Bangladesh Institute of Computational Chemistry and Biochemistry

Green, Bangladesh

Bangladesh Institute of Computational Chemistry and Biochemistry

Green, Bangladesh

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Hoque M.M.,Bangladesh University of Engineering and Technology | Hoque M.M.,Bangladesh Institute of Computational Chemistry and Biochemistry | Halim M.A.,Bangladesh Institute of Computational Chemistry and Biochemistry | Sarwar M.G.,Scripps Research Institute | Khan M.W.,Bangladesh University of Engineering and Technology
Journal of Physical Organic Chemistry | Year: 2015

This study reports a facial regio-selective synthesis of 2-alkyl-N-ethanoyl indoles from substituted-N-ethanoyl anilines employing palladium (II) chloride, which acts as a cyclization catalyst. The mechanistic trait of palladium-based cyclization is also explored by employing density functional theory. In a two-step mechanism, the palladium, which attaches to the ethylene carbons, promotes the proton transfer and cyclization. The gas-phase barrier height of the first transition state is 37kcal/mol, indicating the rate-determining step of this reaction. Incorporating acetonitrile through the solvation model on density solvation model reduces the barrier height to 31kcal/mol. In the presence of solvent, the electron-releasing (-CH3) group has a greater influence on the reduction of the barrier height compared with the electron-withdrawing group (-Cl). These results further confirm that solvent plays an important role on palladium-catalyzed proton transfer and cyclization. For unveiling structural, spectroscopic, and photophysical properties, experimental and computational studies are also performed. Thermodynamic analysis discloses that these reactions are exothermic. The highest occupied molecular orbital-lowest unoccupied molecular orbital gap (4.9-5.0eV) confirms that these compounds are more chemically reactive than indole. The calculated UV-Vis spectra by time-dependent density functional theory exhibit strong peaks at 290, 246, and 232nm, in good agreement with the experimental results. Moreover, experimental and computed 1H and 13C NMR chemical shifts of the indole derivatives are well correlated. Copyright © 2015 John Wiley & Sons, Ltd.


Enamullah M.,Jahangirnagar University | Islam M.K.,Jahangirnagar University | Halim M.A.,Bangladesh Institute of Computational Chemistry and Biochemistry | Janiak C.,Heinrich Heine University Düsseldorf
Journal of Molecular Structure | Year: 2015

Abstract The titled Rh(η4-cod)-enantiopure aminocarboxylate complexes, [Rh(η4-cod) (AA)] {cod = cycloocta-1,5-diene; AA = L-prolinato (1) and D-4-hydroxy-phenylglycinato (2)}, are synthesized from the reaction of enantiopure aminocarboxylate with [Rh(η4-cod) (acetate)]2. Polarimetric measurements confirm the enantiopurity or very similar enantiomeric excess of the complexes in chloroform. Electronic spectra in different solvents exhibit a negative solvatochromism in the solvents of increasing polarity or acceptor number. DSC analyses show an exothermic peak at 269 C (ΔH = -72.42 kJ M-1) for 2, corresponding to an irreversible phase transformation. Cyclic voltammograms reveal a quasi-reversible one electron transfer for [Rh(η4-cod) (l-prolinate)]/[Rh(η4-cod) (l-prolinate)]+ couple in acetonitrile. Electronic spectra calculated by TDDFT reveal the bands at relatively lower energy (>230 nm) due to combined d-d, MLCT and LLCT transitions, while the bands at higher energy only for LLCT, which are very similar to the experimental results. X-ray structure demonstrates a distorted square-planar geometry with N,O-chelation of the l-prolinate ligand to the Rh(η4-cod)-fragment in 1. The crystal packing is evidenced by charge-assisted intermolecular N-H···O and C-H···O interactions to the non-coordinated carboxylate oxygen atom. Hydrogen bonding leads to the formation of supramolecular chains along the a direction of the unit cell. The interchain packing is governed mostly by van-der-Waals forces and reminiscent of a 'herring-bone' packing. © 2015 Elsevier B.V.


Enamullah M.,Jahangirnagar University | Quddus M.A.,Jahangirnagar University | Halim M.A.,Bangladesh Institute of Computational Chemistry and Biochemistry | Islam M.K.,Jahangirnagar University | And 2 more authors.
Inorganica Chimica Acta | Year: 2014

The Schiff bases N-2-(4/6-methyl-pyridyl)salicylaldimine (HL) which are geometric isomers differing in the para- or ortho-position of the methyl group to the pyridyl nitrogen atom react with zinc(II) acetate to give the bis-ligand chelate complexes bis[N-2-(4/6-methyl-pyridyl)salicylaldiminato-κ2N,O]zinc(II) {4-methyl or para (1), 6-methyl or ortho (2)}. The zinc complexes feature an N2O2 chromophore from the two salicylaldiminato moieties with one or two additional weak Zn-N(pyridyl) contacts to give a 4 + 1 or 4 + 2 coordination in 1 or 2, respectively. The difference in metal coordination is traced to competitive alternative C-H···π interactions of the non-coordinated methyl-pyridyl ring in compound 1 which are absent in 2. Instead, the weakly zinc-coordinated methyl-pyridyl rings in 1 and 2 are at the same time engaged in π···π interactions. The latter compound features two C-H···O contacts. DFT calculation produces the similar structural features for 1 and 2. The excited state properties calculated by TDDFT reveal that the complexes have distinctive ligand-ligand (LL) and metal-to-ligand (ML) charge transfer bands. Hirshfeld surface analysis also discloses similar C-H···π and C-H···O interactions in crystals 1 and 2, respectively. © 2014 Elsevier B.V. All Rights Reserved.


Elius Hossain M.,University of Dhaka | Mahmudul Hasan M.,University of Dhaka | Halim M.E.,University of Dhaka | Ehsan M.Q.,University of Dhaka | Halim M.A.,Bangladesh Institute of Computational Chemistry and Biochemistry
Spectrochimica Acta - Part A: Molecular and Biomolecular Spectroscopy | Year: 2015

Some transition metal complexes of phenylalanine of general formula [M(C9H10NO2)2]; where M = Mn(II), Co(II), Ni(II), Cu(II) and Zn(II) are prepared in aqueous medium and characterized by spectroscopic, thermo-gravimetric (TG) and magnetic susceptibility analysis. Density functional theory (DFT) has been employed calculating the equilibrium geometries and vibrational frequencies of those complexes at B3LYP level of theory using 6-31G(d) and SDD basis sets. In addition, frontier molecular orbital and time-dependent density functional theory (TD-DFT) calculations are performed with CAM-B3LYP/6-31+G(d,p) and B3LYP/SDD level of theories. Thermo-gravimetric analysis confirms the composition of the complexes by comparing the experimental and calculated data for C, H, N and metals. Experimental and computed IR results predict a significant change in vibrational frequencies of metal-phenylalanine complexes compared to free ligand. DFT calculation confirms that Mn, Co, Ni and Cu complexes form square planar structure whereas Zn adopts distorted tetrahedral geometry. The metal-oxygen bonds in the optimized geometry of all complexes are shorter compared to the metal-nitrogen bonds which is consistent with a previous study. Cation-binding energy, enthalpy and Gibbs free energy indicates that these complexes are thermodynamically stable. UV-vis and TD-DFT studies reveal that these complexes demonstrate representative metal-to-ligand charge transfer (MLCT) and d-d transitions bands. TG analysis and IR spectra of the metal complexes strongly support the absence of water in crystallization. Magnetic susceptibility data of the complexes exhibits that all except Zn(II) complex are high spin paramagnetic. © 2014 Elsevier B.V. All rights reserved.


Abu Saleh M.,Bangladesh Institute of Computational Chemistry and Biochemistry | Abu Saleh M.,Jahangirnagar University | Solayman M.,Bangladesh Institute of Computational Chemistry and Biochemistry | Solayman M.,Jahangirnagar University | And 5 more authors.
BioMed Research International | Year: 2016

In this study, mitoxantrone and its halogenated derivatives have been designed by density functional theory (DFT) to explore their structural and thermodynamical properties. The performance of these drugs was also evaluated to inhibit DNA topoisomerase type IIα (TOP2A) by molecular docking calculation. Noncovalent interactions play significant role in improving the performance of halogenated drugs. The combined quantum and molecular mechanics calculations revealed that CF3 containing drug shows better preference in inhibiting the TOP2A compared to other modified drugs. Copyright © 2016 Md. Abu Saleh et al.


PubMed | Bangladesh Institute of Computational Chemistry and Biochemistry, Jahangirnagar University, Scripps Research Institute, University Claude Bernard Lyon 1 and Jubail University College
Type: | Journal: BioMed research international | Year: 2016

In this study, mitoxantrone and its halogenated derivatives have been designed by density functional theory (DFT) to explore their structural and thermodynamical properties. The performance of these drugs was also evaluated to inhibit DNA topoisomerase type II (TOP2A) by molecular docking calculation. Noncovalent interactions play significant role in improving the performance of halogenated drugs. The combined quantum and molecular mechanics calculations revealed that CF3 containing drug shows better preference in inhibiting the TOP2A compared to other modified drugs.

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