Harno Pranowo - Academia.edu (original) (raw)
Papers by Harno Pranowo
JC-T (Journal Cis-Trans): Jurnal Kimia dan Terapannya
Model Quantitative structure-activity relationship (QSAR) dari turunan kumarin 3-tersubstitusi 4-... more Model Quantitative structure-activity relationship (QSAR) dari turunan kumarin 3-tersubstitusi 4-anilino terhadap aktivitasnya sebagai anti-kanker pankreas telah berhasil dibuat dan divalidasi. Struktur molekul turunan kumarin 3-tersubstitusi 4-anilino dan aktivitas biologisnya yang digunakan disitasi dari penelitian yang telah dilakukan oleh Luo dkk. Setiap molekul turunan kumarin 3tersubstitusi 4-anilino yang digunakan dioptimasi menggunakan metode kalkulasi DFT/BPV86 6-31G. Model analisis QSAR dibentuk menggunakan metode Multi Linear Regression (MLR) dan model terbaik yang didapatkan adalah: Log IC50 = 4,02 + (-7,126 x qC7) + (-5,709 x qC8) + (6,845 x qC18), n = 18; r 2 train = 0.701; r 2 test = 0.849, Fkal/Ftab = 3,269; SEE = 0.230. Dari model tersebut, nilai Log IC50 terhadap kanker pankreas dari turunan kumarin 3-tersubstitusi 4anilino dapat diperkecil dengan memodifikasi nilai qC7, qC8, dan qC18 menyesuaikan koefisien setiap diskriptor tersebut.
Eter mahkota dikenal sebagai salah satu senyawa pengikat secara spesifik suatu ion logam. Pada ba... more Eter mahkota dikenal sebagai salah satu senyawa pengikat secara spesifik suatu ion logam. Pada banyak kasus, selektifitas eter mahkota mengikuti prinsip kesesuaian antara jejari ion dengan jejari kavitas eter mahkota (kesesuaian struktur). Keberadaan substituen pada eter mahkota dapat mempengaruhi kemudahan eter mahkota dalam menata ulang konformasinya ketika berinteraksi dengan ion logam. Penelitian ini bertujuan untuk mempelajari pengaruh substituen pada struktur senyawa eter mahkota dibenzo-18-mahkota-6 (DBz18C6), dibenzo-16-mahkota-5 (DBz16C5) dan benzo-15-mahkota-5 (Bz15C5) dan interaksi senyawa eter mahkota tersebut dengan kation logam. Analisis data didasarkan pada hasil perhitungan kimia komputasi dengan metode semi empiris MNDO/d. Langkah awal adalah penentuan struktur teroptimasi dari semua eter mahkota. Langkah selanjutnya adalah memasukkan kation logam Li+, Na+ dan Zn2+ untuk berinteraksi dengan eter mahkota. Data yang akan diperoleh dari perhitungan semiempiris adalah p...
Indonesian Journal of Chemistry, 2021
Potential energy curves (PECs) and energy profiles of atomic O attack on coronene as a model for ... more Potential energy curves (PECs) and energy profiles of atomic O attack on coronene as a model for graphene/graphitic surface and interstellar reaction surface have been computed at the unrestricted B3LYP/cc-pVDZ level of theory to elaborate on atomic O attack mechanism and chemisorption on coronene. The PECs were generated by scanning the O atom distance to the closest carbon atom on "top" and "bridge" positions in the coronene, while fully relaxed geometries in the triplet state were investigated to gain the energy profile. We found that the most favorable geometry as the final product was the chemically bound O on the "bridge" site in the singlet state with an interaction energy of –29.2 kcal/mol. We recommended a plausible mechanism of atomic O attack and chemisorption reaction on coronene or generally graphitic surface starting from the non-interacting O atom and coronene systems into the chemically bound O atom on coronene.
Chiang Mai University Journal of Natural Sciences, 2020
In this study, we make QSAR models from 29 of BA derivatives’ HIV maturation inhibition activitie... more In this study, we make QSAR models from 29 of BA derivatives’ HIV maturation inhibition activities against their 3D descriptors. The best model involve 5 descriptors as follows: 1/log EC50 = -462.275 + (69.213 × TDB6u) + (723.745 × TDB6e) + (-0.576 × FPSA-3) + (0.849 × RDF140u) + (0.302 × RDF80e) r2 training = 0.7918; Q2 test = 0.9644; r2test = 0.9798; and r2m-test = 0.9445 TDB6u and TDB6e are the 3d topological distance-based autocorrelation-lag 6 /unweighted and weighted by Sanderson electronegati-vities, respectively. FPSA-3 is the value of charge weighted partial positive surface area / total molecular surface area. RDF140u is radial distribution function-140 / unweighted. RDF80e is radial distribution function-080/weighted by relative Sanderson electronegativities. The QSAR model was then used to design and predict some of the new BA derivatives’ HIV maturation activities. The best predicted compound had pEC50 value of -0.838 and EC50 value of 0.064 nM with the chemical IUPAC n...
Journal of Computational Chemistry, 2020
The impact of solvent flexibility and electron correlation on the simulation results of Cu2+ in l... more The impact of solvent flexibility and electron correlation on the simulation results of Cu2+ in liquid ammonia has been investigated via an ab initio quantum mechanical charge field molecular dynamics (QMCF MD) simulation approach. To achieve this, three different simulation systems were considered in this study, namely Cu2+ in rigid and flexible ammonia at Hartree-Fock (HF) level of theory, as well as resolution of identity second order Møller-Plesset (MP2) perturbation theory in the rigid body case. In all cases, a stable octahedral [Cu(NH3 )6 ]2+ complex subject to dynamic Jahn-Teller distortions without the occurrence of ligand exchange was observed. The Cu2+ - NH3 distance in the first shell agrees well with the experimental and other theoretical data. In all three cases, the structural data shows that the rigid-body ammonia model in conjunction with the HF level of theory provides accurate data for the first solvation shell, while at the same time, the computational demand and thus the achievable simulation time are much more beneficial. The vibrational analysis of the Cu2+ - NH3 interaction yields similar force constants in the three investigated systems indicating that there is no distinct difference on the dynamical properties of the first solvation shell. In addition to the QMCF MD simulations, a number of natural bond orbital (NBO) analyses were carried out, confirming the strong electrostatic character of the Cu2+ - NH3 interaction.
Asian Journal of Chemistry, 2018
Synthesis of new asymmetrical curcumin analogue of 1-(3,4-dimethoxy-phenyl)-5-(4-hydroxy-3-methox... more Synthesis of new asymmetrical curcumin analogue of 1-(3,4-dimethoxy-phenyl)-5-(4-hydroxy-3-methoxy-phenyl)-penta-1,4-dien-3-one via condensation reaction between vanillinacetone and veratraldehyde in ethanol has been performed. The in vitro anti-inflammatory activities of the synthesized compounds showed excellent anti-inflammatory activity. In vitro anti-inammatory activity by using inhibition of albumin denaturation technique compared to standard dichlorofenac. Molecular docking studies were performed, where docking of the compound into 6COX active site suggested that it could exert its anti-inflammatory potential by cyclooxygenase inhibition.
Indonesian Journal of Chemistry, 2010
Determination of solvation structure of Ni2+ ion in water has been achieved using Monte Carlo met... more Determination of solvation structure of Ni2+ ion in water has been achieved using Monte Carlo method using canonic assemble (NVT constant). Simulation of a Ni2+ ion in 215 H2O molecules has been done under NVT condition (298.15 K). The results showed that number of H2O molecules surround Ni2+ ion were 8 molecules in first shell and 17 molecules in second shell, interaction energy of Ni2+-H2O in first shell was -68.7 kcal/mol and in second shell was -9.8 kcal/mol, and there were two angles of O-Ni2+-O, i.e. 74o and 142o. According to those results, the solvation structure of Ni2+ ion in water was cubic antisymetric. Keywords: Water simulation, Monte Carlo simulation
![Research paper thumbnail of MOLECULAR MODELLING OF Mn<sup>+</sup>.[DBz16C5] COMPLEXES, M = Li<sup>+</sup>, Na<sup>+</sup> AND Zn<sup>2+</sup> BASED ON MNDO/d SEMIEMPIRICAL METHOD](https://attachments.academia-assets.com/101893855/thumbnails/1.jpg)
](Indonesian Journal of Chemistry, 2010
The effect of substituent on dibenzo-16-crown-5 (DBz16C5) and interaction between these crown eth... more The effect of substituent on dibenzo-16-crown-5 (DBz16C5) and interaction between these crown ether with metal cations was evaluated using computational chemistry calculations. Substituens where are connected to the benzene ring on the DBz16C5 are -COOH, -Br, -COOC2H5, -CHO, -CH=CHCO2H, -CH=CHCO2C2H5 and -CH(OH)CH3. The analysis based on computational chemistry calculation using MNDO/d semi empirical method was done. The first step is structure optimization of crown ether followed by optimization of crown ether-metals cation complexes Mn+.[DBz16C5], where M is Li+, Na+ and Zn2+. Interactions of the crown ether and cation were discussed in term of the structure parameter of crown ether, atomic charges and energy interaction of the crown ether-metals cation. Electron donating groups increase the capability of crown ether to bind cation by means of induction effect, while electron withdrawing groups reduce the ability of crown ether to bind cation. Any substituent on the benzene in DBz...
Indonesian Journal of Chemistry, 2018
Study of substituent effect on properties of platinum(II) porphyrin had been performed using DFT ... more Study of substituent effect on properties of platinum(II) porphyrin had been performed using DFT method. The aim of the study is to investigate the effect of substituent group on the electronic and optical properties of the platinum(II) porphyrin. Geometry optimization was conducted using DFT/B3LYP/LANL2DZ to obtain molecular structure, electronic structure and energy profile. Band gap energy (Eg), the density of states (DOS), and UV-visible spectra are the semiconductor parameters to study. Computational results show that platinum(II) porphyrin and substituted platinum(II) porphyrin have properties of semiconductor based on Eg value, DOS, and UV-visible spectra. The results show that Mulliken partial charges of electron withdrawing substituents are higher than the electron donating substituents (CH3, OH, and NH2). Eg values of the complexes with respect to the substituents follow this order: NH2 < OH < NO2 < COOH < I < CH3 < Br < F < H, for DOSHOMO values, t...
Journal of molecular modeling, Jan 27, 2018
Rb(I) ion solvation in liquid ammonia has been studied by an ab initio quantum mechanical charge ... more Rb(I) ion solvation in liquid ammonia has been studied by an ab initio quantum mechanical charge field molecular dynamics simulation, and the first solvation shell structure has been analyzed using natural bond orbital. The simulation was performed for an ion and 593 ammonia molecules in a box with a length of 29.03 Å corresponding to a liquid ammonia density of 0.69 g/mL at 235.16 K. The quantum mechanical calculation was carried out for atomic interactions in the radius of 6.4 Å from the ion using LANL2DZ ECP and DZP (Dunning) basis sets for Rb(I) ion and ammonia respectively. The trajectories of the simulation were analyzed in terms of radial, angular, and coordination number distribution functions, vibration, and mean residence time (MRT). Two solvation shell regions are observed for the Rb(I)-N as well as the Rb(I)-H. The maximum distance of Rb(I)-N in the first solvation shell is in accordance with experimental data where a coordination number of 8 is favorable. A non-single c...
This work is licensed under a Creative Commons Attribution 4.0 License. You are free to copy, dis... more This work is licensed under a Creative Commons Attribution 4.0 License. You are free to copy, distribute and perform the work. You must attribute the work in the manner specified by the author or licensor.
Indonesian Journal of Chemistry, 2013
The hydration of α-pinene has been studied in the presence of Y-zeolite (Si/Al = 2.89) as a solid... more The hydration of α-pinene has been studied in the presence of Y-zeolite (Si/Al = 2.89) as a solid acid catalyst. The reaction was performed in batch reactor in isopropyl alcohol at various temperature and reaction time with magnetic stirrer. The acid catalyst hydration reaction of a-pinene yields a complex mixture of monoterpenes, alcohols and hydrocarbons. The selectivity of α-terpineol (the monocyclic alcohol) as main product was 59.20% with a conversion of 83.83% and the non alcoholic as the isomerization co-product as 30% after 60 min at 65 °C. The conversion and selectivity to α-terpineol increase significantly with in increase in temperature and reaction times.
Indonesian Journal of Chemistry, 2015
A QM/MM molecular dynamics (MD) simulation has been carried out using three-body corrected pair p... more A QM/MM molecular dynamics (MD) simulation has been carried out using three-body corrected pair potential to investigate the structural and dynamical properties of Zr4+ in dilute aqueous solution. Structural data in the form of radial distribution function, coordination number distribution, and angular distribution function were obtained. The results indicate eight water molecules coordinate to zirconium ion and have two angles of O-Zr4+-O, i.e. 72.0° and 140.0° with a Zr4+-O distance of 2.34 Å. According to these results, the hydration structure of Zr4+ ion in water was more or less well-defined square antiprismatic geometry. The dynamical properties have been characterized by the ligand’s mean residence time (MRT) and Zr4+-O stretching frequencies. The inclusion of the three-body correction was important for the description of the hydrated Zr4+ ion, and the results indicated in good agreement with experimental values.
Chiang Mai University Journal of Natural Sciences, 2021
Quantitative structure-activity relationships (QSAR) proposes a model that relates the biological... more Quantitative structure-activity relationships (QSAR) proposes a model that relates the biological activities of drugs to their chemical structures, and the interaction between the drug and its target enzyme is revealed by molecular docking research. These studies were conducted on chalcone to produce a model that could design highly potent breast anticancer MCF7 cells. The compounds were optimized using ab initio using a basis set 6-31G, then their descriptors calculated using this method. Genetic Function Algorithm (GFA) was used to select descriptors and build the model. One of the six models generated was found to be the best with internal and external squared correlation coefficient (R2) of 0.743 and 0.744, respectively, adjusted squared correlation coefficient (adjusted R2) of 0.700, Standard estimate of error (SEE) of 0.198, Fcalc/Ftable of 6.423, and Predicted residual sum of squares (PRESS) of 1.177. The QSAR equation is pIC50 = 3.869 + (1.427 x qC1) + (4. 027 x qC10) + (0.8...
Berkala Ilmiah Mipa, Jul 25, 2014
Methylation of gallic acid has been conducted by the use of dimethyl sulfate (DMS) or dimethyl ca... more Methylation of gallic acid has been conducted by the use of dimethyl sulfate (DMS) or dimethyl carbonate (DMC) as methylating agents. Methylation of gallic acid using DMS was carried out by various methods, i.e. mild condition at ambient temperature, reflux and sonication. The best method was achieved by methylation under reflux yielded 48.9% efficiency of 3,4,5trimethoxybenzoic acid. Methylation of gallic acid with DMC was performed with several variations on the type and amount of base and phase transfer catalyst (PTC). In addition, green methods sonochemistry and microwave irradiation have also been done. Unfortunately, the methylation of gallic acid failed to give 3,4,5-trimethoxybenzoic acid. Methylation of gallic acid using green reagent DMC gave high yield at mole ratio of gallic acid : DMC : K2CO3 : KI : PTC of tetrabuthyl ammonium bromide (TBAB) = 5 : 320 : 20 : 5 : 8 under reflux for 10 hours and produced 75.96% of methyl 3,4,5trimethoxybenzoate. Atom economy of gallic acid methylation method using DMC is 37.95%, which is not very different from that of DMS method (30.47%). However, the methylation method using DMC produced by products, which have the lower toxicity compared to that of methylation using DMS.
Indonesian Journal of Chemistry, 2010
In order to describe the cobalt-water interaction correctly, a new ab initio potential was develo... more In order to describe the cobalt-water interaction correctly, a new ab initio potential was developed consisting of pair interaction terms as well as three-body contributions. Within this approach, it was possible to correct for the well-known failures of pair potentials in describing solvation phenomena of such ions. A first-shell coordination number of 6 in agreement with experimental data were obtained from Monte Carlo simulations of a single cobalt (II) ion in water. The structure of hydrated ion is discussed in terms of radial density functions and coordination number, energy and angular distributions. Keywords: MC Simulations, cobalt(II), hydration, three-body correction
Indonesian Journal of Chemistry, Nov 3, 2011
Thymelaeaceae is one of Indonesia's traditional medicines. Chemical constituent has been isolated... more Thymelaeaceae is one of Indonesia's traditional medicines. Chemical constituent has been isolated from ethyl acetate extract of leaves of mahkota dewa. Sample was extracted with methanol, concentrated then extracted by n-hexane, chloroform and ethyl acetate. The ethyl acetate extract was separated and fractionated by column chromatography. The first fraction was purified by TLC preparative and recrystalization. Compound was isolated as red-brown spherical crystal in 8 mg (m.p. 129-131°C). Its spot gave dark fluoroscence at TLC plate (UV 366 ) with Rf of 0.3 at TLC chromatogram with eluent of n-hexane : ethyl acetate (7:3); 0.6 with n-hexane : ethyl acetate (1:1); 0.9 with -hexane : ethyl acetate (4:6). This compound was dissolved in methanol. Compound was identified by UV, IR, 1 H NMR, 13 C NMR and NMR 2 dimension (HMQC, COSY, HMBC and DEPT-135) spectroscopic as 2,6,4'-trihydroxy-4-methoxybenzophenon. This compound as well as the ethyl acetate extract showed antioxidant activity on DPPH with IC 50 was 10.57 and 101.06 μg/mL, respectively. This compound showed strong antioxidant activity on DPPH, almost to the standard antioxidant activity of quercetin (IC 50 of 2.93 μg/mL)
Indonesian Journal of Chemistry, Jun 22, 2010
6 -anhidroeritromisin-A is a new derivative of erythromycin which is synthesized through biosyn... more 6 -anhidroeritromisin-A is a new derivative of erythromycin which is synthesized through biosynthetic engineering technique. The molecular docking in rRNA 23S Deinoccocus radiodurans are accomplished to determine the model and strength of binding to the target macromolecule. The molecular docking of erythromycin-A and 6-deoksieritromisin-A to the same macromolecule is used as a control. The docking result of the 6 anhidroeritromisin-A shows that it occupies the same cavity as of the experimental erythromycin-A in the same macromolecule. The binding position of 6 -anhidroeritromisin-A is not exactly same as erythromycin-A and 6deoksieritromisin-A due to the presence of 6 unsaturated double bond. However the hydroxyl group(OH) at C-6 does not have an apparent effect on the binding model to rRNA23S D. radiodurans.
JC-T (Journal Cis-Trans): Jurnal Kimia dan Terapannya
Model Quantitative structure-activity relationship (QSAR) dari turunan kumarin 3-tersubstitusi 4-... more Model Quantitative structure-activity relationship (QSAR) dari turunan kumarin 3-tersubstitusi 4-anilino terhadap aktivitasnya sebagai anti-kanker pankreas telah berhasil dibuat dan divalidasi. Struktur molekul turunan kumarin 3-tersubstitusi 4-anilino dan aktivitas biologisnya yang digunakan disitasi dari penelitian yang telah dilakukan oleh Luo dkk. Setiap molekul turunan kumarin 3tersubstitusi 4-anilino yang digunakan dioptimasi menggunakan metode kalkulasi DFT/BPV86 6-31G. Model analisis QSAR dibentuk menggunakan metode Multi Linear Regression (MLR) dan model terbaik yang didapatkan adalah: Log IC50 = 4,02 + (-7,126 x qC7) + (-5,709 x qC8) + (6,845 x qC18), n = 18; r 2 train = 0.701; r 2 test = 0.849, Fkal/Ftab = 3,269; SEE = 0.230. Dari model tersebut, nilai Log IC50 terhadap kanker pankreas dari turunan kumarin 3-tersubstitusi 4anilino dapat diperkecil dengan memodifikasi nilai qC7, qC8, dan qC18 menyesuaikan koefisien setiap diskriptor tersebut.
Eter mahkota dikenal sebagai salah satu senyawa pengikat secara spesifik suatu ion logam. Pada ba... more Eter mahkota dikenal sebagai salah satu senyawa pengikat secara spesifik suatu ion logam. Pada banyak kasus, selektifitas eter mahkota mengikuti prinsip kesesuaian antara jejari ion dengan jejari kavitas eter mahkota (kesesuaian struktur). Keberadaan substituen pada eter mahkota dapat mempengaruhi kemudahan eter mahkota dalam menata ulang konformasinya ketika berinteraksi dengan ion logam. Penelitian ini bertujuan untuk mempelajari pengaruh substituen pada struktur senyawa eter mahkota dibenzo-18-mahkota-6 (DBz18C6), dibenzo-16-mahkota-5 (DBz16C5) dan benzo-15-mahkota-5 (Bz15C5) dan interaksi senyawa eter mahkota tersebut dengan kation logam. Analisis data didasarkan pada hasil perhitungan kimia komputasi dengan metode semi empiris MNDO/d. Langkah awal adalah penentuan struktur teroptimasi dari semua eter mahkota. Langkah selanjutnya adalah memasukkan kation logam Li+, Na+ dan Zn2+ untuk berinteraksi dengan eter mahkota. Data yang akan diperoleh dari perhitungan semiempiris adalah p...
Indonesian Journal of Chemistry, 2021
Potential energy curves (PECs) and energy profiles of atomic O attack on coronene as a model for ... more Potential energy curves (PECs) and energy profiles of atomic O attack on coronene as a model for graphene/graphitic surface and interstellar reaction surface have been computed at the unrestricted B3LYP/cc-pVDZ level of theory to elaborate on atomic O attack mechanism and chemisorption on coronene. The PECs were generated by scanning the O atom distance to the closest carbon atom on "top" and "bridge" positions in the coronene, while fully relaxed geometries in the triplet state were investigated to gain the energy profile. We found that the most favorable geometry as the final product was the chemically bound O on the "bridge" site in the singlet state with an interaction energy of –29.2 kcal/mol. We recommended a plausible mechanism of atomic O attack and chemisorption reaction on coronene or generally graphitic surface starting from the non-interacting O atom and coronene systems into the chemically bound O atom on coronene.
Chiang Mai University Journal of Natural Sciences, 2020
In this study, we make QSAR models from 29 of BA derivatives’ HIV maturation inhibition activitie... more In this study, we make QSAR models from 29 of BA derivatives’ HIV maturation inhibition activities against their 3D descriptors. The best model involve 5 descriptors as follows: 1/log EC50 = -462.275 + (69.213 × TDB6u) + (723.745 × TDB6e) + (-0.576 × FPSA-3) + (0.849 × RDF140u) + (0.302 × RDF80e) r2 training = 0.7918; Q2 test = 0.9644; r2test = 0.9798; and r2m-test = 0.9445 TDB6u and TDB6e are the 3d topological distance-based autocorrelation-lag 6 /unweighted and weighted by Sanderson electronegati-vities, respectively. FPSA-3 is the value of charge weighted partial positive surface area / total molecular surface area. RDF140u is radial distribution function-140 / unweighted. RDF80e is radial distribution function-080/weighted by relative Sanderson electronegativities. The QSAR model was then used to design and predict some of the new BA derivatives’ HIV maturation activities. The best predicted compound had pEC50 value of -0.838 and EC50 value of 0.064 nM with the chemical IUPAC n...
Journal of Computational Chemistry, 2020
The impact of solvent flexibility and electron correlation on the simulation results of Cu2+ in l... more The impact of solvent flexibility and electron correlation on the simulation results of Cu2+ in liquid ammonia has been investigated via an ab initio quantum mechanical charge field molecular dynamics (QMCF MD) simulation approach. To achieve this, three different simulation systems were considered in this study, namely Cu2+ in rigid and flexible ammonia at Hartree-Fock (HF) level of theory, as well as resolution of identity second order Møller-Plesset (MP2) perturbation theory in the rigid body case. In all cases, a stable octahedral [Cu(NH3 )6 ]2+ complex subject to dynamic Jahn-Teller distortions without the occurrence of ligand exchange was observed. The Cu2+ - NH3 distance in the first shell agrees well with the experimental and other theoretical data. In all three cases, the structural data shows that the rigid-body ammonia model in conjunction with the HF level of theory provides accurate data for the first solvation shell, while at the same time, the computational demand and thus the achievable simulation time are much more beneficial. The vibrational analysis of the Cu2+ - NH3 interaction yields similar force constants in the three investigated systems indicating that there is no distinct difference on the dynamical properties of the first solvation shell. In addition to the QMCF MD simulations, a number of natural bond orbital (NBO) analyses were carried out, confirming the strong electrostatic character of the Cu2+ - NH3 interaction.
Asian Journal of Chemistry, 2018
Synthesis of new asymmetrical curcumin analogue of 1-(3,4-dimethoxy-phenyl)-5-(4-hydroxy-3-methox... more Synthesis of new asymmetrical curcumin analogue of 1-(3,4-dimethoxy-phenyl)-5-(4-hydroxy-3-methoxy-phenyl)-penta-1,4-dien-3-one via condensation reaction between vanillinacetone and veratraldehyde in ethanol has been performed. The in vitro anti-inflammatory activities of the synthesized compounds showed excellent anti-inflammatory activity. In vitro anti-inammatory activity by using inhibition of albumin denaturation technique compared to standard dichlorofenac. Molecular docking studies were performed, where docking of the compound into 6COX active site suggested that it could exert its anti-inflammatory potential by cyclooxygenase inhibition.
Indonesian Journal of Chemistry, 2010
Determination of solvation structure of Ni2+ ion in water has been achieved using Monte Carlo met... more Determination of solvation structure of Ni2+ ion in water has been achieved using Monte Carlo method using canonic assemble (NVT constant). Simulation of a Ni2+ ion in 215 H2O molecules has been done under NVT condition (298.15 K). The results showed that number of H2O molecules surround Ni2+ ion were 8 molecules in first shell and 17 molecules in second shell, interaction energy of Ni2+-H2O in first shell was -68.7 kcal/mol and in second shell was -9.8 kcal/mol, and there were two angles of O-Ni2+-O, i.e. 74o and 142o. According to those results, the solvation structure of Ni2+ ion in water was cubic antisymetric. Keywords: Water simulation, Monte Carlo simulation
Indonesian Journal of Chemistry, 2010
The effect of substituent on dibenzo-16-crown-5 (DBz16C5) and interaction between these crown eth... more The effect of substituent on dibenzo-16-crown-5 (DBz16C5) and interaction between these crown ether with metal cations was evaluated using computational chemistry calculations. Substituens where are connected to the benzene ring on the DBz16C5 are -COOH, -Br, -COOC2H5, -CHO, -CH=CHCO2H, -CH=CHCO2C2H5 and -CH(OH)CH3. The analysis based on computational chemistry calculation using MNDO/d semi empirical method was done. The first step is structure optimization of crown ether followed by optimization of crown ether-metals cation complexes Mn+.[DBz16C5], where M is Li+, Na+ and Zn2+. Interactions of the crown ether and cation were discussed in term of the structure parameter of crown ether, atomic charges and energy interaction of the crown ether-metals cation. Electron donating groups increase the capability of crown ether to bind cation by means of induction effect, while electron withdrawing groups reduce the ability of crown ether to bind cation. Any substituent on the benzene in DBz...
Indonesian Journal of Chemistry, 2018
Study of substituent effect on properties of platinum(II) porphyrin had been performed using DFT ... more Study of substituent effect on properties of platinum(II) porphyrin had been performed using DFT method. The aim of the study is to investigate the effect of substituent group on the electronic and optical properties of the platinum(II) porphyrin. Geometry optimization was conducted using DFT/B3LYP/LANL2DZ to obtain molecular structure, electronic structure and energy profile. Band gap energy (Eg), the density of states (DOS), and UV-visible spectra are the semiconductor parameters to study. Computational results show that platinum(II) porphyrin and substituted platinum(II) porphyrin have properties of semiconductor based on Eg value, DOS, and UV-visible spectra. The results show that Mulliken partial charges of electron withdrawing substituents are higher than the electron donating substituents (CH3, OH, and NH2). Eg values of the complexes with respect to the substituents follow this order: NH2 < OH < NO2 < COOH < I < CH3 < Br < F < H, for DOSHOMO values, t...
Journal of molecular modeling, Jan 27, 2018
Rb(I) ion solvation in liquid ammonia has been studied by an ab initio quantum mechanical charge ... more Rb(I) ion solvation in liquid ammonia has been studied by an ab initio quantum mechanical charge field molecular dynamics simulation, and the first solvation shell structure has been analyzed using natural bond orbital. The simulation was performed for an ion and 593 ammonia molecules in a box with a length of 29.03 Å corresponding to a liquid ammonia density of 0.69 g/mL at 235.16 K. The quantum mechanical calculation was carried out for atomic interactions in the radius of 6.4 Å from the ion using LANL2DZ ECP and DZP (Dunning) basis sets for Rb(I) ion and ammonia respectively. The trajectories of the simulation were analyzed in terms of radial, angular, and coordination number distribution functions, vibration, and mean residence time (MRT). Two solvation shell regions are observed for the Rb(I)-N as well as the Rb(I)-H. The maximum distance of Rb(I)-N in the first solvation shell is in accordance with experimental data where a coordination number of 8 is favorable. A non-single c...
This work is licensed under a Creative Commons Attribution 4.0 License. You are free to copy, dis... more This work is licensed under a Creative Commons Attribution 4.0 License. You are free to copy, distribute and perform the work. You must attribute the work in the manner specified by the author or licensor.
Indonesian Journal of Chemistry, 2013
The hydration of α-pinene has been studied in the presence of Y-zeolite (Si/Al = 2.89) as a solid... more The hydration of α-pinene has been studied in the presence of Y-zeolite (Si/Al = 2.89) as a solid acid catalyst. The reaction was performed in batch reactor in isopropyl alcohol at various temperature and reaction time with magnetic stirrer. The acid catalyst hydration reaction of a-pinene yields a complex mixture of monoterpenes, alcohols and hydrocarbons. The selectivity of α-terpineol (the monocyclic alcohol) as main product was 59.20% with a conversion of 83.83% and the non alcoholic as the isomerization co-product as 30% after 60 min at 65 °C. The conversion and selectivity to α-terpineol increase significantly with in increase in temperature and reaction times.
Indonesian Journal of Chemistry, 2015
A QM/MM molecular dynamics (MD) simulation has been carried out using three-body corrected pair p... more A QM/MM molecular dynamics (MD) simulation has been carried out using three-body corrected pair potential to investigate the structural and dynamical properties of Zr4+ in dilute aqueous solution. Structural data in the form of radial distribution function, coordination number distribution, and angular distribution function were obtained. The results indicate eight water molecules coordinate to zirconium ion and have two angles of O-Zr4+-O, i.e. 72.0° and 140.0° with a Zr4+-O distance of 2.34 Å. According to these results, the hydration structure of Zr4+ ion in water was more or less well-defined square antiprismatic geometry. The dynamical properties have been characterized by the ligand’s mean residence time (MRT) and Zr4+-O stretching frequencies. The inclusion of the three-body correction was important for the description of the hydrated Zr4+ ion, and the results indicated in good agreement with experimental values.
Chiang Mai University Journal of Natural Sciences, 2021
Quantitative structure-activity relationships (QSAR) proposes a model that relates the biological... more Quantitative structure-activity relationships (QSAR) proposes a model that relates the biological activities of drugs to their chemical structures, and the interaction between the drug and its target enzyme is revealed by molecular docking research. These studies were conducted on chalcone to produce a model that could design highly potent breast anticancer MCF7 cells. The compounds were optimized using ab initio using a basis set 6-31G, then their descriptors calculated using this method. Genetic Function Algorithm (GFA) was used to select descriptors and build the model. One of the six models generated was found to be the best with internal and external squared correlation coefficient (R2) of 0.743 and 0.744, respectively, adjusted squared correlation coefficient (adjusted R2) of 0.700, Standard estimate of error (SEE) of 0.198, Fcalc/Ftable of 6.423, and Predicted residual sum of squares (PRESS) of 1.177. The QSAR equation is pIC50 = 3.869 + (1.427 x qC1) + (4. 027 x qC10) + (0.8...
Berkala Ilmiah Mipa, Jul 25, 2014
Methylation of gallic acid has been conducted by the use of dimethyl sulfate (DMS) or dimethyl ca... more Methylation of gallic acid has been conducted by the use of dimethyl sulfate (DMS) or dimethyl carbonate (DMC) as methylating agents. Methylation of gallic acid using DMS was carried out by various methods, i.e. mild condition at ambient temperature, reflux and sonication. The best method was achieved by methylation under reflux yielded 48.9% efficiency of 3,4,5trimethoxybenzoic acid. Methylation of gallic acid with DMC was performed with several variations on the type and amount of base and phase transfer catalyst (PTC). In addition, green methods sonochemistry and microwave irradiation have also been done. Unfortunately, the methylation of gallic acid failed to give 3,4,5-trimethoxybenzoic acid. Methylation of gallic acid using green reagent DMC gave high yield at mole ratio of gallic acid : DMC : K2CO3 : KI : PTC of tetrabuthyl ammonium bromide (TBAB) = 5 : 320 : 20 : 5 : 8 under reflux for 10 hours and produced 75.96% of methyl 3,4,5trimethoxybenzoate. Atom economy of gallic acid methylation method using DMC is 37.95%, which is not very different from that of DMS method (30.47%). However, the methylation method using DMC produced by products, which have the lower toxicity compared to that of methylation using DMS.
Indonesian Journal of Chemistry, 2010
In order to describe the cobalt-water interaction correctly, a new ab initio potential was develo... more In order to describe the cobalt-water interaction correctly, a new ab initio potential was developed consisting of pair interaction terms as well as three-body contributions. Within this approach, it was possible to correct for the well-known failures of pair potentials in describing solvation phenomena of such ions. A first-shell coordination number of 6 in agreement with experimental data were obtained from Monte Carlo simulations of a single cobalt (II) ion in water. The structure of hydrated ion is discussed in terms of radial density functions and coordination number, energy and angular distributions. Keywords: MC Simulations, cobalt(II), hydration, three-body correction
Indonesian Journal of Chemistry, Nov 3, 2011
Thymelaeaceae is one of Indonesia's traditional medicines. Chemical constituent has been isolated... more Thymelaeaceae is one of Indonesia's traditional medicines. Chemical constituent has been isolated from ethyl acetate extract of leaves of mahkota dewa. Sample was extracted with methanol, concentrated then extracted by n-hexane, chloroform and ethyl acetate. The ethyl acetate extract was separated and fractionated by column chromatography. The first fraction was purified by TLC preparative and recrystalization. Compound was isolated as red-brown spherical crystal in 8 mg (m.p. 129-131°C). Its spot gave dark fluoroscence at TLC plate (UV 366 ) with Rf of 0.3 at TLC chromatogram with eluent of n-hexane : ethyl acetate (7:3); 0.6 with n-hexane : ethyl acetate (1:1); 0.9 with -hexane : ethyl acetate (4:6). This compound was dissolved in methanol. Compound was identified by UV, IR, 1 H NMR, 13 C NMR and NMR 2 dimension (HMQC, COSY, HMBC and DEPT-135) spectroscopic as 2,6,4'-trihydroxy-4-methoxybenzophenon. This compound as well as the ethyl acetate extract showed antioxidant activity on DPPH with IC 50 was 10.57 and 101.06 μg/mL, respectively. This compound showed strong antioxidant activity on DPPH, almost to the standard antioxidant activity of quercetin (IC 50 of 2.93 μg/mL)
Indonesian Journal of Chemistry, Jun 22, 2010
6 -anhidroeritromisin-A is a new derivative of erythromycin which is synthesized through biosyn... more 6 -anhidroeritromisin-A is a new derivative of erythromycin which is synthesized through biosynthetic engineering technique. The molecular docking in rRNA 23S Deinoccocus radiodurans are accomplished to determine the model and strength of binding to the target macromolecule. The molecular docking of erythromycin-A and 6-deoksieritromisin-A to the same macromolecule is used as a control. The docking result of the 6 anhidroeritromisin-A shows that it occupies the same cavity as of the experimental erythromycin-A in the same macromolecule. The binding position of 6 -anhidroeritromisin-A is not exactly same as erythromycin-A and 6deoksieritromisin-A due to the presence of 6 unsaturated double bond. However the hydroxyl group(OH) at C-6 does not have an apparent effect on the binding model to rRNA23S D. radiodurans.