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At least 1,675 records · Page 93

Combined Experimental and Computational Investigation of the Elementary Reaction of Ground State Atomic Carbon (C; 3 P j ) with Pyridine (C 5 H 5 N; X 1 A 1 ) via Ring Expansion and Ring Degradation Pathways

In t his work, we explored the elementary reaction of atomic carbon (C; 3 P j ) with pyridine (C 5 H 5 N; X 1 A 1 ) at a collision energy of 34 ± 4 kJ mol-1 utilizing the crossed molecular beams technique. Forwardconvolution fitting of the data was combined with high-level electronic structure calculations and statistical (RRKM) calculations on the triplet C 6 H 5 N potential energy surface (PES). These investigations reveal that the reaction dynamics are indirect and dominated by large range reactive impact parameters leading via barrier-less addition to the nitrogen atom and to two chemically non-equivalent ‘aromatic’ carbon-carbon bonds forming three distinct collision complexes. At least two reaction pathways through atomic hydrogen loss were identified on the triplet surface. These channels involve multiple isomerization steps of the initial collision complexes via ring-opening and ring expansion forming an acyclic 1-ethynyl-3-isocyanoallyl radical (P1; 2 A”) and a hitherto unreported seven-membered 1-aza-2-dehydrocyclohepta-2,4,6-trien-4-yl radical isomer (P3; 2 A), respectively. For RRKM calculations at zero collision energy, representing conditions in cold molecular clouds, the ring expansion product P3 is formed nearly exclusively for the atomic hydrogen loss channel. Based on the computations, the molecular fragmentation channel eliminating acetylene (C 2 H 2 ) plus 3-cyano-2-propen-1-ylidene (P6; 3 A”) plays also an important role the reaction of atomic carbon with pyridine proposing a probable destruction pathway of interstellar pyridine. Lastly, these results are also discussed in light of the isoelectronic carbon – benzene (C 6 H 6 ; X 1 A 1 ) system with important implications to the rapid degradation of nitrogen-bearing polycyclic aromatic hydrocarbons (NPAHs) in the interstellar medium compared to mass growth processes of PAH counterparts through ring expansion.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Cation, Anion, and Radical Isomers of C4H4N: Computational Characterization and Implications for Astrophysical and Planetary Environments

Nitrogen-containing ions and molecules in the gas phase have been detected in non-Earth environments such as dark molecular clouds and more recently in the atmosphere of Saturn's moon Titan. These molecules may serve as precursors to larger heterocyclic structures that provide the foundation of complex biological molecules. On Titan, molecules of m/z 66 have been detected by the Cassini mission, and species of the empirical formula C 4 H 4 N may contribute to this signature. We have characterized seven isomers of C 4 H 4 N in anionic, neutral radical, and cationic states using density functional theory. Structures were optimized using the range-separated hybrid ωB97X-V with the cc-pVTZ and aug-cc-pVTZ basis sets. Anionic and radical C4H4N favor cyclic structures with aromatic and quasi-aromatic electron arrangements, respectively. Interestingly, ionization from the radical surface to the cation induces significant changes in structural stability, and the global minimum for positively charged isomers is CH 2 CCHCNH + , a pseudo-linear species reminiscent of cyanoallene. Select formation pathways to these structures from Titan's existing or postulated gas-phase species, reactions that are also relevant for other astrophysical environments, are discussed. By characterizing C 4 H 4 N isomers, we have identified energetically stable anionic, radical, and cationic structures that may be present in Titan's atmosphere and dark molecular clouds.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Dynamics of Hydrophobic Core Phenylalanine Residues Probed by Solid-State Deuteron NMR

We conducted a detailed investigation of the dynamics of two phenylalanine side chains in the hydrophobic core of the villin headpiece subdomain protein (HP36) in the hydrated powder state over the 298–80 K temperature range. We utilized static deuteron NMR measurements of longitudinal relaxation and line shapes supplemented with computational modeling. The temperature dependence of the relaxation times reveals the presence of two main mechanisms that can be attributed to the ring-flips, dominating at high temperatures, and small-angle fluctuations, dominating at low temperatures. The relaxation is non- exponential at all temperatures with the extent of non-exponentiality increasing from higher to lower temperatures. This behavior suggests a distribution of conformers with unique values of activation energies. The central values of the activation energies for the ring-flipping motions are among the smallest reported for aromatic residues in peptides and proteins and point to a very mobile hydrophobic core. The analysis of the widths of the distributions, in combination with the earlier results on the dynamics of flanking methyl groups (Vugmeyster et al., J. Phys. Chem. 2013, 117, 6129–6137), suggests that the hydrophobic core undergoes concerted fluctuations. There is a pronounced effect of dehydration on the ring-flipping motions, which shifts the distribution toward more rigid conformers. The cross-over temperature between the regions of dominance of the small-angle fluctuations and ring-flips shifts from 195 K in the hydrated protein to 278 K in the dry one. This result points to the role of solvent in the onset of the concerted fluctuations of the core and highlights aromatic residues as markers of the protein dynamical transitions.

Environmental Molecular Sciences Laboratory↗

Single-Molecule Electron Transport in Peptoids

Peptoids are structural analogs of peptides in which side chains are appended to the backbone nitrogen rather than the α-carbon. The sequence-defined modularity of peptoids enables precise control over structure−function relationships, enabling applications in energy storage and biomedical materials. Despite recent progress, the role of sequence and conformation on electron transport in peptoid molecules is not fully understood. Here, we synthesize a library of peptoid oligomers and characterize their molecular electronic properties using the scanning tunneling microscope-break junction (STM-BJ) technique. Our results show well-defined electron transport behavior for peptoid sequences containing aromatic side groups lacking hydrogen bonds (H-bonds) and without chemical substitutions at the N−C α position. This behavior fundamentally differs from electron transport in peptides, where H-bond interactions give rise to higher conductance states. All-atom molecular dynamics (MD) simulations are used to understand the conformational heterogeneity of peptoids, and molecular conformations obtained from MD simulations are used in quantum mechanical calculations based on the nonequilibrium Green’s function−density functional theory (NEGF-DFT) formalism. In all cases, computational results are in reasonable qualitative agreement with experiments. Our work demonstrates that the conductance behavior of peptoids depends on monomer identity, including side-chain aromaticity and substitution at the N−C α position. Overall, this work provides new insights into the structure−function relationships governing electron transport in peptoid-based materials and establishes design rules for peptoid-based molecular junctions.

Charge transport↗

Coarse-Grained Molecular Simulation of the Hierarchical Self-Assembly of π-Conjugated Optoelectronic Peptides

Self-assembled aggregates of peptides containing aromatic groups possess optoelectronic properties that make them attractive targets for the fabrication of biocompatible electronics. Molecular-level understanding of how the microscopic peptide chemistry influences the properties of the aggregates is vital for rational peptide design. We construct a coarse-grained model of Asp-Phe-Ala-Gly-OPV3-Gly-Ala-Phe-Asp (DFAG-OPV3-GAFD) peptides containing OPV3 (distyrylbenzene) π-conjugated cores explicitly parameterized against all-atom calculations and perform molecular dynamics simulations of the self-assembly of hundreds of molecules over hundreds of nanoseconds. We observe a hierarchical assembly mechanism wherein ~2-8 peptides assemble into stacks with aligned aromatic cores that subsequently form elliptical aggregates and ultimately a branched network with a fractal dimensionality of ~1.5. The assembly dynamics are well described by a Smoluchowski coagulation process for which we extract rate constants from the molecular simulations to both furnish insight into the microscopic assembly kinetics and extrapolate our aggregation predictions to time and length scales beyond the reach of molecular simulation. Lastly, this study presents new molecular-level understanding of the morphology and dynamics of the spontaneous self-assembly of DFAG-OPV3-GAFD peptides and establishes a systematic protocol to develop coarse-grained models of optoelectronic peptides for the exploration and design of π-conjugated peptides with tunable optoelectronic properties.

36 MATERIALS SCIENCE↗

Identifying the Thermal Decomposition Mechanism of Guaiacol on Pt(111): An Integrated X-ray Photoelectron Spectroscopy and Density Functional Theory Study

Using a concerted effort from both experiment and theory, we determine the thermal decomposition mechanism for guaiacol on Pt(111), a reaction of interest in the area of bio-oil upgrading. This work serves as a demonstration of the power of combining in situ temperature-programmed X-ray photoelectron spectroscopy cos (TPXPS) and density functional theory (DFT) to elucidate complex reaction mechanisms occurring on heterogeneous surfaces. At low temperature (230 K), guaiacol was found to chemisorb with the aromatic ring parallel to the Pt(111) surface with five distinct carbon species and three oxygen species. As the temperature was increased, TPXPS showed several significant changes to the surface species. The increase in the species associated with the decomposition of the functional groups of guaiacol is followed by their subsequent disappearance and an increase in the nonaromatic carbon signal. On the basis of an energetic analysis of the various mechanisms using DFT, along with the comparison of the experimentally and theoretically derived core-level binding energies, we determined that guaiacol's decomposition mechanism occurs via the dehydrogenation of both the methyl and hydroxyl functional groups, followed by demethylation of the CH2 or CH group to form 1,2-benzoquinone. Further heating to above 375 K likely breaks the aromatic ring and results in the rapid formation and desorption of CO, accounting for the disappearance of the 0 is signal above 450 K These results show that a knowledgeable application of TPXPS and DFT can result in the quantitative identification of surface species during complex reactions, providing insight useful for the design of future heterogeneous surfaces.

Hensley, Alyssa J. R. (ORCID:0000000273821286)↗

Optical Absorbance Enhancement in PbS QD/Cinnamate Ligand Complexes

We studied the optical absorption enhancement in colloidal suspensions of PbS quantum dots (QD) upon ligand exchange from oleate to a series of cinnamate ligands. By combining experiments and ab initio simulations, we elucidate physical parameters that govern the optical absorption enhancement. We find that, within the cinnamate/PbS QD system, the optical absorption enhancement scales linearly with the electronic gap of the ligand, indicating that the ligand/QD coupling occurs equally efficient between the QD and ligand HOMO and their respective LUMO levels. Disruption of the conjugation that connects the aromatic ring and its substituents to the QD core causes a reduction of the electronic coupling. Our results further support the notion that the ligand/QD complex should be considered as a distinct chemical system with emergent behavior rather than a QD core with ligands whose sole purpose is to passivate surface dangling bonds and prevent agglomeration.

Kroupa, Daniel M.↗

Insights into Supramolecular Sites Responsible for Complete Separation of Biomass-Derived Phenolics and Glucose in Metal–Organic Framework NU-1000

The molecular origins of adsorption of lignin-derived phenolics to metal–organic framework NU-1000 are investigated from aqueous solution as well as in competitive mode with glucose present in the same aqueous mixture. A comparison of adsorption equilibrium constants ($K_{ads}$) for phenolics functionalized with either carboxylic acid or aldehyde substituents demonstrated only a slight increase (less than a factor of 6) for the former according to both experiments and calculations. This small difference in $K_{ads}$ between aldehyde and carboxylic-acid substituted adsorbates is consistent with the pyrene unit of NU-1000 as the adsorption site, rather than the zirconia nodes, while at saturation coverage, the adsorption capacity suggests multiple guests per pyrene. Experimental standard free energies of adsorption directly correlated with the molecular size and electronic structure calculations confirmed this direct relationship, with the pyrene units as adsorption site. The underlying origins of this relationship are grounded in noncovalent $π–π$ interactions as being responsible for adsorption, the same interactions present in the condensed phase of the phenolics, which to a large extent govern their heat of vaporization. Thus, NU-1000 acts as a preformed aromatic cavity for driving aromatic guest adsorption from aqueous solution and does so specifically without causing detectable glucose adsorption from aqueous solution, thereby achieving complete glucose–phenolics separations. The reusability of NU-1000 during an adsorption/desorption cycle was good, even with some of the phenolic compounds with greatest affinity not easiliy removed with water and ethanol washes at room temperature. A competitive adsorption experiment gave an upper bound for $K_{ads}$ for glucose of at most 0.18 M –1 , which can be compared with $K_{ads}$ for the phenolics investigated here, which fell in the range of 443–42 639 M –1 . The actual value of $K_{ads}$ for glucose may be much closer to zero given the lack of observed glucose uptake with NU-1000 as adsorbent.

09 BIOMASS FUELS↗

Understanding the Nature of Amino Acid Interactions with Pd(111) or Pd–Au Bimetallic Catalysts in the Aqueous Phase

In this study, the interaction of methionine (Met) with different bimetallic-segregated surfaces comprising a uniform distribution of strips and islands of Au on the Pd(111) surface was examined using molecular dynamics (MD) simulations. Out of all the segregated and uniformly doped surfaces studied, the design of Pd–Au islands showed some reduction in the interaction energy (E int = -43.7 kJ/mol) as compared to that of the pure Pd(111) surface (E int = -50 kJ/mol) for a single Met molecule. However, at a higher coverage of 9 Met molecules/simulation cell, none of the Pd–Au alloy surfaces showed any improvement as compared to the Pd(111) surface. In order to develop a comprehensive understanding of the nature of the nonbonded interaction of aqueous biogenic impurities with the Pd catalyst surface, the MD study was extended to include a variety of aliphatic, S-containing, aromatic, and polar amino acids. The potential of mean force (PMF) profiles were observed to be distinct for each class of amino acids with substantial differences among amino acids with acidic and basic side chains. The side chains of all the polar and aromatic amino acids showed direct contact with the surface while aliphatic amino acids had their hydrophobic side chain aligned away from the surface. Interestingly, lysine (Lys) and tyrosine (Tyr) were the only two amino acids which interacted preferentially via the distant backbone nitrogen and backbone oxygen, respectively, despite their side chains being in direct contact with the metal surface. The strength of interaction was correlated with the size of the amino acid; the interaction energies were observed to be the maximum for large molecules such as arginine (Arg, E int = -87.7 kJ/mol) and tryptophan (Trp, E int = -73.4 kJ/mol), while it was a minimum for aliphatic amino acids such as alanine (Ala, E int = -10.9 kJ/mol). Lastly, the study is focused on examining the sensitivity of the choice of the preferential interaction site, conformational preferences, and interaction energies to the side-chain specificity.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Comparisons of bpy and phen Ligand Backbones in Cr-Mediated (Co-)Electrocatalytic CO 2 Reduction

Due to the rise in atmospheric carbon dioxide (CO 2 ) concentrations, there is a need for the development of new strategies to enhance the selectivity and activity of the electrocatalytic conversion of CO 2 to value-added products. The incorporation of redox mediators (RMs) as co-catalysts to enhance the transfer of redox equivalents during catalysis has been gaining more attention in recent years across a variety of small molecule transformations. We have shown that using Cr-centered complexes with sulfone-based RMs leads to an enhancement of CO 2 reduction electrocatalysis under protic conditions via an inner-sphere mechanism. In these co-catalytic systems, an oxygen atom of the reduced RM binds to the Cr center to form a key intermediate stabilized by pancake bonding between the reduced aromatic components of the catalyst ligand backbone and the RM. This interaction facilitates the transfer of an electron and accesses a more kinetically favorable reaction pathway. Here, we show that expanding the aromatic character of the ligand backbone of the catalyst as well as the RM can cause a greater enhancement of co-electrocatalytic activity. These results suggest that further activity improvements can be achieved by focusing on the kinetic and thermodynamic parameters which control association between the catalyst and RM.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Tackling the Capacity Fading Issue of Li–S Battery by a Functional Additive—Hexafluorobenzene

Due to the strong electron-withdrawing fluorine groups, the aromatic ring of hexafluorobenzene (HFB) becomes more electron-deficient and strongly interacts with the lone-pair electrons of the medium. When used as an electrolyte additive for Li-S cell, HFB preferably coordinates with low-order lithium sulfides Li 2 S and Li 2 S 2 and subsequently reacts and converts both into active aromatic sulfides-bis(pentafluorophenyl) disulfides and bis-(pentafluorophenyl) polysulfides in situ-thus facilitating the utilization of the electronically insulating Li 2 S and Li 2 S 2 and improving the cycling stability of the Li-S cell. Finally, this research opens a new avenue to tackle the inherent issues associated with the Li-S chemistry.

25 ENERGY STORAGE↗

Understanding Electron Transport in Disk-Shaped Triphenylene-Tris(naphthaleneimidazole)s through Structural Modification and Theoretical Investigation

We report that disk-shaped molecules with large aromatic π-surfaces are a class of organic semiconductors in which the charge-carrier transport properties could be greatly facilitated by preferred intermolecular stacking of the π-surfaces. The optical and electronic properties are not only determined by the core aromatic structure of these disk-shaped molecules but are also strongly dependent on the side chains, which directly impact the molecular self-assembly behavior in condensed phases. Triphenylene-tris(naphthaleneimidazole) (TP-TNI) is a recently reported n-type semiconductor featuring a large π-core and branched side chains, with an electron-transporting mobility reaching 10 -4 cm 2 V -1 s -1 . To further improve material performance, a detailed study is needed to understand the dependence of carrier transport properties on both the core electronic structure and side chain. Here, we present the detailed synthesis and characterization of a TP-TNI derivative bearing linear side chains, which has demonstrated a field-effect electron-transport mobility of up to 1.3 × 10 -3 cm 2 V -1 s -1 . The more than 1 order improvement in electron-transport properties over the branched side chain homologue can be correlated to ordered twisted packing in the thin film, as revealed by in situ variable temperature grazing incidence wide-angle X-ray scattering studies. In conclusion, in-depth theoretical understanding of the frontier orbitals, reorganization energies, and charge-transfer integrals of TP-TNI molecules has provided further insight into the relationship between the molecular stacking geometry and charge-transport properties.

36 MATERIALS SCIENCE↗

Intra-molecular Charge Transfer and Electron Delocalization in Non-fullerene Organic Solar Cells

Two types of electron acceptors were synthesized by coupling two kinds of electron-rich cores with four equivalent perylene diimides (PDIs) at the a position. With fully aromatic cores, TPB and TPSe have pi-orbitals spread continuously over the whole aromatic conjugated backbone, unlike TPC and TPSi, which contain isolated PDI units due to the use of a tetrahedron carbon or silicon linker. Density functional theory calculations of the projected density of states showed that the highest occupied molecular orbital (HOMO) and lowest unoccupied molecular orbital (LUMO) for TPB are localized in separate regions of space. Further, the LUMO of TPB shows a greater contribution from the orbitals belonging to the connective core of the molecules than that of TPC. Overall, the properties of the HOMO and LUMO point at increased intra-molecular delocalization of negative charge carriers for TPB and TPSe than for TPC and TPSi and hence at a more facile intra-molecular charge transfer for the former. The film absorption and emission spectra showed evidences for the inter -molecular electron delocalization in TPB and TPSe, which is consistent with the network structure revealed by X-ray diffraction studies on single crystals of TPB. These features benefit the formation of charge transfer states and/or facilitate charge transport. Thus, higher electron mobility and higher charge dissociation probabilities under J sc condition were observed in blend films of TPB:PTB7-Th and TPSe:PTB7-Th than those in TPC:PTB7Th and TPSi:PTB7-Th blend films. As a result, the J sc and fill factor values of 15.02 mA/cm 2 , 0.58 and 14.36 mA/cm 2 , 0.55 for TPB- and TPSe-based solar cell are observed, whereas those for TPC and TPSi are 11.55 mA/cm 2 , 0.47 and 10.35 mA/cm 2 , 0.42, respectively.

14 SOLAR ENERGY↗

Aqueous-Based Polyimine Functionalization of Cellulose Nanofibrils for Effective Drying and Polymer Composite Reinforcement

Here a simple strategy was developed to synthesize polyimine-coated cellulose nanofibrils (CNF) for effective CNF drying and composite reinforcement. The polyimine was synthesized in an aqueous medium using a selective hydrophilic and hydrophobic component that forces the polyimine to precipitate, which prevents the reverse imine reaction. The polyimine coating allowed the CNF to be easily oven-dried while maintaining a fibrillar morphology to provide mechanical reinforcement in poly(ethylene terephthalate glycol) (PETG) composites. In comparison, poor mechanical performance and a heterogeneous fracture surface were observed when the coated CNF were incorporated into poly(l-lactide) (PLA) composites. It is hypothesized that intermolecular aromatic–aromatic interactions are formed at the interface between fibers and the polymer matrix in the PETG system, while no such phenomena occur in the PLA system. Overall, this facile strategy to produce modified, easily dried CNF can be adapted to produce polyimine-coated CNF with unique functionalities that are useful in a range of applications.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Thermally Induced Structural Transitions in Epoxy Thermoset Polymer Networks and Their Spectroscopic Responses

The polymer network structure of epoxy thermosets plays a significant role in its final material properties. However, the effects of mild thermal exposure on these network structures are poorly studied. In this work, wide-angle X-ray scattering was used to investigate the polymer network structure of two epoxy thermosets: homopolymerized bisphenol A (BPA) epoxy resin and BPA epoxy resin cured with a polyether amine hardener (BPA/T-403). Using density functional theory and wide-angle X-ray scattering, insights into the polymer network structure were obtained. Diffraction features were determined to originate from hardener-to-hardener molecular distance, perpendicular π–π stacking of aromatic p-phenylene rings, and the average carbon–carbon distance in the polymer. Thermal exposure was found to permanently alter these structural features for both thermosets, with an increase in the π–π stacking distance. Homopolymerized BPA had an additional decrease in the hardener-to-hardener distance. These structural alterations were found to be detectable using Fourier transform infrared spectroscopy and Raman spectroscopy, with changes in the hardener-to-hardener distance having the largest variations in the resulting spectra specifically at the aromatic and ether frequencies.

36 MATERIALS SCIENCE↗

Using Biomimetic Polymers in Place of Noncollagenous Proteins to Achieve Functional Remineralization of Dentin Tissues

In calcified tissues such as bones and teeth, mineralization is regulated by an extracellular matrix, which includes non-collagenous proteins (NCP). This natural process has been adapted or mimicked to restore tissues following physical damage or demineralization by using polyanionic acids in place of NCPs, but the remineralized tissues fail to fully recover their mechanical properties. Here we show that pre-treatment with certain amphiphilic peptoids, a class of peptide-like polymers consisting of N-substituted glycines that have defined monomer sequences, enhances ordering and mineralization of collagen and induces functional remineralization of dentin lesions in vitro. In the vicinity of dentin tubules, the newly formed apatite nano-crystals are co-aligned with the c-axis parallel to the tubular periphery and recovery of tissue ultrastructure is accompanied by development of high mechanical strength. The observed effects are highly sequence-dependent with alternating polar and non-polar groups leading to positive outcomes while diblock sequences have no effect. The observations suggest aromatic groups interact with the collagen while the hydrophilic side chains bind the mineralizing constituents and highlight the potential of synthetic sequence-defined biomimetic polymers to serve as NCP mimics in tissue remineralization.

Chien, Yung-Ching↗

β-O-4 Bond Cleavage Mechanism for Lignin Model Compounds over Pd Catalysts Identified by Combination of First-Principles Calculations and Experiments

Lignin in lignocellulosic biomass is the only renewable source for aromatic compounds, and effective valorization of lignin remains a significant challenge in biomass conversion processes. Here, we have performed density functional theory calculations and experiments to investigate the cleavage mechanism of the C–O ether bond in the lignin model compound 2-phenoxy-1-phenylethanol with a β-O-4 linkage over a Pd(111) catalyst surface model. We propose the favorable reaction pathway to proceed as follows: the dilignol reactant gets dehydrogenated first on the α-carbon and then on the -OH group to generate its corresponding ketone 2-phenoxy-1-phenylethanone; the ketone continues to get dehydrogenated on the β-carbon by first a equilibrated keto–enol tautomerization to its enol form and then -OH dehydrogenation; finally, the C–O ether bond cleavage happens afterward, leading to one-aromatic-ring surface intermediates followed by hydrogenation to yield acetophenone and phenol.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗