X-ray photoelectron spectroscopic investigations of Cu-Ni, Au-Ag, Ni-Pd, and Cu-Pd bimetallic clusters

Core-level binding energies of the component metals in bimetallic clusters of various compositions in the Ni-Cu, Au-Ag, Ni-Pd, and Cu-Pd systems have been measured as functions of coverage or cluster size, after having characterized the clusters with respect to sizes and compositions. The core-level binding energy shifts, relative to the bulk metals, at large coverages or cluster size, Delta E(a), are found to be identical to those of bulk alloys. By substracting the Delta E(a) values from the observed binding energy shifts, Delta E, we obtain the shifts, Delta E(c), due to cluster size. The Delta E(c) values in all the alloy systems increase with the decrease in cluster size. These results establish the additivity of the binding energy shifts due to alloying and cluster size effects in bimetallic clusters.

Density-matrix renormalization-group study of low-lying excitations of polyacene within a Pariser-Parr-Pople model

We have carried out symmetrized density-matrix renormalization-group calculations to study the nature of excited states of long polyacene oligomers within a Pariser-Parr-Pople Hamiltonian. We have used the C-2 symmetry, the electron-hole symmetry, and the spin parity of the system in our calculations. We find that there is a crossover in the lowest dipole forbidden two-photon state and the lowest dipole allowed excited state with size of the oligomer. In the long system limit, the two-photon state lies below the lowest dipole allowed excited state. The triplet state lies well below the two-photon state and energetically does not correspond to its description as being made up of two triplets. These results are in agreement with the general trends in linear conjugated polymers. However, unlike in linear polyenes wherein the two-photon state is a localized excitation, we find that in polyacenes, the two-photon excitation is spread out over the system. We have doped the systems with a hole and an electron and have calculated the charge excitation gap. Using the charge gap and the optical gap, we estimate the binding energy of the 1(1)B(-) exciton to be 2.09 eV. We have also studied doubly doped polyacenes and find that the bipolaron in these systems, to be composed of two separated polarons, as indicated by the calculated charge-density profile and charge-charge correlation function. We have studied bond orders in various states in order to get an idea of the excited state geometry of the system. We find that the ground state, the triplet state, the dipole allowed state, and the polaron excitations correspond to lengthening of the rung bonds in the interior of the oligomer while the two-photon excitation corresponds to the rung bond lengths having two maxima in the system.

Calcium-Decorated Carbyne Networks as Hydrogen Storage Media

Among the carbon allotropes, carbyne chains appear outstandingly accessible for sorption and very light. Hydrogen adsorption on calcium-decorated carbyne chain was studied using ab initio density functional calculations. The estimation of surface area of carbyne gives the value four times larger than that of graphene, which makes carbyne attractive as a storage scaffold medium. Furthermore, calculations show that a Ca-decorated carbyne can adsorb up to 6 H(2) molecules per Ca atom with a binding energy of similar to 0.2 eV, desirable for reversible storage, and the hydrogen storage capacity can exceed similar to 8 wt %. Unlike recently reported transition metal-decorated carbon nanostructures, which suffer from the metal clustering diminishing the storage capacity, the clustering of Ca atoms on carbyne is energetically unfavorable. Thermodynamics of adsorption of H(2) molecules on the Ca atom was also investigated using equilibrium grand partition function.

A resistometric study of solute–solute interaction in dilute aluminium–silver alloys

The experimentally determined apparent vacancy formation energy values in dilute aluminium—silver alloys showed a divergence from calculated values at higher solute fractions. This is explained in terms of a solute—solute interaction energy of the order of 0.10 ev which exists when the binding energy between a vacancy and a solute atom pair is reduced to zero.

First-Principles Study of the Effect of Organic Ligands on the Crystal Structure of CdS Nanoparticles

We show with the aid of first-principles electronic structure calculations that suitable choice of the capping ligands may be an important control parameter for crystal structure engineering of nanoparticles. Our calculations on CdS nanocrystals reveal that the binding energy of model trioctylphosphine molecules on the (001) facets of zincblende nanocrystals is larger compared to that on wurtzite facets. Similarly, the binding energy of model cis-oleic acid is found to be dominant for the (10 (1) over bar0) facets of wurtzite structure. As a consequence, trioctylphosphine as a capping agent stabilizes the zincblende structure while cis-oleic acid stabilizes the wurtzite phase by influencing the surface energy, which has a sizable contribution to the energetics of a nanocrystal. Our detailed analysis suggests that the binding of molecules on the nanocrystalline facets depends on the surface topology of the facets, the coordination of the surface atoms where the capping molecule is likely to attach, and the conformation of the capping molecule.

Molecular Docking Studies of Novel Palmitoyl-ligands for Cyclooxygenase-2

An in silico approach was adopted to identify potential cyclooxygenase-2 inhibitors through molecular docking studies. The in vivo studies indicated that synthetic palmitoyl derivatives of salicylic acid, para amino phenol, para amino benzoic acid, and anthranilic acid possessed significant pharmacological activities like anti-inflammatory, analgesic, and antipyretic activities. None of the tested substances produced any significant gastric lesions in experimental animals. In an attempt to understand the ligandprotein interactions in terms of the binding affinity, the above synthetic molecules were subjected to docking analysis using AutoDock. The palmitoyl derivatives palmitoyl anthranilic acid, palmitoyl para amino benzoic acid, palmitoyl para amino phenol, and palmitoyl salicylic acid showed better binding energy than the known inhibitor diclofenac bound to 1PXX. All the palmitoyl derivatives made similar interactions with the binding site residues of cyclooxygenase-2 as compared to that of the known inhibitor. Thus, structure-based drug discovery approach was successfully employed to identify some promising pro-drugs for the treatment of pain and inflammation.

Interaction of nucleic acids with carbon nanotubes and dendrimers

Nucleic acid interaction with nanoscale objects like carbon nanotubes (CNTs) and dendrimers is of fundamental interest because of their potential application in CNT separation, gene therapy and antisense therapy. Combining nucleic acids with CNTs and dendrimers also opens the door towards controllable self-assembly to generate various supra-molecular and nano-structures with desired morphologies. The interaction between these nanoscale objects also serve as a model system for studying DNA compaction, which is a fundamental process in chromatin organization. By using fully atomistic simulations, here we report various aspects of the interactions and binding modes of DNA and small interfering RNA (siRNA) with CNTs, graphene and dendrimers. Our results give a microscopic picture and mechanism of the adsorption of single- and double-strand DNA (ssDNA and dsDNA) on CNT and graphene. The nucleic acid-CNT interaction is dominated by the dispersive van der Waals (vdW) interaction. In contrast, the complexation of DNA (both ssDNA and dsDNA) and siRNA with various generations of poly-amido-amine (PAMAM) dendrimers is governed by electrostatic interactions. Our results reveal that both the DNA and siRNA form stable complex with the PAMAM dendrimer at a physiological pH when the dendrimer is positively charged due to the protonation of the primary amines. The size and binding energy of the complex increase with increase in dendrimer generation. We also give a summary of the current status in these fields and discuss future prospects.

First principles calculations of H-storage in sorption materials

A review of various contributions of first principles calculations in the area of hydrogen storage, particularly for the carbon-based sorption materials, is presented. Carbon-based sorption materials are considered as promising hydrogen storage media due to their light weight and large surface area. Depending upon the hybridization state of carbon, these materials can bind the hydrogen via various mechanisms, including physisorption, Kubas and chemical bonding. While attractive binding energy range of Kubas bonding has led to design of several promising storage systems, in reality the experiments remain very few due to materials design challenges that are yet to be overcome. Finally, we will discuss the spillover process, which deals with the catalytic chemisorption of hydrogen, and arguably is the most promising approach for reversibly storing hydrogen under ambient conditions.

Methane and carbon dioxide adsorption on edge-functionalized graphene: a comparative DFT study

With a view towards optimizing gas storage and separation in crystalline and disordered nanoporous carbon-based materials, we use ab initio density functional theory calculations to explore the effect of chemical functionalization on gas binding to exposed edges within model carbon nanostructures. We test the geometry, energetics, and charge distribution of in-plane and out-of-plane binding of CO2 and CH4 to model zigzag graphene nanoribbons edge-functionalized with COOH, OH, NH2, H2PO3, NO2, and CH3. Although different choices for the exchange-correlation functional lead to a spread of values for the binding energy, trends across the functional groups are largely preserved for each choice, as are the final orientations of the adsorbed gas molecules. We find binding of CO2 to exceed that of CH4 by roughly a factor of two. However, the two gases follow very similar trends with changes in the attached functional group, despite different molecular symmetries. Our results indicate that the presence of NH2, H2PO3, NO2, and COOH functional groups can significantly enhance gas binding, making the edges potentially viable binding sites in materials with high concentrations of edge carbons. To first order, in-plane binding strength correlates with the larger permanent and induced dipole moments on these groups. Implications for tailoring carbon structures for increased gas uptake and improved CO2/CH4 selectivity are discussed. (C) 2012 American Institute of Physics. http://dx.doi.org/10.1063/1.4736568]

Structure of a carbon nanotube-dendrimer composite

Using all atomistic molecular dynamics (MD) simulations we report a microscopic picture of the carbon nanotube (6,5)-dendrimer complex for PAMAM dendrimers of generations 2 to 4. We study the compact wrapping conformations of the dendrimer onto the nanotube surface for all the three generations of PAMAM dendrimer. A high degree of wrapping for the non-protonated dendrimer is observed as compared to the protonated dendrimer. For comparison, we also study the interaction of another dendrimer, poly(propyl ether imine) (PETIM), with the nanotube. The results of the distance of closest approach as well as the number of close contacts between the nanotube and the dendrimer reveal that the PAMAM dendrimer interacts strongly as compared to the PETIM dendrimer. We also calculate the binding energy between the nanotube and the dendrimer using MM/PBSA methods and attribute the strong binding to the charge transfer between them. Dendrimer wrapping on the CNT will make it soluble and the dendrimer can act as an efficient dispersing agent for the nanotubes.

Effective Mass-Driven Structural Transition in a Mn-Doped ZnS Nanoplatelet

Mn doping in ZnS nanoplatelets has been shown to induce a structural transition from the wurtzite to the zinc blende phase. We trace the origin of this transition to quantum confinement effects, which shift the valence band maximum of the wurtzite and zinc blende polyrnorphs of ZnS at different rates as a function of the nanocrystal size, arising from different effective hole masses in the two structures. This modifies the covalency associated with Mn incorporation and is reflected in the size-dependent binding energy difference for the two structures.

Comprehensive investigations on DNa center dot center dot center dot A (D = H/F) complexes show why `sodium bonding' is not commonly observed

A comprehensive study of D-Na center dot center dot center dot A (D = H/F) complexes has been done using advanced ab initio and atoms in molecule (AIM) theoretical analyses. The correlation between electron density at bond critical point and binding energy gives a distinguishing feature for hydrogen bonding, different from the `electrostatic complexes' formed by LiD and NaD. Moreover, the LiD/NaD dimers have both linear and anti-parallel minima, as expected for electrostatic dipole-dipole interactions. The HF dimer has a quasi-linear minimum and the anti-parallel structure is a saddle point. Clearly, characterizing hydrogen bonding as `nothing but electrostatic interaction between two dipoles' is grossly in error.

Selenium adsorption on Au(111) and Ag(111) surfaces: adsorbed selenium and selenide films

Results of a high resolution photoemission and electrochemistry study of Se adsorption Au(111) and Ag(111) surfaces performed by immersion of pristine samples into an aqeuous solution of Na2Se are presented. Cyclic voltammetry on Au shows formation of selenium adsorbed species and the structures observed in reductive desorption are to the atomic and polymeric species observed in XPS. In the case of Au(111) XPS spectra in the Se(3d) region indeed show two main features attributed to Se chemisorbed atomically and polymeric Se-8 features.' Smaller structures due to other types of Se conformations were also observed. The Au(4f) peak line, shape does not show core level, shifts: indicative of Au selenide formation the case of silver, XPS spectra for the Ag(3d) show a broadening of the peak and a deconvolution into Ag-B bulk like Ag-Se components shows that the Ag-Se is located at a lower binding energy, an effect similar to oxidation and sulfidation of Ag. The Se(3d) XPS spectrum is found to be substantially different from the Au case and dominated by atomic type Se due to the selenide, though a smaller intensity Se structure at an energy similar to the Se-8 structure for Au is also observed. Changes in the valence band region. related to Se adsorption are reported.

Li diffusion through doped and defected graphene

We investigate the effect of nitrogen and boron doping on Li diffusion through defected graphene using first principles based density functional theory. While a high energy barrier rules out the possibility of Li-diffusion through the pristine graphene, the barrier reduces with the incorporation of defects. Among the most common defects in pristine graphene, Li diffusion through the divacancy encounters the lowest energy barrier of 1.34 eV. The effect of nitrogen and boron doping on the Li diffusion through doped defected-graphene sheets has been studied. N-doping in graphene with a monovacancy reduces the energy barrier significantly. The barrier reduces with the increasing number of N atoms. On the other hand, for N doped graphene with a divacancy, Li binds in the plane of the sheet, with an enhanced binding energy. The B doping in graphene with a monovacancy leads to the enhancement of the barrier. However, in the case of B-doped graphene with a divacancy, the barrier reduces to 1.54 eV, which could lead to good kinetics. The barriers do not change significantly with B concentration. Therefore, divacancy, B and N doped defected graphene has emerged as a better alternative to pristine graphene as an anode material for Li ion battery.

Fe as Hydrogen/Halogen Bond Acceptor in Square Pyramidal Fe(CO)(5)

Hydrogen bonded complexes formed between the square pyramidal Fe(CO)(5) with HX (X = F, Cl, Br), showing X-H center dot center dot center dot Fe interactions, have been investigated theoretically using density functional theory (DFT) including dispersion correction. Geometry, interaction energy, and large red shift of about 400 cm(-1) in the FIX stretching frequency confirm X-H center dot center dot center dot Fe hydrogen bond formation. In the (CO)(5)Fe center dot center dot center dot HBr complex, following the significant red shift, the HBr stretching mode is coupled with the carbonyl stretching modes. This clearly affects the correlation between frequency shift and binding energy, which is a hallmark of hydrogen bonds. Atoms in Molecule (AIM) theoretical analyses show the presence of a bond critical point between the iron and the hydrogen of FIX and significant mutual penetration. These X-H center dot center dot center dot Fe hydrogen bonds follow most but not all of the eight criteria proposed by Koch and Popelier (J. Phys. Chem. 1995, 99, 9747) based on their investigations on C-H center dot center dot center dot O hydrogen bonds. Natural bond orbital (NBO) analysis indicates charge transfer from the organometallic system to the hydrogen bond donor. However, there is no correlation between the extent of charge transfer and interaction,energy, contrary to what is proposed in the recent IUPAC recommendation (Pure Appl.. Chem. 2011, 83, 1637). The ``hydrogen bond radius'' for iron has been determined to be 1.60 +/- 0.02 angstrom, and not surprisingly it is between the covalent (127 angstrom) and van der Waals (2.0) radii of Fe. DFT and AIM theoretical studies reveal that Fe in square pyramidal Fe(CO)(5) can also form halogen bond with CIF and ClH as ``halogen bond donor''. Both these complexes show mutual penetration as well, though the Fe center dot center dot center dot Cl distance is closer to the sum of van der Waals radii of Fe and Cl in (CO)5Fe center dot center dot center dot ClH, and it is about 1 angstrom less in (CO)(5)Fe center dot center dot center dot ClF.