Displaying publications 1 - 20 of 31 in total

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  1. Neves RF, Jones DB, Lopes MC, Blanco F, García G, Ratnavelu K, et al.
    J Chem Phys, 2015 May 21;142(19):194305.
    PMID: 26001459 DOI: 10.1063/1.4921313
    We report on measurements of integral cross sections (ICSs) for electron impact excitation of a series of composite vibrational modes and electronic-states in phenol, where the energy range of those experiments was 15-250 eV. There are currently no other results against which we can directly compare those measured data. We also report results from our independent atom model with screened additivity rule correction computations, namely, for the inelastic ICS (all discrete electronic states and neutral dissociation) and the total ionisation ICS. In addition, for the relevant dipole-allowed excited electronic states, we also report f-scaled Born-level and energy-corrected and f-scaled Born-level (BEf-scaled) ICS. Where possible, our measured and calculated ICSs are compared against one another with the general level of accord between them being satisfactory to within the measurement uncertainties.
    Matched MeSH terms: Quantum Theory*
  2. Dehghan MR, Ahmadi S, Mosapour Kotena Z, Niakousari M
    J Mol Graph Model, 2021 06;105:107862.
    PMID: 33588350 DOI: 10.1016/j.jmgm.2021.107862
    Metal nanoclusters have been considered as a new class of chemical sensors due to their unique electronic structures and the particular physicochemical properties. The interaction of N2 molecule with neutral and ionic magnesium nanoclusters Mg17q(q=0,±1), as well as neutral magnesium nanoclusters with the centrality of beryllium and calcium Mg16M (M=Be, Mg, and Ca) have been investigated using CAM-B3LYP/6-311+G(d) level of theory in the gas phase. The electronic properties of magnesium nanoclusters were significantly affected by the adsorption of N2 molecule. The NBO analysis revealed a charge transfer from the adsorbed N2 molecule to the nanocluster. Based on the adsorption energies and enthalpies, a thermodynamically favorable chemisorption process was predicted for the Mg16Ca-N2 complex. The negative value of the Gibbs free energy of Mg16Ca-N2 confirmed the spontaneous adsorption process. The estimated recovery time for Mg16Ca-N2 complex for 8-MR (0.089 s) and 4-MRs (0.075 s) illustrated a possible desorption process for N2 molecule from the surface of Mg16Ca. Our finding also revealed the Mg16Ca has the ability to use as a sensor for detection and absorption of N2 molecule.
    Matched MeSH terms: Quantum Theory*
  3. Al-Dabbagh MM, Salim N, Himmat M, Ahmed A, Saeed F
    Molecules, 2015;20(10):18107-27.
    PMID: 26445039 DOI: 10.3390/molecules201018107
    One of the most widely-used techniques for ligand-based virtual screening is similarity searching. This study adopted the concepts of quantum mechanics to present as state-of-the-art similarity method of molecules inspired from quantum theory. The representation of molecular compounds in mathematical quantum space plays a vital role in the development of quantum-based similarity approach. One of the key concepts of quantum theory is the use of complex numbers. Hence, this study proposed three various techniques to embed and to re-represent the molecular compounds to correspond with complex numbers format. The quantum-based similarity method that developed in this study depending on complex pure Hilbert space of molecules called Standard Quantum-Based (SQB). The recall of retrieved active molecules were at top 1% and top 5%, and significant test is used to evaluate our proposed methods. The MDL drug data report (MDDR), maximum unbiased validation (MUV) and Directory of Useful Decoys (DUD) data sets were used for experiments and were represented by 2D fingerprints. Simulated virtual screening experiment show that the effectiveness of SQB method was significantly increased due to the role of representational power of molecular compounds in complex numbers forms compared to Tanimoto benchmark similarity measure.
    Matched MeSH terms: Quantum Theory
  4. Anouar el H, Weber JF
    PMID: 23880409 DOI: 10.1016/j.saa.2013.06.114
    Natural styrylpyrones isolated from fungi are known for various biological activities including antioxidant activity by scavenging free radicals. UV/vis spectra play an important role in elucidating chemical structures of these compounds via identification of chromophore units. With the aim of predicting the UV/vis spectra of a series of natural styrylpyrones, we tested TD-DFT, CIS and ZINDO methods in gas and in PCM solvent. The results showed that the individual or combined B3P86 and B3LYP hybrid functionals are suitable to predict the maximum wavelength absorption bands (λmax) for styrylpyrones. The structure property relationship (SPR) study emphasized the role of (i) structural parameters (e.g., hydrogen bond and the length of conjugated double bonds) and (ii) electronic descriptors (e.g., ionization potential, electronic affinity, hardness and electrophilicity) in bathochromic and hypsochromic shifts of maximum wavelength absorption bands (λmax) of styrylpyrone derivatives.
    Matched MeSH terms: Quantum Theory*
  5. Rodrigues A, Olivato PR, Zukerman-Schpector J, Maganhi SH, Reis AK, Tiekink ER
    J Phys Chem A, 2015 Aug 13;119(32):8714-23.
    PMID: 26213179 DOI: 10.1021/acs.jpca.5b04019
    The X-ray single crystal analysis of isomeric ortho, meta, and para bromo-substituted α-methylsulfonyl-α-diethoxyphosphoryl acetophenones showed that this class of compound adopts synclinal (gauche) conformations for both [-P(O)(OEt)2] and [-S(O)2Me] groups, with respect to the carbonyl functional group. The phosphonate, sulfonyl, and carbonyl functional groups are joined through an intramolecular network of attractive interactions, as detected by molecular orbital calculations at the M06-2X/6-31G(d,p) level. These interactions are responsible for the more stable conformations in the gas phase, which also persist in the solid-state structures. The main structural distinction in the title compounds relates to the torsion angle of the aryl group (with respect to the carbonyl group), which gives rise to different interactions in the crystal packing, due to the different positions of the Br atom.
    Matched MeSH terms: Quantum Theory
  6. Poznanski RR, Cacha LA, Latif AZA, Salleh SH, Ali J, Yupapin P, et al.
    J Integr Neurosci, 2019 03 30;18(1):1-10.
    PMID: 31091842 DOI: 10.31083/j.jin.2019.01.105
    The physicality of subjectivity is explained through a theoretical conceptualization of guidance waves informing meaning in negentropically entangled non-electrolytic brain regions. Subjectivity manifests its influence at the microscopic scale of matter originating from de Broglie 'hidden' thermodynamics as action of guidance waves. The preconscious experienceability of subjectivity is associated with a nested hierarchy of microprocesses, which are actualized as a continuum of patterns of discrete atomic microfeels (or "qualia"). The mechanism is suggested to be through negentropic entanglement of hierarchical thermodynamic transfer of information as thermo-qubits originating from nonpolarized regions of actin-binding proteinaceous structures of nonsynaptic spines. The resultant continuous stream of intrinsic information entails a negentropic action (or experiential flow of thermo-quantum internal energy that results in a negentropic force) which is encoded through the non-zero real component of the mean approximation of the negentropic force as a 'consciousness code'. Consciousness consisting of two major subprocesses: (1) preconscious experienceability and (2) conscious experience. Both are encapsulated by nonreductive physicalism and panexperiential materialism. The subprocess (1) governing "subjectivity" carries many microprocesses leading to the actualization of discrete atomic microfeels by the 'consciousness code'. These atomic microfeels constitute internal energy that results in the transfer intrinsic information in terms of thermo-qubits. These thermo-qubits are realized as thermal entropy and sensed by subprocess (2) governing "self-awareness" in conscious experience.
    Matched MeSH terms: Quantum Theory
  7. Zainuri DA, Abdullah M, Zaini MF, Bakhtiar H, Arshad S, Abdul Razak I
    PLoS One, 2021;16(9):e0257808.
    PMID: 34582495 DOI: 10.1371/journal.pone.0257808
    The Ultraviolet-visible (UV-Vis) spectra indicate that anthracenyl chalcones (ACs) have high maximum wavelengths and good transparency windows for optical applications and are suitable for optoelectronic applications owing to their HOMO-LUMO energy gaps (2.93 and 2.76 eV). Different donor substituents on the AC affect their dipole moments and nonlinear optical (NLO) responses. The positive, negative, and neutral electrostatic potential regions of the molecules were identified using molecular electrostatic potential (MEP). The stability of the molecule on account of hyperconjugative interactions and accompanying charge delocalization was analyzed using natural bond orbital (NBO) analysis. Open and closed aperture Z-scans were performed using a continuous-wave frequency-doubled diode-pumped solid-state (DPSS) laser to measure the nonlinear absorption and nonlinear refractive index coefficients, respectively. The valley-to-peak profile of AC indicated a negative nonlinear refractive index coefficient. The obtained single crystals possess reverse saturation absorption due to excited-state absorption. The structural and nonlinear optical properties of the molecules have been discussed, along with the role of anthracene substitution for enhancing the nonlinear optical properties. The calculated third-order susceptibility value was 1.10 x10-4 esu at an intensity of 4.1 kW/cm2, higher than the reported values for related chalcone derivatives. The NLO response for both ACs offers excellent potential in optical switching and limiting applications.
    Matched MeSH terms: Quantum Theory
  8. 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: Quantum Theory*
  9. Arifin K, Daud WR, Kassim MB
    PMID: 24508875 DOI: 10.1016/j.saa.2013.12.107
    Bis(dithiolene) tungsten carbonyl complex, W(S2C2Ph2)2(CO)2 was successfully synthesized and the structure, frontier molecular orbital and optical properties of the complex were investigated theoretically using density functional theory calculations. The investigation started with a molecular structure construction, followed by an optimization of the structural geometry using generalized-gradient approximation (GGA) in a double numeric plus polarization (DNP) basis set at three different functional calculation approaches. Vibrational frequency analysis was used to confirm the optimized geometry of two possible conformations of [W(S2C2Ph2)2(CO)2], which showed distorted octahedral geometry. Electronic structure and optical characterization were done on the ground states. Metal to ligand and ligand to metal charge transfer were dominant in this system.
    Matched MeSH terms: Quantum Theory*
  10. Mosapour Kotena Z, Behjatmanesh-Ardakani R, Hashim R, Manickam Achari V
    J Mol Model, 2013 Feb;19(2):589-99.
    PMID: 22972691 DOI: 10.1007/s00894-012-1576-z
    Density functional theory calculations on two glycosides, namely, n-octyl-β-D-glucopyranoside (C(8)O-β-Glc) and n-octyl-β-D-galactopyranoside (C(8)O-β-Gal) were performed for geometry optimization at the B3LYP/6-31G level. Both molecules are stereoisomers (epimers) differing only in the orientation of the hydroxyl group at the C4 position. Thus it is interesting to investigate electronically the effect of the direction (axial/equatorial) of the hydroxyl group at the C4 position. The structure parameters of X-H∙∙∙Y intramolecular hydrogen bonds were analyzed, while the nature of these bonds and the intramolecular interactions were considered using the atoms in molecules (AIM) approach. Natural bond orbital analysis (NBO) was used to determine bond orders, charge and lone pair electrons on each atom and effective non-bonding interactions. We have also reported electronic energy and dipole moment in gas and solution phases. Further, the electronic properties such as the highest occupied molecular orbital, lowest unoccupied molecular orbital, ionization energy, electron affinity, electronic chemical potential, chemical hardness, softness and electrophilicity index, are also presented here for both C(8)O-β-Glc and C(8)O-β-Gal. These results show that, while C(8)O-β-Glc possess- only one hydrogen bond, C(8)O-β-Gal has two intramolecular hydrogen bonds, which further confirms the anomalous stability of the latter in self-assembly phenomena.
    Matched MeSH terms: Quantum Theory*
  11. Eltayeb NE, Teoh SG, Adnan R, Teh JB, Fun HK
    J Fluoresc, 2011 Jul;21(4):1393-400.
    PMID: 21222144 DOI: 10.1007/s10895-010-0822-y
    A series of Zn(II)-Schiff bases I, II and III complexes were synthesized by reaction of o-phenylenediamine with 3-methylsalicylaldehyde, 4-methylsalicylaldehyde and 5-methylsalicylaldehyde. These complexes were characterized using FT-IR, UV-Vis, Diffuse reflectance UV-Vis, elemental analysis and conductivity. Complex III was characterized by XRD single crystal, which crystallizes in the triclinic system, space group P-1, with lattice parameters a=9.5444(2) Å, b=11.9407(2) Å, c=21.1732(3) Å, V=2390.24(7) Å(3), D ( c )=1.408 Mg m(-3), Z=4, F(000)=1050, GOF=0.981, R1=0.0502, wR2=0.1205. Luminescence property of these complexes was investigated in DMF solution and in the solid state. Computational study of the electronic properties of complex III showed good agreement with the experimental data.
    Matched MeSH terms: Quantum Theory*
  12. Shawkataly OB, Goh CP, Tariq A, Khan IA, Fun HK, Rosli MM
    PLoS One, 2015;10(3):e0119620.
    PMID: 25798915 DOI: 10.1371/journal.pone.0119620
    A series of complexes of the type LAuCl where L = tris(p-tolylarsane), tris(m-tolylarsane), bis(diphenylarsano)ethane, and tris(naphthyl)arsane have been synthesized. All of the new complexes, 1-4, have been fully characterized by means of ¹H NMR and ¹³C NMR spectroscopy and single crystal X-ray crystallography. The structures of complexes 1-4 have been determined from X-ray diffraction data. The linear molecules have an average bond distance between gold-arsenic and gold-chlorine of 2.3390Å and 2.2846Å, respectively. Aurophilic interaction was prominent in complex 1 and 3, whereas complex 2 and 4 do not show any such interaction. The intermolecular gold interaction bond length was affected by the electronegativity of the molecule. The computed values calculated at DFT level using B3LYP function are in good agreement with the experimental results.
    Matched MeSH terms: Quantum Theory*
  13. Kumar CS, Parlak C, Tursun M, Fun HK, Rhyman L, Ramasami P, et al.
    PMID: 25767992 DOI: 10.1016/j.saa.2015.02.079
    The structure of 3-iodobenzaldehyde (3IB) was characterized by FT-IR, Raman and single-crystal X-ray diffraction techniques. The conformational isomers, optimized geometric parameters, normal mode frequencies and corresponding vibrational assignments of 3IB were examined using density functional theory (DFT) method, with the Becke-3-Lee-Yang-Parr (B3LYP) functional and the 6-311+G(3df,p) basis set for all atoms except for iodine. The LANL2DZ effective core basis set was used for iodine. Potential energy distribution (PED) analysis of normal modes was performed to identify characteristic frequencies. 3IB crystallizes in monoclinic space group P21/c with the O-trans form. There is a good agreement between the theoretically predicted structural parameters, and vibrational frequencies and those obtained experimentally. In order to understand halogen effect, 3-halogenobenzaldehyde [XC6H4CHO; X=F, Cl and Br] was also studied theoretically. The free energy difference between the isomers is small but the rotational barrier is about 8kcal/mol. An atypical behavior of fluorine affecting conformational preference is observed.
    Matched MeSH terms: Quantum Theory*
  14. Chua EG, Wise MJ, Khosravi Y, Seow SW, Amoyo AA, Pettersson S, et al.
    DNA Res, 2017 Feb 01;24(1):37-49.
    PMID: 27803027 DOI: 10.1093/dnares/dsw046
    Helicobacter pylori is a highly successful gastric pathogen. High genomic plasticity allows its adaptation to changing host environments. Complete genomes of H. pylori clinical isolate UM032 and its mice-adapted serial derivatives 298 and 299, generated using both PacBio RS and Illumina MiSeq sequencing technologies, were compared to identify novel elements responsible for host-adaptation. The acquisition of a jhp0562-like allele, which encodes for a galactosyltransferase, was identified in the mice-adapted strains. Our analysis implies a new β-1,4-galactosyltransferase role for this enzyme, essential for Ley antigen expression. Intragenomic recombination between babA and babB genes was also observed. Further, we expanded on the list of candidate genes whose expression patterns have been mediated by upstream homopolymer-length alterations to facilitate host adaption. Importantly, greater than four-fold reduction of mRNA levels was demonstrated in five genes. Among the down-regulated genes, three encode for outer membrane proteins, including BabA, BabB and HopD. As expected, a substantial reduction in BabA protein abundance was detected in mice-adapted strains 298 and 299 via Western analysis. Our results suggest that the expression of Ley antigen and reduced outer membrane protein expressions may facilitate H. pylori colonisation of mouse gastric epithelium.
    Matched MeSH terms: Quantum Theory*
  15. Junaedi S, Al-Amiery AA, Kadihum A, Kadhum AA, Mohamad AB
    Int J Mol Sci, 2013 Jun 04;14(6):11915-28.
    PMID: 23736696 DOI: 10.3390/ijms140611915
    1,5-Dimethyl-4-((2-methylbenzylidene)amino)-2-phenyl-1H-pyrazol-3(2H)-one (DMPO) was synthesized to be evaluated as a corrosion inhibitor. The corrosion inhibitory effects of DMPO on mild steel in 1.0 M HCl were investigated using electrochemical impedance spectroscopy (EIS), potentiodynamic polarization, open circuit potential (OCP) and electrochemical frequency modulation (EFM). The results showed that DMPO inhibited mild steel corrosion in acid solution and indicated that the inhibition efficiency increased with increasing inhibitor concentration. Changes in the impedance parameters suggested an adsorption of DMPO onto the mild steel surface, leading to the formation of protective films. The novel synthesized corrosion inhibitor was characterized using UV-Vis, FT-IR and NMR spectral analyses. Electronic properties such as highest occupied molecular orbital energy, lowest unoccupied molecular orbital energy (EHOMO and ELUMO, respectively) and dipole moment (μ) were calculated and discussed. The results showed that the corrosion inhibition efficiency increased with an increase in the EHOMO values but with a decrease in the ELUMO value.
    Matched MeSH terms: Quantum Theory*
  16. Nguan H, Ahmadi S, Hashim R
    J Mol Model, 2012 Dec;18(12):5041-50.
    PMID: 22752540 DOI: 10.1007/s00894-012-1497-x
    A theoretical study of a series of five glucose based glycolipid crown ethers and their complexes with Na(+) and K(+) was performed using the density functional theory with B3LYP/6-31 G* to obtain the optimized geometrical structures and electronic properties. The local nucleophilicity of the five molecules was investigated using Fukui function, while the global nucleophilicity was calculated from the ionization potential and electron affinity. The structures and coordination of the complexes were studied to identify the best match of the glycolipid crown ethers with cations. In general, it was found that the oxygen atoms pairs O2 and O3 (or O4 and O6) on the sugar ring are constrained from moving toward the cation, which results in a weaker O-cation coordination strength for the oxygen pair compared to the other oxygen atoms in the crown ether ring. The thermodynamic properties of the binding of the complexes and the exchange reaction in gas phase were evaluated. The cation selectivity pattern among the five molecules was in good agreement with the experiment.
    Matched MeSH terms: Quantum Theory
  17. Wahab HA, Amaro RE, Cournia Z
    J Chem Inf Model, 2018 11 26;58(11):2175-2177.
    PMID: 30277769 DOI: 10.1021/acs.jcim.8b00642
    Matched MeSH terms: Quantum Theory
  18. Salim F, Yunus YM, Anouar EH, Awang K, Langat M, Cordell GA, et al.
    J Nat Prod, 2019 11 22;82(11):2933-2940.
    PMID: 31686505 DOI: 10.1021/acs.jnatprod.8b00380
    The structure elucidation of three new alkaloids named isoformosaninol (1), formosaninol (2), and longiflorine (3), isolated from the leaves of Uncaria longiflora var. pteropoda (Miq.) Ridsdale, along with their biosynthetic pathways are discussed. Their absolute structures were determined through a combination of physical data interpretation and quantum chemical calculations using the time-dependent density functional theory (TDDFT) method.
    Matched MeSH terms: Quantum Theory
  19. Abosadiya HM, Anouar el H, Hasbullah SA, Yamin BM
    PMID: 25748989 DOI: 10.1016/j.saa.2015.01.092
    A new isomers of thiourea derivatives, namely N-(4-chlorobutanoyl)-N'-(2-methylphenyl)-thiourea (1a), N-(4-chlorobutanoyl)-N'-(3-methylphenyl)thiourea (1b) and N-(4-chlorobutanoyl)-N'-(4-methylphenyl)thiourea (1c) have been synthesized by refluxing mixture of equimolar amounts of 4-chlorobutanoylisothiocyanate with 2, 3 or 4-toluidine, respectively. The three isomers were characterized by spectroscopic (UV/vis, FT-IR and NMR) and X-ray crystallography techniques. To investigate the isomerization effect on spectroscopic data, DFT and TD-DFT calculations have been carried out using five hybrid functionals (B3LYP, B3P86, CAM-B3LYP, M06-2X and PBE0) to predict UV/vis absorption bands (n→π∗ and π→π∗), (1)H and (13)C NMR chemical shifts, FT-IR vibration modes and X-ray parameters (bonds, bond angles and torsion angles) for 1a, 1b and 1c isomers. The results showed that the isomerization effect is significant on λ(MAX) absorption bands, while for IR and NMR the effect is negligible. In accordance with previous studies, B3LYP, B3P86 and PBE0 gave the most reliable to predict the excitation energies of thiourea derivatives.
    Matched MeSH terms: Quantum Theory*
  20. Anouar el H, Zakaria NS, Alsalme A, Shah SA
    Mini Rev Med Chem, 2015;15(14):1148-58.
    PMID: 26205959
    A natural pentacyclic triterpenoid oleanolic acid 1 and its biotransformed metabolites 2-3 are potential α-glucosidase inhibitors. To elucidate the inhibitory mechanism of compounds 1, 2 and 3 against α-glucosidase, we calculated (i) their electronic and optical properties using DFT and TD-DFT at the B3LYP/6-31G(d) level in gas and IEF-PCM solvent; and (ii) their binding energies to α-glucosidase via docking study. DFT results showed that the α-glucosidase inhibtion is mainly depend on the polarity parameters of the studied compounds. Docking results revealed that the activity increased with binding energies (i.e. the stability of ligand-receptor complex). The specroscopic data of oleanolic acid 1 and its metabolites 2 and 3 are well predicetd for 13C NMR chemical shifts (R2=99%) and 1H NMR chemical shifts (R2=90%); and for (ii) UV/vis spectra. The assignments and interpretation of NMR chemical shifts and bathochromic shift of λMAX absorption bands are discussed.
    Matched MeSH terms: Quantum Theory*
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