Rahul V. Pinjari

Electronic Structure, Molecular Electrostatic Potential, and NMR Chemical Shifts in Cucurbit[n]urils (n = 5-8), Ferrocene, and Their Complexes

Electronic structure and molecular electrostatic potential (MESP) in ferrocene (FC), cucurbit[n]urils (CB[n]) with n = 5-8, and their host-guest complexes are obtained within the framework of density functional theory. MESP topography that is employed to gauge the dimensions of the CB[n] cavity estimates that the cavity height increases from 7.25 to 7.70 A along CB[n] homologue series, whereas the diameter of the CB[8] (8.57 A) cavity is larger than twice that of CB[5] (3.91 A). MESP investigations reveal deeper minima near ureido oxygens in CB[5] along with large electron-rich regions at its portal. A lateral interaction of the guest FC with hydrophilic exterior of the CB[n] portal and its encapsulation within hydrophobic cavity of the host are analyzed. The present calculations suggest that CB[5] does not yield stable complexes in either case. FC interacts laterally with CB[6], and inclusion of the guest occurs, both parallel as well as perpendicular to the CB[n] axis, in the cavity of higher homologue. Self-consistent reaction field studies indicate that, in the presence of water as a solvent, encapsulation of FC in parallel fashion is favored within CB[7] and CB[8] cavities. NMR chemical shifts (delta(H)) of CB[n] protons remain practically unchanged with an increase in the cavity size; however, they are influenced significantly by water. The spectra thus obtained in aqueous solution agree with those observed experimentally. The delta(H) values in FC-CB[n] complexes indicate deshielding of FC protons directed toward portals, while those pointing toward nitrogens exhibit up-shifts in the spectra.

Density functional investigations on the charge distribution, vibrational spectra, and NMR chemical shifts in cucurbit[n]uril (n = 5-12) hosts.

Electronic structure, charge distribution, and vibrational frequencies of cucurbit[n]uril, CB[n] (n = 5-12), hosts have been derived using the density functional methods. CB[n] conformers with different orientations of methylene group connecting glycouril units have been investigated. The conformers that possess uniform CB[n] cavity turn out to be of lowest energy, and molecular electrostatic potential (MESP) herein engender shallow minima near ureido oxygens along the series. MESP topography has been utilized to estimate the cavity height and diameter; the ratio of which governs the shape (circular or elliptical) of the cavity. When this ratio is larger than unity (for CB[n] with n >or= 8), an elliptical host cavity is noticed. Calculated vibrational spectra reveal that carbonyl stretching frequency shift in successive CB[n] homologue decreases steadily from 1760 cm(-1) in CB[5] to 1742 cm(-1) in CB[12]. An increase in glycouril units along the CB[n] series influences significantly the intensity profile of C horizontal lineO and C-N stretching vibrations in the calculated infrared spectra. Furthermore, calculated (1)H chemical shifts predict that one of methylene protons directing outside the host cavity are deshielded, whereas the remaining proton near the carbonyl group exhibits downshifted signal in the NMR spectra.

On the Binding of SF6 to Cucurbit[6]uril Host: Density Functional Investigations

Interactions of sulfur hexafluoride (SF(6)) with cucurbit[6]uril (CB[6]) have been investigated using the density functional calculations. An encapsulation of guest within CB[6] cavity as well as its binding to either exterior host protons or portal uredio oxygens have been analyzed. The present calculations predict that the complexes with the complete inclusion of SF(6) are favored over those possessing lateral or external interactions. The interactions between fluorine and ureido carbons (F---C) of the host contribute to lowering of energy of the complex. Normal mode analyses from the calculated vibrational spectra show a red-shifted stretching (approximately 928 cm(-1)) of S-F bonds perpendicular to the CB[6] cavity axis when SF(6) is encapsulated in the host cavity. On the other hand, S-F bonds parallel to the cavity axis exhibit a blue shift as compared to the corresponding vibration of the isolated guest. These frequency shifts of S-F bonds have further been analyzed by mapping the difference electron density on the bond critical point(s) (bcp) in molecular electron density (MED) topography and natural bond orbital (NBO) analyses. A depletion of electron density at the bcp along with an enhanced electron density in antibonding S-F* orbital engender weakening of the bond. Concomitant redistribution of electron density leads to the strengthening of S-F bonds parallel to the cavity axis (directing toward either portals). (1)H NMR reveals that the protons directing toward CB[n] portals are not influenced by encapsulation of the guest, which is in consonant with experimentally measured NMR spectra.

Electronic Structure and Normal Vibrations in (+)-Catechin and (−)-Epicatechin Encapsulated β-Cyclodextrin

Host-guest interactions between beta-cyclodextrin (beta-CD) and flavan-3-Ol enantiomers (guest) namely, (+)-catechin (CA) or (-)-epicatechin (EC), have been analyzed within the framework of density functional theory. Both CA and EC consist of two phenol rings, I and II, and a pyran ring, III, which facilitate a variety of binding patterns with the host, beta-CD. The minimum energy beta-CD-CA complex reveals that ring II of CA interacts with primary hydroxyls of the upper rim and the phenol ring I engenders hydrogen-bonded interactions with secondary hydroxyl from the lower rim of CD. On the other hand, the O-H...O interactions between ring I and primary hydroxyls of beta-CD along with those between one of hydroxyl of ring II and secondary hydroxyl of the host render large stability to the beta-CD-EC complex. Structures of both beta-CD-CA and beta-CD-EC complexes thus obtained are in consonant with those inferred from the experimental NMR data and exhibit distinct features in infrared spectra. The frequency shifts of characteristic vibrations in infrared spectra of these complexes compared to the unbound individual host or guest in its free state have been analyzed with the use of natural bond orbital analyses and combining difference electron density maps with bond critical points in molecular electron density topography.

Electronic Structure and 1H NMR Chemical Shifts in Host-Guest Complexes of Cucurbit[6]uril and sym-Tetramethyl Cucurbit[6]uril with Imidazole Derivatives

Binding patterns and (1)H NMR chemical shifts in the complexes of protonated N-(4-hydroxylphenyl)imidazole (g1), N-(4-aminophenyl)imidazole (g2), 2-phenylimidazole (g3) guests with cucurbit[6]uril (CB[6]), and sym-substituted tetramethyl cucurbit[6]uril (TMeCB[6]) in the gas phase as well as in water have been investigated using the density functional theory. It has been shown that the inclusion complexes of g1 and g2 with CB[6] or TMeCB[6] exhibit selective encapsulation of the phenyl moiety with its substituents binding to portal oxygens on the lower rim of the host and imidazole protons facilitate C-H···O interactions externally with upper rim ureido oxygens. On the other hand, the lowest-energy g3 complex encapsulates the imidazole ring within the host, engendering N-H···O interactions with portal oxygens on the upper rim of the host with the phenyl ring residing outside the cavity owing to an absence of para-substituent and show qualitatively different host-guest binding patterns. Calculated (1)H NMR spectra of the complexes in water reveal shielding of phenyl ring protons within the host cavity which exhibit signals at 0.2-0.5 ppm, whereas the protons of the imidazole ring participating in hydrogen bonded interactions exhibit deshielding, and the corresponding (1)H NMR signals are downshifted by 1.1-1.5 ppm in the spectra compared to those in the unbound guest. (1)H NMR chemical shifts of inclusion complexes thus obtained are in consonant with δ(H) patterns observed in experiments reported in the literature.

Binding of rhodamine B and kiton red S to cucurbit[7]uril: density functional investigations

AbstractThe binding of the laser dyes rhodamine B (RhB) and sulforhodamine B (kiton red S or KRS) to a cucurbit[7]uril (CB[7]) host has been investigated using density functional theory. Both guests (RhB and KRS) contain two N,N-diethylamino groups on a xanthene core. The lowest-energy structure of these host–guest complexes has one of the N,N-diethylamino groups encapsulated within the host cavity, that engenders C–H···O interactions with portals, while the remaining noninteracting diethylamino group resides outside the cavity. The 1H NMR chemical shifts derived using the gauge-independent atomic orbital method are consistent with those observed in experiments. FigureBinding modes of the fluorescent dyes RhB and KRS to a CB[7] host

Molecular Orbital Simulations of Metal 1s2p Resonant Inelastic X-ray Scattering.

For first-row transition metals, high-resolution 3d electronic structure information can be obtained using resonant inelastic X-ray scattering (RIXS). In the hard X-ray region, a K pre-edge (1s→3d) excitation can be followed by monitoring the dipole-allowed Kα (2p→1s) or Kβ (3p→1s) emission, processes labeled 1s2p or 1s3p RIXS. Here the restricted active space (RAS) approach, which is a molecular orbital method, is used for the first time to study hard X-ray RIXS processes. This is achieved by including the two sets of core orbitals in different partitions of the active space. Transition intensities are calculated using both first- and second-order expansions of the wave vector, including, but not limited to, electric dipoles and quadrupoles. The accuracy of the approach is tested for 1s2p RIXS of iron hexacyanides [Fe(CN)6](n-) in ferrous and ferric oxidation states. RAS simulations accurately describe the multiplet structures and the role of 2p and 3d spin-orbit coupling on energies and selection rules. Compared to experiment, relative energies of the two [Fe(CN)6](3-) resonances deviate by 0.2 eV in both incident energy and energy transfer directions, and multiplet splittings in [Fe(CN)6](4-) are reproduced within 0.1 eV. These values are similar to what can be expected for valence excitations. The development opens the modeling of hard X-ray scattering processes for both solution catalysts and enzymatic systems.

Theoretical studies on the electronic structure, charge distribution and vibrational spectra of diglyme–M+-AsF6− (M = Li, Na, K)

Electronic structure and the vibrational spectra of CH(3)(OCH(2)CH(2))(2)OCH(3)-M(+)-AsF(6)(-) (M=Li, Na, K) have been obtained using the density functional theory. Lithium ion exhibits a pentavalent coordination via 3 oxygens from diglyme and two fluorines of AsF(6)(-) whereas Na(+) and K(+) exhibit coordinate number 6 with 3 fluorines of the anion binding to alkali metal in these complexes. Analysis of calculated spectra reveal that the CH(2) wag (840-1120 cm(-1)) vibrations in the complex are sensitive to metal ion coordination. A frequency downshift relative to the free anion has been predicted for the vibrations of AsF(6)(-) anion when the fluorines are directly bonded (denoted by F) to metal ion. Consequent reorganization of electron density in the complex engenders a frequency shift in the opposite direction for As-F vibrations wherein the fluorine atoms are not coordinating to the alkali metal ion. An approach based on the molecular electron density topography coupled with the difference electron density map explains the direction of the frequency shifts of C-O-C and the As-F stretchings compared to those of free diglyme or AsF(6) anion. A new method, which includes the color-mapping function for the difference molecular electron density (MED), superimposed on the bond critical points in MED topography has been suggested to explain the direction of the frequency shifts in a single attempt.

Cu(II) conjugation along the transformation of a vitamin K3 derivative to a dinaphthoquinone methide radical

1,1′-Methide-bi-vitamin K3 (B) has been isolated as a dinaphthoquinone methide radical (DNQM) by the transformation of 1-imino(acetylhydrazino)-vitamin K3 (A). The transformation follows a biomimetic activation pathway mediated via Cu(II) ion catalyzed oxidative coupling. Single crystal X-ray and electron spin resonance (ESR) experiments combined with density functional calculations elucidate the “resonance structure” of the DNQM radical (B). Fluorescence investigations reveal that DNQM facilitates interaction with the cysteine residue. As compared to the parent substrate, B shows a depletion in the level of GSH, triggering apoptosis in HeLa cells.