76 results on '"Natarajan Sathiyamoorthy Venkataramanan"'
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2. Intermolecular hydrogen bond interactions in water clusters of zwitterionic glycine: DFT, MESP, AIM, RDG, and molecular dynamics analysis
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Natarajan Sathiyamoorthy, Venkataramanan, Suvitha, Ambigapathy, Abdul Rahim, Sirajunnisa, and Sahara, Ryoji
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- 2024
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3. Molecular insights into the complex formation between dodecamethylcucurbit[6]uril and phenylenediamine isomers
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Natarajan Sathiyamoorthy, Venkataramanan, Suvitha, Ambigapathy, and Sahara, Ryoji
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- 2022
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4. Intermolecular interactions in microhydrated ribonucleoside and deoxyribonucleoside: A computational study
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Natarajan Sathiyamoorthy, Venkataramanan, Suvitha, Ambigapathy, Sahara, Ryoji, and Kawazoe, Yoshiyuki
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- 2021
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5. Unveiling the gemcitabine drug complexation with cucurbit[n]urils (n=6-8): A computational analysis
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Natarajan Sathiyamoorthy Venkataramanan, Ambigapathy Suvitha, Ryoji Sahara, and Yoshiyuki Kawazoe
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Physical and Theoretical Chemistry ,Condensed Matter Physics - Abstract
In this work, the DFT-D3 method was employed to investigate the complex formation capability of gemcitabine drug with host cucurbit[n]uril Q[n] (n = 6,7 and8) molecules. The density functional theory studies demonstrate that the most stable configuration is a fully encapsulated complex. In the gemcitabine@[6] and gemcitabine@[7] encapsulated systems the gemcitabine amino -NH2 and the alcoholic group in the carbohydrate bonds with the carbonyl units of Q[n]. The addition of sodium ions leads to the partial exclusion of the gemcitabine molecule and the sodium atoms lie close to the carbonyl portal of Q[7]. Thermodynamic parameters computed for the complexation process exhibit high negative entropy change implying that the encapsulation process is spontaneous and is an enthalpy-driven process. Frontier molecular orbitals are located mainly on the gemcitabine uracil ring, before and after encapsulation formation, indicating that the encapsulation happens by pure physical adsorption. Quantitative molecular electrostatic potentials demonstrate a shift in charge occurs during the complex formation and is more pronounced in gemcitabine@Q[7]. AIM topological analysis illustrates that these complexes are stabilized by various noncovalent interactions including HBs and C···F interactions. The 2D RDG plots exhibit the presence of strong HBs and weak van der Waals interactions and the presence of steric repulsion. The isosurface NCI diagram shows predominant steric interaction in the gemcitabine@Q[6] complex. The NCI isosurface for gemcitabine encapsulated complexes with Q[7] and Q[8] host displays that the green patches are uniformly distributed in all directions. Finally, EDA results demonstrate Paulis repulsive energy is predominant in the gemcitabine@Q[6] complex, while the orbital and dispersion energies stabilize the gemcitabine@Q[7] complex.
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- 2022
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6. The structure, stability, thermochemistry, and bonding in SO3-(H2O)n (n=1–7) clusters: a computational analysis
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Ambigapathy Suvitha, Natarajan Sathiyamoorthy Venkataramanan, and Ryoji Sahara
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Physical and Theoretical Chemistry ,Condensed Matter Physics - Abstract
The structure, stability, and intermolecular interactions in SO3-(H2O)n(n = 1 -7) clusters were investigated using density functional and wave functional methods. The putative global minimum shows the SO3molecule tends to be on the surface water clusters. The increase in the number of water molecules chalcogen bond distance between water molecules and SO3decreases, while the maximum number of water molecules coordinated to the SO3molecule remains at three. The calculated solvation energy increases with the increase in the number of water molecules and it does not saturate, which indicates that the addition of water molecules can add up to the existing water cluster network. The interaction energy between water molecules and SO3was less than the solvation energy conforming to the cluster forming of water molecules. The Gibbs free energy and entropy values decrease with the increase in cluster size, signifying the amount of water molecule decide the sequential hydration process. Thermochemistry data at various temperatures show that low-temperature regions found in the upper part of the troposphere favor hydration formation. Molecular electrostatic potentials (MESP) show reduced Vs,max value of π-hole on sulfur atom, and increased value on hydrogens of water molecules which results in the addition of water which leads to the sequential addition of water molecules to the water network. The quantum theory of atoms in molecules (QTAIM) shows the presence of S···O, O···H interactions between SO3and water molecules. Between water molecules O···H, H-bonding interactions were observed, and in larger clusters, O···O interaction was also noticed. QTAIM analysis shows the water–water HBs in these clusters are weak H-bond, while the SO3-water interaction can be classified as medium H-bonds which was further supported by the NCI and 2D RDG plots.
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- 2022
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7. Review for "Noncovalent chalcogen and tetrel bonding interactions: Spectroscopic study of halide–carbonyl sulfide complexes"
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Natarajan Sathiyamoorthy, Venkataramanan, primary
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- 2022
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8. Demonstration of the first known 1:2 host-guest encapsulation of a platinum anticancer complex within a macrocycle
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Natarajan Sathiyamoorthy Venkataramanan, Yvonne E. Moussa, and Nial J. Wheate
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010405 organic chemistry ,Hydrogen bond ,Chemistry ,Guanosine ,chemistry.chemical_element ,General Chemistry ,010402 general chemistry ,Condensed Matter Physics ,Electrostatics ,01 natural sciences ,0104 chemical sciences ,chemistry.chemical_compound ,Crystallography ,Proton NMR ,Molecule ,Platinum ,Spectroscopy ,Stoichiometry ,Food Science - Abstract
This study examined the ability of the para-sulfonatocalix[8]arene (sCX[8]) macrocycle to encapsulate [Pt(H2O)2(R,R-dach)]2+, the active aquated component of oxaliplatin. Both the free 1R,2R-diaminocyclohexane (dach) ligand and [Pt(H2O)2(R,R-dach)]2+ formed host-guest complexes with sCX[8], as indicated by 1H nuclear magnetic resonance (NMR) spectroscopy and molecular modelling. This interaction uniquely occurred in a 1:2 host-guest stoichiometric ratio, such that one platinum molecule was bound at each of the two sCX[8] pseudo-cavities. The 1H NMR data showed this binding to be predominantly stabilised by hydrophobic effects, hydrogen bonds and electrostatic interactions, the latter of which were evidenced by the lack of host-guest complex formation for the uncharged [PtCl2(R,R-dach)] derivative. Contrastingly, molecular modelling results indicated that host-guest complex formation was predominantly due to hydrogen bonds and electrostatic interactions at the surface of the macrocycle, such that the dach groups of [Pt(H2O)2(R,R-dach)]2+ were projecting away from, and not bound through hydrophobic effects with, the pseudo-cavities of sCX[8]. Guanosine 5′-monophosphate binding studies demonstrated that complexation with the macrocycle did not affect the ability of [Pt(H2O)2(R,R-dach)]2+ to interact with its target, but rather, it was capable of doing so while still bound to sCX[8]. In total, these findings point to the potential role of sCX[8] as a delivery vehicle for other charged platinum complexes.
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- 2019
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9. Unraveling the binding nature of hexane with quinone functionalized pillar[5]quinone: a computational study
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Natarajan Sathiyamoorthy Venkataramanan, Yoshuyuki Kawazoe, and A. Suvitha
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Exergonic reaction ,010405 organic chemistry ,Chemistry ,General Chemistry ,Pillararene ,010402 general chemistry ,Condensed Matter Physics ,01 natural sciences ,0104 chemical sciences ,Quinone ,Hexane ,chemistry.chemical_compound ,Computational chemistry ,Electrophile ,Moiety ,Molecule ,Density functional theory ,Food Science - Abstract
The nature of host–guest interactions between the hexane and pillar[5]arene and its quinone modified pillararenes has been studied using dispersion-corrected density functional theory and wave functional methods. The introduction of quinone in pillararene prompted flexibility in structure and the electrophilicity of pillararenes increases with the number of quinone moiety. Thermochemical as well as energetic results indicate that hexane binding is favorable on all studied systems. The presence of quinone reduces the exothermicity, and exergonic nature and the decrease in temperature increases the free energy of formation. Molecular electrostatic potential analysis indicates the existence of charge transfer between the host and guest molecules. Quantum theory of atoms in molecule analysis reveals in the quinone functionalized pillararenes, the number of interactions arising from quinone is less than that on the 1,4-alkoxybenzene unit. Noncovalent interaction analysis shows a larger area of interactions correspond to C–H···π interactions in the encapsulated complexes. EDA results reveal that dispersion ΔEdisp interaction followed by electrostatic attraction ΔEelstat contributes mainly for the attractive terms. These insights can be used to tune further and improve the binding ability of pillararene guest towards linear host molecules.
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- 2019
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10. Electronic structure, stability, and cooperativity of chalcogen bonding in sulfur dioxide and hydrated sulfur dioxide clusters: a DFT study and wave functional analysis
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Natarajan Sathiyamoorthy Venkataramanan
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Chalcogen ,Crystallography ,Hydrogen bond ,Chemistry ,Intermolecular force ,Binding energy ,Atoms in molecules ,Molecule ,Density functional theory ,Electronic structure ,Physical and Theoretical Chemistry ,Condensed Matter Physics - Abstract
Density functional theory calculations and wave functional analysis are used to examine the (SO2)n and (SO2)n–H2O clusters with n = 1–7. The nature of interactions is explored by molecular electrostatic potentials, electron density distribution, atoms in molecules, noncovalent interaction, and energy decomposition analysis. The putative global minimum of SO2 molecules has a 3D growth pattern with tetrahedral. In the hydrated SO2 clusters, the pure hydrogen bond isomers are less stable than the O···S chalcogen bond isomers. The cluster absorption energy of SO2 on water increases with the size of sulfur dioxide, implying reactivity of sulfur dioxide with water increases with size. The presence of cooperativity was evident from the excellent linearity plot of binding energy/polarizability vs the number of SO2 molecules. Molecular electrostatic potential analysis elucidates the reason for the facile formation of S···O chalcogen than hydrogen bonding in hydrated sulfur dioxide. Atoms in molecule analysis characterize the bonds chalcogen and H bonds to be weak and electrostatic dominant. EDA analysis shows electrostatic interaction is dominated in complexes with more intermolecular chalcogen bonding and orbital interaction for systems with intermolecular H-bonding. The reduced density gradient (RDG) analysis of sulfur dioxide clusters has blue patches and green patches due to S···O chalcogen bonding O···O electrostatic interaction. The RDG analysis of hydrated sulfur dioxide clusters shows intensive blue patches and green patches for the existence of S···O chalcogen and hydrogen bonding respectively. Thus, the presence of strong electrostatic S···O chalcogen interaction and weak H bonds acts cooperatively and stabilize the hydrated sulfur dioxide clusters.
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- 2021
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11. A computational study on the complexation of bisbenzimidazolyl derivatives with cucurbituril and cyclohexylcucurbituril
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Natarajan Sathiyamoorthy Venkataramanan, Y. Kawazoe, Ambigapathy Suvitha, and R. Sahara
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010405 organic chemistry ,Chemistry ,Hydrogen bond ,Enthalpy ,General Chemistry ,010402 general chemistry ,Condensed Matter Physics ,01 natural sciences ,0104 chemical sciences ,Crystallography ,chemistry.chemical_compound ,Covalent bond ,Cucurbituril ,Molecule ,Density functional theory ,Reactivity (chemistry) ,Methylene ,Food Science - Abstract
The binding properties of 1,w- bisbenzimidazolyl derivatives with cucurbit[6]uril (CB6) and cyclohexanocucurbit[6]uril (CCB6) host, for 1:1 stoichiometry, have been studied using density functional theory. The distance between the two benimidazole acidic hydrogen’s along with the flexible butyl spacer group play a vital role in the complexation with host. The energetic analysis exhibits strong complexation ability of guests with CB6 than CCB6 host. The computed enthalpy and free energy change were negative indicating the encapsulation process to be spontaneous and thermodynamically favorable and enthalpy driven. The global reactivity descriptors based charge transfer calculations show that charge transfer occurs from the guest to host molecule which was supported by the electron density difference map. The main factors for the higher stability of stable complex was the presence of C-H····O = C hydrogen bonding interactions in addition to the weak C···O, C···N, N···O, C···H, H···N type of interactions. AIM topological parameters and NCI analysis reveals the existence of weak interaction, mainly of electrostatic in nature and more number of hydrogen bonds are present in stable complexes. EDA analysis demonstrates the presence of noncovalent and electrostatic interaction with partial covalent character in the encapsulated complexes. The lower stability of CCB6 complexes compare to CB6 are due to the presence of positive Vs,max values of cyclohexanone methylene hydrogen’s on CCB6 host.
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- 2021
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12. Sustainable Metallocavitand for Flue Gas-Selective Sorption: A Multiscale Study
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Natarajan Sathiyamoorthy Venkataramanan and Biswajit Mohanty
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Hydrogen ,Chemistry ,Hydrogen bond ,chemistry.chemical_element ,02 engineering and technology ,010402 general chemistry ,021001 nanoscience & nanotechnology ,01 natural sciences ,0104 chemical sciences ,Surfaces, Coatings and Films ,Electronic, Optical and Magnetic Materials ,symbols.namesake ,General Energy ,Adsorption ,Covalent bond ,Selective adsorption ,symbols ,Physical chemistry ,Molecule ,Density functional theory ,Physical and Theoretical Chemistry ,van der Waals force ,0210 nano-technology - Abstract
We have used density functional theory, Grand canonical Monte Carlo (GCMC), and ideal adsorption solution theory (IAST) to understand the selective adsorption of flue within the cavity of porous metallocavitand pillarplex (PPX) molecule. Energies associated with the guest@PPX complex formation depict the effectiveness of encapsulation of guest within PPX. PPX is noted to have high selectivity toward the adsorption of Br2, HBr, CS2, H2S, and NO2 over their respective congeners. The strength of bonding and nature of the interaction is deciphered via quantum theory of atoms in molecule, noncovalent interaction, and energy decomposition analysis scheme. The molecules containing acidic hydrogen, viz., H2O, H2S, HF, HCl, and HBr, make hydrogen bonding with the −N atom of the pyrazole ring, and F2 and Cl2 make partially covalent bonding interaction with the −Au atom of PPX. The interaction is mostly of the van der Waals type, except in F2, Cl2, NO, and HF, in which the cumulative contribution of orbital, electro...
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- 2019
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13. Investigation of potential anti-malarial lead candidate 2-(4-fluorobenzylthio)-5-(5-bromothiophen-2-yl)-1,3,4-oxadiazole: Insights from crystal structure, DFT, QTAIM and hybrid QM/MM binding energy analysis
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Lamya H. Al-Wahaibi, Natarajan Sathiyamoorthy Venkataramanan, Abdul-Malek S. Al-Tamimi, Subbiah Thamotharan, Judith Percino, Nandakumar Santhosh Kumar, Ali A. El-Emam, and Hazem A. Ghabbour
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biology ,010405 organic chemistry ,Chemistry ,Organic Chemistry ,Binding energy ,Oxadiazole ,Crystal structure ,010402 general chemistry ,01 natural sciences ,0104 chemical sciences ,Analytical Chemistry ,Inorganic Chemistry ,QM/MM ,chemistry.chemical_compound ,Crystallography ,Dihydrofolate reductase ,biology.protein ,Molecule ,Single crystal ,Spectroscopy ,Natural bond orbital - Abstract
A combined study involving single crystal X-ray diffraction and various theoretical approaches has been used to characterize the 2-(4-fluorobenzylthio)-5-(5-bromothiophen-2-yl)-1,3,4-oxadiazole compound. The crystal structure is primarily stabilized by intermolecular C H···π, C H⋯N and C H⋯F. A short and very rare halogen-halogen contact (Br⋯F) which adopts type I trans geometry along with the S⋯S, N⋯S contacts, which play an important role in the stabilization of the crystal packing. The importance of these contacts is established through various theoretical approaches such as QTAIM and NBO analysis. A detailed CSD analysis of Br⋯F contacts is performed to understand the geometrical preference. A detailed in silico analysis is performed to explore the binding potential of the title compound against the Plasmodium falciparum dihydrofolate reductase (PfDHFR). The results clearly suggest that the title compound may be a promising anti-malarial lead candidate by inhibiting the DHFR target and halogenated fragments of the molecule are important for the stabilization of the protein-ligand complex formation.
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- 2019
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14. Structure, stability, and nature of bonding between high energy water clusters confined inside cucurbituril: A computational study
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Ambigapathy Suvitha, Natarajan Sathiyamoorthy Venkataramanan, and Ryoji Sahara
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010304 chemical physics ,Chemistry ,Binding energy ,Intermolecular force ,010402 general chemistry ,Condensed Matter Physics ,01 natural sciences ,Biochemistry ,0104 chemical sciences ,Molecular dynamics ,Chemical physics ,Intramolecular force ,0103 physical sciences ,Potential energy surface ,Cluster (physics) ,Molecule ,Density functional theory ,Physical and Theoretical Chemistry - Abstract
The structure and stability of the high energy water molecules inside the CB7 cavity was studied using the dispersion corrected density functional theory (DFT) and molecular dynamics (MD). The intermolecular distance between the O and H in the water molecule was found to decrease upon the encapsulation of water molecules inside the cavity, indicating the increase in the stability of water clusters. The computed binding energies were found to be sensitive to the choice of functional. Energy decomposition analysis (EDA) shows that the repulsive Pauli interaction decides the stability of the water complex. In all the encapsulated systems, except the eight water clusters, the electrostatic interactions have supremacy over the dispersive term, due to the large polarization induced by the water clusters. Molecular electrostatic potentials of entrapped systems show the charge distribution between CB7 and water clusters. QTAIM analysis indicates the existence of noncovalent intramolecular interactions between CB7 and water clusters and ellipticity values to be least for 8H2O@CB7. The topological of ρ(r) fields at the urido nitrogen plane in CB7, proves the stronger bonding with water molecules. Thus, entrapped water molecules are not electronically innocent inside the cage and have noncovalent interaction with hydrophobic part of CB7 molecule. Atom centered Density Matrix Propagation (ADMP) molecular dynamic studies shows that the water clusters are stable with respect to their isolated cluster geometry, inside the cucurbituril and the change in potential energy surface is due to the distortion in the geometry of the CB7 unit.
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- 2019
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15. Deciphering the nature of interactions in nandrolone/testosterone encapsulated cucurbituril complexes: a computational study
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Maaouia Souissi, R. Sahara, Ambigapathy Suvitha, and Natarajan Sathiyamoorthy Venkataramanan
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Steric effects ,010405 organic chemistry ,Chemistry ,Hydrogen bond ,Intermolecular force ,General Chemistry ,010402 general chemistry ,Condensed Matter Physics ,01 natural sciences ,0104 chemical sciences ,symbols.namesake ,Crystallography ,Nandrolone ,Cucurbituril ,symbols ,medicine ,Molecule ,Density functional theory ,van der Waals force ,Food Science ,medicine.drug - Abstract
The intention of the study is to find the nature of interactions that exist in inclusion complexes formed between the steroids, nandrolone, and testosterone with cucurbit[n]urnils (n = 7 and 8) host, using density functional theory incorporated with empirical dispersion correction. Upon encapsulation, nandrolone caused a larger geometrical distortion in cucurbit[8]uril geometry, while testosterone inclusion complex is formed with a larger number of intermolecular hydrogen bonds. The molecular electrostatic potential examination shows that the positive potential observed on the eight-membered ring in CB7 got reduced upon encapsulation, while on the nandrolone the negative potential on carbonyl unit has increased. AIM analysis shows that in inclusion complexes, the observed electron density are higher for the interactions between the oxygen atoms of carbonyl fringe of cucurbituril molecule and the steroid molecules. The NCI isosurface of nandrolone@CB7 has green patches in between the nandrolone and cucurbituril molecule, evenly distributed. In the testosterone@CB7, along with the green patches, red patches, due to the steric crowding between the testosterone and cucurbit[7]uril, were observed. The energy decomposition analysis parameters show that Pauli’s repulsive term was highest for nandrolone@CB7. When testosterone is the guest, repulsive energy was found to be larger than nandrolone guest. From the above interference, it can be confirmed that the steric hindrance that arises during the interaction of testosterone with CB7 reduces the stability of the complex, and the nandrolone best fit inside the CB7 cavity with the combination of hydrogen bonding and weak van der Waals bonding as intermolecular interactions.
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- 2018
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16. Unravelling the nature of binding of cubane and substituted cubanes within cucurbiturils: A DFT and NCI study
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Yoshiyuki Kawazoe, Natarajan Sathiyamoorthy Venkataramanan, and Ambigapathy Suvitha
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chemistry.chemical_classification ,010405 organic chemistry ,010402 general chemistry ,Condensed Matter Physics ,Electrostatics ,01 natural sciences ,Atomic and Molecular Physics, and Optics ,0104 chemical sciences ,Electronic, Optical and Magnetic Materials ,Gibbs free energy ,chemistry.chemical_compound ,Crystallography ,symbols.namesake ,Electron transfer ,chemistry ,Cubane ,Cucurbituril ,Materials Chemistry ,symbols ,Molecule ,Non-covalent interactions ,Density functional theory ,Physical and Theoretical Chemistry ,Spectroscopy - Abstract
The nature of interactions between the neutral, charged and substituted cubane, within cucurbituril host were analyzed employing the dispersion corrected density functional theory. The structural comparison between the inclusion complexes of CB7 and CB8 shows a best fit for the CB7. The computed Gibbs free energy for the formation of inclusion complexes by the neutral guests were close to the experimental estimate. The dicationic guest within CB has the highest strain energy with least strain on the host. The conceptual DFT based analysis ECT analysis shows a charge transfer from the host to guest in neutral systems, while for the dicationic guest an electron transfer from guest to host has been noticed, which was further conformed from the quantitative MESP values. The computed NICS values on the cubane, are not affected by the introduction of charge/substituents implying that cubane part act as a spacer group while the functional groups present on the cubane dictates the charge transfer. In AIM analysis, the ρ value is least for the complex cubane@CB7 and highest for the cubane functionalized dicationic complex@CB complexes. The NCI-RDG analysis for the inclusion complex with dicarboxylic guest, the spike at higher density region undergoes a shift, reflecting the increase in repulsive energy. In the inclusion complexes of CB7 the patch escalation in the NCI isosurface occurs evenly in CB7 than on the CB8 inclusion complexes, signifying the fit-induced extra stability of the CB7 inclusion complexes. EDA analysis shows that the Pauli repulsive energy increase with the increase in the size of the guest molecule and among the guest the dicationic has the highest repulsive energy. The presence of higher amount of electrostatic interactions in the dicationic complex has remunerated the dispersion contribution in the dicationic complexes.
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- 2018
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17. Nature of bonding and cooperativity in linear DMSO clusters: A DFT, AIM and NCI analysis
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Natarajan Sathiyamoorthy Venkataramanan and Ambigapathy Suvitha
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Models, Molecular ,Static Electricity ,Physics::Medical Physics ,Binding energy ,Molecular Conformation ,Cooperativity ,Trimer ,010402 general chemistry ,01 natural sciences ,Materials Chemistry ,Molecule ,Dimethyl Sulfoxide ,Physical and Theoretical Chemistry ,Spectroscopy ,010405 organic chemistry ,Hydrogen bond ,Chemistry ,Atoms in molecules ,Hydrogen Bonding ,Hydrogen atom ,Computer Graphics and Computer-Aided Design ,0104 chemical sciences ,Crystallography ,Models, Chemical ,Quantum Theory ,Density functional theory ,Algorithms - Abstract
This study aims to cast light on the nature of interactions and cooperativity that exists in linear dimethyl sulfoxide (DMSO) clusters using dispersion corrected density functional theory. In the linear DMSO, DMSO molecules in the middle of the clusters are bound strongly than at the terminal. The plot of the total binding energy of the clusters vs the cluster size and mean polarizabilities vs cluster size shows an excellent linearity demonstrating the presence of cooperativity effect. The computed incremental binding energy of the clusters remains nearly constant, implying that DMSO addition at the terminal site can happen to form an infinite chain. In the linear clusters, two σ-hole at the terminal DMSO molecules were found and the value on it was found to increase with the increase in cluster size. The quantum theory of atoms in molecules topography shows the existence of hydrogen and SO⋯S type in linear tetramer and larger clusters. In the dimer and trimer SO⋯OS type of interaction exists. In 2D non-covalent interactions plot, additional peaks in the regions which contribute to the stabilization of the clusters were observed and it splits in the trimer and intensifies in the larger clusters. In the trimer and larger clusters in addition to the blue patches due to hydrogen bonds, additional, light blue patches were seen between the hydrogen atom of the methyl groups and the sulphur atom of the nearby DMSO molecule. Thus, in addition to the strong H-bonds, strong electrostatic interactions between the sulphur atom and methyl hydrogens exists in the linear clusters.
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- 2018
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18. Theoretical investigations of two adamantane derivatives: A combined X-ray, DFT, QTAIM analysis and molecular docking
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Judith Percino, Fatmah A.M. Al-Omary, Lamya H. Al-Wahaibi, Subramaniam Sujay, Ali A. El-Emam, Natarajan Sathiyamoorthy Venkataramanan, Subbiah Thamotharan, Gangadharan Ganesh Muthu, and Hazem A. Ghabbour
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010405 organic chemistry ,Chemistry ,Hydrogen bond ,Adamantane ,Organic Chemistry ,Cyclohexane conformation ,Intermolecular force ,chemistry.chemical_element ,Crystal structure ,010402 general chemistry ,01 natural sciences ,0104 chemical sciences ,Analytical Chemistry ,Inorganic Chemistry ,Crystal ,Crystallography ,chemistry.chemical_compound ,Fluorine ,HOMO/LUMO ,Spectroscopy - Abstract
A detailed structural analysis of two adamantane derivatives namely, ethyl 2-[(Z)-1-(adamantan-1-yl)-3-(phenyl)isothioureido]acetate I and ethyl 2-[(Z)-1-(adamantan-1-yl)-3-(4-fluorophenyl)isothioureido]acetate II is carried out to understand the effect of fluorine substitution. The introduction of fluorine atom alters the crystal packing and is completely different from its parent compound. The fluorine substitution drastically reduced the intermolecular H⋯H contacts and this reduction is compensated by intermolecular F⋯H and F⋯F contacts. The relative contributions of various intermolecular contacts present in these structures were quantified using Hirshfeld surface analysis. Energetically significant molecular pairs were identified from the crystal structures of these compounds using PIXEL method. The structures of I and II are optimized in gas and solvent phases using the B3LYP-D3/6-311++G(d,p) level of theory. The quantum theory of atoms-in-molecules (QTAIM) analysis was carried out to estimate the strengths of various intermolecular contacts present in these molecular dimers. The results suggest that the H H bonding take part in the stabilization of crystal structures. The experimental and theoretical UV–Vis results show the variations in HOMO and LUMO energy levels. In silico docking analysis indicates that both compounds I and II may exhibit inhibitory activity against 11-β-hydroxysteroid dehydrogenase 1 (11-β-HSD1).
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- 2018
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19. Piperine Encapsulation within Cucurbit[n]uril (n=6,7): A Combined Experimental and Density Functional Study
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A. Suvitha, Natarajan Sathiyamoorthy Venkataramanan, and Biswajit Mohanty
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chemistry.chemical_classification ,chemistry.chemical_compound ,010405 organic chemistry ,Chemistry ,Cucurbituril ,Piperine ,Non-covalent interactions ,General Chemistry ,010402 general chemistry ,01 natural sciences ,Combinatorial chemistry ,0104 chemical sciences ,Encapsulation (networking) - Published
- 2018
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20. Density functional theory study on the dihydrogen bond cooperativity in the growth behavior of dimethyl sulfoxide clusters
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A. Suvitha, Natarajan Sathiyamoorthy Venkataramanan, and Yoshiyuki Kawazoe
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chemistry.chemical_classification ,010304 chemical physics ,Hydrogen bond ,Intermolecular force ,Interaction energy ,010402 general chemistry ,Condensed Matter Physics ,01 natural sciences ,Atomic and Molecular Physics, and Optics ,0104 chemical sciences ,Electronic, Optical and Magnetic Materials ,Delocalized electron ,Crystallography ,chemistry ,0103 physical sciences ,Materials Chemistry ,Non-covalent interactions ,Dihydrogen bond ,Molecule ,Density functional theory ,Physical and Theoretical Chemistry ,Spectroscopy - Abstract
We have carried out a density functional theory study on the structures of DMSO clusters and analysed the structure and their stability using molecular electrostatic potential and quantum theory of atoms-in-molecules (QTAIM). The ground state geometry of the DMSO clusters, prefer to exist in ouroboros shape. Pair wise interaction energy calculation show the interaction between methyl groups of adjacent DMSO molecules and destabilization is created by the methyl groups which are away from each other. Molecular electrostatic potential analysis shows the existence of σ-hole on the odd numbered clusters, which helps in their highly directional growth. QTAIM analysis show the existence of two intermolecular hydrogen bonds, of type S O ⋯ H C hydrogen bonds and methyl C H ⋯ H C dihydrogen bonds. The computed ρ and Laplacian values were all positive for the intermolecular bonds, supporting the existence of noncovalent interactions. The computed ellipticity for the dihydrogen bonds have values > 2, which confirms the delocalization of electron, are mainly due to the hydrogen-hydrogen interactions of methyl groups. A plot of total hydrogen bonding energy vs the observed total local electron density shows linearity with correlation coefficient of near unity, which indicates the cooperative effects of intermolecular dihydrogen H·H bonds.
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- 2018
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21. Intermolecular interaction in nucleobases and dimethyl sulfoxide/water molecules: A DFT, NBO, AIM and NCI analysis
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Natarajan Sathiyamoorthy Venkataramanan, Yoshiyuki Kawazoe, and A. Suvitha
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Models, Molecular ,Electron density ,Molecular Conformation ,010402 general chemistry ,01 natural sciences ,Nucleobase ,Heterocyclic Compounds ,Computational chemistry ,Materials Chemistry ,Molecule ,Non-covalent interactions ,Dimethyl Sulfoxide ,Physical and Theoretical Chemistry ,Spectroscopy ,chemistry.chemical_classification ,010405 organic chemistry ,Hydrogen bond ,Water ,Hydrogen Bonding ,Computer Graphics and Computer-Aided Design ,0104 chemical sciences ,chemistry ,Covalent bond ,Solvents ,Quantum Theory ,Thermodynamics ,Dispersion (chemistry) ,Natural bond orbital - Abstract
This study aims to cast light on the physico-chemical nature and energetics of interactions between the nucleobases and water/DMSO molecules which occurs through the non-conventional CH⋯O/N-H bonds using a comprehensive quantum-chemical approach. The computed interaction energies do not show any appreciable change for all the nucleobase-solvent complexes, conforming the experimental findings on the hydration enthalpies. Compared to water, DMSO form complexes with high interaction energies. The quantitative molecular electrostatic potentials display a charge transfer during the complexation. NBO analysis shows the nucleobase-DMSO complexes, have higher stabilization energy values than the nucleobase-water complexes. AIM analysis illustrates that the in the nucleobase-DMSO complexes, SO⋯H-N type interaction have strongest hydrogen bond strength with high EHB values. Furthermore, the Laplacian of electron density and total electron density were negative indicating the partial covalent nature of bonding in these systems, while the other bonds are classified as noncovalent interactions. EDA analysis indicates, the electrostatic interaction is more pronounced in the case of nucleobase-water complexes, while the dispersion contribution is more dominant in nucleobase-DMSO complexes. NCI-RDG analysis proves the existence of strong hydrogen bonding in nucleobase-DMSO complex, which supports the AIM results.
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- 2017
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22. Electrochemical investigations of Co3Fe-RGO as a bifunctional catalyst for oxygen reduction and evolution reactions in alkaline media
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Brij Kishore, N. Munichandraiah, Surender Kumar, S. Ranganatha, Divyaratan Kumar, and Natarajan Sathiyamoorthy Venkataramanan
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Materials science ,Alloy ,Inorganic chemistry ,Oxide ,General Physics and Astronomy ,chemistry.chemical_element ,Nanoparticle ,Proton exchange membrane fuel cell ,02 engineering and technology ,engineering.material ,010402 general chemistry ,Electrochemistry ,01 natural sciences ,Oxygen ,Catalysis ,chemistry.chemical_compound ,technology, industry, and agriculture ,Surfaces and Interfaces ,General Chemistry ,equipment and supplies ,021001 nanoscience & nanotechnology ,Condensed Matter Physics ,0104 chemical sciences ,Surfaces, Coatings and Films ,Bifunctional catalyst ,chemistry ,Chemical engineering ,engineering ,0210 nano-technology - Abstract
Nanoparticles of Co 3 Fe alloy is prepared on reduced graphene oxide (RGO) sheets by modified polyol method. Synthesized alloy particles are characterized by various physicochemical techniques. TEM and SEM pictures showed homogeneously dispersed alloy nanoparticles on the RGO sheets. Electrochemistry of alloy nanoparticles is investigated in alkaline medium. The result shows that oxygen evaluation reaction (OER) activity of Co 3 Fe-RGO is higher than Pt-black particles. RDE studies in alkaline medium shows that oxygen reduction reaction (ORR) follow four electron pathway. It is suggest that Co 3 Fe-RGO is an efficient non-precious catalyst for oxygen (ORR/OER) reactions in alkaline electrolyte for PEMFC applications.
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- 2017
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23. Investigation of inclusion complexation of acetaminophen with pillar [5]arene: UV–Vis, NMR and quantum chemical study
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Ashiwini Vijayaraghavan, Natarajan Sathiyamoorthy Venkataramanan, A. Suvitha, and Subbiah Thamotharan
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010405 organic chemistry ,Stereochemistry ,Chemistry ,Binding energy ,Intermolecular force ,Pillar ,010402 general chemistry ,Condensed Matter Physics ,01 natural sciences ,Atomic and Molecular Physics, and Optics ,0104 chemical sciences ,Electronic, Optical and Magnetic Materials ,Crystallography ,Ultraviolet visible spectroscopy ,Materials Chemistry ,Molecule ,Physical and Theoretical Chemistry ,Inclusion (mineral) ,Spectroscopy ,Stoichiometry ,Natural bond orbital - Abstract
We have carried out combined experimental and density functional study on the complexation of acetaminophen and with pillar [5]arene. UV–Vis and NMR studies indicates the stoichiometry between acetaminophen and pillar [5]arene to be 1:1. The computed binding energy and the formation energy show the inclusion complex is stable, and its formation can occur at room temperature. The HOMO-LUMO gap for the inclusion complex is lower than the pristine pillar [5]arene and acetaminophen, which indicates that complex formation can be kinetically controllable. MESP and NBO analysis support the occurrence of charge transfer between the guest and host molecule. AIM analysis establishes the intermolecular bonds in the inclusion complex can be classified under a category with partially noncovalent and with a partial electrostatic in character. NCI isosurface displays blue patches due to H-bonding and green patches due to electrostatic interaction and is evenly distributed inside the pillar [5]arene, that could be responsible for the stabilization of the inclusion complex.
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- 2017
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24. Theoretical Investigation of the Binding of Nucleobases to Cucurbiturils by Dispersion Corrected DFT Approaches
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Natarajan Sathiyamoorthy Venkataramanan and A. Suvitha
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Bridged-Ring Compounds ,Guanine ,Static Electricity ,Binding energy ,Covalent Interaction ,010402 general chemistry ,01 natural sciences ,Nucleobase ,symbols.namesake ,Computational chemistry ,Materials Chemistry ,Physical and Theoretical Chemistry ,Binding Sites ,010405 organic chemistry ,Chemistry ,Intermolecular force ,Imidazoles ,Solvation ,Charge density ,0104 chemical sciences ,Surfaces, Coatings and Films ,Chemical physics ,symbols ,Quantum Theory ,Thermodynamics ,Density functional theory ,van der Waals force - Abstract
The encapsulation of nucleobases inside CB7 has gained prominence due to its use as anticancer and antiviral drugs. With this respect, the nonconvalent interactions existing in the nucleobases encapsulated inside the CB7 cavity have been analyzed employing the dispersion corrected density functional theory. The CBn cavity has the ability to encapsulate two guest nucleobases molecules when they are aligned in parallel configuration. The computed association energy using the two- and three-body correction method computed at B3LYP-D3 level is close to the experimental estimate. The use of dispersion corrected DFs is essential to identify the correct binding energies. The solvation energy plays a vital role in the estimation of association energy. QTAIM analysis shows that the Laplacian of the charge density (∇2ρ) is negative and the presence of covalent interaction between the guest and host molecule. The NCI-RDG isosurface shows the presence of noncovalent intermolecular interactions such as van der Waals a...
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- 2017
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25. Structure, electronic, inclusion complex formation behavior and spectral properties of pillarplex
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A. Suvitha and Natarajan Sathiyamoorthy Venkataramanan
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010405 organic chemistry ,Chemistry ,Binding energy ,General Chemistry ,Electronic structure ,010402 general chemistry ,Condensed Matter Physics ,01 natural sciences ,0104 chemical sciences ,Gibbs free energy ,Metal ,NMR spectra database ,symbols.namesake ,Chemical physics ,visual_art ,visual_art.visual_art_medium ,symbols ,Molecule ,Density functional theory ,Food Science ,Natural bond orbital - Abstract
Electronic structure, vibrational and NMR spectra of metal-Pillarplex (metal = Cu, Ag and Au) and its inclusion complex with 1,8-diaminooctane (DAO) are investigated by using density functional theory. The coordinated metal atoms tune the cavity size and the height of metal-Pillarplex and form a rigid cavity thereby reducing their structural deformation. Cu-Pillarplex undergoes a large deformation both on the host and guest molecule. The calculated Gibbs free energy for the formation of inclusion complex were negative indicating their facile formation at the room temperature. Computed binding energies with various functionals and energy decomposition analysis, shows that dispersion correction is essential in these systems. The low binding energy, and the physical adsorption of guest molecule and HOMO–LUMO spatial diagram indicates, that the Au and Ag-Pillarplex can be used as reversible host for linear alkanes Complexation of guest engenders frequency shift in the vibrational spectra. Calculated 1H NMR reveal that guest protons which are closer to the metal sites experience larger shielding possibly due to C–H→LP* metal interaction. The 15N signal observed for the DAO is nearly identical to that observed for the DAO@metal-Pillarplex. NBO and AIM analysis indicate that metal centers in host, play a major role in stabilizing the guest inside the cavity than the amino group on the guest molecule.
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- 2017
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26. Investigation of 9-(2-hydroxy-4,4-dimethyl-6-oxocyclohex-1-en-1-yl)-3,3-dimethyl-2,3,4,9-tetrahydro-1H-xanthen-1-one: Crystal structure, AIM and NBO analysis
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Subbiah Thamotharan, Kullaiah Byrappa, Natarajan Sathiyamoorthy Venkataramanan, Kothandapani Jagatheeswaran, Shankar Madan Kumar, Subramaniapillai Selva Ganesan, and Mani Udayakumar
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010405 organic chemistry ,Chemistry ,Dimer ,Organic Chemistry ,Intermolecular force ,Crystal structure ,010402 general chemistry ,01 natural sciences ,0104 chemical sciences ,Analytical Chemistry ,Inorganic Chemistry ,Crystal ,Crystallography ,chemistry.chemical_compound ,Molecular vibration ,Molecule ,Single crystal ,Spectroscopy ,Natural bond orbital - Abstract
Single crystal X-ray analysis reveals that the 9-(2-hydroxy-4,4-dimethyl-6-oxocyclohex-1-en-1-yl)-3,3-dimethyl-2,3,4,9-tetrahydro-1H-xanthen-1-one, crystallizes in the centrosymmetric space group P21/c. In the crystal, molecules form as a dimer through a keto-enol type hydrogen-bonding pattern along with intermolecular C H⋯O interactions. The crystal structure of the title compound is further stabilized by intermolecular H⋯H interactions. Various intermolecular interactions present in the crystal structure are quantified by Hirshfeld surface analysis, PIXEL energy, NBO, AIM and DFT calculations. The energetics of the title compound is also compared with that of the two closely related analogs. Further, the vibrational modes of the interacting groups are characterized using both the experimental and simulated FT-IR and FT-Raman spectra. The experimental and calculated UV–visible spectra are compared and agree well. The time-dependent DFT spectra suggest that the ligand-to-ligand charge transfer within the molecule is responsible for the intense absorbance.
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- 2017
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27. Trapping of organophosphorus chemical nerve agents by pillar[5]arene: A DFT, AIM, NCI and EDA analysis
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Natarajan Sathiyamoorthy Venkataramanan and A. Suvitha
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chemistry.chemical_classification ,010405 organic chemistry ,Stereochemistry ,Hydrogen bond ,Dimethyl methylphosphonate ,Binding energy ,Charge density ,General Chemistry ,010402 general chemistry ,Condensed Matter Physics ,01 natural sciences ,0104 chemical sciences ,Gibbs free energy ,chemistry.chemical_compound ,Crystallography ,symbols.namesake ,chemistry ,symbols ,Molecule ,Non-covalent interactions ,van der Waals force ,Food Science - Abstract
The encapsulation of organophosphorus (OP) nerve agents by pillar[5]arene (P5) molecule, shows that adsorption occurs with a larger structural reorganization of the host molecule. The computed binding energies shows that the complexes formed are more stable inside the cavity. Tabun was found to have the highest binding energy among the studied OPs. The computed Gibbs free energy is negative for Dimethyl methylphosphonate, sarin and tabun, and are positive for soman (GD) and ethyl-S-dimethylaminoethyl methylphosphonothiolate (VX). The inclusion complexes were found to have lower band gap. The quantum theory of Atoms-in-molecules analysis shows that ρ values were positive which implies the existence of noncovalent interactions. The Laplacian of the charge density ∇2ρ for bond critical points bonds are small and are negative which indicates the depletion of electronic charge along the bond paths and existence of an electrostatic nature of bonding between the guest and host molecule. The noncovalent interactions analysis clearly shows the existence of hydrogen bonding and van der Waals bonding in these inclusion complexes. The energy decomposition analysis shows that the, interaction between the P5 and the larger guest molecules VX and GD are mainly due to electrostatic interaction and for small guest, the interactions are mostly of van der Waals type.
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- 2017
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28. Structural investigation of (2E)-2-(ethoxycarbonyl)-3-[(4-methoxyphenyl)amino]prop-2-enoic acid: X-ray crystal structure, spectroscopy and DFT
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Tom Sundius, Perumal Venkatesan, Andivelu Ilangovan, V. Rajakannan, Natarajan Sathiyamoorthy Venkataramanan, and Subbiah Thamotharan
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Lattice energy ,010405 organic chemistry ,Chemistry ,Organic Chemistry ,Intermolecular force ,Crystal structure ,010402 general chemistry ,01 natural sciences ,Acceptor ,0104 chemical sciences ,Analytical Chemistry ,Inorganic Chemistry ,Crystallography ,Computational chemistry ,Intramolecular force ,Molecule ,HOMO/LUMO ,Spectroscopy ,Natural bond orbital - Abstract
The title compound, (2E)-2-(ethoxycarbonyl)-3-[(4-methoxyphenyl)amino]prop-2-enoic acid is characterized by means of X-ray crystallography, spectroscopic methods and quantum chemical calculations. The title compound crystallizes in centrosymmetric space group P21/c. Moreover, the crystal structure is primarily stabilized through intramolecular N H⋯O and O H⋯O and intermolecular N H⋯O and C H⋯O interactions along with carbonyl⋯carbonyl and C H⋯C contacts. These intermolecular interactions are analysed and quantified by using Hirshfeld surface analysis, PIXEL energy, NBO, AIM and DFT calculations. The overall lattice energies of the title and parent compounds suggest that the title compound is stabilized by a 4.5 kcal mol−1 higher energy than the parent compound. The additional stabilization force comes from the methoxy substitution on the title molecule, which is evident since the methoxy group is involved in the intermolecular C H⋯O interaction as an acceptor. The vibrational modes of the interacting groups are investigated using both experimental and theoretical FT-IR and FT-Raman spectra. The experimental and theoretical UV–Vis spectra agree well. The time dependent DFT spectra show that the ligand-to-ligand charge transfer is responsible for the intense absorbance of the compound.
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- 2016
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29. Structure, stability and reactivity of neutral and charged monomeric chromium oxide clusters
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Natarajan Sathiyamoorthy Venkataramanan, Sourabh S. Nair, D. Vignesh, A. Suvitha, and S. Prakash
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Coordination number ,Inorganic chemistry ,chemistry.chemical_element ,02 engineering and technology ,010402 general chemistry ,021001 nanoscience & nanotechnology ,Condensed Matter Physics ,01 natural sciences ,Biochemistry ,Oxygen ,Dissociation (chemistry) ,0104 chemical sciences ,chemistry.chemical_compound ,Crystallography ,Monomer ,Fragmentation (mass spectrometry) ,chemistry ,Cluster (physics) ,Chromium oxide ,Ozonide ,Physical and Theoretical Chemistry ,0210 nano-technology - Abstract
We report a density–functional study on monomeric chromium oxide cluster: The maximum coordination number of the CrOn cluster was eight. The computed fragmentation energies for the various dissociation channels of oxygen, shows that oxo releases in these monomeric clusters are less likely to occur compared to the dioxygen and ozonide release. We have observed the existence of neutral CrOn clusters with n
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- 2016
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30. A theoretical exploration of the intermolecular interactions between resveratrol and water: a DFT and AIM analysis
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Y. Kawazoe, Natarajan Sathiyamoorthy Venkataramanan, Ambigapathy Suvitha, and Ryoji Sahara
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Aqueous solution ,010304 chemical physics ,Hydrogen ,Chemistry ,Hydrogen bond ,Organic Chemistry ,Intermolecular force ,chemistry.chemical_element ,010402 general chemistry ,01 natural sciences ,Catalysis ,0104 chemical sciences ,Computer Science Applications ,Inorganic Chemistry ,symbols.namesake ,Computational Theory and Mathematics ,Computational chemistry ,Phase (matter) ,0103 physical sciences ,symbols ,Molecule ,Density functional theory ,Physical and Theoretical Chemistry ,van der Waals force - Abstract
The polyphenolic compound resveratrol, classified under stilbenes, offers a broad range of health advantages, including neuroprotection and playing a role in autophagy in the nervous system. However, resveratrol has poor water solubility and is soluble in the gel phase in liposomal membranes. The main aim of this work was to understand the nature of the interactions between resveratrol and water molecules. In the present study, we used the dispersion corrected density functional theory (DFT) method to study hydrogen bonding interactions. Eight different geometries of resveratrol-water complexes were identified by optimizing the geometries by placing water at various locations. We observed the two lowest energy structures to be isoenergetic. In most complexes, water interaction occurs with phenolic hydrogen as all the phenolic hydroxyl groups have identical Vs,max values. Energy decomposition analysis shows that the dispersion contribution was minimal in these complexes, while electrostatic and orbital contributions were larger. Complex formation between water and the resveratrol molecule results in a blue shift in the vibrational frequency, along with an increase in intensity due to the transfer of electron density. The hydrogen bonds in the resveratrol-water complexes have closed-shell interactions with a medium-to-strong bonding nature. Noncovalent index analysis of the complexes shows that, in addition to hydrogen bonding, electrostatic and van der Waal's interactions play a key role in stabilizing the complexes. Graphical abstract Noncovalent index analysis showing that, in addition to hydrogen bonding, electrostatic and van der Waal's interactions play a major role in stabilizing resveratrol-water complexes.
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- 2019
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31. Recent advances in MXenes: from fundamentals to applications
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Abhishek K. Singh, Natarajan Sathiyamoorthy Venkataramanan, Mohammad Khazaei, Seiji Yunoki, and Avanish Mishra
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Elemental composition ,Condensed Matter - Materials Science ,Materials science ,020502 materials ,Materials Science (cond-mat.mtrl-sci) ,FOS: Physical sciences ,Nanotechnology ,02 engineering and technology ,High surface ,0205 materials engineering ,Chemical diversity ,General Materials Science ,MAX phases ,MXenes ,Science, technology and society - Abstract
The family of MAX phases and their derivative MXenes are continuously growing in terms of both crystalline and composition varieties. In the last couple of years, several breakthroughs have been achieved that boosted the synthesis of novel MAX phases with ordered double transition metals and, consequently, the synthesis of novel MXenes with a higher chemical diversity and structural complexity, rarely seen in other families of two-dimensional (2D) materials. Considering the various elemental composition possibilities, surface functional tunability, various magnetic orders, and large spin–orbit coupling, MXenes can truly be considered as multifunctional materials that can be used to realize highly correlated phenomena. In addition, owing to their large surface area, hydrophilicity, adsorption ability, and high surface reactivity, MXenes have attracted attention for many applications, e.g., catalysts, ion batteries, gas storage media, and sensors. Given the fast progress of MXene-based science and technology, it is timely to update our current knowledge on various properties and possible applications. Since many theoretical predictions remain to be experimentally proven, here we mainly emphasize the physics and chemistry that can be observed in MXenes and discuss how these properties can be tuned or used for different applications.
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- 2019
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32. Encapsulation of sulfur, oxygen, and nitrogen mustards by cucurbiturils: a DFT study
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Natarajan Sathiyamoorthy Venkataramanan and Suvitha Ambigapathy
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chemistry.chemical_classification ,Hydrogen bond ,Chemistry ,Intermolecular force ,Atoms in molecules ,General Chemistry ,Interaction energy ,Condensed Matter Physics ,Bond order ,Crystallography ,Computational chemistry ,Molecule ,Non-covalent interactions ,Lone pair ,Food Science - Abstract
A density functional theory analysis on the encapsulation of sulphur mustard (HD), oxygen mustard (OM), and nitrogen mustard (N1) by cucurbit[7]uril (CB[7]) molecule was carried out using the dispersion corrected B3LYP-D/6-311+G(d,p) method. The encapsulation of HD, OM and N1, have favorable interaction energy and are found to be functional dependent. Amongst the encapsulated molecules, N1@CB[7] has the least highest occupied molecular obitual- lowest unoccupied molecular orbital gap, which indicates that nitrogen mustard can be reversible stored inside CB[7]. Molecular electrostatic potential studies shows that charge transfer occurs between the host and guest molecule during the complexation process. Atoms-in-molecules analysis at the intermolecular bond critical points, have positive charge density, negative Laplacian and close to zero value of total energy density, indicating the depletion of electronic charge along the bond paths, which implies an electrostatic nature of bonding. The natural bond order analysis of N1@CB[7] complex with highest strongest second order perturbation energies are due to the donation of lone pair nitrogen of CB molecule to the guest molecule and the back donation of charge, leads to the high interaction energy. Non covalent index isosurface clearly show the existence of hydrogen bonding and van der Walls intermolecular interaction between the guest molecule and the host CB[7].
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- 2015
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33. Effect of oxygen content and charge on the structure, stability and optoelectronic properties of yttrium oxide clusters
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Natarajan Sathiyamoorthy Venkataramanan
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education.field_of_study ,Valence (chemistry) ,Inorganic chemistry ,Population ,Ionic bonding ,chemistry.chemical_element ,General Chemistry ,Yttrium ,Condensed Matter Physics ,Delocalized electron ,Crystallography ,chemistry ,Physics::Atomic and Molecular Clusters ,Cluster (physics) ,Molecule ,General Materials Science ,Density functional theory ,Physics::Chemical Physics ,education - Abstract
The electronic and geometrical structures of neutral and charged YOn (n=2–12) clusters have been investigated using density functional theory (DFT) with generalized gradient approximation. The oxygen atom in YOn has been found to be in oxo, peroxo and in superoxo forms. The geometrical structures and topologies of small size anionic clusters resemble that of neutral clusters. Yttrium showed higher coordination number than scandium. Computed results reveal the existence of YO10 cluster to have a penta-peroxo oxygen with a homoleptic Y(η2 –O2)5 geometrical configuration. The HOMO–LUMO gaps decrease with increasing n due to the increase in 2p orbital population of oxygen atoms. It has been shown that in these clusters bonding are predominantly ionic in nature and anions are thermodynamically more stable, due to the charge delocalization between the metal atom and oxygen ligands. YO10+ and YO12+ were found to be highly exothermic to release one and two oxygen molecules, while YO11+ dissociates though the ozonide dissociation channel. Computed absorption spectra of small clusters are mainly contributed by yttrium metal d and s valence orbitals. The absorbance spectra, shifts towards lower energy with cluster size increase, while charge has no substantial effect on the absorption spectrum.
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- 2015
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34. Computational study on the interactions of mustard gas with cucurbituril macrocycles
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Yoshiyuki Kawazoe, Hiroshi Mizuseki, Natarajan Sathiyamoorthy Venkataramanan, and A. Suvitha
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Heteroatom ,Intermolecular force ,Sulfur mustard ,Condensed Matter Physics ,Photochemistry ,Atomic and Molecular Physics, and Optics ,chemistry.chemical_compound ,chemistry ,Cucurbituril ,Intramolecular force ,Molecule ,Organic chemistry ,Physical and Theoretical Chemistry ,Absorption (chemistry) ,Macromolecule - Abstract
The study on the absorption of toxic gases such as mustard gas by organic host is essential to the development of inexpensive detection and decontamination equipments. Using quantum chemical methods, we propose cucurbituril as an effective host to capture mustard gas. It was found that stable complexes are formed with the inclusion of the toxic gas molecules inside the cucurbituril cavity, compared with the lateral and exterior interactions. Oxygen mustard has a comparable binding energy with sulfur mustard and hence can be used during experimental investigation. Additionally, during the inclusion complex formation, the presence of heteroatoms helps the guest molecules to undergo a larger structural reorganization to get accommodated inside the cucurbituril macromolecule. Atoms-in-molecules analysis shows the existence of strong intermolecular CH…O bonding between the guest molecules and cucurbituril macromolecule. The presence of an intramolecular CH…Cl type of bonding accounts for the higher stabilization of sulfur mustard inside the cucurbituril macromolecule. © 2015 Wiley Periodicals, Inc.
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- 2015
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35. Self-Reversible Mechanochromism and Thermochromism of a Triphenylamine-Based Molecule: Tunable Fluorescence and Nanofabrication Studies
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Dohyun Moon, P. S. Hariharan, Natarajan Sathiyamoorthy Venkataramanan, and Savarimuthu Philip Anthony
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Thermochromism ,Materials science ,Fluorophore ,Fluorescence in the life sciences ,Photochemistry ,Triphenylamine ,Fluorescence ,Fluorescence spectroscopy ,Surfaces, Coatings and Films ,Electronic, Optical and Magnetic Materials ,chemistry.chemical_compound ,General Energy ,Resonance fluorescence ,chemistry ,Intramolecular force ,Physical and Theoretical Chemistry - Abstract
A triphenylamine-based fluorophore, 4-((4-methoxyphenyl)(phenyl)amino)benzaldehyde (1), exhibits external-stimuli-responsive self-reversible solid-state fluorescence switching, tunable fluorescence, and a rare phenomenon of temperature-dependent fluorescence. Mechanically grinding a crystalline powder of 1 converts the blue fluorescence (λmax = 457 nm) to green (λmax = 502 nm), but blue fluorescence robustly self-recovers within 8 min. X-ray analysis and theoretical studies suggest that the change from a highly twisted molecular conformation and crystalline form into an amorphous phase with more planar conformation is responsible for the fluorescence switching. Self-reversible fluorescence switching did not show a significant change in fluorescence for several cycles of measurement. Interestingly, 1 in toluene showed a rare phenomenon of fluorescence enhancement with increasing temperature via activating more vibrational bands that lead to stronger twisted intramolecular charge-transfer (TICT) emissions. ...
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- 2015
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36. Quantitative analysis of intermolecular interactions in 2,2’-((4-bromophenyl)methylene)bis(3-hydroxy-5,5-dimethylcyclohex-2-en-1-one): insights from crystal structure, PIXEL, Hirshfeld surfaces and QTAIM analysis
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Fernando Robles, Jagatheeswaran Kothandapani, Judith Percino, Kullaiah Byrappa, Subbiah Thamotharan, Subramaniapillai Selva Ganesan, Natarajan Sathiyamoorthy Venkataramanan, and Shankar Madan Kumar
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Lattice energy ,Materials science ,010405 organic chemistry ,Hydrogen bond ,Oscillator strength ,Intermolecular force ,General Chemistry ,Crystal structure ,010402 general chemistry ,01 natural sciences ,0104 chemical sciences ,Crystallography ,chemistry.chemical_compound ,chemistry ,Intramolecular force ,Molecular vibration ,Methylene - Abstract
The crystallographic study of 2,2’-((4-bromophenyl)methylene)bis(3-hydroxy-5,5-dimethylcyclohex-2-en-1-one) reveals that the compound crystallizes in the centrosymmetric space group $$P2_{1}/c$$ . In the solid state, the structure of the title compound exhibits two strong intramolecular $$\hbox {O}{-}\hbox {H}\cdots \hbox { O}$$ hydrogen bonding interactions. Further, molecules of the title compound are self-assembled by weak intermolecular $$\hbox {C}{-}\hbox {H}\cdots \hbox {O}, \pi \cdots \pi $$ and $$\hbox {H}\cdots \hbox { H}$$ and $$\hbox {C}{-}\hbox {H}\cdots \hbox { Br}$$ contacts. Various intermolecular interaction that exist in the crystal structure and their energetics are quantified using PIXEL, DFT and QTAIM analyses. Six different motifs are identified from the PIXEL calculation. Lattice energy calculation suggests that the dispersion energy has the highest contribution for the crystal formation. The relative contributions of various intermolecular contacts in the title compound and its closely related analogs are evaluated using Hirshfeld surface analysis and the decomposed fingerprint plots. The common packing features exist between the title compound and its related analogs are identified. The quantitative molecular electrostatic potential surface diagram depicts the potential binding sites which are in good agreement with the crystal structure of the title compound. The structures of title compound in gas and solvent phases are compared with the experimental structure and reveals that they are superimposed very well. The vibrational modes of the monomer and four most stabilized dimers are characterized using both the experimental and DFT calculations. The UV-Vis spectrum is calculated using time dependent-DFT (TD-DFT) method and compared with experimental spectrum. The results indicate that the calculated energy of absorbance and oscillator strength correlate well with the experimental data. SYNOPSIS. Synthesis and crystal structure analysis of 2,2’-((4-bromophenyl)methylene) bis(3-hydroxy-5,5-dimethylcyclohex-2-en-1-one) are reported. Molecules of this compound are self-assembled by intermolecular $$\hbox {C}{-}\hbox {H}\cdots \hbox {O}$$ , $$\pi \cdots \pi $$ and $$\hbox {H}\cdots \hbox { H}$$ and $$\hbox {C}{-}\hbox {H}\cdots \hbox { Br}$$ interactions. The relative contributions of various intermolecular interactions in the bromo derivative and its closely related analogs are quantified using theoretical approaches.
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- 2018
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37. A theoretical study of the effects of transition metal dopants on the adsorption and dissociation of hydrogen on nickel clusters
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Natarajan Sathiyamoorthy Venkataramanan, Hiroshi Mizuseki, A. Suvitha, and Yoshiyuki Kawazoe
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Hydrogen ,Inorganic chemistry ,chemistry.chemical_element ,Condensed Matter Physics ,Atomic and Molecular Physics, and Optics ,Dissociation (chemistry) ,Catalysis ,Nickel ,Adsorption ,chemistry ,Physisorption ,Transition metal ,Chemisorption ,Physical chemistry ,Physical and Theoretical Chemistry - Abstract
The structure, stability, adsorption, and dissociation of H2 on nickel clusters doped with late transition metals were investigated using density functional theory with the BP86 functional. Molecular hydrogen physisorption occurred at a vertex atom with a low coordination number. Charge transfer between clusters and the H2 molecule stabilized the physisorption. The chemisorption of H2 occurred at the bridge sites, without any structural or spin change of the clusters. Among the pentamer clusters, Cd, Zn, and Au had the lowest chemisorption energies, while Ir and Pt had higher chemisorption energies for hydrogen. The computed reaction energies and activation barriers for the dissociation mechanism showed that dopants such as Rh, Pd, Pt, and Au have endothermic reaction energies and low activation barriers. This facilitates the reversible adsorption/dissociation of the H2 molecule on these metal-doped clusters. The dopant atoms play a major role in modulating the physisorption, chemisorption, and dissociation mechanism of H2 on nickel clusters. V C 2013 Wiley
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- 2013
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38. Loading of a Phenanthroline-Based Platinum(II) Complex onto the Surface of a Carbon Nanotube via pi–pi Stacking
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Natarajan Sathiyamoorthy Venkataramanan, Stephanie Houston, Nial J. Wheate, and A. Suvitha
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Fullerene ,Phenanthroline ,Stacking ,Supramolecular chemistry ,chemistry.chemical_element ,02 engineering and technology ,Carbon nanotube ,010402 general chemistry ,01 natural sciences ,law.invention ,chemistry.chemical_compound ,law ,cancer ,platinum ,carbon nanotube ,Ligand ,General Chemistry ,021001 nanoscience & nanotechnology ,pluronic ,0104 chemical sciences ,phenanthroline ,molecular modelling ,Crystallography ,buckyball ,chemistry ,Physical chemistry ,Self-assembly ,0210 nano-technology ,Platinum - Abstract
Stacking of the metal complex [(5,6-dimethyl-1,10-phenanthroline)(1S,2S-diaminocyclohexane)platinum(ii)]2+ (56MESS) onto the surface of two different fullerenes, a carbon nanotube (CNT), and a C60-buckyball was examined. The metal complex forms a supramolecular complex with multi-walled CNTs but not with buckyballs. Binding of 56MESS to the CNTs is highly efficient (90 %) but can be further stabilized by the addition of the surfactant, pluronic F-127, which resulted in a loading efficiency of 95 %. Molecular modelling shows that binding of 56MESS to the CNT is supported by the large surface area of the fullerene, whereas the more pronounced curvature and lack of a flat surface on the buckyball affects the ability of 56MESS to form bonds to its surface. The loading of 56MESS onto the CNT is via π–π stacking from the metal complex phenanthroline ligand and C–H···π bonding from the diaminocyclohexane ligand. 56MESS has 13 critical bonding points with the CNT, eight of which are π–π stacking bonds, but the metal complex forms only seven bonds with the buckyball. In addition, the loading of 56MESS onto the CNT results in a charge transfer of –0.111 eV; however, charge transfer is almost negligible for binding to the buckyball.
- Published
- 2016
39. Novel Electronic and Magnetic Properties of Two-Dimensional Transition Metal Carbides and Nitrides
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Yoshio Sakka, Yoshiyuki Kawazoe, Mohammad Khazaei, Taizo Sasaki, Natarajan Sathiyamoorthy Venkataramanan, Mehdi Estili, Chan Yeup Chung, and Masao Arai
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Transition metal carbides ,Materials science ,business.industry ,Metallurgy ,Nitride ,Condensed Matter Physics ,Electronic, Optical and Magnetic Materials ,Biomaterials ,symbols.namesake ,Semiconductor ,Thermoelectric effect ,Boltzmann constant ,Electrochemistry ,symbols ,Surface modification ,Physical chemistry ,MAX phases ,MXenes ,business - Abstract
Layered MAX phases are exfoliated into 2D single layers and multilayers, so-called MXenes. Using fi rst-principles calculations, the formation and electronic properties of various MXene systems, M 2 C (M = Sc, Ti, V, Cr, Zr, Nb, Ta) and M 2 N (M = Ti, Cr, Zr) with surfaces chemically functionalized by F, OH, and O groups, are examined. Upon appropriate surface functionalization, Sc 2 C, Ti 2 C, Zr 2 C, and Hf 2 C MXenes are expected to become semiconductors. It is also derived theoretically that functionalized Cr 2 C and Cr 2 N MXenes are magnetic. Thermoelectric calculations based on the Boltzmann theory imply that semiconducting MXenes attain very large Seebeck coeffi cients at low temperatures.
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- 2012
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40. Microsolvation of DMSO: Density functional study on the structure and polaraizabilities
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Natarajan Sathiyamoorthy Venkataramanan
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Hydrogen bond ,Chemistry ,Dimethyl sulfoxide ,Physics::Medical Physics ,Infrared spectroscopy ,Condensed Matter Physics ,Atomic and Molecular Physics, and Optics ,Bond length ,Solvent ,chemistry.chemical_compound ,Polarizability ,Computational chemistry ,Chemical physics ,Molecule ,Physical and Theoretical Chemistry ,Ground state - Abstract
The structure and stability for the association of water with dimethyl sulfoxide (DMSO) are investigated using the density functional M06-2X level theory. Stable complexes are formed by the formation of hydrogen bonding between water and oxygen atom of DMSO molecule, while the electrostatic force between water and DMSO plays a vital role in deciding the structure. The water-DMSO interactions are stronger than the interwater hydrogen bonds, which can be inferred from the shorter DMSO-water bond distance compared with the water– water bond distance. The calculated solvent association energy does not saturate, and it remains favorable to attach additional water molecules to the existing water network. The calculated IR spectra shifts supports the formation stronger hydrogen bonding, while the electrostatic potential (ESP) plot supports the existence of weaker electrostatic interaction in the studied clusters. The polarizabilities for the ground state clusters were found to increase monotonically with the cluster size. The presence of additional electrostatic bonding between water and DMSO, devastates the linear hydrogen-bonding network. V C 2011 Wiley Periodicals, Inc.
- Published
- 2011
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41. Single walled carbon nanotubes functionalized with hydrides as potential hydrogen storage media: A survey of intermolecular interactions
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Velappa Jayaraman Surya, Yoshiyuki Kawazoe, Natarajan Sathiyamoorthy Venkataramanan, K. Iyakutti, and Hiroshi Mizuseki
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chemistry.chemical_classification ,Materials science ,Hydrogen ,Intermolecular force ,chemistry.chemical_element ,Nanotechnology ,Carbon nanotube ,Condensed Matter Physics ,Electrostatics ,Electronic, Optical and Magnetic Materials ,law.invention ,symbols.namesake ,Hydrogen storage ,Chemical engineering ,chemistry ,law ,symbols ,Non-covalent interactions ,Molecule ,van der Waals force - Abstract
In this paper, we have analyzed the intermolecular interactions between H2 and single walled carbon nanotube (SWCNT)–hydride complexes and project their capability as a practicable hydrogen storage medium (HSM). In this respect, we have investigated the type of interactions namely van der Waals, electrostatic, and orbital interactions to understand the molecular hydrogen binding affinity of various systems. We found that the charge transfer effects coupled with induced electrostatic interactions are responsible for synergetic action of SWCNT and hydrides on adsorption of H2 molecules at ambient conditions. Also we have calculated the thermodynamically usable capacity of hydrogen in all the systems. This study enables one to identify and design potential hydrogen storage materials.
- Published
- 2011
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42. Electronic structures and spectra of symmetric meso-substituted porphyrin: DFT and TDDFT-PCM investigations
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Yoshiyuki Kawazoe, Hiroshi Mizuseki, A. Suvitha, Hitoshi Nejo, and Natarajan Sathiyamoorthy Venkataramanan
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Oscillator strength ,Solvation ,Free base ,Time-dependent density functional theory ,Condensed Matter Physics ,Ring (chemistry) ,Photochemistry ,Porphyrin ,Atomic and Molecular Physics, and Optics ,chemistry.chemical_compound ,Crystallography ,chemistry ,Bathochromic shift ,Polar effect ,Physical and Theoretical Chemistry - Abstract
DFT and TDDFT calculations at the level of PBE0/6-31G(d)/6-31+G(d) were performed systematically on seven porphyrins with symmetrical meso-substitutents. Our results show that the planarity of the free base porphyrin (BP) are affected by the introduction of substitutents at the meso-position of the ring. Geometrical studies show that the introduction of electron-withdrawing groups brings about in-plane deformation in the porphyrin ring, whereas the bulky substitutents make an out-of-plane deformation. However, FMO's diagram shows that electron-withdrawing groups alter the degeneracy of the HOMO and HOMO −1 orbtial. Up on introduction of substituents at the meso-position, the Q band FMOs transitions were the same as in the case of free BP; however, the oscillator strength is changed. Electron releasing substituted at the meso-position shows bathochromic shift in the Q band region. However, the intensity or the hyperchromic shift is higher for the electron withdrawing groups. Solvation studies show that Q bands are blue shifted and B bands are red shifted, whereas the intensity of the B bands was highly enhanced compared with the Q bands. These theoretical studies would be helpful in designing new porphyrins for the photodynamic therapy and dye-sensitized solar cell applications. © 2010 Wiley Periodicals, Inc. Int J Quantum Chem, 2011
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- 2011
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43. Theoretical investigation on the alkali-metal doped BN fullerene as a material for hydrogen storage
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Natarajan Sathiyamoorthy Venkataramanan, Rodion Vladimirovich Belosludov, Ryunosuke Note, Ryoji Sahara, Hiroshi Mizuseki, and Yoshiyuki Kawazoe
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Hydrogen ,Cryo-adsorption ,Binding energy ,Inorganic chemistry ,General Physics and Astronomy ,chemistry.chemical_element ,Hydrogen atom abstraction ,Hydrogen storage ,Adsorption ,chemistry ,Chemisorption ,Physical chemistry ,Molecule ,Physical and Theoretical Chemistry - Abstract
First-principles calculations have been used to investigate hydrogen adsorption on alkali atom doped B 36 N 36 clusters. The alkali atom adsorption takes place near the six tetragonal bridge sites available on the cage, thereby avoiding the notorious clustering problem. Adsorption of alkali atoms involves a charge transfer process, creating positively charged alkali atoms and this polarizes the H 2 molecules thereby, increasing their binding energy. Li atom has been found to adsorb up to three hydrogen molecules with an average binding energy of 0.189 eV. The fully doped Li 6 B 36 N 36 cluster has been found to hold up to 18 hydrogen molecules with the average binding energy of 0.146 eV. This corresponds to a gravimetric density of hydrogen storage of 3.7 wt.%. Chemisorption on the Li 6 B 36 N 36 has been found to be an exothermic reaction, in which 60 hydrogen atoms chemisorbed with an average chemisorption energy of −2.13 eV. Thus, the maximum hydrogen storage capacity of Li doped BN fullerene is 8.9 wt.% in which 60 hydrogen atoms were chemisorbed and 12 hydrogen molecules were adsorbed in molecular form.
- Published
- 2010
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44. Quantum chemical study on the alkali atom doped calix[4]arene as hydrogen storage material
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Hiroshi Mizuseki, Ryoji Sahara, Yoshiyuki Kawazoe, and Natarajan Sathiyamoorthy Venkataramanan
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General Computer Science ,Hydrogen ,Chemistry ,Inorganic chemistry ,Binding energy ,General Physics and Astronomy ,chemistry.chemical_element ,General Chemistry ,Alkali metal ,Condensed Matter::Materials Science ,Computational Mathematics ,Dipole ,Hydrogen storage ,Adsorption ,Mechanics of Materials ,Physics::Atomic and Molecular Clusters ,Physical chemistry ,Molecule ,General Materials Science ,Metal-organic framework ,Physics::Atomic Physics ,Physics::Chemical Physics - Abstract
We have demonstrated that doping alkali cations in charged state can improve the hydrogen adsorption significantly in the molecular form. In addition, the number of hydrogen molecules adsorbed by Li cation doped benzene system was 3 while Na and K doped benzene were able to adsorb up to 6 hydrogen molecules. In general the adsorption energies of alkali atoms and the binding energy/H2 for hydrogen are underestimated by the hybrid B3LYP functional, while MP2 functional provides higher binding energy. The nature of interaction between hydrogen and the alkali center was mainly due to be dipole – quardupole and dipole – induced dipole electrostatic interaction. Further, we extended the present single benzene system to the curved calixarene system. The calixarene ring was able to adsorb up to five alkali atoms, one inside the cavity and 4 on the walls of the cavity and this system was capable to adsorb up to 30 H2 molecules in molecular form at low temperature.
- Published
- 2010
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45. Titanium-Doped Nickel Clusters TiNin (n = 1−12): Geometry, Electronic, Magnetic, and Hydrogen Adsorption Properties
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Hiroshi Mizuseki, Yoshiyuki Kawazoe, R. Sahara, and Natarajan Sathiyamoorthy Venkataramanan
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Pseudopotential ,Condensed Matter::Materials Science ,Crystallography ,Nickel ,Hydrogen ,chemistry ,Chemisorption ,Hydride ,Atom ,Binding energy ,chemistry.chemical_element ,Density functional theory ,Physical and Theoretical Chemistry - Abstract
Using the first principles method, we study the growth behavior and electronic and magnetic properties of TiNi(n) (n = 1-12) clusters to clarify the effect of Ti modulation on the nickel nanostructures. Furthermore, chemisorption of H(2) was studied to understand the chemical reactivity of H(2) on the small Ni- and Ti-doped Ni clusters. The calculations are performed using the plane wave pseudopotential approach under the density functional theory and generalized gradient approximation for the exchange and correlation functional. The optimized geometries of TiNi(n-1) clusters indicate that the substitution of Ti brings a substantial structural reconstruction from 3D structure to a layer structure in which Ti atom is found to coordinate with Ni atoms to a maximum extent. This is accompanied by a significant enhancement in binding energies and reduction in chemical reactivity. Furthermore, the magnetic moments of the small Ti-doped Ni clusters are quenched because of the antiferromagnetic alignment of the Ti electrons. The lowest-energy structure of H(2) chemisorbed on Ni clusters shows that hydrogen prefers to adsorb on the edge site with two hydrogen atoms on these clusters in neighboring sites as the preferred arrangement. The incorporation of Ti atom improves the chemisorption energy of Ni clusters. Bader charge analysis indicates that with the formation of metal hydride, the H atoms withdraw charges from the metal centers, making them lose an electron, and carry a positive charge over them. Furthermore, Ti doping is found to enhance the chemical reactivity of Ni clusters.
- Published
- 2010
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46. HYDROGEN STORAGE ON NANOFULLERENE CAGES
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Hiroshi Mizuseki, Natarajan Sathiyamoorthy Venkataramanan, and Yoshiyuki Kawazoe
- Subjects
Materials science ,Dopant ,Hydrogen ,Doping ,Binding energy ,Inorganic chemistry ,chemistry.chemical_element ,Condensed Matter Physics ,Alkali metal ,Hydrogen storage ,chemistry ,Chemical physics ,General Materials Science ,Density functional theory ,Boron - Abstract
In this paper, we discuss and compare various nanocage materials proposed theoretically as storage medium for hydrogen. Doping of transition elements leads to clustering which reduces the gravimetric density of hydrogen, while doping of alkali and alkali-earth metals on the nanocage materials, such as carborides, boronitride, and boron cages, were stabilized by the charger transfer from the dopant to the nanocage. Further, the alkali or alkali-earth elements exist with a charge, which are found to be responsible for the higher uptake of hydrogen, through a dipole–dipole and change-induced dipole interaction. The binding energies of hydrogen on these systems were found to be in the range of 0.1 eV to 0.2 eV, which are ideal for the practical applications in a reversible system.
- Published
- 2009
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47. Clustering of functional molecules on a single-walled carbon-nanotube surface and its effect on hydrogen storage
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Velappa Jayaraman Surya, Yoshiyuki Kawazoe, K. Iyakutti, Natarajan Sathiyamoorthy Venkataramanan, and M. Rajarajeswari
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Surface (mathematics) ,Stereochemistry ,Chemistry ,Carbon nanotube ,Condensed Matter Physics ,Electronic, Optical and Magnetic Materials ,law.invention ,Hydrogen storage ,Adsorption ,Functional importance ,Chemical engineering ,law ,Surface modification ,Molecule ,Cluster analysis - Abstract
This first-principles study deals with the effect of clustering of different functional molecules adsorbed on the surface of the single-walled carbon nanotubes (SWCNT S ) (5, 5). Here we report the results of our investigation on the effect of clustering on storage capacity, the nature of H 2 bonding and strength of H 2 binding. The investigation is carried out for (5, 5) SWCNT functionalized with different types of hydrogen-rich molecules such as AlH 3 , NH 3 , BH 3 and NiH 2 . In the case of AlH 3 , the clustering turns into dimerization with the adsorption of H 2 . This is distinctly different from the other three cases. Weak clustering is observed for full coverage of NH 3 molecules. The clustering starts with higher coverage of H 2 molecules in the case of SWCNT functionalized with BH 3 molecules. The clusters of NiH 2 molecules, chemisorbed on the surface of carbon nanotube, are observed. Our study indicates that depending upon the materials used for the functionalization, the clustering pattern is different and the effect on the above-mentioned factors is also different.
- Published
- 2009
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48. Theoretical insights into the formation, structure, and electronic properties of anticancer oxaliplatin drug and cucurbit[n]urils n = 5 to 8
- Author
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Natarajan Sathiyamoorthy Venkataramanan, A. Suvitha, Nobiaki Ohuchi, Yoshiyuki Kawazoe, and Hiroshi Mizuseki
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Aqueous solution ,Hydrogen bond ,Stereochemistry ,General Chemistry ,Condensed Matter Physics ,Metal ,chemistry.chemical_compound ,Crystallography ,chemistry ,Cucurbituril ,visual_art ,visual_art.visual_art_medium ,Amine gas treating ,Carboxylate ,HOMO/LUMO ,Food Science ,Natural bond orbital - Abstract
Geometries, formation and electronic properties of cucurbit[n]uril-oxaliplatin n = 5–8, host-guest complexes are investigated with DFT calculations. The formation of inclusion complexes of CB[n]-oxaliplatin are facile in CB[n] n = 6–8. In the complex, the cyclohexyl group is found to be deep inside the cavity, with the formation of a hydrogen bonding between the portal oxygen atoms and the amine nitrogen of the oxaliplatin guest. NBO analysis shows the transfer of charge from the metal center to the CB[7] unit and the existence of hydrogen bonding between the oxygen portal and amine nitrogen. The HOMO orbital is localized on the carboxylate group and the LUMO orbital are localized on the cucurbituril unit in CB[7]-oxaliplatin complex. The strength of the interaction determined here reflects the ability of CB[n] to act as a host for suitably oxaliplatin guests, even in aqueous solution.
- Published
- 2009
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49. Structures of small YnAlm clusters (n+m⩽6): A DFT study
- Author
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Natarajan Sathiyamoorthy Venkataramanan, Ambigapathy Suvitha, Ryunosuke Note, and Yoshiyuki Kawazoe
- Subjects
Zirconium ,Band gap ,Ab initio ,chemistry.chemical_element ,Yttrium ,Condensed Matter Physics ,Biochemistry ,Crystallography ,chemistry ,Transition metal ,Chemical physics ,Cluster (physics) ,Physical and Theoretical Chemistry ,Bimetallic strip ,Basis set - Abstract
We conducted DFT studies on the YnAlm binary clusters of size n + m 6 6, to study electronic propertyvariation, using the PBE1PBE method and Lanl2DZ as basis set. The ground-state geometries of yttrium(n P 4) prefer 3D geometry and Al (m 6 5) desires planar geometry. Yttrium clusters were stabilizedby the addition of one or two aluminum atoms. The shape and geometry of the clusters has a profoundinfluence on their band gap and stability. With an increase in the Al composition, segregation was foundto occur in the bimetallic systems with the geometry and shape depending on the aluminum composi-tion. The bimetallic clusters have higher electron affinity and stability. 2009 Elsevier B.V. All rights reserved. 1. IntroductionStudies on bimetallic clusters have received great attentionowing to their chemical and physical properties, which can betuned by varying the composition, atomic ordering, and size ofthe clusters [1]. Their surface structures, compositions, and segre-gation properties are of interest; moreover, these studies havebeen important in determining chemical reactivity which hasled to widespread applications in electronics, engineering andcatalysis [2]. Though large advances have been made in experi-mental physics to produce size-selected clusters, they lack theability to directly explore and assign cluster geometries and dis-criminate between possible isomers. Of particular interest arealuminum alloys which are light weight, high strength, and corro-sion resistance. Hence much research has been carried out tostudy the bimetallic clusters of aluminum [3–5]. Studies on thesubstitution of the transition metal show that they increase thestability of the materials. However, theoretical studies of suchclusters have faced difficulties due to the presence of d electrons,with complicated electronic ground-states structure with differ-ent spin multiplicities [6].Yttrium shows great promise as a catalyst [7]. Yttrium in itscomposites such as Yttrium Aluminum Granite (YAG), finds appli-cations in optical sensors with high sensitivity or in X-ray detec-tion material [8]. Moreover, yttrium can be added to reduce thegrain size in chromium, molybdenum, zirconium, and titanium,and to increase the strength of aluminum and magnesium alloys[9]. Besides, yttrium alloys are extensively used in bulk metallicglasses [10]. Aluminum and its alloy clusters were found be capa-ble of acting as reversible hydrogen storage materials [11]. Onlyrecently, attention has been paid to the structure and stabilityof monometallic yttrium clusters by using the DFT method[12,13]. In a recent study, Yuan et al. reported on the structureand electronic properties of small yttrium clusters of size n =2–17 and observed that the growth evaluation favors 3D clustersformation with a oscillatory behavior in their HOMO–LUMOgap. On the contrary, much attention was paid to ab initio anddensity functional modeling of aluminum clusters [14–18]. Ahl-richs and Elliot investigated the structure stability of aluminumclusters and observed that the 2D planar configurations were ofthe lowest energy for clusters of m = 5. The nature of the hetero-metallic bond has been extensively studied using experimentaland theoretical methods [19,20]. Theoretical investigations havebeen done on CuAl clusters [21], Al–Ti clusters [3], Al–Ni clus-ters [4], Al–B clusters [22], Al–Si clusters [5], and Al–Fe clusters[23].With the view to understanding the structure, stability andproperties, of the type YnAlm (m + n 6 6), we have made a theoret-ical investigation on the small bimetallic clusters over the com-plete composition range from pure yttrium to pure aluminumcluster. We present the results obtained for various YAl clustersaccording to the composition of the clusters and have comparedtheir properties with monometallic clusters.
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- 2009
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50. Probing the Structure, Stability and Hydrogen Adsorption of Lithium Functionalized Isoreticular MOF-5 (Fe, Cu, Co, Ni and Zn) by Density Functional Theory
- Author
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Natarajan Sathiyamoorthy Venkataramanan, Hiroshi Mizuseki, Ryoji Sahara, and Yoshiyuki Kawazoe
- Subjects
Materials science ,Hydrogen ,Density functional Theory (DFT) ,Iron ,Inorganic chemistry ,chemistry.chemical_element ,Zinc ,Lithium ,Article ,Catalysis ,lcsh:Chemistry ,Inorganic Chemistry ,Metal ,Adsorption ,Nickel ,Organic Chemicals ,Physical and Theoretical Chemistry ,lcsh:QH301-705.5 ,Molecular Biology ,Spectroscopy ,Metal-organic frameworks (MOF’s) ,Hydrogen storage: Li-functionalization ,Organic Chemistry ,Cobalt ,General Medicine ,Computer Science Applications ,lcsh:Biology (General) ,lcsh:QD1-999 ,chemistry ,Metals ,visual_art ,visual_art.visual_art_medium ,Density functional theory ,Copper - Abstract
Li adsorption on isoreticular MOFs with metal Fe, Cu, Co, Ni and Zn was studied using density function theory. Li functionalization shows a considerable structural change associated with a volume change in isoreticular MOF-5 except for the Zn metal center. Hydrogen binding energies on Li functionalized MOFs are seen to be in the range of 0.2 eV, which is the desired value for an ideal reversible storage system. This study has clearly shown that Li doping is possible only in Zn-based MOF-5, which would be better candidate to reversibly store hydrogen.
- Published
- 2009
- Full Text
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