Displaying publications 21 - 40 of 352 in total

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  1. Chidan Kumar CS, Panicker CY, Fun HK, Mary YS, Harikumar B, Chandraju S, et al.
    PMID: 24607470 DOI: 10.1016/j.saa.2014.01.145
    2-(4-Chlorophenyl)-2-oxoethyl 3-nitrobenzoate is synthesized by reacting 4-chlorophenacyl bromide with 3-nitrobenzoic acid using a slight excess of potassium or sodium carbonate in DMF medium at room temperature. The structure of the compound was confirmed by IR and single-crystal X-ray diffraction studies. FT-IR spectrum of 2-(4-chlorophenyl)-2-oxoethyl 3-nitrobenzoate was recorded and analyzed. The crystal structure is also described. The vibrational wavenumbers were computed using HF and DFT methods and are assigned with the help of potential energy distribution method. The first hyperpolarizability and infrared intensities are also reported. The geometrical parameters of the title compound obtained from XRD studies are in agreement with the calculated (DFT) values. The stability of the molecule arising from hyper-conjugative interaction and charge delocalization has been analyzed using NBO analysis. The HOMO and LUMO analysis are used to determine the charge transfer within the molecule. MEP was performed by the DFT method.
    Matched MeSH terms: Models, Molecular
  2. Naqeebullah, Farina Y, Chan KM, Mun LK, Rajab NF, Ooi TC
    Molecules, 2013 Jul 22;18(7):8696-711.
    PMID: 23881054 DOI: 10.3390/molecules18078696
    Three diorganotin(IV) complexes of the general formula R2Sn[RcC(O)N(RN)O] (Rc = aryl, RN = Alkyl) have been synthesized by refluxing in toluene the corresponding diorganotin(IV) oxides with the free ligand N-methyl p-fluorobenzohydroxamic acid, using a Dean and Stark water separator. The ligand was derived from the reaction of the corresponding p-fluorobenzoyl chloride and N-methylhydroxylamine hydrochloride in the presence of sodium hydrogen carbonate. The isolated free ligand and its respective diorganotin compounds have been characterized by elemental analysis, IR and 1H-, 13C-, 119Sn-NMR spectroscopies. The crystal structures of the diorganotin complexes have been confirmed by single crystal X-ray diffraction methods. The investigations carried out on the diorganotin(IV) complexes of N-methyl p-fluorobenzohydroxamic acid confirmed a 1:2 stoichiometry. The complex formation took place through the O,O-coordination via the carbonyl oxygen and subsequent deprotonated hydroxyl group to the tin atom. The crystal structures of three diorganotin complexes were determined and were found to adopt six coordination geometries at the tin centre with coordination to two ligand moieties.
    Matched MeSH terms: Models, Molecular
  3. Hamzah R, Bakar MA, Khairuddean M, Mohammed IA, Adnan R
    Molecules, 2012 Sep 12;17(9):10974-93.
    PMID: 22971583 DOI: 10.3390/molecules170910974
    A structural study of epoxidized natural rubber (ENR-50) and its cyclic dithiocarbonate derivative was carried out using NMR spectroscopy techniques. The overlapping (1)H-NMR signals of ENR-50 at δ 1.56, 1.68-1.70, 2.06, 2.15-2.17 ppm were successfully assigned. In this work, the C=S and quaternary carbon of cyclic dithiocarbonate. All other (1)H- and (13)C-NMR chemical shifts of the derivative remain unchanged with respect to the ENR-50.
    Matched MeSH terms: Models, Molecular
  4. Das Arulsamy A, Kregar Z, Eleršič K, Modic M, Subramani US
    Phys Chem Chem Phys, 2011 Sep 7;13(33):15175-81.
    PMID: 21776515 DOI: 10.1039/c1cp20138g
    Hydrogen produced from the photocatalytic splitting of water is one of the reliable alternatives to replace the polluting fossil and the radioactive nuclear fuels. Here, we provide unequivocal evidence for the existence of blue- and red-shifting O-H covalent bonds within a single water molecule adsorbed on the MgO surface as a result of asymmetric displacement polarizabilities. The adsorbed H-O-H on MgO gives rise to one weaker H-O bond, while the other O-H covalent bond from the same adsorbed water molecule compensates this effect with a stronger bond. The weaker bond (nearest to the surface), the interlayer tunneling electrons and the silver substrate are shown to be the causes for the smallest dissociative activation energy on the MgO monolayer. The origin that is responsible to initiate the splitting mechanism is proven to be due to the changes in the polarizability of an adsorbed water molecule, which are further supported by the temperature-dependent static dielectric constant measurements for water below the first-order electronic-phase transition temperature.
    Matched MeSH terms: Models, Molecular
  5. Raj SS, Fun HK, Zhao PS, Jian FF, Lu LD, Yang XJ, et al.
    Acta Crystallogr C, 2000 Jul;56 ( Pt 7):742-3.
    PMID: 10935066
    Matched MeSH terms: Models, Molecular
  6. Ng SW, Shanmuga Sundara Raj S, Fun HK, Razak IA, Hook JM
    Acta Crystallogr C, 2000 Aug;56 ( Pt 8):966-8.
    PMID: 10944291
    catena-Poly[dicyclohexylammonium [tributyltin-mu-(4-oxo-4H-pyran-2,6-dicarboxylato-O(2):O( 6))]], (C(12)H(24)N)[Sn(C(7)H(2)O(6))(C(4)H(9))(3)], consists of 4-oxo-4H-pyran-2,6-dicarboxylato groups that axially link adjacent tributyltin units into a linear polyanionic chain. The ammonium counter-ions surround the chain, and each cation forms a pair of hydrogen bonds to the double-bond carbonyl O atoms of the same dianionic group. The chain propagates in a zigzag manner along the c axis of the monoclinic cell. In catena-poly[methyl(phenyl)ammonium [tributyltin-mu-(pyridine-2,6-dicarboxylato-O(2):O(6))]], (C(7)H(10)N)[Sn(C(7)H(3)NO(4))(C(4)H(9))(3)], the pyridine-2, 6-dicarboxylato groups also link the tributyltin groups into a chain, but the hydrogen-bonded chain propagates linearly on the ac face of the monoclinic cell.
    Matched MeSH terms: Models, Molecular
  7. Hendrickson WA, Ward KB
    Biochem Biophys Res Commun, 1975 Oct 27;66(4):1349-56.
    PMID: 5
    Matched MeSH terms: Models, Molecular
  8. Nakamukai S, Ise Y, Ohtsuka S, Okada S, Matsunaga S
    Biosci Biotechnol Biochem, 2019 Nov;83(11):1985-1988.
    PMID: 31250707 DOI: 10.1080/09168451.2019.1630258
    N6-Isopentenyladenosine (i6A) was isolated from a marine sponge Oceanapia sp. as the major cytotoxic constituent along with N6-isopentenyladenosine 5'-monophosphate (i6AP) which was inactive. The structures of i6A and i6AP were assigned by a combination of the analysis of NMR spectroscopy and mass spectrometry. This is the first isolation of i6A and i6AP from a marine sponge.
    Matched MeSH terms: Models, Molecular
  9. Mazlan SNHS, Ali MSM, Rahman RNZRA, Sabri S, Jonet MA, Leow TC
    Int J Biol Macromol, 2018 Nov;119:1188-1194.
    PMID: 30102982 DOI: 10.1016/j.ijbiomac.2018.08.022
    GDSL esterase J15 (EstJ15) is a member of Family II of lipolytic enzyme. The enzyme was further classified in subgroup SGNH hydrolase due to the presence of highly conserve motif, Ser-Gly-Asn-His in four conserved blocks I, II, III, and V, respectively. X-ray quality crystal of EstJ15 was obtained from optimized formulation containing 0.10 M ammonium sulphate, 0.15 M sodium cacodylate trihydrate pH 6.5, and 20% PEG 8000. The crystal structure of EstJ15 was solved at 1.38 Å with one molecule per asymmetric unit. The structure exhibits α/β hydrolase fold and shared low amino acid sequence identity of 23% with the passenger domain of the autotransporter EstA of Pseudomonas aeruginosa. The active site is located at the centre of the structure, formed a narrow tunnel that hinder long substrates to be catalysed which was proven by the protein-ligand docking analysis. This study facilitates the understanding of high substrate specificity of EstJ15 and provide insights on its catalytic mechanism.
    Matched MeSH terms: Models, Molecular
  10. Tabandeh M, Goh EW, Salman AA, Heidelberg T, Duali Hussen RS
    Carbohydr Res, 2018 Nov;469:14-22.
    PMID: 30196011 DOI: 10.1016/j.carres.2018.08.016
    Two azide-terminated oligoethylene oxide spacered glycolipids have been synthesized, and their assembly behavior has been studied in comparison to the corresponding base surfactants. The results suggest potential of the Guerbet lactoside-based compound for targeted drug delivery, while a coiling of the ethylene oxide linker disfavors the application of the glucoside.
    Matched MeSH terms: Models, Molecular
  11. Pantong W, Pederick JL, Maenpuen S, Tinikul R, Jayapalan JJ, Jovcevski B, et al.
    Protein Sci, 2023 Jun;32(6):e4654.
    PMID: 37165541 DOI: 10.1002/pro.4654
    Methylenetetrahydrofolate reductase (MTHFR) is a key metabolic enzyme in colonization and virulence of Neisseria meningitidis, a causative agent of meningococcal diseases. Here, the biochemical and structural properties of MTHFR from a virulent strain of N. meningitidis serogroup B (NmMTHFR) were characterized. Unlike other orthologs, NmMTHFR functions as a unique homohexamer, composed of three homo-dimerization partners, as shown in our 2.7 Å resolution crystal structure. Six active sites were formed solely within monomers and located away from the oligomerization interfaces. Flavin adenine dinucleotide cofactor formed hydrogen bonds with conserved sidechains, positioning its isoalloxazine ring adjacent to the overlapping binding sites of nicotinamide adenine dinucleotide (NADH) coenzyme and CH2 -H4 folate substrate. NmMTHFR utilized NADH (Km  = 44 μM) as an electron donor in the NAD(P)H-CH2 -H4 folate oxidoreductase assay, but not nicotinamide adenine dinucleotide phosphate (NADPH) which is the donor required in human MTHFR. In silico analysis and mutagenesis studies highlighted the significant difference in orientation of helix α7A (Phe215-Thr225) with that in the human enzyme. The extended sidechain of Met221 on helix α7A plays a role in stabilizing the folded structure of NADH in the hydrophobic box. This supports the NADH specificity by restricting the phosphate group of NADPH that causes steric clashes with Glu26. The movement of Met221 sidechain allows the CH2 -H4 folate substrate to bind. The unique topology of its NADH and CH2 -H4 folate binding pockets makes NmMTHFR a promising drug target for the development of new antimicrobial agents that may possess reduced off-target side effects.
    Matched MeSH terms: Models, Molecular
  12. Liu Y, Marshall NM, Yu SS, Kim W, Gao YG, Robinson H, et al.
    Inorg Chem, 2023 Jul 24;62(29):11618-11625.
    PMID: 37424080 DOI: 10.1021/acs.inorgchem.3c01365
    In order to investigate the effects of the secondary coordination sphere in fine-tuning redox potentials (E°') of type 1 blue copper (T1Cu) in cupredoxins, we have introduced M13F, M44F, and G116F mutations both individually and in combination in the secondary coordination sphere of the T1Cu center of azurin (Az) from Pseudomonas aeruginosa. These variants were found to differentially influence the E°' of T1Cu, with M13F Az decreasing E°', M44F Az increasing E°', and G116F Az showing a negligible effect. In addition, combining the M13F and M44F mutations increases E°' by 26 mV relative to WT-Az, which is very close to the combined effect of E°' by each mutation. Furthermore, combining G116F with either M13F or M44F mutation resulted in negative and positive cooperative effects, respectively. Crystal structures of M13F/M44F-Az, M13F/G116F-Az, and M44F/G116F-Az combined with that of G116F-Az reveal these changes arise from steric effects and fine-tuning of hydrogen bond networks around the copper-binding His117 residue. The insights gained from this study would provide another step toward the development of redox-active proteins with tunable redox properties for many biological and biotechnological applications.
    Matched MeSH terms: Models, Molecular
  13. Yusof NA, Kamaruddin S, Abu Bakar FD, Mahadi NM, Abdul Murad AM
    Cell Stress Chaperones, 2019 Mar;24(2):351-368.
    PMID: 30649671 DOI: 10.1007/s12192-019-00969-1
    Studies on TCP1-1 ring complex (TRiC) chaperonin have shown its indispensable role in folding cytosolic proteins in eukaryotes. In a psychrophilic organism, extreme cold temperature creates a low-energy environment that potentially causes protein denaturation with loss of activity. We hypothesized that TRiC may undergo evolution in terms of its structural molecular adaptation in order to facilitate protein folding in low-energy environment. To test this hypothesis, we isolated G. antarctica TRiC (GaTRiC) and found that the expression of GaTRiC mRNA in G. antarctica was consistently expressed at all temperatures indicating their importance in cell regulation. Moreover, we showed GaTRiC has the ability of a chaperonin whereby denatured luciferase can be folded to the functional stage in its presence. Structurally, three categories of residue substitutions were found in α, β, and δ subunits: (i) bulky/polar side chains to alanine or valine, (ii) charged residues to alanine, and (iii) isoleucine to valine that would be expected to increase intramolecular flexibility within the GaTRiC. The residue substitutions observed in the built structures possibly affect the hydrophobic, hydrogen bonds, and ionic and aromatic interactions which lead to an increase in structural flexibility. Our structural and functional analysis explains some possible structural features which may contribute to cold adaptation of the psychrophilic TRiC folding chamber.
    Matched MeSH terms: Models, Molecular
  14. Rosli AN, Ahmad MR, Alias Y, Zain SM, Lee VS, Woi PM
    J Mol Model, 2014 Dec;20(12):2533.
    PMID: 25433601 DOI: 10.1007/s00894-014-2533-9
    Design of neutral receptor molecules (ionophores) for beryllium(II) using unsaturated carbonitrile models has been carried out via density functional theory, G3, and G4 calculations. The first part of this work focuses on gas phase binding energies between beryllium(II) and 2-cyano butadiene (2-CN BD), 3-cyano propene (3-CN P), and simpler models with two separate fragments; acrylonitrile and ethylene. Interactions between beryllium(II) and cyano nitrogen and terminal olefin in the models have been examined in terms of geometrical changes, distribution of charge over the entire π-system, and rehybridization of vinyl carbon orbitals. NMR shieldings and vibrational frequencies probed charge centers and strength of interactions. The six-membered cyclic complexes have planar structures with the rehybridized carbon slightly out of plane (16° in 2-CN BD). G3 results show that in 2-CN BD complex participation of vinyl carbon further stabilizes the cyclic adduct by 16.3 kcal mol(-1), whereas, in simpler models, interaction between beryllium(II) and acetonitrile is favorable by 46.4 kcal mol(-1) compared with that of ethylene. The terminal vinyl carbon in 2-CN BD rehybridizes to sp (3) with an increase of 7 % of s character to allow interaction with beryllium(II). G4 calculations show that the Be(II) and 2-CN BD complex is more strongly bound than those with Mg(II) and Ca(II) by 98.5 and 139.2 kcal mol(-1) (-1), respectively. QST2 method shows that the cyclic and acyclic forms of Be(II)-2-CN BD complexes are separated by 12.3 kcal mol(-1) barrier height. Overlap population analysis reveals that Ca(II) can be discriminated based on its tendency to form ionic interaction with the receptor models.
    Matched MeSH terms: Models, Molecular*
  15. Almansour AI, Kumar RS, Arumugam N, Basiri A, Kia Y, Ali MA
    Biomed Res Int, 2015;2015:965987.
    PMID: 25710037 DOI: 10.1155/2015/965987
    A series of hexahydro-1,6-naphthyridines were synthesized in good yields by the reaction of 3,5-bis[(E)-arylmethylidene]tetrahydro-4(1H)-pyridinones with cyanoacetamide in the presence of sodium ethoxide under simple mixing at ambient temperature for 6-10 minutes and were assayed for their acetylcholinesterase (AChE) inhibitory activity using colorimetric Ellman's method. Compound 4e with methoxy substituent at ortho-position of the phenyl rings displayed the maximum inhibitory activity with IC50 value of 2.12 μM. Molecular modeling simulation of 4e was performed using three-dimensional structure of Torpedo californica AChE (TcAChE) enzyme to disclose binding interaction and orientation of this molecule into the active site gorge of the receptor.
    Matched MeSH terms: Models, Molecular*
  16. Arunagiri C, Subashini A, Saranya M, Thomas Muthiah P, Thanigaimani K, Abdul Razak I
    PMID: 25084236 DOI: 10.1016/j.saa.2014.07.016
    The molecular structure of a new Schiff base, 2-[4-hydroxy benzylidene]-amino naphthalene (HBAN) has been examined by HF and B3LYP/6-311++G(d,p) calculations. The X-ray structure was determined in order to establish the conformation of the molecule. The compound, C17H13NO, crystallizes in the orthorhombic, P212121 space group with the cell dimension, a=6.2867(2), b=10.2108(3), c=19.2950(6) Å, α=β=γ=90° and z=4. The asymmetric unit contains a molecule of a Schiff base. A strong intermolecular O-H⋯N and a weak C-H⋯O hydrogen bonds stabilized the crystal structure. The vibrational spectra of HBAN have been calculated using density functional theoretical computation and compared with the experimental. The study is extended to the HOMO-LUMO analysis to calculate the energy gap (Δ), Ionization potential (I), Electron Affinity (A), Global Hardness (η), Chemical Potential (μ) and Global Electrophilicity (w). The calculated HOMO and LUMO energy reveals that the charge transfer occurs within the molecule.
    Matched MeSH terms: Models, Molecular*
  17. Chidan Kumar CS, Fun HK, Parlak C, Rhyman L, Ramasami P, Tursun M, et al.
    PMID: 24858359 DOI: 10.1016/j.saa.2014.04.155
    A novel (2E)-1-(5-chlorothiophen-2-yl)-3-(naphthalen-2-yl)prop-2-en-1-one [C17H11ClOS] compound has been synthesized and its structure has been characterized by FT-IR, Raman and single-crystal X-ray diffraction techniques. The isomers, optimized geometrical parameters, normal mode frequencies and corresponding vibrational assignments of the compound have been examined by means of the density functional theory method, employing, the Becke-3-Lee-Yang-Parr functional and the 6-311+G(3df,p) basis set. Reliable vibrational assignments and molecular orbitals have been investigated by the potential energy distribution and natural bonding orbital analyses, respectively. The compound crystallizes in the monoclinic space group P2₁/c with the unit cell parameters a=5.7827(8)Å, b=14.590(2)Å, c=16.138(2)Å and β=89.987 (°). The CC bond of the central enone group adopts an E configuration. There is a good agreement between the theoretically predicted structural parameters and vibrational frequencies and those obtained experimentally.
    Matched MeSH terms: Models, Molecular*
  18. Jumbri K, Abdul Rahman MB, Abdulmalek E, Ahmad H, Micaelo NM
    Phys Chem Chem Phys, 2014 Jul 21;16(27):14036-46.
    PMID: 24901033 DOI: 10.1039/c4cp01159g
    Molecular dynamics simulation and biophysical analysis were employed to reveal the characteristics and the influence of ionic liquids (ILs) on the structural properties of DNA. Both computational and experimental evidence indicate that DNA retains its native B-conformation in ILs. Simulation data show that the hydration shells around the DNA phosphate group were the main criteria for DNA stabilization in this ionic media. Stronger hydration shells reduce the binding ability of ILs' cations to the DNA phosphate group, thus destabilizing the DNA. The simulation results also indicated that the DNA structure maintains its duplex conformation when solvated by ILs at different temperatures up to 373.15 K. The result further suggests that the thermal stability of DNA at high temperatures is related to the solvent thermodynamics, especially entropy and enthalpy of water. All the molecular simulation results were consistent with the experimental findings. The understanding of the properties of IL-DNA could be used as a basis for future development of specific ILs for nucleic acid technology.
    Matched MeSH terms: Models, Molecular*
  19. Chidan Kumar CS, Fun HK, Tursun M, Ooi CW, Chandraju S, Quah CK, et al.
    Spectrochim Acta A Mol Biomol Spectrosc, 2014 Apr 24;124:595-602.
    PMID: 24509537 DOI: 10.1016/j.saa.2014.01.063
    2-(4-Chlorophenyl)-2-oxoethyl 2-chlorobenzoate has been synthesized, its structural and vibrational properties have been reported using FT-IR and single-crystal X-ray diffraction (XRD) studies. The conformational analysis, optimized geometric parameters, normal mode frequencies and corresponding vibrational assignments of the synthesized compound (C15H10Cl2O3) have been examined by means of Becke-3-Lee-Yang-Parr (B3LYP) density functional theory (DFT) method together with 6-31++G(d,p) basis set. Furthermore, reliable conformational investigation and vibrational assignments have been made by the potential energy surface (PES) and potential energy distribution (PED) analyses, respectively. Calculations are performed with two possible conformations. The title compound crystallizes in orthorhombic space group Pbca with the unit cell dimensions a=12.312(5) Å, b=8.103(3) Å, c=27.565(11) Å, V=2750.0(19) Å(3). B3LYP method provides satisfactory evidence for the prediction of vibrational wavenumbers and structural parameters.
    Matched MeSH terms: Models, Molecular*
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