Theoretical Appraisal of Cyclopropenone: Aggregation and Complexes with Water.

Cyclopropenone (HCCOCH, "CPN") is an exotic quasi-aromatic cyclic carbene that abounds in the interstellar medium (ISM). Astronomical observations suggest that (i) stagnate CPN exhibits a tendency to polymerize and that (ii) interactions may occur between CPN and water that is also ubiquitous in the ISM. In this light, density functional theory investigations reveal cooperative hydrogen bonding, which leads to stable polymeric conformations of (CPN)n, tracked up to n = 14. Stable agglomerations with water, however, constitute at best only two CPN and two water molecules, signifying that while CPN exhibits remarkable cooperativity for "cohesive" clustering via hydrogen bonding, this tendency is markedly diminished for "hetero"-interactions. Multifaceted data are employed to probe cogent molecular descriptors, such as structure and energetics of various conformers, vibrational spectroscopic response, molecular electrostatic potential (MESP), effective atomic charges: all these, in unison, describe the evolution of the characteristics upon cluster formation. Salient stretching frequency shifts, as well as charge redistribution gleaned from MESP morphology, have a direct bearing on variegated hydrogen bonding patterns: linear, nonlinear, as well as bifurcated. In particular, characteristic C-H, C═O stretching, and O-H vibrations in the water complexes reveal a "softening" (downshift) of frequencies. While small conformers have markedly distinct MESP variations, the differences become less pronounced with incremental clustering, an effect substantiated by corresponding emergent atomic charges.

A halophilic Chromohalobacter species from estuarine coastal waters as a detoxifier of manganese, as well as a novel bio-catalyst for synthesis of n-butyl acetate.

Anthropogenic pollution due to ferro-manganese ore transport by barges through the Mandovi estuary in Goa, India is a major environmental concern. In this study a manganese (Mn) tolerant, moderately halophilic Chromohalobacter sp. belonging to the family Halomonadaceae was isolated from the sediments of a solar saltern adjacent to this Mandovi estuary. Using techniques of Atomic absorption spectroscopy, Scanning electron microscopy-Energy dispersive X-ray spectroscopy, Fourier-transform infrared spectroscopy and Atomic Force Microscopy, the Chromohalobacter sp. was explored for its ability to tolerate and immobilize Mn in amended and unamended media with 20% natural salt concentration (w/v). In aqueous media supplemented with 0.1 mM Mn, the Chromohalobacter sp. was capable of sequestering up to 76% Mn with an average immobilization rate of 8 mg Mn /g /day. Growth rate kinetic analysis using Gompertz mathematical functions was found to model the experimental data well. The model inferred that the maximum growth rate of Chromohalobacter sp. was at 10% natural salt concentration (w/v). The Chromohalobacter sp. was further found to be multimetal tolerant showing high tolerance to Iron (Fe), Nickel (Ni) and Cobalt (Co), (each at 4 mM), and tolerated Manganese (Mn) up to 6 mM. Morphologically, the Chromohalobacter sp. was a non-spore forming, Gram negative motile rod (0.726 µ× 1.33 µ). The adaptative mechanism of Chromohalobacter sp. to elevated Mn concentrations (1 mM) resulted in the reduction of its cell size to 0.339 µ× 0.997 µ and the synthesis of an extracellular slime, immobilizing Mn from the liquid phase forming Manganese oxide, as confirmed by Scanning Electron Microscopy. The expression of Mnx genes for manganese oxidation further substantiated the finding. This bacterial synthesized manganese oxide also displayed catalytic activity (∼50% conversion) for the esterification of butan-1-ol with CH3COOH to yield n-butyl acetate. This Chromohalobacter sp. being indigenous to marine salterns, has adapted to high concentrations of heavy metals and high salinities and can withstand this extremely stressed environment, and thus holds a tremendous potential as an environmentally friendly "green bioremediator" of Mn from euryhaline environments. The study also adds to the limited knowledge about metal-microbe interactions in extreme environments. Further, since Chromohalobacter sp. exhibits commendable catalytic activity for the synthesis of n-butyl acetate, it would have several potential industrial applications.

Selective recognition and extraction of arsenate by a urea-functionalized tripodal receptor from competitive aqueous media.

A second-generation hydrogen bond donor (HBD) anion receptor with an inner amide cavity and an outer urea cavity can selectively and efficiently extract arsenate (AsO43-) from water in the presence of competitive oxoanions and halides. The X-ray structure showed encapsulation of AsO43- in a π-stacked dimeric capsular assembly of the receptor, the first crystallography-based example of pentavalent AsO43- trianion recognition by a HBD receptor.

Cyclopropenylidene: Clustering and Interaction with Water Molecules.

Cyclopropenylidene (c-C3H2, abbreviated CPD) is a highly reactive, planar, partially aromatic carbene discovered in the interstellar medium, and, also recently, in the outer solar system. It is demonstrated herein on cogent quantum chemical grounds that CPD which possesses an electric dipole moment of 3.4 D is capable of forming stable dimer and trimer clusters through hydrogen-bonding. These attributes of CPD are conducive to the formation of stable hydrogen-bonded conformations with one- and two-water molecules. Having determined its consistency with the second-order Møller-Plesset perturbation theory MP2, we employ the ωB97xD hybrid density functional theory in conjunction with a 6-311++G(2d,2p) basis set for a credible description of noncovalent interactions involved in clustering. Molecular electrostatic potential (MESP) and characteristic vibrational frequency shifts upon clustering are presented.

Synergistic Antibacterial Potential and Cell Surface Topology Study of Carbon Nanodots and Tetracycline Against E. coli.

Increasing drugs and antibiotic resistance against pathogenic bacteria create the necessity to explore novel biocompatible antibacterial materials. This study investigated the antibacterial effect of carbon dot (C-dot) against E. coli and suggested an effective synergistic dose of tetracycline with C-dot, using mathematical modeling of antibacterial data. Colony count and growth curve studies clearly show an enhanced antibacterial activity against E. coli synergistically treated with C-dot and tetracycline, even at a concentration ten times lower than the minimum inhibitory concentration (MIC). The Richards model-fit of growth curve clearly showed an increase in doubling time, reduction in growth rate, and early stationary phase in the synergistic treatment with 42% reduction in the growth rate (µm) compared to the control. Morphological studies of E. coli synergistically treated with C-dot + tetracycline showed cell damage and deposition of C-dots on the bacterial cell membrane in scanning electron microscopy imaging. We further validated the topological changes, cell surface roughness, and significant changes in the height profile (ΔZ) with the control and treated E. coli cells viewed under an atomic force microscope. We confirmed that the effective antibacterial doses of C-dot and tetracycline were much lower than the MIC in a synergistic treatment.

Many-body van der Waals interactions in molecules and condensed matter.

This work reviews the increasing evidence that many-body van der Waals (vdW) or dispersion interactions play a crucial role in the structure, stability and function of a wide variety of systems in biology, chemistry and physics. Starting with the exact expression for the electron correlation energy provided by the adiabatic connection fluctuation-dissipation theorem, we derive both pairwise and many-body interatomic methods for computing the long-range dispersion energy by considering a model system of coupled quantum harmonic oscillators within the random-phase approximation. By coupling this approach to density functional theory, the resulting many-body dispersion (MBD) method provides an accurate and efficient scheme for computing the frequency-dependent polarizability and many-body vdW energy in molecules and materials with a finite electronic gap. A select collection of applications are presented that ascertain the fundamental importance of these non-bonded interactions across the spectrum of intermolecular (the S22 and S66 benchmark databases), intramolecular (conformational energies of alanine tetrapeptide) and supramolecular (binding energy of the 'buckyball catcher') complexes, as well as molecular crystals (cohesive energies in oligoacenes). These applications demonstrate that electrodynamic response screening and beyond-pairwise many-body vdW interactions--both captured at the MBD level of theory--play a quantitative, and sometimes even qualitative, role in describing the properties considered herein. This work is then concluded with an in-depth discussion of the challenges that remain in the future development of reliable (accurate and efficient) methods for treating many-body vdW interactions in complex materials and provides a roadmap for navigating many of the research avenues that are yet to be explored.

Encapsulation of alkyl and aryl derivatives of quaternary ammonium cations within cucurbit[n]uril (n = 6,7) and their inverted diastereomers: density functional investigations.

Electronic structure, vibrational frequencies, and ¹H chemical shifts of inclusion complexes between CB[n] (n = 6,7) or their inverted iCB[n] diastereomer hosts and quaternary diammonium viz., 1,6-hexyldiammonium (HDA) or p-xylyldiammonium (XYL) cationic guests are obtained from the density functional calculations. The interaction of CB[n] or iCB[n] with HDA (guest) conduce inclusion complexes in which the guest attains gauche conformation within the host cavity. The lowest energy XYL complexes of CB[6] or iCB[6] are comprised of one ammonium group orienting parallel to aromatic ring. The CB[7] or iCB[7] complexes of XYL on the other hand, reveal ammonium group(s) perpendicular to aromatic ring of the guest. The ureido C=O and N--H stretching vibrations on complexation engender frequency down-shift in the calculated spectra. This can be attributed to C--H-- --O and N--H-- --O interactions in the complex. The inverting of glycouril unit in iCB[n] renders a frequency shift (12 cm⁻¹) for the C=O stretching in the opposite direction. Molecular electron density topography and natural bond orbital analyses have been used to explain the direction of frequency shifts. Calculated ¹H NMR reveal that guest protons within the host cavity not participating in hydrogen bonding interactions, exhibit shielded signals compared to isolated XYL or HDA. Likewise the inverted protons in the iCB[6]-XYL complex led to up-field signals in calculated ¹H NMR as a result of C-H-- -π interactions.

Scaling laws for van der Waals interactions in nanostructured materials.

Van der Waals interactions have a fundamental role in biology, physics and chemistry, in particular in the self-assembly and the ensuing function of nanostructured materials. Here we utilize an efficient microscopic method to demonstrate that van der Waals interactions in nanomaterials act at distances greater than typically assumed, and can be characterized by different scaling laws depending on the dimensionality and size of the system. Specifically, we study the behaviour of van der Waals interactions in single-layer and multilayer graphene, fullerenes of varying size, single-wall carbon nanotubes and graphene nanoribbons. As a function of nanostructure size, the van der Waals coefficients follow unusual trends for all of the considered systems, and deviate significantly from the conventionally employed pairwise-additive picture. We propose that the peculiar van der Waals interactions in nanostructured materials could be exploited to control their self-assembly.

Dispersion Interactions with Density-Functional Theory: Benchmarking Semiempirical and Interatomic Pairwise Corrected Density Functionals.

We present a comparative assessment of the accuracy of two different approaches for evaluating dispersion interactions: interatomic pairwise corrections and semiempirical meta-generalized-gradient-approximation (meta-GGA)-based functionals. This is achieved by employing conventional (semi)local and (screened-)hybrid functionals, as well as semiempirical hybrid and nonhybrid meta-GGA functionals of the M06 family, with and without interatomic pairwise Tkatchenko-Scheffler corrections. All of those are tested against the benchmark S22 set of weakly bound systems, a representative larger molecular complex (dimer of NiPc molecules), and a representative dispersively bound solid (hexagonal boron nitride). For the S22 database, we also compare our results with those obtained from the pairwise correction of Grimme (DFT-D3) and nonlocal Langreth-Lundqvist functionals (vdW-DF1 and vdW-DF2). We find that the semiempirical kinetic-energy-density dependence introduced in the M06 functionals mimics some of the nonlocal correlation needed to describe dispersion. However, long-range contributions are still missing. Pair-wise interatomic corrections, applied to conventional semilocal or hybrid functionals, or to M06 functionals, provide for a satisfactory level of accuracy irrespectively of the underlying functional. Specifically, screened-hybrid functionals such as the Heyd-Scuseria-Ernzerhof (HSE) approach reduce self-interaction errors in systems possessing both localized and delocalized orbitals and can be applied to both finite and extended systems. Therefore, they serve as a useful underlying functional for dispersion corrections.

Synthesis, electronic structure, DNA and protein binding, DNA cleavage, and anticancer activity of fluorophore-labeled copper(II) complexes.

Two mononuclear fluorophore-labeled copper(II) complexes [Cu(nip)(acac)](+)(2) and [Cu(nip)2](2+) (3), where fluorophore is 2-(naphthalen-1-yl)-1H-imidazo[4,5-f][1,10]phenanthroline (nip) (1) and acac is acetylacetone, have been synthesized and characterized by various techniques. The ligand 1 and complex 2 are structurally characterized by single-crystal X-ray diffraction. The coordination geometries around the copper are square planar in solid as well as solution state as evidenced by electron paramagnetic resonance (EPR) spectroscopy. The density functional calculations carried out on 1-3 have shown that electron-rich regions in the highest occupied orbital are localized on the naphthalene and partly on the phenanthroline moiety. Both complexes 2 and 3 in dimethyl sulfoxide (DMSO) exhibit near square planar structure around the metal ion in their ground state. Time-dependent density functional theory (TD-DFT) calculations reveal that Cu(II) ion in complex 2 shows tetrahedral coordination around the metal while 3 retains its square planar geometry in the lowest excited state. The interaction of complexes with calf-thymus DNA (CT DNA) has been explored by using absorption, emission, thermal denaturation, and viscosity studies, and the intercalating mode of DNA binding has been proposed. The complexes cleave DNA oxidatively without any exogenous additives. The protein binding ability has been monitored by quenching of tryptophan emission in the presence of complexes using bovine serum albumin (BSA) as model protein. The compounds showed dynamic quenching behavior. Further, the anticancer activity of the complexes on MCF-7 (human breast cancer), HeLa (human cervical cancer), HL-60 (human promyelocytic leukemia), and MCF-12A (normal epithelial) cell lines has been studied. It has been observed that 3 exhibits higher cytotoxicity than 2, and the cells undergo apoptotic cell death.

Electronic structure and normal vibrations in (+)-catechin and (-)-epicatechin encapsulated beta-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.

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.