Chiranjib Majumder

A theoretical study on the interaction of aromatic amino acids with graphene and single walled carbon nanotube

In this study we have investigated the interaction of phenylalanine (Phe), histidine (His), tyrosine (Tyr), and tryptophan (Tryp) molecules with graphene and single walled carbon nanotubes (CNTs) with an aim to understand the effect of curvature on the non-covalent interaction. The calculations are performed using density functional theory and the Moller-Plesset second-order perturbation theory (MP2) within linear combination of atomic orbitals-molecular orbital (LCAO-MO) approach. Using these methods, the equilibrium configurations of these complexes were found to be very similar, i.e., the aromatic rings of the amino acids prefer to orient in parallel with respect to the plane of the substrates, which bears the signature of weak pi-pi interactions. The binding strength follows the trend: His<Phe<Tyr<Tryp. Although the qualitative trend in binding energy is almost similar between the planar graphene and rolled nanotube structure but they differ in terms of the absolute magnitude. For the nanotube, the binding strength of these molecules is found to be weaker than the graphene sheet. To get an insight about the nature of these interactions, we have calculated the polarizability of the aromatic motifs of the amino acids. Remarkably, we find excellent correlation between the polarizability and the strength of the interaction; the higher the polarizability, greater is the binding strength. Moreover, we have analyzed the electronic densities of state spectrum before and after adsorption of the amino acid moieties. The results reveal that the Fermi level of the free CNT is red-shifted by the adsorption of the amino acids and the degree of shift is consistent with the trend in polarizability of these molecules.

Structural and electronic properties of Sin,Sin+, and AlSin−1 (n=2–13) clusters: Theoretical investigation based on ab initio molecular orbital theory

The geometric and electronic structures of Sin, Sin+, and AlSin−1 clusters (2⩽n⩽13) have been investigated using the ab initio molecular orbital theory under the density functional theory formalism. The hybrid exchange-correlation energy function (B3LYP) and a standard split-valence basis set with polarization functions [6-31G(d)] were employed for this purpose. Relative stabilities of these clusters have been analyzed based on their binding energies, second difference in energy (Δ 2E) and fragmentation behavior. The equilibrium geometry of the neutral and charged Sin clusters show similar structural growth. However, significant differences have been observed in the electronic structure leading to their different stability pattern. While for neutral clusters, the Si10 is magic, the extra stability of the Si11+ cluster over the Si10+ and Si12+ bears evidence for the magic behavior of the Si11+ cluster, which is in excellent agreement with the recent experimental observations. Similarly for AlSin−1 clusters...

Structural investigation of thiophene thiol adsorption on Au nanoclusters: Influence of back bonds

The adsorption of thiolate radicals on the Au24 nanocluster truncated from the Au (111) surface is investigated using first principles electronic structure calculations under the density functional theory formalism. Particular emphasis is given to understanding the chemical interactions at the gold-sulfur interface. In order to describe the influence of the back bonds at the thiolate sites we have carried out adsorption studies with thiophene 2-thiolate (-ST) and thiophen–2-yl-methanethiolate (-SCH2T) along with atomic sulfur (S), mercapto (-SH), and methylthiolate (-SCH3). The results suggest that the adsorption geometry at the gold-sulfur interface is strongly dependent on the local environment of the terminal sulfur atom. The interfacial charge transfer is found to be localized along the Au-S bonds and does not influence the molecular structure of the thiophene ring.

CO Oxidation by BN−Fullerene Cage: Effect of Impurity on the Chemical Reactivity

Using state of the art spin-polarized density functional theory it is found that a chemically inert (BN)(36) cluster can be activated by incorporating magnetic nanoparticles inside it. To illustrate this aspect we have calculated the geometries and electronic structure of Fe(BN)(36) and Fe(4)(BN)(36) clusters, which showed the appearance of gap states localized on the impurity atoms. The reaction of O(2) molecules with these clusters results in weak interaction and an elongation of the O-O bond. Further interaction of this complex species with an incoming CO molecule leads to the formation of CO(2). The reaction mechanism has been investigated via Langmuir-Hinshelwood and Elay-Rideal routes, and the minimum energy path calculations are performed using the elastic band method. These results have implications in designing novel materials based on metal nanoparticles for potential applications as industrial catalyst.

Structural and electronic properties of Sin, Sin−, and PSin−1 clusters (2⩽n⩽13): Theoretical investigation based on ab initio molecular orbital theory

The geometric and electronic structures of Si(n), Si(n)-, and PSi(n-1) clusters (2 < or = n < or = 13) have been investigated using the ab initio molecular orbital theory formalism. The hybrid exchange-correlation energy functional (B3LYP) and a standard split-valence basis set with polarization functions (6-31+G(d)) were employed to optimize geometrical configurations. The total energies of the lowest energy isomers thus obtained were recalculated at the MP2/aug-cc-pVTZ level of theory. Unlike positively charged clusters, which showed similar structural behavior as that of neutral clusters [Nigam et al., J. Chem. Phys. 121, 7756 (2004)], significant geometrical changes were observed between Si(n) and Si(n)- clusters for n = 6, 8, 11, and 13. However, the geometries of P substituted silicon clusters show similar growth as that of negatively charged Si(n) clusters with small local distortions. The relative stability as a function of cluster size has been verified based on their binding energies, second difference in energy (Delta2 E), and fragmentation behavior. In general, the average binding energy of Si(n)- clusters is found to be higher than that of Si(n) clusters. For isoelectronic PSi(n-1) clusters, it is found that although for small clusters (n < 4) substitution of P atom improves the binding energy of Si(n) clusters, for larger clusters (n > or = 4) the effect is opposite. The fragmentation behavior of these clusters reveals that while small clusters prefer to evaporate monomer, the larger ones dissociate into two stable clusters of smaller size. The adiabatic electron affinities of Si(n) clusters and vertical detachment energies of Si(n)- clusters were calculated and compared with available experimental results. Finally, a good agreement between experimental and our theoretical results suggests good prediction of the lowest energy isomeric structures for all clusters calculated in the present study.

Atomic and electronic structures of neutral and charged Pbn clusters (n=2-15): theoretical investigation based on density functional theory.

The geometric and electronic structures of the Pbn+ clusters (n=2-15) have been investigated and compared with neutral clusters. The search for several low-lying isomers was carried out under the framework of the density functional theory formalism using the generalized gradient approximation for the exchange correlation energy. The wave functions were expanded using a plane wave basis set and the electron-ion interactions have been described by the projector augmented wave method. The ground state geometries of the singly positively charged Pbn+ clusters showed compact growth pattern as those observed for neutrals with small local distortions. Based on the total energy of the lowest energy isomers, a systematic analysis was carried out to obtain the physicochemical properties, viz., binding energy, second order difference in energy, and fragmentation behavior. It is found that n=4, 7, 10, and 13 clusters are more stable than their neighbors, reflecting good agreement with experimental observation. The chemical stability of these clusters was analyzed by evaluating their energy gap between the highest occupied and lowest unoccupied molecular orbitals and adiabatic ionization potentials. The results revealed that, although Pb13 showed higher stability from the total energy analysis, its energy gap and ionization potential do not follow the trend. Albeit of higher stability in terms of binding energy, the lower ionization potential of Pb13 is interesting which has been explained based on its electronic structure through the density of states and electron shell filling model of spherical clusters.

THEORETICAL STUDY OF DONOR–SPACER–ACCEPTOR STRUCTURE MOLECULE FOR STABLE MOLECULAR RECTIFIER

Recently, field of molecular electronics has attracted strong attention as a “post-silicon technology” to enable future nanoscale electronic devices. To realize this molecular device, unimolecular rectifying function is one of the most fundamental requirements using nanotechnology. In the present study, the geometric and electronic structures of alkyl derivative C37H50N4O4 (PNX) molecule, (donor – spacer – acceptor), a candidate for a molecular rectifying device, has been investigated theoretically using ab initio quantum mechanical calculations. The results suggest that in such donor-acceptor molecular complexes, while the lowest unoccupied orbital concentrates on the acceptor subunit, the highest occupied molecular orbital is localized on the donor subunit. After the optimization of the structure by B3LYP/6-31(d), the approximate potential differences for the optimized PNX molecule have been estimated at the B3LYP/6-311++G(d,p) level of theory, which achieves quite good agreement with experimentally reported results.

Multiphoton ionisation of acetone at 355 nm: a time-of-flight mass spectrometry study

Abstract Multiphoton ionisation/fragmentation of acetone has been studied at λ=355 nm using time-of-flight mass spectrometry. A broad peak at m/e=43 is observed which shows a three-photon laser power dependence. The results suggest that three-photon ionisation at 355 nm produces vibrationally excited acetone ions which undergo fast dissociation. The broadening of the m/e=43 peak is found to depend on the laser power in the low laser intensity region. Under high laser intensity conditions, a bimodal distribution of m/e=43 peak was observed which has been assigned to two different isomeric product channels. The results provide clear evidence for partial isomerisation of the keto form of the acetone radical cation to the enol form. On ionisation at 355 nm, CH3COC2H5 fragments into two channels corresponding to (CH3CO+) and (C2H5CO+) in the ratio of approximately 3:1.

Interactions of a conjugated molecular diode with small metal clusters of Cu, Ag, and Au: First-principles calculations

The geometries and electronic structures of a thiol-terminated molecular diode interacting with group-11 metal clusters (Cu, Ag, Au) have been investigated using density functional theory with a hybrid exchange-correlation energy functional. The charge transfer and bonding nature at the metal-molecule interface are illustrated from natural bond orbital analysis. The metal-sulfur bonds are found to be directional, and the charge transfer is localized along the bond. The extent of charge transfer to the terminal sulfur is higher for bonding with Cu and Ag (∼0.40) than with Au (∼0.17). The electronic conduction across the molecular diode has been analyzed from the change in the electronic structure and the shape of the molecular orbitals of the free molecule and metal-molecule complexes. The results suggest that while the inclusion of Au scarcely affects the unoccupied molecular orbitals, the effect is more pronounced in the cases of Cu and Ag. The threshold energy for conduction estimated for these metal-molecule complexes indicates a higher required bias voltage for Au than for Cu and Ag.

Ground state geometries and energetics of ALnLi (n = 1, 13) clusters using ab initio density-based molecular dynamics

Abstract Based on orbital-free ab initio molecular dynamics calculations, the geometries and energetics of lithium-doped aluminium clusters (Al n Li, n = 1, 13) have been investigated. It is seen that, a single impurity of Li affects the geometries of small ( n 3 Li, Al 6 Li and Al 13 Li clusters, which are in contrast with our earlier results on Li n Al. The results indicate that the Li atom segregates to the surface of the aluminium cluster and prefers to form a tetrahedron, wherever possible, with one of the triangular faces of Al atoms. In particular, for Al 13 Li, the Al 13 core takes the most symmetric icosahedral form with the Li atom occupying the outer ‘hollow-site’.