Browsing by Author "Pandithavidana, D.R."

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Comparative Study of Antioxidant Potential of Selected Dietary Vitamins; Computational Insights
(Molecules, 2019) Pandithavidana, D.R.; Jayawardana, S.B.
Density functional theory (DFT) was used to explore the antioxidant properties of some naturally occurring dietary vitamins, and the reaction enthalpies related to various mechanisms of primary antioxidant action, i.e., hydrogen atom transfer, single electron transfer–proton transfer, and sequential proton loss–electron transfer were discussed in detail. B3LYP, M05-2X, and M06-2X functionals were utilized in this work. For aqueous phase studies, the integral equation formalism polarized continuum model (IEF–PCM) was employed. From the outcomes, hydrogen atom transfer (HAT) was the most probable mechanism for the antioxidant action of this class of compounds. Comparison of found results with experimental data (available in literature), vitamin C possesses the lowest enthalpy values for both proton a nity (PA) and bond dissociation energy (BDE)in the aqueous phase, suggesting it as the most promising candidate as an antioxidant. Accordingly, these computational insights encourage the design of structurally novel, simple vitamins which will be more economical and beneficial in the pharmaceutical industry.
Computational design and investigation of antioxidant activity of phenolic compounds and their derivatives
(Proceedings of the 73rd Annual Sessions of Sri Lanka Association for the Advancement of Science, 2017) Surangika, K.H.K.; Pandithavidana, D.R.
Among various types of antioxidants, phenolic antioxidants form an important class of compounds, which serves to inhibit the oxidation of materials of both commercial and biological importance. Density functional theory (DFT) calculations (BP86 level of theory and 6-311++ G (2df, 2p) basis set) have been performed on some structurally simple phenolic antioxidants first, and then on novel designed, phenolic derivatives. Moreover, the polarity of the solvent medium has been included in calculating bond dissociation energy (BDE) and ionization potentials (IP). Both H-atom transfer (HAT mechanism) and single electron transfer (SET mechanism) pathways have been investigated by calculating the phenolic O—H bond dissociation energy (BDE) and ionization potentials (IP) in three different phases (gas, aqueous and cyclohexane). How the antioxidant activity of phenolic derivatives is perturbed by electron donor and withdrawing substituents present at ortho, meta, and para positions and the dimerized of phenolic derivatives have also been computationally investigated. The presence of electron donating substituents on the structure at the ortho and para positions of the phenol increased the antioxidant activity significantly. When secondary and tertiary amine groups were introduced to phenolic antioxidants, the BDE and IP values decreased noticeably (IP from 7.04 to 5.23 and 1.97 eV, BDE from 71.01 to 70.62 and 69.00 kcal/mol). In aqueous phase the designed phenolic antioxidants showed better activity owing to Hydrogen bonding. The effect of solvent on IP values was higher than on BDE, showing that the SET mechanism was highly solvent dependent compared to HAT mechanism. These theoretical computational predictions were superimposable with experimental results reported in literature. When designed novel amino derivatives were dimerized and those monomers were linked through conjugated alkyl chains, they demonstrateded much better antioxidant properties (lower BDE) than the monomers themselves (68.05 to 65.04 kcal/mol).
Computational Investigation of Antioxidant Activity of Dietary Vitamins; DFT Study
(International Postgraduate Research Conference 2019, Faculty of Graduate Studies, University of Kelaniya, Sri Lanka, 2019) Jayawardana, S.B.; Pandithavidana, D.R.
Among numerous types of antioxidant compounds, dietary vitamins form an important class of chain-breaking compounds which have a potential to quench reactive radical intermediates produced during the oxidative processes of both biological and commercial importance materials. According to the recent investigations, the possible role of antioxidants in prevention of human diseases has taken a leading role. Antioxidants are also capable to defend against number of disease conditions such as aging, atherosclerosis, cancer, asthma, arthritis and autoimmune diseases. Antioxidants as external supplements are used to maintain the concentration of free radicals as low as possible and to avoid the oxidative stress. They are heavily used in food industry to maintain the quality of the ready-to-eat foods, and to boost the shelf life. The computational chemistry has become a versatile tool to investigate wide range of thermodynamic properties which are hardly measurable, as well as to predict the trends between them. The efficiency of an antioxidant can be successfully estimated by analyzing the potential energy surface (PES) of the reaction with a certain radical. This potential energy surface permits calculation of the activation and reaction energies, entailing that both kinetic and thermodynamic approaches to the interested reaction are presented. As well as the computed parameters provide useful information on the radical scavenging power without considering reaction pathway. Density functional theory (DFT) was used to explore the antioxidant properties of some naturally occurring dietary vitamins, and the reaction enthalpies related to various mechanisms of primary antioxidant action, i.e., hydrogen atom transfer (HAT), single electron transfer–proton transfer (SET–PT), and sequential proton loss–electron transfer (SPLET) have been investigated in detail. B3LYP, M05-2X, and M06-2X functionals were utilized in this work. For aqueous phase studies, the integral equation formalism polarized continuum model (IEF–PCM) was employed. From the outcomes, hydrogen atom transfer (HAT) was the most probable mechanism for the antioxidant action of this class of compounds. Comparison of found results with experimental data (available in literature), vitamin C possesses the lowest enthalpy values for both proton affinity (PA) and bond dissociation energy (BDE) in the aqueous phase, suggesting it as the most promising candidate as an antioxidant. Accordingly, these computational insights encourage the design of structurally novel, simple vitamins which will be more economical and beneficial in the pharmaceutical industry.
Computational investigation of cyclic 8-membered enediyne chemistry
(Sri Lanka Association for the Advancement of Science, 2014) Adhihetty, P.K.; Rathnayake, P.V.G.M.; Pandithavidana, D.R.
Computational Investigation of Pesticide Induced Oxidative Stress and Its Impact on the Chronic Kidney Disease of Unknown Etiology (CKDu)
(19th Conference on Postgraduate Research, International Postgraduate Research Conference 2018, Faculty of Graduate Studies,University of Kelaniya, Sri Lanka, 2018) Deshan, T.M.V.; Pandithavidana, D.R.
The chronic kidney disease of unknown etiology (CKDu) has been a major health issue in Sri Lanka within the last three decades. It has been a burden problem mainly for the rural agricultural community. Many investigative efforts have been carried out to identify its unknown origin and several risk factors which have been associated. But levels of any of the pollutants or conditions reported have not been consistent or correlated with the prevalence of the disease as it is named (as the sole cause of CKDu). A possible link between oxidative stress and the progression of the disease has been identified. The environmental factors which favor the development of oxidative stress are prevalent in those affected areas. The study of “pesticide induced oxidative stress” has been a topic of research interest. Alterations in the balance between the production of free radicals and the antioxidant defenses were recognized as one of the main causes. The secondary interactions between small ligands and macromolecules were computationally investigated using AutoDock molecular docking program. In this computational study, four major pesticides were docked with different enzymes which directly related to mechanisms in generating oxidative stress. The strength of the binding of the pesticide in the binding site of the corresponding enzyme was used to emphasize its potential interaction with the enzyme. According to molecular docking investigations, it was evident that three organophospahates; Profenofos, Diazinon and Chlrofyrifos possessed relatively similar binding energies at the active site compared to the inducer for Cytochrome P450 A34 enzyme. Profenofos showed the lowest Gibbs binding energy among three. The computational studies predicted that these pesticides might serve as potent inducers or substrates for the enzyme. Imidacloprid was not metabolized by the enzyme as it didn’t show any interactions at the active site. None of the pesticides would act as a potent inhibitor of the enzyme. Further, computational simulations revealed that these organophosphates behaved as potent enzyme inducers as well as substrates which involved in bio activation. These computed results directed to a feasible mechanism to disclose how reactive oxygen species were generated to cause oxidative stress. The location of binding pocket and the strength of binding at the active site of the enzyme were important parameters used to generate these predictions. This computational study has been utilized to predict mechanistic steps related to the “pesticide induced oxidative stress” which is a causative factor for the multi factorial origin of CKDu.
Computational investigation of thermodynamic and kinetic feasibilities of cyclopropenone decarbonylation mechanism
(Sri Lanka Association for the Advancement of Science, 2014) Rathnayaka, R.M.S.C.; Rathnayaka, P.V.G.M.; Pandithavidana, D.R.
De novo synthesis and properties of analogues of the self-assembling chlorosomal bacteriochlorophylls
(New Journal of Chemistry, 2011) Mass, O.; Pandithavidana, D.R.; Ptaszek, M.; Santiago, K.; Springer, J.W.; Jiao, J.; Tang, Q.; Kirmaier, C.; Bocian, D.; Holten, D.; Lindsey, J.S.
Natural photosynthetic pigments bacteriochlorophyllsc, d and e in green bacteria undergo self-assembly to create an organized antenna system known as the chlorosome, which collects photons and funnels the resulting excitation energy toward the reaction centers. Mimicry of chlorosome function is a central problem in supramolecular chemistry and artificial photosynthesis, and may have relevance for the design of photosynthesis-inspired solar cells. The main challenge in preparing artificial chlorosomes remains the synthesis of the appropriate pigment (chlorin) equipped with a set of functional groups suitable to direct the assembly and assure efficient energy transfer. Prior approaches have entailed derivatization of porphyrins or semisynthesis beginning with chlorophylls. This paper reports a third approach, the de novo synthesis of macrocycles that contain the same hydrocarbon skeleton as chlorosomal bacteriochlorophylls. The synthesis here of Zn(II) 3-(1-hydroxyethyl)-10-aryl-131-oxophorbines (the aryl group consists of phenyl, mesityl, or pentafluorophenyl) entails selective bromination of a 3,13-diacetyl-10-arylchlorin, palladium-catalyzed 131-oxophorbine formation, and selective reduction of the 3-acetyl group using BH3�tBuNH2. Each macrocycle contains a geminal dimethyl group in the pyrroline ring to provide stability toward adventitious dehydrogenation. A Zn(II) 7-(1-hydroxyethyl)-10-phenyl-17-oxochlorin also has been prepared. Altogether, 30 new hydroporphyrins were synthesized. The UV-Vis absorption spectra of the new chlorosomal bacteriochlorophyll mimics reveal a bathochromic shift of [similar]1800 cm?1 of the Qy band in nonpolar solvent, indicating extensive assembly in solution. The Zn(II) 3-(1-hydroxyethyl)-10-aryl-131-oxophorbines differ in the propensity to form assemblies based on the 10-substituent in the following order: mesityl
Density functional theory simulation of structural, electronic and thermodynamic properties of nonylphenol ethoxylate surfactants
(Sri Lanka Association for the Advancement of Science, 2015) Jayalath, W.I.M.; Pandithavidana, D.R.
Enhancement of physical properties of red clay based superior quality cookware.
(Faculty of Science, University of Kelaniya Sri Lanka, 2023) Dulaj, M.H.T.; Gunathilaka, H.M.B.I.; Arachchige, R.C.W.; Pandithavidana, D.R.; Kottegoda, I.R.M.
Red clay-based cookware has been used for centuries mainly due to its aesthetic appearance, eco-friendliness as well as the ability to enhance the quality and taste of foods. However, at present, cookware manufacturers can't stay in business without freshcutting-edge properties because the growing demand for superior quality cookware that not only performs well but also has enhanced physical properties such as durability, resistance to cracking, and improved thermal shock resistance. As a remediation, the present study explores various techniques that can be employed to enhance the physical properties of red clay-based cookware, by adding reinforcing materials (Ball clay, Quartz, and Feldspar), varying firing temperatures, and advanced-manufacturing techniques like casting clay methods. Eight samples with different compositions were prepared using red clay, four different weight percentages were chosen for each clay type from 15 wt.%, 20 wt.%, 25wt.%, and 30 wt.% in Colombo and Beliattha samples. Their physical properties such as density of a casing clay slip, drying or firing shrinkage, loss on ignition, water absorption, modulus of rupture (MOR), and thermal shock resistance were investigated with repetition. Among the prepared samples, low shrinkage was observed in each clay type resulting reduced risk of defects from warping and cracking. Colombo clay is more suitable inthat respect. Due to higher MOR value, Beliatta clay has higher strength, durability, andstronger thermal shock resistance as well. Low water absorption was shown by Beliatta clay, indicating a more solid and impermeable structure, making the cookware lessprone to discoloration, cracking, or degradation. Therefore, Beliatta clay is more suitable than Colombo clay to fabricate cookware. Overall, it was found that different compositions of red clay could be successfully incorporated to improve the properties of claybased cookware. This study demonstrates that enhancement of the MOR value, low water absorption and low shrinkage for cookware manufacturers, researchers, and enthusiasts who are interested in improving the quality and performance of red clay-based cookware.
Molecular Docking Analysis to Elucidate the Potential Drug Action of Phytochemicals Present in Ashwagandharishta towards Memory Related Disorders
(19th Conference on Postgraduate Research, International Postgraduate Research Conference 2018, Faculty of Graduate Studies,University of Kelaniya, Sri Lanka, 2018) Munaweera, R.R.K.W.; Pandithavidana, D.R.
Ashwagandharishta is an Ayurveda medicine that is used to treat psychiatric conditions, dullness, memory related diseases, sluggishness, epilepsy, depression, anxiety, schizophrenia. The main plant ingredient used to prepare this is Withaniasomnifera. It contains various classes of secondary metabolites such as steroidal lactones, phytosterols, sitoindosides and alkaloids. Memory-related disorders are closely associated with the defects in cholinergic neurotransmission. Repairing mechanisms for theses defects provide promising treatment strategies for these kinds of disorders. The most abundant receptor found in cholinergic neurotransmission is nicotinic acetylcholine receptor. Alpha-7 nicotinic acetylcholine receptor is a sub type of nicotinic acetylcholine receptor and has been identified as one of the most useful drug target for the treatment of nervous system related disorders. Potential agonists of alpha-7 nicotinic acetylcholine receptor have shown to be enhancers of cognitive performance when memory related disorders are treated. Molecular docking analyses have been carried out to identify any possible secondary metabolites present in Ashwagandharishta that could act as agonists of alpha-7 nicotinic acetylcholine receptor using AutoDock4 software package. Four possible phytochemicals have been selected based on drug likeness, blood brain barrier penetrability and agonistic binding ability with the receptor. Their docked conformations, binding at correct binding site, binding energies and dissociation constants (kI) have been further investigated computationally Based on the molecular docking studies it was revealed that anaferine and anahygrine possessed lower binding energies with compared to the binding energy of nicotine while cuscohygrine showed relatively higher energy in binding. When kI (dissociation constant) values were compared, anaferine and anahygrine possessed relatively higher values than that of nicotine. According to computational studies, cuscohygrine and palletierine showed some tendency to bind nonspecifically at other sites of the receptor. However, nonspecific bindings for anaferine and anahygrine were not energetically favorable. According this computational investigation, it has been found that two phytochemicals (anaferine and anahygrine) show promising agonistic activity towards the receptor. Thus anaferine and anahygrine have high possibility to serve as alpha-7nAChR agonists which show potential drug action towards memory related disorders.
Palette of lipophilic bioconjugatable bacteriochlorins for construction of biohybrid light-harvesting architectures
(Chemical Science, 2013) Reddy, K.R.; Pandithavidana, D.R.; Parkes-Loach, P.S.; Loach, P.A.; Bocian, D.F.; Holten, D.; Lindsey, J.S.
The challenge of creating both pigment building blocks and scaffolding to organize a large number of such pigments has long constituted a central impediment to the construction of artificial light-harvesting architectures. Light-harvesting (LH) antennas in photosynthetic bacteria are formed in a two-tiered self-assembly process wherein (1) a peptide dyad containing two bacteriochlorophyll a molecules forms, and (2) the dyads associate to form cyclic oligomers composed of 8 or 9 dyads in LH2 and 15 or 16 in LH1 of purple photosynthetic bacteria. While such antenna systems generally have near-quantitative transfer of excitation energy among pigments, only a fraction of the solar spectrum is typically absorbed. A platform architecture for study of light-harvesting phenomena has been developed that employs native photosynthetic peptide analogs, native bacteriochlorophyll a, and synthetic near-infrared-absorbing bacteriochlorins. Herein, the syntheses of 10 lipophilic bacteriochlorins are reported, of which 7 contain bioconjugatable handles (maleimide, iodoacetamide, formyl, carboxylic acid) for attachment to the peptide chassis. The bioconjugatable bacteriochlorins typically exhibit a long-wavelength absorption band in the range 710 to 820 nm, fluorescence yield of 0.1?0.2, and lifetime of the lowest singlet excited state of 2?5 ns. The ?-helical structure of the native-like peptide is retained upon conjugation with a synthetic bacteriochlorin, as judged by single-reflection infrared studies. Static and time-resolved optical studies of the oligomeric biohybrid architectures in aqueous detergent solution reveal efficient ([similar]90%) excitation energy transfer from the attached bacteriochlorin to the native-like bacteriochlorophyll a sites. The biohybrid light-harvesting architectures thus exploit the self-constituting features of the natural systems yet enable versatile incorporation of members from a palette of synthetic chromophores, thereby opening the door to a wide variety of studies in artificial photosynthesis.