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At least 199 records · Page 11

Chlorination of Hydrogenated Silicon Nanosheets Revealed by Solid-State Nuclear Magnetic Resonance Spectroscopy

We report two-dimensional silicon nanosheets (Si-NS) synthesized by topotactic deintercalation of CaSi 2 are hypothesized to consist of buckled layers of sp 3 -hybridized silicon atoms that are bonded to three other framework Si atoms and a terminal atom or functional group such as H, Cl, or OH. Here, we apply 1 H{ 35 Cl} and 29 Si{ 35 Cl} Resonance-Echo Saturation-Pulse DOuble-Resonance (RESPDOR) solid-state NMR experiments to directly confirm the presence of chlorinated Si atoms within Si-NS. Plotting the 1 H{ 35 Cl} RESPDOR dephasing as a function of the 35 Cl saturation pulse offset reveals that the 35 Cl quadrupolar coupling constant (C Q ) is 38 MHz, consistent with Cl atoms that are covalently bonded to silicon. Modeling the 1 H{ 35 Cl} RESPDOR dephasing curve shows that the Si–Si interlayer spacing is approximately 6 Å. Plane-wave density functional theory (DFT) calculations show that the direct band gap transition of the Si-NS decreases with increasing chlorination and hydroxylation, suggesting that the band gap of Si-NS can be tuned by modifying the terminal atoms or functional groups.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Pt-Assisted Carbon Remediation of Mo2C Materials for CO Disproportionation

Using the CO disproportionation (Boudouard) reaction as a probe reaction, an in-depth analysis of temperature-programmed pulse response data shows that the addition of Pt to Mo2C mitigates deactivation of Mo active sites by acting as a carbon collector. CO2 production on Mo2C and Pt/Mo2C materials is dependent on both the activation energy and the CO surface concentration. Detailed plane-wave density functional theory calculations of the CO adsorption and disproportion reactions on Mo2C-supported Pt nanoparticles (NPs) are reported. The Mo2C was modeled by the ß-Mo2C (100) surface, and the Pt/Mo2C interface was modeled by the addition of 12 Pt atoms to the Mo2C (100) surface (12Pt@Mo2C). The potential energy surfaces of the Boudouard reaction were calculated on pure Mo2C, 12Pt@Mo2C, and Pt (111) surfaces. CO dissociation readily occurs on the Mo2C (100) surface, but not on the Pt (111) surface, with the former being exothermic and the latter being endothermic. At the Pt/Mo2C interface, CO dissociation is still exothermic, but with a larger energy barrier. The Boudouard reaction takes place on the Mo2C region, where CO2 is formed from a surface O atom dissociated from one CO molecule in reaction with another CO molecule, leaving one C atom on the surface. C adsorption is preferential on the Pt site in comparison to the Mo site. The supported Pt domains can collect the remaining C atoms, facilitating further CO2 formation on the active Mo sites. A Bader charge analysis shows that the surface metal-carbon bond is a mixture of covalent and ionic bonds, whereas the surface metal-oxygen bond is ionic. Electron localization function (ELF) and partial charge density calculations agree well with the Bader charge analysis. These computational results are consistent with experimental observations of the interaction of CO with Mo2C nanotube supported Pt domains in the transient regime under far from equilibrium conditions. The Boudouard reaction is an important side reaction, and the unexpected role found for Pt as a carbon collector, with Mo serving as a disproportionation site, provides a unique vantage point for understanding carbon and coke formation on catalytic materials.

Pt-assisted carbon remediation, Pt/Mo2C interface,↗

Density functional theory study on the coupling and reactions of diferuloylputrescine as a lignin monomer

Diferuloylputrescine has been found in a variety of plant species, and recent work has provided evidence of its covalent bonding into lignin. Results from nuclear magnetic resonance spectroscopy revealed the presence of bonding patterns consistent with homo-coupling of diferuloylputrescine and the possibility of cross-coupling with lignin. In the present work, density functional theory calculations have been applied to assess the energetics associated with radical coupling, rearomatization, and dehydrogenation for possible homo-coupled dimers of diferuloylputrescine and cross-coupled dimers of diferuloylputrescine and coniferyl alcohol. Furthermore, the values obtained for these reaction energetics are consistent with those reported for monolignols and other novel lignin monomers. As such, this study shows that there would be no thermodynamic impediment to the incorporation of diferuloylputrescine into the lignin polymer and its addition to the growing list of non-canonical lignin monomers.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Charge Regulation Stabilizes the Formation of Ionic Liquid‐Based Amphiphilic Oligomer Droplet Interface Bilayers

Amphiphilic charged oligomers (oligodimethylsiloxane – methylimidazolium cation, ODMS-MIM (+) ), assemble into bilayers using the droplet interface bilayer (DIB) platform, possess similar size and functionality as phospholipid bilayers, but exhibit increased stability. The oligomer ionic headgroups (MIM (+) ) are covalently bound to monodisperse, short-chain (n = 13) hydrophobic tails (ODMS). These self-assemble as monolayer brushes at the oil–aqueous interface of water droplets that are influenced by both the charged cationic headgroups, and the nature of the covalently attached tails in the organic phase. Charge regulation (CR) stabilizes the formation of ordered, molecularly close-packed brush phases, which results in highly insulating, stable DIB membranes, with contributions from specific ion-pairing effects, Debye screening, and voltage-dependent electrocompressive stresses. In the oil phase, interactions between hexadecane, a good solvent for ODMS, and the hydrophobic tails result in extended waiting times for bilayer formation compared to phospholipid DIBs, for which hexadecane is a poor solvent. Close agreement between experimental values and predictions for two key parameters, the critical membrane thickness, h c , and maximal grafted headgroup density, Γ 0 , validate an electrostatic CR model consisting of adsorption and partial neutralization of counterions at a charged interface.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Homoleptic Perchlorophenyl “Ate” Complexes of Thorium(IV) and Uranium(IV)

The reaction of AnCl 4 (DME) n (An = Th, n = 2; U, n = 0) with 5 equiv of LiC 6 Cl 5 in Et 2 O resulted in the formation of homoleptic actinide-aryl “ate” complexes [Li(DME) 2 (Et 2 O)] 2 [Li(DME) 2 ][Th(C 6 Cl 5 ) 5 ] 3 ([Li][1]) and [Li(Et 2 O) 4 ][U(C 6 Cl 5 ) 5 ] ([Li][2]). Similarly, the reaction of AnCl 4 (DME)n (An = Th, n = 2; U, n = 0) with 3 equiv of LiC 6 Cl 5 in Et 2 O resulted in the formation of heteroleptic actinide-aryl “ate” complexes [Li(DME) 2 (Et 2 O)][Li(Et 2 O) 2 ][ThCl 3 (C 6 Cl 5 ) 3 ] ([Li][3]) and [Li(Et 2 O) 3 ][UCl 2 (C 6 Cl 5 ) 3 ] ([Li][4]). Density functional calculations show that the An–C ipso σ-bonds are considerably more covalent for the uranium complexes vs the thorium analogues, in line with past results. Additionally, good agreement between experiment and calculations is obtained for the 13 C ipso NMR chemical shifts in [Li][1] and [Li][3]. Here, the calculations demonstrate a deshielding by ca. 29 ppm from spin–orbit coupling effects originating at Th, which is a direct consequence of 5f orbital participation in the Th–C bonds.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Structural Anisotropy Determining the Oxygen Evolution Mechanism of Strongly Correlated Perovskite Nickelate Electrocatalyst

The regulation of reactive centers by involving the participation of lattice oxygen has been reported as an effective strategy for lowering the reaction barrier for the oxygen evolution reaction (OER). However, the control of the OER pathway by taking advantage of the intrinsic properties of catalysts remains a challenging task. Herein, we adopt perovskite nickelate (i.e., NdNiO3 (NNO)) and establish the link between structural anisotropy and the OER catalytic mechanism. The results elucidate that NNO with (100), (110), and (111) orientations display similar oxidative states and metal–oxygen covalency characteristics but distinct OER activities following the order of (100) > (110) > (111). Density function theory (DFT) results confirm that film orientation is a critical determinant of the reaction mechanism. The OER on (100)-NNO favors proceeding via a lattice-oxygen-mediated mechanism (LOM). In contrast, the reaction on (110)-NNO and (111)-NNO follows the adsorbate evolution mechanism (AEM). The anisotropic oxygen vacancy formation energy and stability are strongly correlated to the reaction mechanism and performance, which can be described in brief by the metal–oxygen bond valence. Furthermore, our results are a step toward achieving the long-sought convenient approach to tune the OER mechanism, which is applicable for a wide range of sustainable energy-related devices.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Effect of the abolition of intersubunit salt bridges on allosteric protein structural dynamics

A salt bridge, one of the representative structural factors established by non-covalent interactions, plays a crucial role in stabilizing the structure and regulating the protein function, but its role in dynamic processes has been elusive. Here, to scrutinize the structural and functional roles of the salt bridge in the process of performing the protein function, we investigated the effects of salt bridges on the allosteric structural transition of homodimeric hemoglobin (HbI) by applying time-resolved X-ray solution scattering (TRXSS) to the K30D mutant, in which the interfacial salt bridges of the wild type (WT) are abolished. The TRXSS data of K30D are consistent with the kinetic model that requires one monomer intermediate in addition to three structurally distinct dimer intermediates (I 1 , I 2 , and I 3 ) observed in WT and other mutants. The kinetic and structural analyses show that K30D has an accelerated biphasic transition from I 2 to I 3 by more than nine times compared to WT and lacks significant structural changes in the transition from R-like I 2 to T-like I 3 observed in WT, unveiling that the loss of the salt bridges interrupts the R–T allosteric transition of HbI. Besides, the correlation between the bimolecular CO recombination rates in K30D, WT, and other mutants reveals that the bimolecular CO recombination is abnormally decelerated in K30D, indicating that the salt bridges also affect the cooperative ligand binding in HbI. These comparisons of the structural dynamics and kinetics of K30D and WT show that the interfacial salt bridges not only assist the physical connection of two subunits but also play a critical role in the global structural signal transduction of one subunit to the other subunit via a series of well-organized structural transitions.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Chemical bonding in actinyl( V / VI ) dipyriamethyrin complexes for the actinide series from americium to californium: a computational investigation

The separation of minor actinides in their dioxocation (i.e., actinyl) form in high-valence oxidation states requires efficient ligands for their complexation. Here, in this work, we evaluate the complexation properties of actinyls including americyl, curyl, berkelyl, and californyl in their pentavalent and hexavalent oxidation states with the dipyriamethyrin ligand (L) using density functional theory calculations. The calculated bond parameters show shorter An&#x2550O yl bonds with covalent character and longer An–N bonds with ionic character. The bonding between the actinyl cation and the ligand anion shows a flow of charges from the ligand to actinyl in all [An V/VI O 2 –L] 1–/0 complexes. However, across the series, backdonation of charges from the metal to the ligand becomes prominent and stabilizes the complexes. The thermodynamic parameters in the gas phase and solution suggest that the complex formation reaction is spontaneous for [Cf V/VI O 2 –L] 1–/0 complexes and spontaneous at elevated temperatures (>298.15 K) for all other complexes. Spin–orbit corrections have a quantitative impact while the overall trend remains the same. Energy decomposition analysis (EDA) reveals that the interaction between actinyl and the ligand is mainly due to electrostatic contributions that decrease from Am to Cf along with an increase in orbital contributions due to the backdonation of charges from the actinyl metal center to the ligand that greatly stabilizes the Cf complex. The repulsive Pauli energy contribution is observed to increase in the case of [An V O 2 –L] 1– complexes from Am to Cf while a decrease is observed among [An VI O 2 –L] 0 complexes, showing minimum repulsion in [Cf VI O 2 –L] 0 complex formation. Overall, the hexavalent actinyl complexes show greater stability (increasing from Am to Cf) than their pentavalent counterparts.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Simulation studies for surfaces and materials strength

Computer simulation studies were conducted to investigate materials properties. All the calculations were carried out using atomic level simulation techniques which are based on semiempirical or model functions. During this project, functions with varying degrees of complexity were derived and employed in simulations. Investigations include covalently bonded materials as well as systems involving metal atoms. For small clusters calculated results provided information on various energy- and structure-related properties along with vibrational characteristics. Also, energy barriers for configurational transitions were calculated for selected cases. Simulation calculations for surfaces produced new results in areas related to surface energies, reconstructions and relaxations, surface defects, surface stresses as well as adsorption and nucleation processes. Simulations were also performed on bulk materials. Calculated results provided an atomic level understanding on energetics and structures of point defects, crystal stability, elastic properties, and materials strength for various systems. Calculations involving polymeric materials include studies of polar polymer melts and polymer/solid interfaces. Simulations employing specially developed codes provided significant information about energetics and conformational characteristics of different polymeric chains.

Halicioglu, Timur↗

Cell sorting apparatus

Polymeric functional microspheres containing metal or metal compounds are formed by addition polymerization of a covalently bondable olefinic monomer such as hydroxyethylmethacrylate in the presence of finely divided metal or metal oxide particles, such as iron, gold, platinum or magnetite, which are embedded in the resulting microspheres. The microspheres can be covalently bonded to chemotherapeutic agents, antibodies, or other proteins providing a means for labeling or separating labeled cells. Labeled cells or microspheres can be concentrated at a specific body location such as in the vicinity of a malignant tumor by applying a magnetic field to the location and then introducing the magnetically attractable microspheres or cells into the circulatory system of the subject. Labeled cells can be separated from a cell mixture by applying a predetermined magnetic field to a tube in which the mixture is flowing. After collection of the labeled cells, the magnetic field is discontinued and the labeled sub-cell population recovered.

Yen, Shiao-Ping S.↗

Method for producing a biological reagent

Polymeric functional microspheres containing metal or metal compounds are formed by addition polymerization of a covalently bondable olefinic monomer such as hydroxyethylmethacrylate in the presence of finely divided metal or metal oxide particles, such as iron, gold, platinum or magnetite, which are embedded in the resulting microspheres. The microspheres can be covalently bonded to chemotherapeutic agents, antibodies, or other proteins providing a means for labeling or separating labeled cells. Labeled cells or microspheres can be concentrated at a specific body location such as in the vicinity of a malignant tumor by applying a magnetic field to the location and then introducing the magnetically attractable microspheres or cells into the circulatory system of the subject. Labeled cells can be separated from a cell mixture by applying a predetermined magnetic field to a tube in which the mixture is flowing. After collection of the labeled cells, the magnetic field is discontinued and the labeled sub-cell population recovered.

Yen, Shiao-Ping S.↗

Metal containing polymeric functional microspheres

Polymeric functional microspheres containing metal or metal compounds are formed by addition polymerization of a covalently bondable olefinic monomer such as hydroxyethylmethacrylate in the presence of finely divided metal or metal oxide particles, such as iron, gold, platinum or magnetite, which are embedded in the resulting microspheres. The microspheres can be covalently bonded to chemotherapeutic agents, antibodies, or other proteins providing a means for labeling or separating labeled cells. Labeled cells or microspheres can be concentrated at a specific body location such as in the vicinity of a malignant tumor by applying a magnetic field to the location and then introducing the magnetically attractable microspheres or cells into the circulatory system of the subject. Labeled cells can be separated from a cell mixture by applying a predetermined magnetic field to a tube in which the mixture is flowing. After collection of the labeled cells, the magnetic field is discontinued and the labeled sub-cell population recovered.

Yen, Shiao-Ping S.↗

Isolation of Ce( IV ) centered polyoxoalkoxide sandwich-type complexes allows comparison of metal–oxygen bond covalency

The new Ce III centered sandwich-type complex (TBA) 3 [Ce{W 4 O 13 (OMe) 4 MoNO} 2 ] is reported. The redox properties of this molecule, and its all-molybdenum analogue, (TBA) 3 [Ce{Mo 5 O 13 (OMe) 4 NO} 2 ], were investigated using cyclic voltammetry. The data reveals the presence of reversible Ce IV /Ce III redox couples at modest potentials. One electron oxidation of the complexes provides facile access to the corresponding Ce IV derivatives, which were fully characterized. 17 O NMR spectroscopy reveals that the chemical shifts of the oxygen nuclei directly bound to Ce IV are much higher than the corresponding signals in isostructural, diamagnetic, Zr IV , Hf IV , or Th IV centered complexes. Density functional theory (DFT) calculations indicate that the increase in chemical shift correlates with an increase in the covalency of the M IV –O bonds, illustrating that 17 O NMR spectroscopy is a powerful experimental tool for interrogating the nature of metal oxygen bonding in diamagnetic complexes.

Shiels, Dominic [Univ. of Rochester, NY (United St↗

Molecular basis for dual functions in pilus assembly modulated by the lid of a pilus-specific sortase

The biphasic assembly of Gram-positive pili begins with the covalent polymerization of distinct pilins catalyzed by a pilus-specific sortase, followed by the cell wall anchoring of the resulting polymers mediated by the housekeeping sortase. In Actinomyces oris, the pilus-specific sortase SrtC2 not only polymerizes FimA pilins to assemble type 2 fimbriae with CafA at the tip, but it can also act as the anchoring sortase, linking both FimA polymers and SrtC1-catalyzed FimP polymers (type 1 fimbriae) to peptidoglycan when the housekeeping sortase SrtA is inactive. To date, the structure-function determinants governing the unique substrate specificity and dual enzymatic activity of SrtC2 have not been illuminated. Here, we present the crystal structure of SrtC2 solved to 2.10-Å resolution. SrtC2 harbors a canonical sortase fold and a lid typical for class C sortases and additional features specific to SrtC2. Structural, biochemical, and mutational analyses of SrtC2 reveal that the extended lid of SrtC2 modulates its dual activity. Specifically, we demonstrate that the polymerizing activity of SrtC2 is still maintained by alanine-substitution, partial deletion, and replacement of the SrtC2 lid with the SrtC1 lid. Strikingly, pilus incorporation of CafA is significantly reduced by these mutations, leading to compromised polymicrobial interactions mediated by CafA. In a srtA mutant, the partial deletion of the SrtC2 lid reduces surface anchoring of FimP polymers, and the lid-swapping mutation enhances this process, while both mutations diminish surface anchoring of FimA pili. Evidently, the extended lid of SrtC2 enables the enzyme the cell wall-anchoring activity in a substrate-selective fashion.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Quantum chemical topology and natural bond orbital analysis of M–O covalency in M(OC 6 H 5 ) 4 (M = Ti, Zr, Hf, Ce, Th, Pa, U, Np)

Covalency is complex yet central to our understanding of chemical bonding, particularly in the actinide series. In this work, we assess covalency in a series of isostructural d and f transition element compounds M(OC 6 H 5 ) 4 (M = Ti, Zr, Hf, Ce, Th, Pa, U, Np) using scalar relativistic hybrid density functional theory in conjunction with the Natural Bond Orbital (NBO), quantum theory of atoms in molecules (QTAIM) and interacting quantum atoms (IQA) approaches. The IQA exchange–correlation covalency metric is evaluated for the first time for actinides other than uranium, in order to assess its applicability in the 5f series. It is found to have excellent correlation with NBO and QTAIM covalency metrics, making it a promising addition to the computational toolkit for analysing metal–ligand bonding. Our range of metrics agree that the actinide-oxygen bonds are the most covalent of the elements studied, with those of the heavier group 4 elements the least. Within the early actinide series, Th stands apart from the other three elements considered, being consistently the least covalent.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Structural Insights into Mechanisms Underlying Mitochondrial and Bacterial Cytochrome c Synthases

Mitochondrial holocytochrome c synthase (HCCS) is an essential protein in assembling cytochrome c (cyt c) of the electron transport system. HCCS binds heme and covalently attaches the two vinyls of heme to two cysteine thiols of the cyt c CXXCH motif. Human HCCS recognizes both cyt c and cytochrome c1 of complex III (cytochrome bc1). HCCS is mutated in some human diseases and it has been investigated recombinantly by mutational, biochemical, and reconstitution studies in the past decade. Here, we employ structural prediction programs (e.g., AlphaFold 3) on HCCS and its two substrates, heme and cytochrome c. The results, when combined with spectroscopic and functional analyses of HCCS and variants, provide insights into the structural basis for heme binding, apocyt c binding, covalent attachment, and release of the holocyt c product. Results from in vitro reconstitution of purified human HCCS using cyt c and cyt c1 peptides as acceptors are consistent with the structural modeling of substrate binding. Reconstitution of HCCS and cyt c1 provides an approach to studying cyt c1 assembly, which has been refractile to recombinant in vivo reconstitution (unlike HCCS and cyt c). We propose a structural basis for release of the holocyt c product from HCCS based on in vitro studies and on cryoEM structures of the bacterial cyt c synthase (CcsBA) active site. We analyze the kinetoplastid mitochondrial synthase (KCCS), and hypothesize a molecular evolutionary path from mitochondrial endosymbiosis to the current HCCS.

Biochemistry & Molecular Biology↗

Assessment of DFT methods for the prediction of detachment energies and electronic structures of complex and multiply charged anions

Here, in this work, we assess the ability of different density functional theory methods to reproduce the vertical/adiabatic detachment energies (VDEs/ADEs) of a series of 40 anions, including monoanion versus multiply charged anions (MCAs) and covalent versus noncovalent interaction. The statistical analysis of errors is firstly performed by comparing the theoretical values with the experimental benchmark data obtained from the negative ion photoelectron spectroscopy (NIPES). The proposed optimally tuned range-separated (OTRS) functionals are proved to not only well reproduce the experimental VDEs/ADEs, but also simulate experimental NIPES. The result implies a more serious issue of delocalization error for MCAs and a balanced description of electron-rich/- deficient region of anions is necessary. The radius of the spherically symmetric average electron localization function (ELF) region is demonstrated as a useful descriptor for the characterization of electronic structure of anionic systems and a quasilinear fitting model is proposed to efficiently obtain their OTRS parameters.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Fracture Prediction of Epoxy Resin using Morse Bond Potential Embedded in GAFF using Molecular Dynamics Simulations

A generic method is developed to investigate the fracture behavior of an epoxy resin using atomistic molecular (MD) dynamics simulations. The epoxy system consisted of the stoichiometric mixture of tetra-/tri-functional epoxies and di-functional hardener molecules and was cured with a step-growth crosslinking algorithm. A hybrid force field (hFF) in which Morse bond function were added in second generation-general Amber Force Field (GAFF2) was used to capture bond breaking of the crosslinked epoxy system under uniaxial deformation. The Morse bond parameters for covalent bonds in the crosslinked backbone were fit to dissociation curves computed by CASPT2/6-311+G**. After the systems in various crosslink densities were obtained and equilibrated, the full length of stress-strain (𝜎-𝜀) curve was produced including initial elastic regime, yielding, plastic flow, strain hardening, and progressive failure. We found that the hFF was effective in studying the dissociation of crosslinked polymers and understanding the failure mechanism. In the results, the hFF delivered the same elastic property obtained from the unmodified force field GAFF. The stress-strain curve, however, began to be distinct in the plastic regime due to broken covalent bonds capable of altering the tensile behavior. Once the stress reached maximum, it progressively decreased until the ultimate failure (𝜎=0). Since hFF employed the existing GAFF functions with including a minimal change of its bond potential, this approach is easier to perform and computationally more efficient for unveiling the fracture behavior of polymer materials at the molecular level than other approaches with reactive force fields. We expect this approach will be utilized to accelerate the material-by-design process for thermosets by incorporate data from molecular models.

Changwoon Jang↗