Browsing by Author "Deogratias, Geradius"

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Effect of Electron Donor Groups on Optoelectronic Properties of Betalain Dyes: A DFT Study
(wiley, 2025-05) Tsere, Melkizedeck; Costa, Rene; Deogratias, Geradius; Pogrebnaya, Tatiana; Pogrebnoi, Alexander; Machunda, Revocatus; Al-Qurashi, Ohoud; Wazzan, Nuha; Babu, Nambury
A sensitizer is a vital component of dye-sensitized solar cells(DSSCs); it absorbs incident photons, excites electrons, and facil-itates charge transfer to the semiconductor. In the present work,modification of betalain dyes through grafting of electron donorgroups has been performed. The reported optoelectronic properties of the investigated dyes are determined using densityfunctional theory (DFT) and time-dependent DFT methods. The investigated sensitizers exhibit maximum absorption between400 and 442 nm with light-harvesting efficiencies exceeding 93%.Favorable interactions are observed between the dyes and the hydrogenated TiO2 cluster, (TiO2)6H3. The obtained binding energies range from 1.39 to 0.97 eV in the gas phase and 0.31 to 0.03 eV in water. The electronic spectra of the dye@TiO2 complexes show broader and intensive bands with bathochromicshifts when compared to the individual dyes. The charge density distribution in the complexes indicates appropriate ability of thedyes for charge injection to the semiconductor. Among the considered dyes, the most promising candidates for use in DSSCs have been selected.
Enhancing the optoelectronic properties of blended triphenylamine-betalain based dyes through tailoring the anchoring unit: a theoretical investigation
(Taylor & Francis, 2024-11-25) Tsere, Melkizedeck; Costa, Rene; Deogratias, Geradius; Al-Qurashi, Ohoud; Wazzan, Nuha; Pogrebnaya, Tatiana; Pogrebnoi, Alexander; Machunda, Revocatus
A series triphenyl-betalain organic dyes featuring carboxylic acid and nitro anchoring groups CH = C(X)COOH for the A1-X dyes and -CH = C(X)NO2 for the A2-X dyes, respectively, where X = CN, CH3, CCl3 and CF3 was evaluated for dye sensitised solar cells application. The geometrical structures, molecular orbitals and energies, light absorption patterns, free energies of electron injection and dye regeneration and binding to the semiconductor have been explored using DFT/TD-DFT methods. The nitro-based anchoring group resulted in pronounced red-shift in absorption spectra between 111 and 317 nm compared to carboxylic acid-based dyes. Attachment of the dyes to the semiconductor was modelled via binding to (TiO2)6H3 cluster; A2-X dyes exhibited more stable Dye@TiO2 complexes with binding energies (BEs) ranging between −4.08 and −2.88 eV compared to A1-X dyes with BEs range of −1.11 to −0.05 eV. The results evince that the dyes with CH = C(X)NO2 anchoring groups could be promising materials for light harvesting application.
Ensemble-based screening of natural products and FDA-approved drugs identified potent inhibitors of SARS-CoV-2 that work with two distinct mechanisms
(Elsevier Ltd., 2021-06) Shadrack, Daniel; Deogratias, Geradius; Kiruri, Lucy; Swai, Hulda; Vianney, John-Mary; Nyandoro, Stephen
The 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.
Ensemble-based screening of natural products and FDA-approved drugs identified potent inhibitors of SARS-CoV-2 that work with two distinct mechanisms
(Elsevier Inc., 2021-02-23) Shadrack, Daniel; Deogratias, Geradius; Kiruri, Lucy; Swai, Hulda; Vianney, John-Mary; Nyandoro, Stephen
The 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.
Investigation of optoelectronic properties of triphenylamine-based dyes featuring heterocyclic anchoring groups for DSSCs’ applications: a theoretical study
(Springer Nature Switzerland AG., 2020-08-05) Deogratias, Geradius; Al-Qurashi, Ohoud S.; Wazzan, Nuha; Seriani, Nicola; Pogrebnaya, Tatiana P.; Pogrebnoi, Alexander M.
Design 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.
Luteolin: a blocker of SARS-CoV-2 cell entry based on relaxed complex scheme, molecular dynamics simulation, and metadynamics
(Springer Nature, 2021-07-08) Shadrack, Daniel; Deogratias, Geradius; Kiruri, Lucy; Onoka, Isaac; Vianney, John-Mary; Swai, Hulda; Nyandoro, Stephen
Natural 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.
A Molecular Investigation of the Solvent Influence on Inter- and Intra-Molecular Hydrogen Bond Interaction of Linamarin
(MDPI, 2022-02-11) Paul, Lucas; Deogratias, Geradius; Shadrack, Daniel; Mudogo, Celestin; Mtei, Kelvin; Machunda, Revocatus; Paluch, Andrew; Ntie‐Kang, Fidele
Linamarin 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
(NM-AIST, 2021-06) Deogratias, Geradius
Triphenylamine 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.
(Elsevier Inc., 2020-01-01) Deogratias, Geradius; Seriani, Nicola; Pogrebnaya, Tatiana; Pogrebnoi, Alexander
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.