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  1. An evaluation of the reliability of the characterization of the porous structure of activated carbons based on incomplete nitrogen adsorption isotherms
    Kwiatkowski M, Hameed BH
    J Mol Model, 2017 Aug;23(8):238.
    PMID: 28735499 DOI: 10.1007/s00894-017-3402-0
    The paper presents the results of research devoted to reliability evaluation of the analysis of results of the porous structure of activated carbons based on incomplete nitrogen adsorption isotherms using the BET, t-plot, and NLDFT methods, as well as the LBET method comprising the unique numerical fast multivariant procedure of adsorption system identification. The research involved the application of the nitrogen adsorption isotherms obtained for five samples of activated carbons produced from waste materials of organic origin by way of chemical activation with potassium hydroxide, sodium hydroxide, and potassium carbonate with the use of microwave heating. The analyses performed pointed to a good correlation between the results obtained using the BET, t-plot, NLDFT, and LBET methods. Moreover, the parameters of the porous structure determined using these methods based on incomplete adsorption isotherms of nitrogen are in fact as reliable as these methods allow.
  2. Analysis of phase stability, elastic, electronic, thermal, and optical properties of Sc1-xYxN via ab initio methods
    Gagui S, Meradji H, Ghemid S, Naeem S, Haq BU, Ahmed R, et al.
    J Mol Model, 2022 Dec 21;29(1):14.
    PMID: 36542150 DOI: 10.1007/s00894-022-05412-4
    Understanding the physical properties of a material is crucial to know its applicability for practical applications. In this study, we investigate the phase stability, elastic, electronic, thermal, and optical properties of the ternary alloying of the scandium and yttrium nitrides (Sc1-xYxN) for different compositions. To do so, we apply a "density functional theory (DFT)" based scheme of calculations named as "full potential (FP) linearized (L) augmented plane wave plus local orbitals (APW + lo) method" realized in the WIEN2k computational package. At first, the phase stability of the investigated compositions of the mentioned alloy is determined. The analysis of our calculations shows that Sc1-xYxN alloy is stable in rock salt crystal structure for all investigated compositions. Next to that, the elastic properties of the rock-salt phase of the studied ternary alloy Sc1-xYxN at all above said compositions were done at the level of "Wu-Cohen generalized gradient approximation (Wu-GGA)" within DFT. However, Trans-Blaha (TB) approximation of the "modified Becke-Johson (mBJ)" potential is also used in combination with Wu-GGA where the thermal properties are calculated at the level of the "quasi-harmonic Debye model." The obtained results for the absorption coefficients, and optical bandgap, represent that the title alloy may be a suitable candidate for the applications in optoelectronic devices.
  3. Atomistic simulation studies of the α/β-glucoside and galactoside in anhydrous bilayers: effect of the anomeric and epimeric configurations
    Ahmadi S, Manickam Achari V, Nguan H, Hashim R
    J Mol Model, 2014 Mar;20(3):2165.
    PMID: 24623320 DOI: 10.1007/s00894-014-2165-0
    Fully atomistic molecular dynamics simulation studies of thermotropic bilayers were performed using a set of glycosides namely n-octyl-β-D-glucopyranoside (β-C8Glc), n-octyl-α-D-glucopyranoside (α-C8Glc), n-octyl-β-D-galactopyranoside (β-C8Gal), and n-octyl-α-D-galactopyranoside (α-C8Gal) to investigate the stereochemical relationship of the epimeric/anomeric quartet liner glycolipids with the same octyl chain group. The results showed that, the anomeric stereochemistry or the axial/equatorial orientation of C1-O1 (α/β) is an important factor controlling the area and d-spacing of glycolipid bilayer systems in the thermotropic phase. The head group tilt angle and the chain ordering properties are affected by the anomeric effect. In addition, the L(C) phase of β-C8Gal, is tilting less compared to those in the fluid L(α). The stereochemistry of the C4-epimeric (axial/equatorial) and anomeric (α/β) centers simultaneously influence the inter-molecular hydrogen bond. Thus, the trend in the values of the hydrogen bond for these glycosides is β-C8Gal > α-C8Glc > β-C8Glc > α-C8Gal. The four bilayer systems showed anomalous diffusion behavior with an observed trend for the diffusion coefficients; and this trend is β-C8Gal > β-C8Glc > α-C8Gal > α-C8Glc. The "bent" configuration of the α-anomer results in an increase of the hydrophobic area, chain vibration and chain disorganization. Since thermal energy is dispensed more entropically for the chain region, the overall molecular diffusion decreases.
  4. COSMO-RS-based assessment of thermodynamic tools in predicting the polar and non-polar solvents efficiency in vegetable oil extraction
    Al-Maari MA, Hizaddin HF, Salleh MZM, Hayyan A
    J Mol Model, 2024 Feb 17;30(3):73.
    PMID: 38368310 DOI: 10.1007/s00894-024-05876-6
    CONTEXT: One of the prevalent methods for evaluating separation performance is to predict the interactions of solvent and solute molecules. The infinite dilution activity coefficient, Gibbs free energy, and sigma profiles provided insights into the solubilization of a solute and revealed the intensity of the solution's molecular interactions. The effective thermodynamic tools (infinite dilution activity coefficient, Gibbs free energy) were evaluated for predicting the efficiency of 18 polar and non-polar organic solvents in rubber seed oil (RSO) extraction. An infinite dilution activity coefficient was computed to evaluate the solubility of the rubber seed oil model compound (linoleic acid) in the organic solvents. Gibbs free energy was evaluated to show the energy change associated with the molecules mixing process and forecast the miscibility of linoleic acid molecules in the solvents. Moreover, the study examined the sigma profiles and sigma surfaces of organic solvents and linoleic acid to acquire a deeper insight into their similarities and how they interact molecularly. According to the computational prediction and experimental verification, the thermodynamic properties of Gibbs free energy and activity coefficient proved to be highly effective tools for screening polar and moderately polar solvents, predicting the molecular interactions with solute. Whereas the sigma profile and sigma surface were found to be the most efficient tools for evaluating the efficacy of non-polar solvents. Solvents with moderate polarity, such as tetrahydrofuran and diethyl ether, as well as non-polar solvents like pentane, heptane, and n-hexane, proved to be effective and favorable for oil extraction, resulting in the highest oil yields of approximately 27.0%. Overall, the COSMO-RS method demonstrates its utility in estimating the solubility of RSO in organic solvents, enabling early identification of the most effective solvent.

    METHODS: The initial geometry optimization of every component was conducted through density functional theory (DFT) using TmoleX software. A single-point density functional theory (DFT) computation using Becke Perdew 86 (BP86) and the Triple-Zeta Valence Potential (TZVPD) was performed to produce.cosmo files. COSMO-RS calculations were performed by applying the parameterization file BP_TZVPD_FINE_19.ctd using COSMOthermX software. The practical extraction of oil from plant seeds was performed using a sonicator bath to verify the accuracy of the COSMO-RS predictions.

  5. Comparative modelling studies of fruit bromelain using molecular dynamics simulation
    Pang WC, Ramli ANM, Hamid AAA
    J Mol Model, 2020 May 16;26(6):142.
    PMID: 32417971 DOI: 10.1007/s00894-020-04398-1
    Fruit bromelain is a cysteine protease accumulated in pineapple fruits. This proteolytic enzyme has received high demand for industrial and therapeutic applications. In this study, fruit bromelain sequences QIM61759, QIM61760 and QIM61761 were retrieved from the National Center for Biotechnology Information (NCBI) Genbank Database. The tertiary structure of fruit bromelain QIM61759, QIM61760 and QIM61761 was generated by using MODELLER. The result revealed that the local stereochemical quality of the generated models was improved by using multiple templates during modelling process. Moreover, by comparing with the available papain model, structural analysis provides an insight on how pro-peptide functions as a scaffold in fruit bromelain folding and contributing to inactivation of mature protein. The structural analysis also disclosed the similarities and differences between these models. Lastly, thermal stability of fruit bromelain was studied. Molecular dynamics simulation of fruit bromelain structures at several selected temperatures demonstrated how fruit bromelain responds to elevation of temperature.
  6. Computational docking of L-arginine and its structural analogues to C-terminal domain of Escherichia coli arginine repressor protein (ArgRc)
    Kueh R, Rahman NA, Merican AF
    J Mol Model, 2003 Apr;9(2):88-98.
    PMID: 12707802
    The arginine repressor (ArgR) of Escherichia coli binds to six L-arginine molecules that act as its co-repressor in order to bind to DNA. The binding of L-arginine molecules as well as its structural analogues is compared by means of computational docking. A grid-based energy evaluation method combined with a Monte Carlo simulated annealing process was used in the automated docking. For all ligands, the docking procedure proposed more than one binding site in the C-terminal domain of ArgR (ArgRc). Interaction patterns of ArgRc with L-arginine were also observed for L-canavanine and L-citrulline. L-lysine and L-homoarginine, on the other hand, were shown to bind poorly at the binding site. Figure A general overview of the sites found from docking the various ligands into ArgRc ( grey ribbons). Red coloured sticks: residues in binding site H that was selected for docking
  7. Computational evaluation of unsaturated carbonitriles as neutral receptor model for beryllium(II) recognition
    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.
  8. Computational investigation of the microstructural characteristics and physical properties of glycerol-based deep eutectic solvents
    Aissaoui T, Benguerba Y, AlOmar MK, AlNashef IM
    J Mol Model, 2017 Sep 14;23(10):277.
    PMID: 28913646 DOI: 10.1007/s00894-017-3450-5
    Recently, there has been significant interest in the possibility of using deep eutectic solvents (DESs) as novel green media and alternatives to conventional solvents and ionic liquids (ILs) in many applications. Due to their attractive properties, such as their biodegradability, low cost, easy preparation, and nontoxicity, DESs appear to be very promising solvents for use in the field of green chemistry. This computational study investigated six glycerol-based DESs: DES1(glycerol:methyl triphenyl phosphonium bromide), DES2(glycerol:benzyl triphenyl phosphonium chloride), DES3(glycerol:allyl triphenyl phosphonium bromide), DES4(glycerol:choline chloride), DES5(glycerol:N,N-diethylethanolammonium chloride), and DES6(glycerol:tetra-n-butylammonium bromide). The chemical structures and combination mechanisms as well as the sigma profiles and sigma potentials of the studied DESs were explored in detail. Moreover, density, viscosity, vapor pressure, and IR analytical data were predicted and compared with the corresponding experimental values reported in the literature for these DESs. To achieve these goals, the conductor-like screening model for realistic solvents (COSMO-RS) and the Amsterdam Density Functional (ADF) software package were used. The predicted results were found to be in good agreement with the corresponding experimental values reported in the literature. Further theoretical investigations are needed to confirm the experimental results-regarding both properties and applications-reported for these DESs.
  9. DFT study of glucose based glycolipid crown ethers and their complexes with alkali metal cations Na(+) and K(+)
    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.
  10. DFT-B3LYP study of interactions between host biphenyl-1-aza-18-crown-6 ether derivatives and guest Cd(2+): NBO, NEDA, and QTAIM analyses
    Behjatmanesh-Ardakani R, Pourroustaei-Ardakani F, Taghdiri M, Kotena ZM
    J Mol Model, 2016 07;22(7):149.
    PMID: 27271162 DOI: 10.1007/s00894-016-3012-2
    This report present the results of natural energy decomposition analysis (NEDA), natural bond orbital (NBO), and quantum theory of atoms in molecules (QTAIM) calculations of three derivatives of biphenyl-1-aza-18-crown-6 ether and their 1:1 complexes with Cd(2+). All calculations used the B3LYP density functional theory in combination with the 6-311G and WTBS basis sets for ligands and Cd(2+) ion, respectively. Ligands 1 and 3 have a single 1-aza-18-crown-6, substituent; ligand 2 has two such substituents. The results show that, in the optimized geometries of the complexes, the distance between N and Cd(2+) is greater than the distance between O and Cd(2+). NBO and QTAIM data confirm these results. There was no stabilization energy or bond critical point for N · · · Cd(2+) in NBO or QTAIM, respectively. Data show that the O · · · Cd(2+) interaction is a kind of closed shell interaction. The trend of the calculated stabilization energy was similar to the experimental data. Different contributions of interaction energies for complex formation were analyzed by NEDA, and the results show that the main component of the interactions is accounted for by polarization.
  11. Development and application of fragment-based de novo inhibitor design approaches against Plasmodium falciparum GST
    Al-Qattan MNM, Mordi MN
    J Mol Model, 2023 Aug 16;29(9):281.
    PMID: 37584781 DOI: 10.1007/s00894-023-05650-0
    CONTEXT: Modulation of disease progression is frequently started by identifying biochemical pathway catalyzed by biomolecule that is prone to inhibition by small molecular weight ligands. Such ligands (leads) can be obtained from natural resources or synthetic libraries. However, de novo design based on fragments assembly and optimization is showing increasing success. Plasmodium falciparum parasite depends on glutathione-S-transferase (PfGST) in buffering oxidative heme as an approach to resist some antimalarials. Therefore, PfGST is considered an attractive target for drug development. In this research, fragment-based approaches were used to design molecules that can fit to glutathione (GSH) binding site (G-site) of PfGST.

    METHODS: The involved approaches build molecules from fragments that are either isosteric to GSH sub-moieties (ligand-based) or successfully docked to GSH binding sub-pockets (structure-based). Compared to reference GST inhibitor of S-hexyl GSH, ligands with improved rigidity, synthetic accessibility, and affinity to receptor were successfully designed. The method involves joining fragments to create ligands. The ligands were then explored using molecular docking, Cartesian coordinate's optimization, and simplified free energy determination as well as MD simulation and MMPBSA calculations. Several tools were used which include OPENEYE toolkit, Open Babel, Autodock Vina, Gromacs, and SwissParam server, and molecular mechanics force field of MMFF94 for optimization and CHARMM27 for MD simulation. In addition, in-house scripts written in Matlab were used to control fragments connection and automation of the tools.

  12. Diffusional behavior and guest conformational analysis of hexadecane-1,16-diol and hexadecane in urea crystal model via molecular dynamics simulation approach
    Mustafa SF, Maarof H, Ahmed R, Abdallah HH
    J Mol Model, 2016 Dec;22(12):290.
    PMID: 27866329
    Diffusion at the atomic or molecular level is a source of many physical, chemical, and biological processes taking place in plentiful materials. This work is an endeavor toward investigating the diffusional behavior of two different type of guests, hexadecane-1,16-diol and hexadecane enclathration in urea tunnel architecture, whereby the correlation of the diffusion mechanism with the guest's structural and conformational properties is explored. To carry out this study, molecular dynamics simulation approach is adopted. It is found that hexadecane-1,16-diol exhibit slower diffusion with an average diffusion coefficient value [Formula: see text], where hexadecane diffuse more rapidly with an average diffusion coefficient value [Formula: see text]. It is also observed that the structural properties influence the guest's travel distance and torsion angle distribution of the trans and gauche conformational proportion. Furthermore, the observed high energy barrier accounted for hexadecane-1,16-diol and low energy barrier for hexadecane along urea tunnel systems was analyzed. The comparison of our obtained results are in close agreement with the available experimental measurements, i.e., gauche proportion properties between two different guest molecules correlate well with Raman spectroscopy investigation on α,ω-dihalogenoalkane/urea inclusion compounds. Our calculations also successfully endorse the structure-property relation between the two systems.
  13. Docking of sialic acid analogues against influenza A hemagglutinin: a correlational study between experimentally measured and computationally estimated affinities
    Al-qattan MN, Mordi MN
    J Mol Model, 2010 May;16(5):1047-58.
    PMID: 19911202 DOI: 10.1007/s00894-009-0618-7
    A molecular docking tool of AutoDock3.05 was evaluated for its ability to reproduce experimentally determined affinities of various sialic acid analogues toward hemagglutinin of influenza A virus. With the exception of those with a C6-modified glycerol side chain, the experimental binding affinities of most sialic acid analogues (C2, C4 and C5-substituted) determined by viral hemadsorption inhibition assay, hemagglutination inhibition assay and nuclear magnetic resonance correlated well with the computationally estimated free energy of binding. Sialic acid analogues with modified glycerol side chains showed only poor correlation between the experimentally determined hemagglutinin inhibitor affinities and AutoDock3.05 scores, suggesting high mobility of the glutamic acid side chain at the glycerol binding pocket, which is difficult to simulate using a flexi-rigid molecular docking approach. In conclusion, except for some glycerol-substituted sialic acid analogues, the results showed the effectiveness of AutoDock3.05 searching and scoring functions in estimating affinities of sialic acid analogues toward influenza A hemagglutinin, making it a reliable tool for screening a database of virtually designed sialic acid analogues for hemagglutinin inhibitors.
  14. Does cation break the cyano bond? A critical evaluation of nitrile-cation interaction
    Woi PM, Bakar MA, Rosli AN, Lee VS, Ahmad MR, Zain S, et al.
    J Mol Model, 2014 May;20(5):2219.
    PMID: 24770548 DOI: 10.1007/s00894-014-2219-3
    DFT and G4 results reveal that cations display the following trends in imparting its positive charge to acrylonitrile; H⁺ > Li⁺ > Na⁺ > K⁺ for group I and Be²⁺ > Mg²⁺ > Ca²⁺ for group II. Solvation by water molecules and interaction with cation make the cyano bond more polarized and exhibits ketene-imine character. Bond order in nitrile-cation complexes has been predicted based on the s character of the covalent bond orbitals. Mulliken, CHELPG, and NPA charges are in good agreement in predicting positive charge buildup and GIAO nuclear deshileding on C1. G4 enthalpies show that Mg²⁺ is more strongly bound to acrylonitrile than to acetonitrile by 3 kcal mol⁻¹, and the proton affinity of the former is higher by 0.8 kcal mol⁻¹. G4 enthalpies of reductions support prior experimental observation that metalated conjugated nitriles show enhanced reactivity toward weak nucleophiles to afford Michael addition products.
  15. Effect of donor strength of extended alkyl auxiliary groups on optoelectronic and charge transport properties of novel naphtha[2,1-b:6,5-b']difuran derivatives: simple yet effective strategy
    Chaudhry AR, Ahmed R, Irfan A, Shaari A, Isa AR, Muhammad S, et al.
    J Mol Model, 2015 Aug;21(8):199.
    PMID: 26177706 DOI: 10.1007/s00894-015-2743-9
    The present study spotlights the designing of new derivatives of 2,7-bis (4-octylphenyl) naphtho [2,1-b:6,5-b'] difuran (C8-DPNDF) by substituting the alkyl groups (methyl, ethyl, propyl, butyl, pentyl, hexyl, and heptyl groups) at para position. Density functional theory (DFT) and time-dependent density functional theory (TD-DFT) methods are employed to optimize the molecular structures in ground and first excited states, respectively. Several electro-optical properties including hole/electron reorganization energies (λh/λe), electron affinities (EAs), ionization potentials (IPs), molecular electrostatic potentials (MEP), and frontier molecular orbitals (FMOs) have been evaluated. Furthermore their transfer integrals and intrinsic mobilities values have also been calculated. From this study, it is found that hole mobility of octyl containing derivative is raised to 4.69 cm(2) V(-1) s(-1). Moreover with attaching octyl group, hole transfer integral values have also been enhanced in newly designed derivatives. The balanced hole and electron reorganization energies, and improved transfer integrals lead to enhanced mobility in derivatives with octyl group, highlighting them as an efficient hole transfer material. Unlike the other electro-optical properties, the intrinsic hole mobility has increased because of transfer integral values of octyl containing derivative C8-DPNDF due to the dense and close crystal packing of C8-DPNDF. However, photostability of furan-based materials has not changed by increasing length of extended alkyl chain. Thus our present investigation highlights the importance of alkyl auxiliary groups that are often neglected/replaced with simple methyl group to save computation costs. Graphical Abstract The hole and electron reorganization energies of naphtho[2,1-b:6,5-b']difuran derivatives.
  16. Evaluation of hydrogen bonds formation in the selected rare sugars based on 6-31G* and 6-311 +  + G(d,p) basis sets
    Mosapour Kotena Z, Razi M, Ahmadi S
    J Mol Model, 2021 Oct 09;27(11):315.
    PMID: 34625848 DOI: 10.1007/s00894-021-04916-9
    Rare sugars are monosaccharides with tremendous potential for applications in pharmaceutical, cosmetics, nutraceutical, and flavors industries. The four rare sugars, including gulose, allose, altrose, and talose, are stereoisomers that are different in the hydroxyl group orientation (axial or equatorial) on the C2-4 atoms. The basis sets effect in evaluation of the possibility intramolecular hydrogen bonding (H-bonds) in the selected rare sugars was studied from 6-31G* to 6-311 ++ G(d,p) basis sets using DFT, AIM, and NBO methods. The results show that the selected rare sugars are more stable at 6-311 ++ G(d,p) basis sets compared to 6-31G* because their electronic energies were reduced between 158 and 164 (kcal.mol-1). The overall effect of basis set enhancement is to decrease H-bond energies in the range of  1.25 to 2.51 (kcal.mol-1) and stabilization energies between 2 and 5 (kcal.mol-1) in the selected rare sugars at the DFT level of theory. The intramolecular H-bond distances, H-bond energies obtained from the AIM analysis, and also the second-order stabilization energies obtained from the NBO analysis were fluctuated largely depending on the basis set. In summary, it was found that the use of 6-311 ++ G(d,p) basis set to be more efficient results in rare sugars geometry than the 6-31G* basis set.
  17. First principles investigations of vinazene molecule and molecular crystal: a prospective candidate for organic photovoltaic applications
    Mohamad M, Ahmed R, Shaari A, Goumri-Said S
    J Mol Model, 2015 Feb;21(2):27.
    PMID: 25631921 DOI: 10.1007/s00894-015-2582-8
    Escalating demand for sustainable energy resources, because of the rapid exhaustion of conventional energy resources as well as to maintain the environmental level of carbon dioxide (CO2) to avoid its adverse effect on the climate, has led to the exploitation of photovoltaic technology manifold more than ever. In this regard organic materials have attracted great attention on account of demonstrating their potential to harvest solar energy at an affordable rate for photovoltaic technology. 2-vinyl-4,5-dicyanoimidazole (vinazene) is considered as a suitable material over the fullerenes for photovoltaic applications because of its particular chemical and physical nature. In the present study, DFT approaches are employed to provide an exposition of optoelectronic properties of vinazene molecule and molecular crystal. To gain insight into its properties, different forms of exchange correlation energy functional/potential such as LDA, GGA, BLYP, and BL3YP are used. Calculated electronic structure of vinazene molecule has been displayed via HOMO-LUMO isosurfaces, whereas electronic structure of the vinazene molecular crystal, via electronic band structure, is presented. The calculated electronic and optical properties were analyzed and compared as well. Our results endorse vinazene as a suitable material for organic photovoltaic applications.
  18. First-principle investigations of structural, electronic, thermal, and mechanical properties of AlP1-xBix alloys
    Oumelaz F, Nemiri O, Boumaza A, Meradji H, Ghemid S, Khenata R, et al.
    J Mol Model, 2023 Mar 31;29(4):124.
    PMID: 37000284 DOI: 10.1007/s00894-023-05497-5
    CONTEXT: In this work, a comprehensive study concerning the physical properties of ternary alloys system (AlP1-xBix) at different concentrations is presented. The obtained results from our first-principle calculations are compared with previously reported studies in the literature and discussed in detail. Our computed results are found in a nice agreement where available with earlier reported results. Electronic band structures at the above-mentioned concentrations are also determined. Likewise, the impact of the varying temperature and pressure on Debye temperature, heat capacity, and entropy is analyzed as well. Furthermore, elastic constants and related elastic moduli results are also computed. Our results show that alloys are stable and found to be in brittle nature. This is the first quantitative study related to ternary alloys (AlP1-xBix) at mentioned concentrations. We soon expect the experimental confirmation of our predictions.

    METHOD: The calculations are performed, at concentrations x=0.0, 0.25, 0.5, 0.75, and 1.0 by using the "full potential (FP) linearized (L) augmented plane wave plus local orbital (APW+lo) method framed within density functional theory (DFT)" as recognized in the "WIEN2k computational code". The "quasi-harmonic Debye model" approach is employed to determine the thermal properties of the title alloys.

  19. Fullerene C60 containing porphyrin-like metal center as drug delivery system for ibuprofen drug
    Alipour E, Alimohammady F, Yumashev A, Maseleno A
    J Mol Model, 2019 Dec 13;26(1):7.
    PMID: 31834504 DOI: 10.1007/s00894-019-4267-1
    Today, drug delivery systems based on nanostructures have become the most efficient to be studied. Recent studies revealed that the fullerenes can be used as drug carriers and transport drugs in a target cell. The aim of the present work is to study the interaction of C60 fullerene containing porphyrin-like transition metal-N4 clusters (TMN4C55, TM = Fe, Co, and Ni) with a non-steroidal anti-inflammatory drug (ibuprofen (Ibp)) by employing the method of the density functional theory. Results showed that the C60 fullerene with TMN4 clusters could significantly enhance the tendency of C60 for adsorption of ibuprofen drug. Also, our ultraviolet-visible results show that the electronic spectra of Ibp/TMN4C55 complexes exhibit a blue shift toward lower wavelengths (higher energies). It was found that the NiN4C55 fullerene had high chemical reactivity, which was important for binding of the drug onto the carrier surface. In order to gain insight into the binding features of Ibp/TMN4C55 complexes, the atoms in molecules analysis was also performed. Our results exhibit the electrostatic features of the Ibp/TMN4C55 bonding. Consequently, this study demonstrated that the TMN4C55 fullerenes could be used as potential carriers for delivery of Ibp drug in the nanomedicine domain. Graphical Abstract The TMN4C55 (TM=Fe, Co, and Ni) fullerenes could be used as potential carriers for delivery of ibuprofen drug in the nanomedicine domain.
  20. Homology modeling of the human 5-HT1A, 5-HT 2A, D1, and D2 receptors: model refinement with molecular dynamics simulations and docking evaluation
    Yap BK, Buckle MJ, Doughty SW
    J Mol Model, 2012 Aug;18(8):3639-55.
    PMID: 22354276 DOI: 10.1007/s00894-012-1368-5
    5-HT(1A) serotonin and D1 dopamine receptor agonists have been postulated to be able to improve negative and cognitive impairment symptoms of schizophrenia, while partial agonists and antagonists of the D2 and 5-HT(2A) receptors have been reported to be effective in reducing positive symptoms. There is therefore a need for well-defined homology models for the design of more selective antipsychotic agents, since no three-dimensional (3D) crystal structures of these receptors are currently available. In this study, homology models were built based on the high-resolution crystal structure of the β(2)-adrenergic receptor (2RH1) and further refined via molecular dynamics simulations in a 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine (POPC) lipid bilayer system with the GROMOS96 53A6 united atom force field. Docking evaluations with representative agonists and antagonists using AutoDock 4.2 revealed binding modes in agreement with experimentally determined site-directed mutagenesis data and significant correlations between the computed and experimental pK (i) values. The models are also able to distinguish between antipsychotic agents with different selectivities and binding affinities for the four receptors, as well as to differentiate active compounds from decoys. Hence, these human 5-HT(1A), 5-HT(2A), D1 and D2 receptor homology models are capable of predicting the activities of novel ligands, and can be used as 3D templates for antipsychotic drug design and discovery.
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