R. Mahesh Kumar

Carbohydrate-Aromatic Interactions: The Role of Curvature on XH···π Interactions

The interaction between the fragment of carbon nanotube (CNT) and carbohydrates has been investigated using MP2 and M05-2X methods using various basis sets in gas phase. Three carbohydrates, viz., beta-d-glucose, beta-d-galactose, and beta-d-xylose with different degree of hydrophobic nature have been selected for this investigation. With a view to assess the effect of curvature on the interaction between the carbohydrates and CNT, calculations on intermolecular complexes comprising of coronene (COR) and carbohydrates have also been carried out in gas phase. Results obtained from electronic structure calculations combined with the Baders electron density analysis reveal that CH...pi interaction is the predominant one in the stabilization of the carbohydrate-CNT and carbohydrate-COR complexes. Furthermore, the importance of OH...pi and lone pair...pi (lp...pi) interactions are also evident from the results. The calculated BEs for the various carbohydrate-CNT and carbohydrate-COR complexes at M05-2X with dual basis set [aug-cc-pVTZ for carbohydrate + cc-pVTZ for both CNT and COR] vary from -2.52 to -5.14 and from -4.14 to -8.04 kcal/mol, respectively. The corresponding BEs obtained from MP2/6-311++G(d,p)//M05-2X/6-31+G(d,p) level of calculation range from -4.92 to -9.93 and from -6.75 to -12.53 kcal/mol. Close scrutiny of the energetics of all the complexes elucidate that the electron correlation energy (dispersion energy) significantly contribute to the stability of these complexes. It is found from the analysis of geometrical parameters and BEs that the interplay of orientation of the X-H (X = C and O) bond to the pi-surface is crucial for the recognition and further stabilization. Molecular electrostatic potential (MESP) isosurfaces of curved and planar surfaces have clearly provided the difference between the pi-electron distributions. Evidences form the energy decomposition analysis elicit that the dispersive interaction plays a significant role in the overall stabilization of the complexes. And, it is possible to observe the delicate balance between the electrostatic interaction and the exchange-repulsion energy.

Structure and Stability of (NG)nCN3Be3+ Clusters and Comparison with (NG)BeY0/+

The noble gas binding ability of CN3Be3(+) clusters was assessed both by ab intio and density functional studies. The global minimum structure of the CN3Be3(+) cluster binds with four noble-gas (NG) atoms, in which the Be atoms are acting as active centers. The electron transfer from the noble gas to the Be atom plays a key role in binding. The dissociation energy of the Be-NG bond gradually increases from He to Rn, maintaining the periodic trend. The HOMO-LUMO gap, an indicator for stability, gives additional insight into these NG-bound clusters. The temperature at which the NG-binding process is thermodynamically feasible was identified. In addition, we investigated the stability of two new neutral NG compounds, (NG)BeSe and (NG)BeTe, and found them to be suitable candidates to be detected experimentally such as (NG)BeO and (NG)BeS. The dissociation energies of the Be-NG bond in monocationic analogues of (NG)BeY (Y=O, S, Se, Te) were found to be larger than in the corresponding neutral counter-parts. Finally, the higher the positive charge on the Be atoms, the higher the dissociation energy for the Be-NG bond becomes.

Studies on the structure and stability of cyclic peptide based nanotubes using oligomeric approach: a computational chemistry investigation.

In this study, an attempt has been made to investigate the structure, dynamics, and stability of cyclic peptide nanotubes (CPNTs) formed by the self-assembly of cyclic peptides (CPs) using classical molecular dynamics (MD) simulation and semiempirical quantum chemistry calculation employing PM6 Hamiltonian with the dispersion correction and hydrogen-bonding interaction (DH2). The structure and energetics of monomer and various oligomeric CPNTs have been investigated by considering the (cyclo-[(D-Ala-L-Ala)(4)]) peptide as the model for CP. Although the formation of CPNTs has been intensively studied, the present study adds valuable information to the de novo design of CPNTs. Various geometrical parameters extracted from the MD simulation reveal that the terminal residues are loosely hydrogen bonded to the inner subunits regardless of degree of oligomerization. The hydrogen bonds present in the inner core regions are stronger than the terminal residues. As the degree of oligomerization increases, the stability of the tube increases due to the hydrogen-bonding and stacking interactions between the subunits. The results show that the binding free energy increases with the extent of oligomerization and reaches saturation beyond pentamer CPNT. In addition, hydrophobic and electrostatic interactions play crucial roles in the formation of CPNTs. Analysis of both structure and energetics of the formation of CPNTs unveils that the self-assembly of dimer, trimer, and tetramer CPNTs are the essential steps in the growth of CPNTs.

On the perturbation of the H-bonding interaction in ethylene glycol clusters upon hydration.

Ab initio and density functional methods have been employed to study the structure, stability, and spectral properties of various ethylene glycol (EG(m)) and ethylene glycol-water (EG(m)W(n)) (m = 1-3, n = 1-4) clusters. The effective fragment potential (EFP) approach was used to explore various possible EG(m)W(n) clusters. Calculated interaction energies of EG(m)W(n) clusters confirm that the hydrogen-bonding interaction between EG molecules is perturbed by the presence of water molecules and vice versa. Further, energy decomposition analysis shows that both electrostatic and polarization interactions predominantly contribute to the stability of these clusters. It was found from the same analysis that ethylene glycol-water interaction is predominant over the ethylene glycol-ethylene glycol and water-water interactions. Overall, the results clearly illustrate that the presence of water disrupts the ethylene glycol-ethylene glycol hydrogen bonds.

Expedient synthesis of coumarin-coupled triazoles via 'click chemistry' leading to the formation of coumarin-triazole-sugar hybrids.

Coumarin-based triazoles were synthesized from 3-azidomethylcoumarin and a terminal acetylenic compound. Uncatalysed thermal conditions result in a mixture of both 1,4- and 1,5-regioisomers or the thermodynamically more stable 1,4-regioisomer, whereas the Cu(I)-catalysed reaction affords only the favourable 1,4-regioisomer. B3LYP/6-31G(d) level of theory has been used to calculate geometry and frequency features of the reactants, transition states (TSs) and products. Computational studies further reveal that 1,4-regioisomeric products are more favourable and also thermodynamically more stable compared to the 1,5-regioisomers.

Studies on the encapsulation of F- in single walled nanotubes of different chiralities using density functional theory calculations and Car-Parrinello molecular dynamics simulations.

In this study, the encapsulation of F(-) in different nanotubes (NTs) has been investigated using electronic structure calculations and Car-Parrinello molecular dynamics simulations. The carbon atoms in the single walled carbon nanotube (CNT) are systematically doped with B and N atoms. The effect of the encapsulation of F(-) in the boron nitride nanotube (BNNT) has also been investigated. Electronic structure calculations show that the (7,0) chirality nanotube forms a more stable endohedral complex (with F(-)) than the other nanotubes. Evidence obtained from the band structure of CNT calculations reveals that the band gap of the CNT is marginally affected by the encapsulation. However, the same encapsulation significantly changes the band gap of the BNNT. The density of states (DOS) derived from the calculations shows significant changes near the Fermi level. The snapshots obtained from the CPMD simulation highlight the fluctuation of the anion inside the tube and there is more fluctuation in BNNT than in CNT.

The role of C–H... π interaction in the stabilization of benzene and adamantane clusters #

AbstractIn this investigation, a systematic attempt has been made to understand the interaction between adamantane and benzene using both ab initio and density functional theory methods. C–H...π type of interaction between C–H groups of adamantane and π cloud of benzene is found as the important attraction for complex formation. The study also reveals that the methylene (-CH2) and methine (-CH) groups of adamantane interact with benzene resulting in different geometrical structures. And it is found that the former complex is stronger than the later. The diamondoid structure of adamantane enables it to interact with a maximum of four benzene molecules, each one along the four faces. The stability of the complex increases with increase in the number of benzene molecules. The energy decomposition analysis of adamantane-benzene complexes using DMA approach shows that the origin of the stability primarily arises from the dispersive interaction. The theory of atoms in molecules (AIM) supports the existence of weak interaction between the two systems. The electrostatic topography features provide clues for the mode of interaction of adamantane with benzene.n Graphical AbstractVarious possible modes of interaction between adamantane and benzene have been studied using ab intio and density functional theory based methods. It is found that adamantane can interact with four benzene rings through C–H…π interactions.

Density Functional Theory Studies on Ice Nanotubes

The structure and stability of quasi one-dimensional (1D) ice nanotubes (INTs) have been investigated using Density Functional Theory (DFT) based Beckes three parameter Lee-Yang-Parr exchange and correlation functional (B3LYP) method employing various basis sets. Four different INTs, namely, (4,0)-INT, (5,0)-INT, (6,0)-INT, and (8,0)-INT with different lengths have been considered in this study. The calculated stabilization energies (SEs) illustrate that the stability of INT is proportional to its length and diameter. Further, the encapsulation of various gas molecules (CO(2), N(2)O, CO, N(2), and H(2)) inside the INTs has also been investigated. The calculated SEs of different endohedral complexes reveal that all these gas molecules are stable inside the tubes. The Baders theory of atoms in molecule (AIM) has been used to characterize intra- and inter-ring H-bonding interactions. The electron density topological parameters derived from AIM theory brings out the difference between the intra- and inter-ring H-bonds of INTs.

Interaction of ethylene glycol–water clusters with aromatic surfaces

The gas phase geometries of ethylene glycol–water (EGmWn) (where m = 0–4, n = 0–4; m + n ≤ 4) clusters adsorbed on a fragment of carbon nanotube have been investigated using density functional theory based M05-2X and ωB97XD methods employing various basis sets. With a view to assess the effect of curvature on the hydrogen bonding pattern between ethylene glycol and water molecules, calculations on intermolecular complexes comprising a planar aromatic surface and EGmWn clusters have been carried out. Results obtained from the electronic structure calculations and Baders electron density analysis reveal that C–H⋯π, O–H⋯π and lone pair⋯π interactions are predominant in the stabilization of EGmWn and the corresponding complexes with fragments of a carbon nanotube and graphene. Further, the role of the π-cloud on the stability of EGmWn is illustrated by comparing the interaction energies of clusters in the presence and absence of an aromatic surface.