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.

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.

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.

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.

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.

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.

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.

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.

Archimedean (4,8)-tessellation of haeckelite ultrathin nanosheets composed of boron and aluminum-group V binary materials.

A compendium of unique haeckelite boron and aluminum-group V binary materials have been assessed for their fundamental thermodynamic and ground state electronic properties within density functional theory. We explore their thermodynamic stability relative to new bulk haeckelite crystal structures and find a number of stable polymorphs of planar and buckled ultrathin nanosheets. The bulk boron and aluminum haeckelite crystals display semiconducting and metallic behavior. From the dispersion curves, we predict the formation of both indirect and direct bandgap crystals. We also discover the existence of a five-coordinate aluminum antimonide crystal hitherto never before observed. Moreover, it is found that a number of the Archimedean four and eight membered ring tessellation planar nanosheets could form should synthesis be attempted. It is predicted that these nanosheets can attain two configurations - planar and buckled. From this work we find that combinations of elements such as boron and nitrogen or phosphorus, and aluminum and nitrogen will likely become true single-atom thick nanosheets. These materials show intrinsic indirect bandgap character, which spans the ultraviolet, visible, and infrared spectrum. In the boron series of these materials, the planar structures show double extrema in the bandstructures with van Hove singularities in the projected density of states at the Fermi energy suggesting strong light-matter interactions. The aluminum series we observe strong charge transfer and larger indirect bandgap nanosheets. This study serves as a starting point for a new class of inorganic bulk and ultrathin film materials, which can have many varied applications in nanotechnology.

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.

Voltage-Induced Misfolding of Zinc-Replete ALS Mutant Superoxide Dismutase-1.

The monomerization of Cu, Zn superoxide dismutase (SOD1) is an early step along pathways of misfolding linked to amyotrophic lateral sclerosis (ALS). Monomerization requires the reversal of two post-translational modifications that are thermodynamically favorable: (i) dissociation of active-site metal ions and (ii) reduction of intramolecular disulfide bonds. This study found, using amide hydrogen/deuterium (H/D) exchange, capillary electrophoresis, and lysine-acetyl protein charge ladders, that ALS-linked A4V SOD1 rapidly monomerizes and partially unfolds in an external electric field (of physiological strength), without loss of metal ions, exposure to disulfide-reducing agents, or Joule heating. Voltage-induced monomerization was not observed for metal-free A4V SOD1, metal-free WT SOD1, or metal-loaded WT SOD1. Computational modeling suggested a mechanism for this counterintuitive effect: subunit macrodipoles of dimeric SOD1 are antiparallel and amplified 2-fold by metal coordination, which increases torque at the dimer interface as subunits rotate to align with the electric field.

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.

Site-specific growth of a Pt shell on Au nanoplates: tailoring their surface plasmonic behavior.

In this report, we tune the surface plasmonic behavior of Au nanoplates depending on the morphology of the Pt shell in which Pt is considered as a less optically inactive element. We describe the synthesis of flat Au nanoplates coated with Pt via rim-preferential or uniform growth methods. Depending on the site-selective growth of Pt on core Au nanoplates, the aspect ratio of the resulting Au@Pt nanoplates was tunable and their corresponding surface plasmon resonance (SPR) bands were controlled accordingly. Although Pt is regarded as an optically weak component in visible and near infrared spectral windows, a Pt coating affects the SPR behavior of core Au nanoplates due to effective surface plasmon (SP) coupling between the Au core and the deposited Pt shell. We systematically investigated the optical properties of uniformly grown (Au@Pt(uni)) and rim-preferentially grown (Au@Pt(rim)) Au@Pt nanoplates by observing their SPR band shifts compared to SPR of Au nanoplates. Due to the structural rigidity conferred by the Pt coating, the Au@Pt nanoplates can be easily transferred to the investigated solvents.

Observation of a quadrupole surface plasmon mode for Au nanorods: effects of surface roughness and crystal facets.

This paper describes how the surface roughness and synthetic methods of Au nanorods affect the optical properties that are often associated with localized surface plasmon resonances. We synthesized Au nanorods with different aspect ratios and surface roughness by using two different synthetic strategies to observe surface plasmon resonance bands. One set of nanorods was prepared in high yield by using a seed-mediated dropwise-addition method with a growth-directing surfactant in aqueous solution (Au nanorods in aqueous phase, GNRA). The other set of Au nanorods were synthesized by the electrochemical deposition of Au onto an anodized aluminum oxide (AAO) template (Au nanorods by AAO template, GNRT). The length of the nanorods was controlled by changing the total charge that was passed through the cell and their diameter was monitored by changing the diameter of the template channel. The as-prepared Au nanorods were optimized to observe a quadrupole mode, which is one of the higher-order surface plasmon bands. Our results showed differences between the optical properties of GNRA and GNRT. The roughness and crystal structure of the Au nanorods affected their optical properties. Smooth and single-crystal surface on GNRA had larger and sharper peaks than GNRT. The discrete dipole approximation (DDA) method was used to calculate the optical properties of the Au nanorods and these results were in good agreement with our experimental results.

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.

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.