Browsing by Author "Deogratias, Geradius"
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Item Hydrophobic π-π stacking interactions and hydrogen bonds drive self-aggregation of luteolin in water(Elsevier, 2022-06-23) Deogratias, Geradius; Shadrack, Daniel M; Munissi, Joan J.E.; Kinunda, Grace A.; Jacob, Fortunatus R.; Mtei, Regina P.; Masalu, Rose J.; Mwakyula, Issakwisa; Kiruri, Lucy W.; Nyandoro, Stephen S.Luteolin is a flavonoid obtained from different plant species. It is known for its versatile biological activities. However, the beneficial effects of luteolin have been limited to small concentrations as a result of poor water solubility. This study aimed at investigating the hydrophobic interaction and hydration of luteolin towards the improvement of its solubility when used as a drug. We report the aggregation properties of luteolin in water by varying the number of monomers using atomistic molecular dynamics simulation. Results show that the equilibrium structure of luteolin occurs in an aggregated state with different structural arrangements. As the monomers size increase, the antiparallel flipped conformation dominates over T-shaped antiparallel, T-shaped parallel, and antiparallel conformations. The formation of intramolecular hydrogen bonding of 0.19 nm between the keto-enol groups results in hydrophobic characteristics. A larger cluster exhibits slow hydrogen bond dynamics for luteolin-luteolin than luteolin-water interaction. Water structure at large cluster size exhibited slow dynamics and low self-diffusion of luteolin. The existence of hydrophobic π-π and hydrogen bonds between luteolin molecules drives strong self-aggregation resulting in poor water solubility. Breakage of these established interactions would result in increased solubility of luteolin in water.Item Hydrophobic π-π stacking interactions and hydrogen bonds drive self-aggregation of luteolin in water(Elsevier, 2022-06-28) Deogratias, Geradius; Shadrack, Daniel M.; Munissi, Joan J.E.; Kinunda, Grace A.; Jacob, Fortunatus R.; Mtei, Regina P.; Masalu, Rose J.; Mwakyula, Issakwisa; Kiruri, Lucy W.; Nyandoro, Stephen S.Luteolin is a flavonoid obtained from different plant species. It is known for its versatile biological activities. However, the beneficial effects of luteolin have been limited to small concentrations as a result of poor water solubility. This study aimed at investigating the hydrophobic interaction and hydration of luteolin towards the improvement of its solubility when used as a drug. We report the aggregation properties of luteolin in water by varying the number of monomers using atomistic molecular dynamics simulation. Results show that the equilibrium structure of luteolin occurs in an aggregated state with different structural arrangements. As the monomers size increase, the antiparallel flipped conformation dominates over T-shaped antiparallel, T-shaped parallel, and antiparallel conformations. The formation of intramolecular hydrogen bonding of 0.19 nm between the keto-enol groups results in hydrophobic characteristics. A larger cluster exhibits slow hydrogen bond dynamics for luteolin-luteolin than luteolin-water interaction. Water structure at large cluster size exhibited slow dynamics and low self-diffusion of luteolin. The existence of hydrophobic π-π and hydrogen bonds between luteolin molecules drives strong self-aggregation resulting in poor water solubility. Breakage of these established interactions would result in increased solubility of luteolin in water.Item Influence of heteroatoms on the optoelectronic properties of triphenylamine-based dyes for DSSCs application: A computational approach(Elsevier, 2022-02-23) Kirenga, Peter; Mkoma, Stelyus L.; Mlowe, Sixberth; Msambwa, Yohana; Kiruri, Lucy W.; Jacob, Fortunatus R.; Mgaya, James E.; Kinunda, Grace A.; Deogratias, GeradiusA series of sensitizers with D-π-π-A architectural framework have been fine-tuned through a variation of het eroatoms (NH, O, Se, and Te) in the π-spacers. Cyanoacrylic acid and hydantoin were used as the acceptor groups. The geometrical and electronic properties were investigated through density functional theory (DFT) and time-dependent DFT (TD-DFT) , respectively. To determine stable dye-TiO2 configuration, the binding energies are reported. The driving force of charge injection and dye regeneration range between 0.00 to − 0.77 eV and − 0.133 to − 1.60 eV, respectively, suggesting spontaneous processes. Chalcogen heteroatoms (S, Se, and Te) improved absorption within the visible and NIR regions. The binding energies of dye on (TiO2)6 cluster range between − 8.32 to − 9.62 eV and − 7.77 to − 8.98 eV for cyanoacrylic acid and hydantoin dyes, respectively. The findings suggest that the inclusion Se and Te heteroatoms may boost the performance of DSSCs when compared to parent materials containing S.Item Influence of heteroatoms on the optoelectronic properties of triphenylamine-based dyes for DSSCs application: A computational approach(Elsevier, 2022-02-27) Kirenga, Peter; Mkoma, Stelyus L.; Mlowe, Sixberth; Msambwa, Yohana; Kiruri, Lucy W.; Jacob, Fortunatus R.; Mgaya, James E.; Kinunda, Grace A.; Deogratias, GeradiusA series of sensitizers with D-π-π-A architectural framework have been fine-tuned through a variation of heteroatoms (NH, O, Se, and Te) in the π-spacers. Cyanoacrylic acid and hydantoin were used as the acceptor groups. The geometrical and electronic properties were investigated through density functional theory (DFT) and time-dependent DFT (TD-DFT) , respectively. To determine stable dye-TiO2 configuration, the binding energies are reported. The driving force of charge injection and dye regeneration range between 0.00 to −0.77 eV and −0.133 to −1.60 eV, respectively, suggesting spontaneous processes. Chalcogen heteroatoms (S, Se, and Te) improved absorption within the visible and NIR regions. The binding energies of dye on (TiO2)6 cluster range between −8.32 to −9.62 eV and −7.77 to −8.98 eV for cyanoacrylic acid and hydantoin dyes, respectively. The findings suggest that the inclusion Se and Te heteroatoms may boost the performance of DSSCs when compared to parent materials containing S.Item Luteolin: a blocker of SARS-CoV-2 cell entry based on relaxed complex scheme, molecular dynamics simulation, and metadynamics(Springer, 2021-07-08) Shadrack, Daniel M.; Deogratias, Geradius; Kiruri, Lucy W.; Onoka, Isaac; Vianney, John-Mary; Swai, Hulda; Nyandoro, Stephen S.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.Item 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 M.; Celestin N., Mudogo; Mtei, Kelvin M.; Machunda, Revocatus L.; Paluch, Andrew S.; Ntie-Kang, FideleLinamarin has been reported to have anticancer activities; however, its extraction and isolation using different solvents yield a low amount. Therefore, understanding the physical properties, such as solvents’ solubility, membrane permeability and lipophilicity and how they are associated 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. Centrally 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 interactions are strongest in water. As a result, the solvation free-energy calculations reveal that linamarin solvation is most favourable in DMSO.Item Optical and electronic properties of para-functionalized triphenylamine-based dyes: a theoretical study(Springer, 2021-11-09) Mkoma, Stelyus L.; Msambwa, Yohana; Jacob, Fortunatus R.; Kiruri, Lucy W.; Kinunda, Grace A.; Mlowe, Sixberth; Deogratias, GeradiusMolecular engineering of dyes has become a popular and most successful approach towards improvement of photovoltaic power conversion efficiency of dye-sensitized solar cells (DSSCs). We report the geometrical, optical, and electronic properties for para-substituted triphenylamine (TPA)-based dyes with D-π-π-A architecture. Results were realized through density functional theory (DFT) and time-dependent density functional theory (TD-DFT) methods. We used B3LYP/6–31 + G(d,p) and CAM-B3LYP/6–31 + G(d,p) level of theory for DFT and TD-DFT, respectively. Six electron-donating (ED) and electron-withdrawing (EW) groups were symmetrically grafted to the para-direction of the phenyl rings. Two anchoring groups namely: cyanoacrylic acid (CA) and hydantoin (HY) were used. Excellent relationships between electronic energies and the Hammett constants (σp) have been reported. The results show that variation of both anchoring groups and substituents significantly affect the absorption of the dyes; maximum absorption for CA dyes was found ranging between 514–571 nm and 470–503 nm for ED and EW groups, respectively, while for HY dyes demonstrated maximum absorption between 502–537 nm and 480–496 nm for ED and EW, respectively. A linear correlation between σp and λmax with R2 > 0.97 was obtained. In addition, the mapping of the HOMO and LUMO energies suggests the intramolecular charge transfer and a strong electronic coupling between dye and semiconductor. Our theoretical calculations show that electron-donating substituents enhance the optoelectronic properties of the dyes. Analysis of chemical descriptors suggests that dyes containing alternative anchoring group HY substituted with –NH2 and –N(CH3)2 may demonstrate improved performance of DSSCs.Item Optical and electronic properties of para‑functionalized triphenylamine‑based dyes: a theoretical study(Springer, 2021-11-09) Mkoma, Stelyus L.; Msambwa, Yohana; Jacob, Fortunatus R.; Kiruri, Lucy W.; Kinunda, Grace A.; Mlowe, Sixberth; Deogratias, GeradiusMolecular engineering of dyes has become a popular andmost successful approach towards improvement of photovoltaic power conversion efciency of dye-sensitized solar cells (DSSCs). We report the geometrical, optical, and electronic proper ties for para-substituted triphenylamine (TPA)-based dyes with D-π-π-A architecture. Results were realized through density functional theory (DFT) and time-dependent density functional theory (TD-DFT) methods. We used B3LYP/6–31+G(d,p) and CAM-B3LYP/6–31+G(d,p) level of theory for DFT and TD-DFT, respectively. Six electron-donating (ED) and electron withdrawing (EW) groups were symmetrically grafted to the para-direction of the phenyl rings. Two anchoring groups namely: cyanoacrylic acid (CA) and hydantoin (HY) were used. Excellent relationships between electronic energies and the Hammett constants (σp) have been reported. The results show that variation of both anchoring groups and substituents significantly affect the absorption of the dyes; maximum absorption for CA dyes was found ranging between 514–571 nm and 470–503 nm for ED and EW groups, respectively, while for HY dyes demonstrated maximum absorption between 502–537 nm and 480–496 nm for ED and EW, respectively. A linear correlation between σp and λmax with R2>0.97 was obtained. In addition, the mapping of the HOMO and LUMO energies suggests the intramolecular charge transfer and a strong electronic coupling between dye and semiconductor. Our theoretical calculations show that electron-donating substituents enhance the optoelectronic properties of the dyes. Analysis of chemical descriptors suggests that dyes containing alternative anchoring group HY substituted with –NH2 and –N(CH3)2 may demonstrate improved performance of DSSCs.