Elucidating the Role of Electron-Donating Groups in Halogen Bonding.

Computational quantum chemical techniques were utilized to systematically examine how electron-donating groups affect the electronic and spectroscopic properties of halogen bond donors and their corresponding complexes. Unlike the majority of studies on halogen bonding, where electron-withdrawing groups are utilized, this work investigates the influence of electron-donating substituents within the halogen bond donors. Statistical analyses were performed on the descriptors of halogen bond donors in a prescribed set of archetype, halo-alkyne, halo-benzene, and halo-ethynyl benzene halogen bond systems. The σ-hole magnitude, binding and interaction energies, and the vibrational X···N local force constant (where X = Cl, Br, I, and At) were found to correlate very well in a monotonic and linear manner with all other properties studied. In addition, enhanced halogen bonds were found when the systems contained electron-donating groups that could form intramolecular hydrogen bonds with the electronegative belt of the halogen atom and adjacent linker features.

Shedding Light on the Vibrational Signatures in Halogen-Bonded Graphitic Carbon Nitride Building Blocks.

The relative contributions of halogen and hydrogen bonding to the interaction between graphitic carbon nitride monomers and halogen bond (XB) donors containing C-X and C≡C bonds were evaluated using computational vibrational spectroscopy. Conventional probes into select vibrational stretching frequencies can often lead to disconnected results. To elucidate this behavior, local mode analyses were performed on the XB donors and complexes identified previously at the M06-2X/aVDZ-PP level of theory. Due to coupling between low and high energy C-X vibrations, the C≡C stretch is deemed a better candidate when analyzing XB complex properties or detecting XB formation. The local force constants support this conclusion, as the C≡C values correlate much better with the σ-hole magnitude than their C-X counterparts. The intermolecular local stretching force constants were also assessed, and it was found that attractive forces other than halogen bonding play a supporting role in complex formation.

Toward Quantum Confinement in Graphitic Carbon Nitride-Based Polymeric Monolayers.

Graphitic carbon nitride (g-C3N4) has garnered much attention due to its potential as an efficient metal-free photocatalyst. This study examines the evolution of properties in zero-dimensional quantum dots up to sizable clusters that mimic extended g-C3N4 monolayers. We employ density functional theory to investigate systematically the structural, electronic, and optical properties of the g-C3N4-based melamine and heptazine building blocks using a "bottom-up" construction of polymeric monolayers. The results from our computations indicate that the melamine- and heptazine-based polymeric g-C3N4 systems must be reduced to at least 2.74 and 4.00 nm, respectively, to observe an increase of its optical gap with a size reduction. The present study also examines the nature of the electronic transitions exhibited by g-C3N4-based monolayers through full natural transition orbital and density of state analyses. The most promising sites for water splitting and subsequent chemical doping studies are identified, which generally correspond to the nitrogen and carbon atoms, respectively.

Interrogating the Interplay between Hydrogen and Halogen Bonding in Graphitic Carbon Nitride Building Blocks.

Two graphitic carbon nitride (g-C3N4) molecular building blocks designed for halogen bond driven assembly are evaluated through computational quantum chemistry. Unlike those typically reported in the literature, these g-C3N4-based acceptors each offer three unique sites for halogen bond formation, which when introduced to their donor counterparts, lead to 1:1, 2:1, and 3:1 donor-acceptor complexes. Although halogen bonding interactions are present in all donor-acceptor complexes considered in the work, intermolecular hydrogen bonding emerges in complexes in which an iodine-based donor is directly involved. The halogen bond complexes identified herein feature linear halogen bonds and supportive intermolecular hydrogen bonds that lead to nearly additive electronic binding energies of up to -9.7 (dimers), -18.6 (trimers), and -26.5 kcal mol-1 (tetramers). Select vibrational stretching frequencies (νC-X and νC≡C), and the perturbative shifts they incur upon halogen bond formation, are interrogated and compared to those observed in pyridine- and pyrimidine-based halogen-bonded complexes reported in the literature.

Aromaticity of unsaturated BEC4 heterocycles (E = N, P, As, Sb, O, S, Se, Te).

A compendium of pnictogen and chalcogen substituted boron heterocycles were assessed for their aromatic character by first principles density functional theory. Group-15 and Group-16 elements were placed at the ortho-, meta-, and para-positions of six-membered rings relative to boron to assess their impact on the aromaticity of the unsaturated heterocycles. Aromaticity was analyzed by a multidimensional approach using nuclear independent chemical shifts, gauge-including magnetically induced current, as well as natural bond orbital and natural resonance theory analyses. Based on these methods, we observe a general decline of aromaticity in heavier pnictaborines while the chalcogen analogues maintain relatively strong aromatic character. These general trends result from complementary π-π* natural bond order interactions that sustain resonance within the ring of each heterocycle establishing a pattern of cyclic delocalization. Consequently, natural resonance theory displays strong resonance, which is corroborated with the signed modulus of ring current, toroidal vortices of current maps, and elevated average induced current throughout the ring. The 1,3-configurations for pnictaborines and chalcogenaborines are generally more aromatic compared to the 1,2- and 1,4-isomers, which contain π-holes that limit diatropism within the heterocycles. However, an energetic trend favors the 1,2-heterocycles in both groups, with a few exceptions driven in large-part by π-donation of the lone pair on the heteroatom to the pz orbital on the adjacent boron resulting in stabilization. The importance of planarity for high aromaticity is demonstrated, especially in the pnictaborine isomers where pyramidalization at the pnictogen is favored, while bond regularity seems a less important criterion.

Confinement and surface effects of aqueous solutions within charged carbon nanotubes.

We have examined the structure of water and aqueous solutions in carbon nanotubes using molecular dynamics simulations. We find confinement changes the structure of water as well as the interactions between ions and their solvation shells. The density and orientation of water at the nanotube walls are strongly dependent on the surface charge and cations/anions present at the interfaces. Decreasing the nanotube diameter alters the ion hydration properties as well as hydrogen bonding structure and formation dynamics. The results indicate that fluid structure and hydrogen bond characteristics in nano-channels can be tuned through modification of tube charge and with ion selection.

1,2-Phosphaborines: hybrid inorganic/organic P-B analogues of benzene.

Photolysis of the cyclic phosphine oligomer [PPh]5 in the presence of pentaarylboroles leads to the formation of 1,2-phosphaborines by the formal insertion of a phenylphosphinidene fragment into the endocyclic CB bond. The solid-state structure features a virtually planar central ring with bond lengths indicating significant delocalization. Appreciable ring current in the 1,2-phosphaborine core, detected in nuclear independent chemical shift (NICS) calculations, are consistent with aromatic character. These products are the first reported 1,2-BPC4 conjugated heterocycles and open a new avenue for BP as a valence isoelectronic substitute for CC in arene systems.

Octahedral and Cubic Gold Nanoframes with Platinum Framework.

Herein, we report a general synthetic pathway to various shapes of three-dimensional (3D) gold nanoframes (NFs) embedded with a Pt skeleton for structural rigidity. The synthetic route comprises three steps: site-specific (edge and vertex) deposition of Pt, etching of inner Au, and regrowth of Au on the Pt framework. Site-specific reduction of Pt on Au nanoparticles (NPs) led to the high-quality of 3D Au NFs with good structural rigidity, which allowed the detailed characterization of the corresponding 3D metal NFs. The synthetic method described here will open new avenues toward many new kinds of 3D metal NFs.

Fabrication of 2D Au nanorings with Pt framework.

Surface plasmonics of nanomaterials has been one of the main research themes in nanoscience. Spherical and elongated nanoparticles show their corresponding unique optical features mainly depending on the physical dimensions. Here we successfully synthesized Au nanorings having Pt framework (Pt@Au nanorings) with high uniformity through wet-chemistry. The synthetic strategy consisted of serial reactions involving site-selective growth of Pt on the rim of Au nanoplates, subsequent etching of Au nanoplates, followed by regrowth of Au on the Pt rim. In this synthetic method, Au(3+) ions exhibited dual functionality as an etchant and a metal precursor. The resultant product, Pt@Au nanorings, exhibited unique localized surface plasmon resonance (LSPR) bands originating from the Au shell. The inner Pt skeleton turns out to be important to hold structural stability.

Transmission line equivalent circuit model applied to a plasmonic grating nanosurface for light trapping.

In this paper, we show how light absorption in a plasmonic grating nanosurface can be calculated by means of a simple, analytical model based on a transmission line equivalent circuit. The nanosurface is a one-dimensional grating etched into a silver metal film covered by a silicon slab. The transmission line model is specified for both transverse electric and transverse magnetic polarizations of the incident light, and it incorporates the effect of the plasmonic modes diffracted by the ridges of the grating. Under the assumption that the adjacent ridges are weakly interacting in terms of diffracted waves, we show that the approximate, closed form expression for the reflection coefficient at the air-silicon interface can be used to evaluate light absorption of the solar cell. The weak-coupling assumption is valid if the grating structure is not closely packed and the excitation direction is close to normal incidence. Also, we show the utility of the circuit theory for understanding how the peaks in the absorption coefficient are related to the resonances of the equivalent transmission model and how this can help in designing more efficient structures.

Distance dependent quenching effect in nanoparticle dimers.

In this paper, we investigate the emission characteristics of a molecule placed in the gap of a nanoparticle dimer configuration. The emission process is described in terms of a local field enhancement factor and the overall quantum yield of the system. The molecule is represented as a dipolar source, with fixed length and fed by a constant current. We first describe the coupled dimer-molecule system and compare these results to a single sphere-molecule system. Next, the effect of dimer size is investigated by changing the radius of the nanoparticles. We find that when the radius increases, a saturation effect occurs that trends towards the case of a radiating dipole between two flat interfaces, which we refer to as a parallel plate waveguide geometry. An analytical solution for the parallel plate waveguide geometry is presented and compared to the results for the spherical dimer configuration. We use this approximation as a reference solution, and also, it provides useful guidelines to understand the physical mechanism behind the energy transfer between the molecule and the dimer. We find that the emission intensity undergoes a quenching effect only when the inter-nanoparticle gap distance of the dimer is very small, meaning that strong coupling prevails over energy engaged in the heating process unless the molecule is extremely close to the metal surface.

Molecular dynamics simulations of the secondary-binding site in disaccharide-modified glycopeptide antibiotics.

Oritavancin is a semisynthetic glycopeptide antibiotic used to treat severe infections by multidrug-resistant Gram-positive pathogens. Oritavancin is known to be a thousand times more potent than vancomycin against Gram-positive bacteria due to the additional interactions with bacterial peptidoglycan (PG) facilitated by a secondary-binding site. The presence of this secondary-binding site is evident in desleucyl-oritavancin, an Edman degradation product of oritavancin, still retaining its potency against Gram-positive bacteria, whereas desleucyl-vancomycin is devoid of any antimicrobial activities. Herein, using explicit solvent molecular dynamics (MD) simulations, steered MD simulations, and umbrella sampling, we show evidence of a secondary-binding site mediated by the disaccharide-modified hydrophobic sidechain of oritavancin interactions with the pentaglycyl-bridge segment of the PG. The interactions were characterized through comparison to the interaction of PG with chloroeremomycin, vancomycin, and the desleucyl analogs of the glycopeptides. Our results show that the enhanced binding of oritavancin to PG over the binding of the other complexes studied is due to an increase in the hydrophobic effect, electrostatic and van der Waals interactions, and not the average number of hydrogen bonds. Our ranking of the binding interactions of the biomolecular complexes directly correlates with the order based on their experimental minimum inhibitory concentrations. The results of our simulations provide insight into the modification of glycopeptides to increase their antimicrobial activities or the design of novel antibiotics against pathogenic Gram-positive bacteria.

Molecular Dynamics Simulation of Atomic Interactions in the Vancomycin Binding Site.

Vancomycin is a glycopeptide antibiotic produced by Amycolaptopsis orientalis used to treat serious infections by Gram-positive pathogens including methicillin-resistant Staphylococcus aureus. Vancomycin inhibits cell wall biosynthesis by targeting lipid II, which is the membrane-bound peptidoglycan precursor. The heptapeptide aglycon structure of vancomycin binds to the d-Ala-d-Ala of the pentapeptide stem structure in lipid II. The third residue of vancomycin aglycon is asparagine, which is not directly involved in the dipeptide binding. Nonetheless, asparagine plays a crucial role in substrate recognition, as the vancomycin analogue with asparagine substituted by aspartic acid (VD) shows a reduction in antibacterial activities. To characterize the function of asparagine, binding of vancomycin and its aspartic-acid-substituted analogue VD to l-Lys-d-Ala-d-Ala and l-Lys-d-Ala-d-Lac was investigated using molecular dynamic simulations. Binding interactions were analyzed using root-mean-square deviation (RMSD), two-dimensional (2D) contour plots, hydrogen bond analysis, and free energy calculations of the complexes. The analysis shows that the aspartate substitution introduced a negative charge to the binding cleft of VD, which altered the aglycon conformation that minimized the repulsive lone pair interaction in the binding of a depsipeptide. Our findings provide new insight for the development of novel glycopeptide antibiotics against the emerging vancomycin-resistant pathogens by chemical modification at the third residue in vancomycin to improve its binding affinity to the d-Ala-d-Lac-terminated peptidoglycan in lipid II found in vancomycin-resistant enterococci and vancomycin-resistant S. aureus.

Surface coating effects on the assembly of gold nanospheres.

Optical spectra and atomic force microscopy (AFM) images of individually selected spheres and mechanically assembled silica-coated gold nanosphere pairs were recorded. The shell served as a means of rigid control of the minimum spacing between the metal cores. The spectra of the assembled spheres were simulated using classical electrodynamics. The observed spectra resulted in superior characterization of the particle assembly geometry, relative to the AFM data. Experimental investigations regarding less-rigid polyvinylpyrrolidone (PVP) sphere coatings were also performed and some comparisons were made.

Design and Catalyzed Activation of Tak-242 Prodrugs for Localized Inhibition of TLR4-Induced Inflammation.

Tak-242 (resatorvid), a Toll-like Receptor 4 (TLR4) inhibitor, has been identified as a potent suppressor of innate inflammation. As a strategy to target Tak-242 to select tissue, four TLR4-inactive prodrugs were synthesized for activation via two different release mechanisms. Two nitrobenzyl Tak-242 prodrugs released the parent drug upon exposure to the exogenous enzyme nitroreductase, while the two propargyl prodrugs were converted to Tak-242 in the presence of Pd0.

Computational and experimental evaluation of nanoparticle coupling.

We present theoretical and experimental studies on the optical properties of dimers composed of octahedron-shaped, gold nanoparticles. The experimental measurements show that the photoluminescence varies quite dramatically as two octahedra are brought into close proximity. AFM images and optical emission have been recorded for dimers in uncoupled and strongly coupled configurations. The former displays a single emission peak, while the latter shows two peaks with the new feature at longer wavelengths. Calculations indicate that the red-shifted peak originates from a strongly coupled plasmon state that oscillates along the extended axis of the dimer. Theoretically, we investigate the distances over which the dimers couple and find this to be particularly plasmon mode dependent. The anisotropic morphology and sharp apexes contribute significantly to the orientational dependence of the interparticle couplings and field properties.

Characterization of Electrospray Ionization (ESI) Parameters on In-ESI Hydrogen/Deuterium Exchange of Carbohydrate-Metal Ion Adducts.

The conformations of glycans are crucial for their biological functions. In-electrospray ionization (ESI) hydrogen/deuterium exchange-mass spectrometry (HDX-MS) is a promising technique for studying carbohydrate conformations since rapidly exchanging functional groups, e.g., hydroxyls, can be labeled on the timeframe of ESI. However, regular application of in-ESI HDX to characterize carbohydrates requires further analysis of the in-ESI HDX methodology. For instance, in this method, HDX occurs concurrently to the analyte transitioning from solution to gas-phase ions. Therefore, there is a possibility of sampling both gas-phase and solution-phase conformations of the analyte. Herein, we differentiate in-ESI HDX of metal-adducted carbohydrates from gas-phase HDX and illustrate that this method analyzes solvated species. We also systematically examine the effects of ESI parameters, including spray solvent composition, auxiliary gas flow rate, sheath gas flow rate, sample infusion rate, sample concentration, and spray voltage, and discuss their effects on in-ESI HDX. Further, we model the structural changes of a trisaccharide, melezitose, and its intramolecular and intermolecular hydrogen bonding in solvents with different compositions of methanol and water. These molecular dynamic simulations support our experimental results and illustrate how an individual ESI parameter can alter the conformations we sample by in-ESI HDX. In total, this work illustrates how the fundamental processes of ESI alter the magnitude of HDX for carbohydrates and suggest parameters that should be considered and/or optimized prior to performing experiments with this in-ESI HDX technique. Graphical Abstract ᅟ.

Synthesis of first row transition metal selenomaltol complexes.

We report an efficient, one-step synthesis of the chelator 3-hydroxy-2-methyl-4-selenopyrone (selenomaltol). Complexes of selenomaltol with Fe(iii), Ni(ii), Cu(ii) and Zn(ii) have been prepared and studied by NMR, X-ray crystallography, cyclic voltammetry, EPR and electronic absorption. The Ni(ii) and Cu(ii) complexes show chemically reversible oxidations which are suggested to be ligand-based. Nuclear independent chemical shifts (NICS) analysis is used to compare aromaticity of the heterocyclic rings of selenomaltol and its chelates. The compounds described here should significantly expand the scope and utility of unusual O,Se-donor chelates.

Manipulating the optical properties of pyramidal nanoparticle arrays.

This paper reports the orientation-dependent optical properties of two-dimensional arrays of anisotropic metallic nanoparticles. These studies were made possible by our simple procedure to encapsulate and manipulate aligned particles having complex three-dimensional (3D) shapes inside a uniform dielectric environment. Using dark field or scattering spectroscopy, we investigated the plasmon resonances of 250-nm Au pyramidal shells embedded in a poly(dimethylsiloxane) (PDMS) matrix. Interestingly, we discovered that the scattering spectra of these particle arrays depended sensitively on the direction and polarization of the incident white light relative to the orientation of the pyramidal shells. Theoretical calculations using the discrete dipole approximation support the experimentally observed dependence on particle orientation with respect to incident field. This work presents an approach to manipulate--by hand--ordered arrays of particles over cm(2) areas and provides new insight into the relationship between the shape of well-defined, 3D particles and their supported plasmon resonance modes.