Abstract

Recent reports have demonstrated that nanoclusters of silver and gold can act as substrates for Raman signal enhancements. This article presents a density functional theory (DFT)-based study to explore how the variations in the nature of the cluster-binding heteroatom in the ligand molecule and the relative orientation of the alkyl group attached to the heteroatom affect the Raman signal enhancement in the ligand molecules. Our calculations involved nitrogen and phosphorus heteroatoms in two simple model molecules, methylphosphine and methylamine, as ligands and four small gold clusters, Aun (n = 6–9). In order to understand the interactions in the cluster-molecule systems, we have calculated various geometrical parameters such as Au–X (X = P, N) distances, ffC–X–Au angles and different bond lengths of free and cluster-bound molecules as well as various interaction energies. We have performed natural bond order (NBO) analysis and have calculated second order stabilization energies for the molecules bound to the gold clusters from the NBO analysis. In addition, we have performed detailed calculations pertaining to the change in polarisability, quantity of molecule to cluster charge transfer as well as molecular orientations relative to the clusters and have studied how these factors influence the Raman scattering cross-sections and vibrational frequency shifts. The quantity of charge transfer and the orientation effect have been found to be important contributors in the chemical Raman enhancement mechanism of the ligand molecules.

Abstract

DNA molecules tagged to metal nanoparticles, especially gold nanoparticles (AuNPs), have been shown to exhibit potential applications in designing and fabrication of novel electronic nano-devices, but the binding mechanism between gold nanoparticles and DNA bases and its implications are not completely understood. In this work, a comprehensive study to examine the effect of structural perturbations offered to DNA base pairs in terms of size expansion and adsorption on a gold cluster (Au3) has been done using density functional theory. Geometric and electronic features of these complexes provide evidences for distortion of certain base pairs depending on the binding site of the cluster. This is further substantiated via normal mode, natural bond orbital (NBO) and atoms in molecules (AIM) analyses. The natural population analysis (NPA) and NBO analysis indicate that complexation greatly affects the charge distribution on the base pairs due to charge transfer between base pair and gold cluster. This charge redistribution may offer a possibility of higher order interactions. Upon complexation, a marked decrease in the HOMO-LUMO gap is observed, which is more profound in cases where size expanded bases are involved due to the extended π-conjugation of the fused benzine rings. This study demonstrates the possibility of combining structural modifications to DNA base pairs and subsequent binding to gold nano particles to modulate and achieve molecular systems with desired optico-electronic properties.

Abstract

Gold cluster–nucleobase complexes have potential applications in designing and fabrication of novel electronic nano-devices, and there has been a surge in research activities in this area recently. Binding of gold clusters (Au3 and Au4) with DNA bases and size-expanded DNA bases (x-bases) have been studied using density functional theory employing high quality basis set. A comprehensive attempt has been made to examine several gold–nucleobase complexes with respect to change in the orientation of Au clusters with respect to all the titratable sites of the bases. Geometric and electronic features of these complexes provided evidences for existence of non-conventional hydrogen bonds, which was further substantiated via vibrational frequency and natural bond orbital (NBO) analysis. The nucleobases, both canonical and size-expanded forms, form stable complexes with both the gold clusters considered …

Abstract

: Preference for a cis/trans peptide bond between residues of dipeptides formed by substituted β2,3 (I) and β3 (II) homoproline is investigated using density functional theory (DFT). Potential energy surfaces for monomer and linear dimers are explored at the B3LYP/6-31G(d,p) level of theory. Minimum energy conformations of the dipeptides are optimized using B3LYP, PBE1PBE, B97D, and M06-2X functionals at the 6-31G(d,p) level of basis set in both the gas phase and solvent phase. The relative free energy difference between the selected conformations is marginal. Results obtained using the functionals M06-2X and B97D on dimers of I and II, respectively, agree with experimental results. The lowest energy conformations predicted by B97D/6-31G(d,p) and M06-2X/6-31G(d,p) levels of theory show greater relative MP2 correlation energy. Dipeptides of I with hydrophilic substituents show preference for a trans peptide bond. Support for cis/trans isomerism in dimers of I with hydrophobic substituents comes from potential energy surfaces and free energy data. Although dipeptides of II with hydrophilic substituents show preference for cis peptide bond, the dipeptides with hydrophobic substituent prefer trans bond.

Abstract

Optimally controlled initiation of intramolecular H-transfer in malonaldehyde is accomplished by designing a sequence of ultrashort (∼80 fs) down-chirped pump-dump ultra violet (UV)-laser pulses through an optically bright electronic excited [S2 (ππ∗)] state as a mediator. The sequence of such laser pulses is theoretically synthesized within the framework of optimal control theory (OCT) and employing the well-known pump-dump scheme of Tannor and Rice [D.J. Tannor, S.A. Rice, J. Chem. Phys. 83, 5013 (1985)]. In the OCT, the control task is framed as the maximization of cost functional defined in terms of an objective function along with the constraints on the field intensity and system dynamics. The latter is monitored by solving the time-dependent Schr¨odinger equation. The initial guess, laser driven dynamics and the optimized pulse structure (i.e., the spectral content and temporal profile) followed by associated mechanism involved in fulfilling the control task are examined in detail and discussed. A comparative account of the dynamical outcomes within the Condon approximation for the transition dipole moment versus its more realistic value calculated ab initio is also presented.

Abstract

In this work we specify various parameters like 1) local quantumness 2) entangling capability 3) classical randomness and give a canonical rep- representation of two qubit mixed quantum states based on them. Here we investigate the correlating capability of a non local Hamiltonian acting on general two qubit states in context of these parameters. In particular we address the questions like: 1.What is the rate of change of the standard measures of correlation like Entanglement (E) and Discord (D). 2.How these measures get affected by the change of the parameters. 3.For what choice of initial parameters, these rates of change of correlation like dE/dt ; dD/dt are maximum. 4.We study its application on bistable and open systems. Our study and analysis are completely based on the mixed quantum states quite unlike to the previous investigations based on pure quantum states.

Abstract

Vpu is an 81-residue protein encoded by human immunodeficiency virus type I (HIV-1) that facilitates viral release from host cells. The protein has a cytoplasmic domain and a helical transmembrane (TM) domain, of which the latter oligomerizes to form cation-specific ion channels. The number of TM domains that constitute the channel is still unclear, with experimental studies indicating the existence of a variety of oligomeric states. In this study, we have examined the possibility of Vpu to exist in tetra-, penta-, and hexameric states using comprehensive molecular dynamics (MD) simulations. By modeling the TM domain as an ideal α-helix, we carried out replica-exchange MD simulations in an implicit membrane environment for obtaining suitable starting structures, which were then subjected to extensive MD simulations in a fully hydrated lipid bilayer environment. The results show that the pentameric form is the most stable oligomeric state (the tetramer and hexamer models lose their initial channel-like structure), with helices in the pentamer being held together by strong van der Waals interactions. Hydrogen bonds between lipid headgroups and basic/hydrophilic residues on the protein are stronger in the pentamer than in the tetramer or the hexamer, indicating that these interactions might play a role in adhering the pentamer to the membrane. Free energy calculations using umbrella sampling technique have been performed to examine the potassium ion permeation through the pentameric pore. The results show a high free energy barrier corresponding to ion transport indicating weak ion channel activity in agreement with previous experimental biophysical studies.

Abstract

t Interaction between metal nanoparticles and biomolecules is important from the view point of developing and designing biosensors. Studies on proline tagged with gold nanoclusters are reported here using density functional theory (DFT) calculations for its structural, electronic and bonding properties. Geometries of the complexes are optimized using the PBE1PBE functional and mixed basis set, i. e., 6-311++G for the amino acid and SDD for the gold clusters. Equilibrium configurations are analyzed in terms of interaction energies, molecular orbitals and charge density. The complexes associated with cluster composed of an odd number of Au atoms show higher stability. Marked decrease in the HOMO-LUMO gaps is observed on complexation. Major components of interaction between the two moieties are: the anchoring N-Au and O-Au bond; and the non covalent interactions between Au and N-H or O-H bonds. The electron affinities and vertical ionization potentials for all complexes are calculated. They show an increased value of electron affinity and ionization potential on complexation. Natural bond orbital (NBO) analysis reveals a charge transfer between the donor (proline) and acceptor (gold cluster). The results indicate that the nature of interaction between the two moieties is partially covalent. Our results will be useful for further experimental studies and may be important for future application

Abstract

Theoretical insights into homo versus heterochiral cyclic trimerization of 5-(aminoethyl)-2-furancarboxylic acid (AEFC) are provided based on density functional theory (DFT) calculations[1]. A comparison of pathways leading to cyclic trimerization explored at M06/6-31G(d,p) and B3LYP/6-31G(d,p) levels of theory indicates signicance of the M06 functional in determining the barrier heights. Kinetic preference for heterochiral cyclization is clearly observed from results obtained at M06/6-31G(d,p) level of theory. Structure analysis of geometries reveals existence of strong hydrogen bonding interactions in the solvated heterochiral tripeptides. Further support comes from IR spectra, NBO and AIM calculations, molecular electrostatic potential and electron density surfaces. Our study shows that for the kind of systems, calculations with solvent molecules, even if a few only, are sucient to substantiate experimental observations. Further study on anion binding anity of the peptides has revealed that while both homo and heterochiral cyclic tripeptides show equal electronic energies of interaction for a uoride ion in gas phase, the homochiral cyclic tripeptide shows relatively larger electronic energy of interaction for chloride and bromide ions ( 4 kcal/mol) compared to that shown by heterochiral cyclic tripeptide. In solvent phase, the peptides possess anity for uoride and chloride ions only. While, heterochiral cyclic peptide shows slightly larger interaction for uoride ion, anity of homochiral peptide for chloride ion is slightly larger than its heterochiral counterpart. Though the heterochiral cyclic tripeptide of AEFC is a stable product with high yield, anion recognition propensities are comparable to that of homochiral cyclic tripeptide.

Abstract

Optimal control theory in combination with time-dependent quantum dynamics is employed to design laser pulses which can perform selective vibrational and rotational excitations in a heteronuclear diatomic system. We have applied the conjugate gradient method for the constrained optimization of a suitably designed functional incorporating the desired objectives and constraints. Laser pulses designed for several excitation processes of the HF molecule were able to achieve predefined dynamical goals with almost 100% yield.