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The modulation of bulk properties including the cohesive strength and the solubility of the asphaltenes, due to the inclusion of graphene nanosheets and the thermoplastic polymer, is probed by performing all-atom classical molecular dynamics (MD) simulations. The impact of morphological heterogeneity, including the size of the aromatic core of the asphaltene molecule, the nature of the heteroatom attached to the aromatic core, the orientation of the graphene nanosheets, and the surface area of the nanomaterial, on the bulk properties of the model systems of nanocomposites and interfaces is explored. The cohesive strength of the asphaltene composites is significantly enhanced by the introduction of graphene nanosheets. The addition of styrene–butadiene–styrene (SBS) block copolymer into the graphene-reinforced asphaltene systems improves the cohesive strength, structural plasticity, and compatibility between the nanomaterial and the asphaltenes. The π–π stacking interaction between the graphitic surface and the aromatic core of the asphaltene is identified to be the major driving force for modulating the cohesive strength. The dispersion interaction maximizes in the hierarchical layered structure compared to the randomly oriented structure of the graphene nanosheets and the asphaltene molecules. The energetics of non-covalent interaction are further assessed within the framework of dispersion-corrected density functional theory (DFT)-based methods. The DFT-derived adsorption energies and thermochemical properties substantiate the stronger interaction and the thermodynamic favorability of the adsorption processes in both the gas phase and solvent medium (toluene). The simulated IR and Raman spectra are also analyzed to reveal the nature of the interaction. [ABSTRACT FROM AUTHOR]

The present review article focuses on the impact of the Jahn-Teller effect (JTE) including hidden JTE and pseudo JTE on the ground and low-lying electronic structures of small transition, main group, and mixed metal clusters. The discussions are based on the results acquired from the quantum chemical analysis involving complete active space multiconfiguration self-consistent field (CASMCSCF or CASSCF) together with multireference singles and doubles configuration interaction (MRSDCI) theories. Related computational results from density functional (DFT) and coupled cluster (CC) theories, and the available experimental evidences on the JT-distorted structures are also included for comparative analysis. The role of the relativistic effects on several heavy metal clusters is discussed in detail, since these effects could lead to either enhancement or the quenching of the JTE. The final section of the review manifests the JT-distortion of several mixed metal clusters of icosahedral symmetry and they are explained through a much simpler shell structure (jellium) model. [ABSTRACT FROM AUTHOR]

The therapeutic effectiveness of the catechol diether analogs against both the wild-type and drug-resistant reverse transcriptase (RT) mutants of HIV strains are investigated by performing molecular docking and hybrid ONIOM calculations. The docking protocol has been used to predict the binding modes of the non-nucleoside inhibitors inside the active site cavity of the viral enzymes. For each enzyme-inhibitor adduct, the predicted docked poses are assessed by employing different scoring function based programs. However, the docking protocol fails to explain satisfactorily the antiviral activities of the drug molecules. Two-layered ONIOM calculations have been carried out to compute the relative binding affinities of the catechol diether derivatives to the binding pockets of RT variants. The binding efficacies of the inhibitors are significantly suppressed by the Y181C and K103N mutations, as revealed by the computed interaction energies at the ONIOM [B3LYP/6-31G(d,p):PM6] level of theory. Deformation energies for each bound ligand conformer are also estimated. The nature of interactions between the drug molecules and the active site residues are analyzed from the reduced density gradient (RDG) isosurfaces. The simulated ECD spectra support the conformational adaption upon inhibitor binding in the binding pockets of HIV strains. [ABSTRACT FROM AUTHOR]

The treatment of brain cancer like glioblastoma multiforme often uses chemotherapeutic drugs like temozolomide, procarbazine, carmustine, and lomustine. Fullerene loaded with these drugs help to cross the blood brain barriers. The adsorptions of the four drug molecules on the surface of the fullerene are studied mostly by using density functional theory (DFT) based method at the M06-2X/6-31G(d) level of calculations. In all four cases, the estimated interactions are noncovalent type and the average adsorption energy lies in between -5 and -11 kcal/mol in the gas phase. In the aqueous and protein environment such interactions are weakened further. The binding affinity is further assessed by performing MP2 based calculations to provide interaction energies with a reasonable accuracy. Stabilities and reactivities of the drug adsorbed fullerene complexes are determined from chemical reactivity descriptors. The attached drug molecules increase the polarity of the pristine C 60 thus facilitating the drug delivery within the biological systems. The semiconducting behavior of C 60 is retained in the C 60 –drug composite systems. The computed DOS, IR, UV spectra, and molecular orbitals in the vicinity of Fermi level are analyzed to reveal the nature of the noncovalent interactions between C 60 and drug molecules. The Wiberg bond order values are used to estimate the strength of the adsorption of the drug molecule on C 60 . In all four C 60 –drug interactions, the chemical characteristics of the drug molecule are least perturbed by the C 60 moiety thereby suggesting it to be a good carrier for the delivery of these brain anticancer drug molecules to the target cells. [ABSTRACT FROM AUTHOR]

Binding capabilities of hydrogen molecules on Li doped metal carbide nanotubes (MCNT, M = Si, Ge, Sn) have been compared from ab initio-based calculations using quantum mechanical /molecular mechanics methodology. Geometry optimizations are carried out at the ONIOM2 (B3LYP/6-31 + G(d)//LANL2DZ:UFF) level of theory with coronene ring as a model in the high layer. Lithium binding energies on each of the pure armchair (5,5) and zigzag (6,0) MCNTs are calculated. Adsorptions of one and two H2 molecules on the Li doped nanotubes are successively studied. In both cases the complexes are found to be stable and the average adsorption energy falls in between −18 and −38 kcal/mol. Stabilities of Li@MCNT, H2/Li@MCNT, and (H2)2/Li@MCNT systems are confirmed from the HOMO-LUMO gap and three chemical reactivity descriptors such as chemical potential, hardness and electrophilicity index. The charge polarization mechanism plays a pivotal role in the H2 adsorption on the surface of Li@MCNT. The dispersion corrected M06-2X functional is also included in the calculation to investigate the changes in the H2 binding properties. The interaction of H2 with the lithium doped MCNT has also been analyzed from the total electron density maps and density of states projected to different atoms. [ABSTRACT FROM AUTHOR]

Adsorptions of small toxic molecules such as CO, N2, HCN, SO2, H2CO, and NH3 on a single-walled (6,0) SnC nanotube (SnCNT) are investigated using Quantum Mechanics/Molecular Mechanics (QM/MM) methodology. The calculations are carried out at the B3LYP/6-311++G(d,p)//LANL2DZ:UFF level of theory. The high layer of the model consists of a pyrene-type ring on the nanotube surface as the adsorption site, where one gas molecule is allowed to interact. Conversely, for the adsorption of the two molecules, a larger site like a coronene ring is used for the high layer. Adsorption energy, Gibbs free energy change, Mulliken charge transfer, and total electron-density maps are computed in each case. The adsorption strength of the gas molecule on the SnCNT surface is also analyzed from the density of states projected to different atoms (PDOS) of the nanotube-adsorbate complexes. The adsorptions of CO and N2 on the (6,0) SnCNT surface require to cross potential barriers, and the corresponding transition structures are identified by ONIOM-IRC calculations. For the remaining four molecules, the processes of adsorption are predicted to be barrier-less. The calculations for the adsorption of H2CO on (5,0) and (7,0) SnCNT surfaces are extended to study the effect of the size of the nanotube. Results for the adsorption of a single molecule on (6,0) SnCNT using B3LYP functional are compared with those obtained from a dispersion corrected functional such as M06-2X. © 2015 Wiley Periodicals, Inc. [ABSTRACT FROM AUTHOR]

Inhibition activities of a series of 4-substituted-2,3,5,6-tetrafluorobenzenesulfonamides against the human carbonic anhydrase II (HCAII) enzyme have been explored by employing molecular docking and hybrid QM/MM methods. The docking protocol has been employed to assess the best pose of each ligand in the active site cavity of the enzyme, and probe the interactions with the amino acid residues. The docking calculations reveal that the inhibitor binds to the catalytic Zn 2+ site through the deprotonated sulfonamide nitrogen atom by making several hydrophobic and hydrogen bond interactions with the side chain residues depending on the substituted moiety. A cross-docking approach has been adopted prior to the hybrid QM/MM calculation to validate the docked poses. A correlation between the experimental dissociation constants and the docked free energies for the enzyme-inhibitor complexes has been established. Two-layered ONIOM calculations based on QM/MM approach have been performed to evaluate the binding efficacy of the inhibitors. The inhibitor potency has been predicted from the computed binding energies after taking into account of the electronic phenomena associated with enzyme-inhibitor interactions. Both the hybrid (B3LYP) and meta-hybrid (M06-2X) functionals are used for the description of the QM region. To improve the correlation between the experimental biological activity and the theoretical results, a three-layered ONIOM calculation has been carried out and verified for some of the selected inhibitors. The charge transfer stabilization energies are calculated via natural bond orbital analysis to recognize the donor-acceptor interaction in the binding pocket of the enzyme. The nature of binding between the inhibitors and HCAII active site is further analyzed from the electron density distribution maps. [ABSTRACT FROM AUTHOR]

Ab initio calculations based on a combined method of density functional theory (DFT) and nonequilibrium Green’s function (NEGF) formalism are performed to study the electrical transport properties of Ge 4 , Sn 2 Ge 2 , and Sn 4 clusters which are coupled to Au(1 1 1) electrodes through sulfur. The current–voltage ( I−V ) curves of these molecular junctions are determined for different bias voltages. Except Sn 4 , these clusters show negative differential resistance (NDR) effects at a certain high-bias range. The contribution of transmission coefficients and number of DOS peaks within the bias window explain I−V characteristics. The contributions of electronic states within the bias window due to presence of a nanocluster and its thiol counterpart are predicted from the bias dependent projected density of states (PDOS) analyses. The NDR effect is further analyzed from the molecular projected self-consistent Hamiltonian states under different external bias voltages. [ABSTRACT FROM AUTHOR]

Highlights: [•] Electron transport properties of zigzag single-walled SnC nanotubes are studied. [•] DFT and NEGF methodologies are used for this purpose. [•] Transmission coefficients and I–V characteristics for three chiralities are computed. [•] NDR in I–V curves are analyzed from transmission spectra and MPSH states. [Copyright &y& Elsevier]

• The structure and energetics for the non-covalent conjugation of the anticancer antibiotics viz. Doxorubicin, Mitomycin, and Epirubicin with C 60 are estimated within the framework of DFT. • The inclusion of dispersion correction via the DFT-D3 approach seems to be critical to anticipating the non-covalent interactions. • The complexation of C 60 with the Doxorubicin molecule is both kinetically and thermodynamically favorable. • The polarity of the pristine C 60 fullerene is enhanced due to the attachment of the drug molecules. • The structural parameters as well as the chemical reactivities of the antineoplastic therapeutics are least perturbed by the surface-molecule interaction. A critical assessment of binding energetics for the non-covalent conjugation of drug molecules with nanocarriers is a cornerstone problem in chemical physics due to the omnipresence of many-body van der Waals (vdW) interactions and thereby entailing a meaningful theoretical approach to decipher the origin of surface-molecule interactions at the nanoscale. Fullerene-C 60 , which possesses a unique spherical structure with a strong apolar character, promised to serve as drug delivery scaffolds through covalent or non-covalent interactions with the bioactive moiety. Herein, we have explored the binding characteristics of three anticancer antibiotics viz. Doxorubicin, Mitomycin, and Epirubicin with C 60 nanocage by performing density functional theory (DFT) based calculations. The essence of surface-molecule interactions is derived from the DFT-based methods in conjunction with semiclassical treatments of the dispersion interaction (D3 approach) and semilocal density functional (M06–2X). Stabilities and reactivities of the drug adsorbed fullerene-C 60 complexes are assessed in both the aqueous and protein core environment. The calculated IR stretching frequencies, Raman scattering activities, optical absorption coefficients, global chemical reactivity descriptors as well as thermochemical properties are subsequently analyzed to reveal the nature of the noncovalent interactions between C 60 and antineoplastic therapeutics. [Display omitted] [ABSTRACT FROM AUTHOR]

Highlights: [•] Adsorptions of small molecules on (6,0)GeCNT are studied using ONIOM calculations. [•] The interactions of N2 and CO are found to be endothermic with a large barrier. [•] Adsorption energy, charge transfer, and DOS are used to determine the binding. [•] SO2, NH3, and H2CO molecules bind strongly towards GeCNT. [ABSTRACT FROM AUTHOR]

Electronic structures of neutral lead–silicon clusters of up to six atoms are determined by global optimization of the potential energy hyper surface using Metropolis Monte Carlo and genetic algorithm (GA) methods followed by a bond strength propensity model, and by local optimization using density functional theory at the B3LYP/aug-cc-pVTZ-pp level. For each cluster, geometries of those stable isomers whose relative energies are within 1.0 eV are reported. Average binding energy per atom, band gap, ionization potential (IP), electron affinity (EA), and vertical detachment energy of the most stable isomer of each type of cluster are computed to study their dependences on the size of the cluster. Polarizability, chemical potential, hardness and electrophilicity index of the most stable isomers are estimated to study their relative stabilities and chemical reactivities. Relative strengths of metal–metal interactions are determined from a study of all one-step fragmentation processes. IR intensities and Raman activities for all the vibrational modes of the most stable isomers are calculated. [ABSTRACT FROM AUTHOR]

Electronic states of the PbSi molecule up to 4 eV have been studied by carrying out ab initio based MRDCI calculations which include relativistic effective core potentials (RECPs) of both the atoms. The use of semicore RECPs of Pb produces better dissociation limits than the full-core one. However, the ³P0-³P1 splitting due to Pb is underestimated by about 4000 cm-1. At least 25 bound electronic states of the Λ-S symmetry are predicted for PbSi. The computed zero-field-splitting in the ground state is about 544 cm-1. A strong spin-orbit mixing changes the nature of the potential energy curves of many Ω states. The overall splitting among the spin components of A³Π is computed to be 4067 cm-1. However, the largest spin-orbit splitting is reported for the ³Δ state. A number of spin-allowed and spin-forbidden transitions are predicted. The partial radiative lifetime for the A³Π-X³Σ- transition is of the order of milliseconds. The computed bond energy in the ground state is 1.68 eV, considering the spin-orbit coupling. The vertical ionization energy for the ionization to the X4Σ- ground state of PbSi+ is about 6.93 eV computed at the same level of calculations. [ABSTRACT FROM AUTHOR]

Negative thermal quenching (NTQ), an abnormal phenomenon that the intensity of photoluminescence (PL) increases with increasing temperature, has essentially been restricted to either bulk semiconductors or very low temperatures. Here, we report a delayed fluorescence copper–organic framework exhibiting negative thermal quenching (NTQ) of photoluminescence, which is driven by the fluctuation between the localized and delocalized form of its imidazole ligand. The process is completely reversible on cooling/heating cycles. This study opens a new avenue to explore the electronically switchable NTQ effect in coordination networks and further to develop the NTQ-based light-emitting diodes. [ABSTRACT FROM AUTHOR]