504 – 556 nm and 637 – 732 nm, respectively. Simulation of the dyes attachment to the TiO 2 surface was undertaken; two models of the crystal surface considered, TiO 2 slab and hydrogenated (TiO 2 ) 6 cluster. Among possible adsorption modes of the dye@TiO 2 complexes, monodentate, bidentate and tridentate, the bidentate mode was found thermodynamically more favourable. In both, individual dyes and dye@TiO 2 complexes, less electronegative dopants contributed to the improvement of the UV-Vis spectra and redistribution of electron density. The calculated energies of the dye@TiO 2 attachment relate to dopant heteroatoms; stronger binding is observed in the complexes with heavier heteroatoms – selenium and tellurium. The adsorption energy magnitudes range between 0.11 − 1.75 eV for the TiO 2 slab and 7.61 − 9.48 eV for (TiO 2 ) 6 cluster. Energy difference between the two binding models was found to correspond to the enthalpy of sublimation of TiO 2 from the TiO 2 anatase. One can anticipate that systematic modification of dyes‟ building blocks may lead to novel materials with suitable characteristics for application in DSSCs

Tuning optoelectronic properties of triphenylamine based dyes through variation of pi-conjugated units and anchoring groups: A DFT/TD-DFT investigation.

This research article published by Elsevier Inc.Dye-sensitized solar cells (DSSCs) have attracted widespread attention due to their unique features. In the present work, molecular engineered triphenylamine based dyes featuring donor-bridge-acceptor architecture have been considered and investigated for suitable properties for DSSCs applications. Hydantoin anchoring group has been introduced replacing the commonly used cyanoacrylic acid to improve the long-term stability of the device. Results on the effects of varied anchoring groups and pi-spacers have been interpreted from the viewpoint of DFT/TD-DFT calculations. Designed sensitizers exhibit suitable light-harvesting efficiencies, excited-state lifetimes, electron injection and regeneration abilities. Red-shifted electronic spectra are observed for three hydantoin dyes compared to others in the same family. Further analysis of chemical descriptors and observation from full-electron donor-acceptor map reveal that the three dyes among nine are potential materials with promising properties towards improving DSSCs performance

Ensemble-based screening of natural products and FDA-approved drugs identified potent inhibitors of SARS-CoV-2 that work with two distinct mechanisms

This research article published by Elsevier Ltd., 2021The recent outbreak of SARS-CoV-2 is responsible for high morbidity and mortality rate across the globe. This requires an urgent identification of drugs and other interventions to overcome this pandemic. Computational drug repurposing represents an alternative approach to provide a more effective approach in search for COVID-19 drugs. Selected natural product known to have antiviral activities were screened, and based on their hits; a similarity search with FDA approved drugs was performed using computational methods. Obtained drugs from similarity search were assessed for their stability and inhibition against SARS-CoV-2 targets. Diosmin (DB08995) was found to be a promising drug that works with two distinct mechanisms, preventing viral replication and viral fusion into the host cell. Isoquercetin (DB12665) and rutin (DB01698) work by inhibiting viral replication and preventing cell entry, respectively. Our analysis based on molecular dynamics simulation and MM-PBSA binding free energy calculation suggests that diosmin, isoquercetin, rutin and other similar flavone glycosides could serve as SARS-CoV-2 inhibitor, hence an alternative solution to treat COVID-19 upon further clinical validation

Luteolin: a blocker of SARS-CoV-2 cell entry based on relaxed complex scheme, molecular dynamics simulation, and metadynamics

This research article published by Springer Nature, 2021Natural products have served human life as medications for centuries. During the outbreak of COVID-19, a number of naturally derived compounds and extracts have been tested or used as potential remedies against COVID-19. Tetradenia riparia extract is one of the plant extracts that have been deployed and claimed to manage and control COVID-19 by some communities in Tanzania and other African countries. The active compounds isolated from T. riparia are known to possess various biological properties including antimalarial and antiviral. However, the underlying mechanism of the active compounds against SARS-CoV-2 remains unknown. Results in the present work have been interpreted from the view point of computational methods including molecular dynamics, free energy methods, and metadynamics to establish the related mechanism of action. Among the constituents of T. riparia studied, luteolin inhibited viral cell entry and was thermodynamically stable. The title compound exhibit residence time and unbinding kinetics of 68.86 ms and 0.014 /ms, respectively. The findings suggest that luteolin could be potent blocker of SARS-CoV-2 cell entry. The study shades lights towards identification of bioactive constituents from T. riparia against COVID-19, and thus bioassay can be carried out to further validate such observations

CCDC 1550298: Experimental Crystal Structure Determination

An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures

CCDC 1550295: Experimental Crystal Structure Determination

An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures