Dissociative Transition State Research Articles

Engaging the Concepts of Bimetallicity and Mechanical Strain for N2 Activation: A Computational Exploration.

N2 activation is a vital step in the process toward NH3 production. NH3 synthesis has been considered a crucial process for the production of value-added chemicals and/or hydrogen carriers over recent years. In this work, density functional theory (ab initio) calculations are implemented for a thorough screening of bimetallic alloy surfaces using Fe, Ru, and Mo as the matrix (host) metals and Ag, Au, Co, Cu, Fe, Mo, Ni, Pd, Pt, Rh, and Rh as heterometals toward exploring the N2 catalytic activation (electronic and chemical characteristics); the monometallic surfaces are used for critical comparison in terms of their N2 activation behavior. In particular, adsorption geometries/energetics, density of states (DOS), and charge transfer are discussed. From the N2 activation on the surfaces, we could precisely capture the transition state of the N2 dissociation reaction/step. The effect of the metal alloying (geometrical and electronic factors) as well as the effect of applied mechanical strain, as a tuning factor of alloying, are both studied and thoroughly discussed. DOS studies revealed that the d-band center moved toward the negative direction for all late-TM-based alloys, thereby allowing the nitrogen molecule to adsorb weakly as compared to the early-TM surface alloys. In terms of the mechanical strain, for most of the alloy surfaces studied, apart from the Mo/Fe(110) one, the N2 binding energy varies as a linear function of the applied strain. The mechanical effect trend is in agreement with the charge transfer descending order followed: Fe/Mo(110) > Rh/Mo(110) > Au/Mo(110) > Pt/Mo(110) > Ni/Mo(110) > Ru/Mo(110) > Cu/Mo(110) > Ag/Mo(110) > Pd/Mo(110) > Au/Mo(110), pointing out that Fe-functionalized Mo(110) surface presents the highest charge transfer of -2.14 |e| to the N2 molecule. This study aspires to provide navigation criteria through the abundant design criteria of N2 activation catalysts.

Photoionization and Dissociative Photoionization of Acetaldehyde in the 10.0-13.7 eV Range by Synchrotron Photoelectron Photoion Coincidence Spectroscopy.

Photoionization and dissociative photoionization of acetaldehyde (CH3CHO) in the 10.0-13.7 eV energy range are studied by using synchrotron radiation double imaging photoelectron photoion coincidence spectroscopy (i2PEPICO). The X2A' and A2A" electronic states of CH3CHO+ as well as the Franck-Condon gap region between these two states have been populated with several vibrational sequences and assigned in the high-resolution slow photoelectron spectrum (SPES). The adiabatic ionization energies (AIEs) of the X2A' and A2A" states are measured at 10.228±0.006 and 12.52±0.05 eV, respectively. The present results show that the X2A' state is a stable state while the A2A" state is fully dissociative to produce CH3CO+, CHO+ and CH4 + fragment ions. The 0 K appearance energies (AE0K) of CH3CO+ and CHO+ fragment ions are determined through the modeling of the breakdown diagram, i. e., AE0K(CH3CO+)=10.89±0.01 eV (including a reverse barrier of ~0.19 eV) and AE0K(CHO+)=11.54±0.05 eV. In addition, the dissociation mechanisms of CH3CHO+ including statistical dissociation, direct bond breaking and isomerization are discussed with the support of the calculated dissociation limits and transition state energies.

Magic cluster sizes of cationic and anionic sodium chloride clusters explained by statistical modeling of the complete phase space.

As one of the main components of sea salt aerosols, sodium chloride is involved in numerous atmospheric processes. Gas-phase clusters are ideal models to study fundamental physical and chemical properties of sodium chloride, which are significantly affected by the cluster size. Of particular interest are magic cluster sizes, which exhibit high intensities in mass spectra. In order to understand the origin of these magic cluster sizes, quantum chemical calculations at the CCSD(T)//DFT level are performed, yielding structures and binding energies of neutral (NaCl)x, anionic (NaCl)xCl- and cationic (NaCl)xNa+ clusters up to x = 8. Our calculations show that the clusters can easily isomerize, enabling dissociation into the lowest-energy isomers of the fragments. Energetics can explain the special stability of (NaCl)4Cl-, but (NaCl)4Na+ actually offers low-lying dissociation channels, despite being a magic cluster size. Collision-induced dissociation experiments reveal that the loss of neutral clusters (NaCl)x, x = 2, 4, is in most cases more favorable than the loss of NaCl or the atomic ion, i.e. sodium chloride clusters actually fragment via the cleavage of the entire cluster, not by evaporating small cluster building blocks. This is rationalized by the calculated high stability of even-numbered neutral clusters (NaCl)x, especially x = 2, 4. Analysis of the density of states and rate constants calculated with a modified Rice-Ramsperger-Kassel-Marcus (RRKM) equation called AWATAR - considering all energetically accessible isomers of reactants and fragments - shows that entropic effects are responsible for the magic cluster character of (NaCl)4Na+. In particular, low-lying vibrational modes provide a high density of states of the near-planar cluster. Together with the small contribution of an atomic ion to the sum of states in a loose transition state for dissociation, this leads to a very small unimolecular rate constant for dissociation into (NaCl)4 and Na+, which is the lowest energy fragmentation pathway. Thus, entropic effects may override energetics for certain magic cluster sizes.

Unveil the potential in hydrogen activation and spillover towards NiMoS by Ni3S2 - A theoretical study

Using density functional theory calculation (DFT) as well as ab initio molecular dynamics (AIMD) simulation, the capabilities of hydrogen dissociation and hydrogen spillover over Ni3S2 (111) surface are examined. The steady state, energy change, transition state of hydrogen dissociation and the spillover pathway, stability of S-H bond during hydrogen spillover are all calculated. The results show that several S-top site and S-Ni-bridge site are available for dissociation, among them, “S1-top”, “S3-top” and “S1-Ni1” sites could be recognized as distinct sites, and one hydrogen molecule could be efficiently dissociated by one S3-top site and the adjacent S1-Ni1 site. The crystal orbital Hamilton population analysis and AIMD simulation for S-H bonds both confirm the tendency towards breaking, then the spillover coordinate calculation gives a self-consistent pathway among three district sites. In short, the Ni3S2 surface shows excellent performance in the aspect of hydrogen dissociation and hydrogen spillover, which displays tremendous potential for hydrogen spillover in NiMoS catalytic system. We hope these findings could shed light on the theory of “remote control” model.

Computational (DFT) and Experimental (NMR) Study of the Chelation of an Iridium Hyperpolarization Transfer Catalyst by Amino Acids

AbstractNon‐hydrogenative Para‐Hydrogen Induced Hyperpolarization (nhPHIP) is a Nuclear Magnetic Resonance (NMR) hyperpolarization technique which has experimentally been used to analyze complex biological samples containing amino acids using the Ir‐IMes hyperpolarization transfer catalyst. A computational study based on Density Function Theory (DFT) was performed on all relevant stereoisomers of [Ir(H)2(IMes)(AA)(Py)] (with AA=glycine, alanine, valine; Py=pyridine), for which R/S chirality and orientation of the amino acid chelation (C/A) were considered. A total of 30 structures were calculated comprising of 6 stereoisomers for achiral glycine, and 12 stereoisomers for each of the chiral amino acids. The abundances derived from the DFT energies confirmed the trends observed in thermal (non‐hyperpolarized) NMR experiments. Additionally, theoretical calculations of electronic (Wiberg bond indices, Natural Bond Orders, Frontier Orbital Analysis), bond dissociation energies, transition states, and activation energies related to interconversion between binding modes, and steric factors (Solid angle) were performed to provide detailed explanations for NMR experimental observations.

Solvent and solvation effects on reactivities and mechanisms of phospho group transfers from phosphate and phosphinate esters to nucleophiles.

Organophosphorus esters fulfil many industrial, agricultural, and household roles. Nature has deployed phosphates and their related anhydrides as energy carriers and reservoirs, as constituents of genetic materials in the form of DNA and RNA, and as intermediates in key biochemical conversions. The transfer of the phosphoryl (PO3) group is thus a ubiquitous biological process that is involved in a variety of transformations at the cellular level such as bioenergy and signals transductions. Significant attention has been paid in the last seven decades to understanding the mechanisms of uncatalyzed (solution) chemistry of the phospho group transfer because of the notion that enzymes convert the dissociative transition state structures in the uncatalyzed reactions into associative ones in the biological processes. In this regard, it has also been proposed that the rate enhancements enacted by enzymes result from the desolvation of the ground state in the hydrophobic active site environments, although theoretical calculations seem to disagree with this position. As a result, some attention has been paid to the study of the effects of solvent change, from water to less polar solvents, in uncatalyzed phospho transfer reactions. Such changes have consequences on the stabilities of the ground and the transition states of reactions which affect reactivities and, sometimes, the mechanisms of reactions. This review seeks to collate and evaluate what is known about solvent effects in this domain, especially their effects on rates of reactions of different classes of organophosphorus esters. The outcome of this exercise shows that a systematized study of solvent effects needs to be undertaken to fully understand the physical organic chemistry of the transfer of phosphates and related molecules from aqueous to substantially hydrophobic environments, since significant knowledge gaps exist.

Enhanced dehalogenation of brominated DBPs by catalyzed electrolysis using Vitamin B12 modified electrodes: Kinetics, mechanisms, and mass balances

Vitamin B12 (VB12) modified electrodes were prepared for the electrocatalytic reductive debromination of tribromoacetic acid (TBAA). Under galvanostatic conditions set as 5 mmol/L VB12 loading, 20 mmol/L Na2SO4 as electrolyte, 10.0 mA/cm2 current density, pH 3, and 298 K, the degradation efficiency of 200 μg/L TBAA at the VB12 modified electrode could reach 99.9 % after 6 h. The debromination of TBAA followed the first-order kinetic model. The masses of carbon and bromine elements were conserved before and after the reaction, together with the qualitative analysis of the degradation products showed the likely degradation pathways as TBAA→dibromoacetic acid (DBAA)→monobromoacetic acid (MBAA)→acetic acid (AA). ESR detection and quenching experiments confirmed the role of atomic H* in TBAA debromination. In-situ Raman spectroscopy showed that the Co-Br bond was strongly enriched to the electrode surface, accelerating the electron transfer. The H2O dissociation performance and transition states searching catalyzed by VB12 were calculated by Density Functional Theory (DFT) and proved that the composite electrode can effectively promote atomic H* generation. Material characterization and electrochemical performance tests showed that the VB12 modified electrode had excellent stability and atomic H* catalytic activity. The electrocatalytic debromination of TBAA at VB12 modified electrodes mainly involves two mechanisms, direct reduction by electron transfer and indirect reduction by the strongly reducing atom H*. The results provide an efficient way to achieve safe removal of brominated DBPs from drinking water after chlorination and before human consumption.

Dissociative Transition State in Hepatitis Delta Virus Ribozyme Catalysis.

Ribonucleases and small nucleolytic ribozymes are both able to catalyze RNA strand cleavage through 2'-O-transphosphorylation, provoking the question of whether protein and RNA enzymes facilitate mechanisms that pass through the same or distinct transition states. Here, we report the primary and secondary 18O kinetic isotope effects for hepatitis delta virus ribozyme catalysis that reveal a dissociative, metaphosphate-like transition state in stark contrast to the late, associative transition states observed for reactions catalyzed by specific base, Zn2+ ions, or ribonuclease A. This new information provides evidence for a discrete ribozyme active site design that modulates the RNA cleavage pathway to pass through an altered transition state.

Kinetics and Pathway Analysis Reveals the Mechanism of a Homogeneous PNP-Iron-Catalyzed Nitrile Hydrogenation.

Nitrile hydrogenation via the in situ-generated PNP-FeII(H)2CO (1) catalyst leads to a previously inexplicable loss of mass balance. Reaction kinetics, reaction progress analysis, in situ pressure nuclear magnetic resonance, and X-ray diffraction analyses reveal a mechanism comprising reversible imine self-condensation and amine-imine condensation cascades that yield >95% primary amine. Imine self-condensation has never been reported in a nitrile hydrogenation mechanism. The reaction is first order in catalyst and hydrogen and zero order in benzonitrile when using 2-propanol as the solvent. Variable-temperature analysis revealed values for ΔG298K⧧ (79.6 ± 26.8 kJ mol-1), ΔH⧧ (90.7 ± 9.7 kJ mol-1), and ΔS⧧ (37 ± 28 J mol-1 K-1), consistent with a solvent-mediated proton-shuttled dissociative transition state. This work provides a basis for future catalyst optimization and essential data for the design of continuous reactors with earth-abundant catalysts.

Structure sensitivity of ethanol steam reforming over the Rh catalyst: Reaction kinetics and deactivation mechanisms

Rh catalyst exhibits high activity and selectivity of hydrogen production for ethanol steam reforming (ESR). In this work, we used density functional theory calculations and microkinetic modeling to study the structure sensitivity of ESR over the Rh catalyst, with stepped Rh(211) and terraced Rh(111) as models. The dominant reaction paths on the two surfaces were determined by pruning a complex network under different conditions. Further microkinetic analysis of the dominant reaction pathways suggested that Rh(211) shows higher activity and CO2 selectivity than Rh(111), but lower stability due to carbon deposition. High steam/ethanol ratio was found to be important to the reaction which can reduce carbon accumulation and improve CO2 selectivity. The transition state of CH3CH2OH dissociation is rate-controlling over both surfaces at high temperatures, while the removal processes of C* is rate controlling on Rh(211) at low temperatures, resulting in deactivation of the step edge sites. After screening several metal dopants over Rh(211), we found that the d-band center is well correlated with carbon adsorption energy, and stability trend is consistent with experiments. Our work could provide understanding of structure sensitivity and guidelines of rational Rh-based catalyst design for the ESR reaction.

Prediction model on hydrolysis kinetics of phthalate monoester: A density functional theory study

As primary degradation products of phthalate esters, phthalate monoesters (MPEs) have been widely detected in various aquatic environments and drawn growing toxicological concerns. Hydrolysis kinetics that is of importance for assessing environmental persistence of chemicals remain elusive for MPEs. Herein, kinetics of base-catalyzed and neutral hydrolysis for 18 MPEs with different leaving groups was investigated by density functional theory calculation. Results indicate that MPEs with leaving groups having pKa of <10 prefer dissociative transition states. MPEs are more persistent than their parents, and their hydrolysis half-lives were calculated to vary from 3.4 min to 79.2 years (pH = 7–9). A quantitative structure-activity relationship model was developed for predicting the hydrolysis kinetics parameters. It was found that pKa of the leaving groups and electronegativity of the MPEs are key factors determining the hydrolysis kinetics. This work may lay a theoretical foundation for better understanding the chemical process that governs MPE persistence in aquatic environments.

Phosphoenolpyruvate Mutase-Catalyzed C-P Bond Formation: Mechanistic Ambiguities and Opportunities.

Phosphonates are produced across all domains of life and used widely in medicine and agriculture. Biosynthesis almost universally originates from the enzyme phosphoenolpyruvate mutase (Ppm), EC 5.4.2.9, which catalyzes O-P bond cleavage in phosphoenolpyruvate (PEP) and forms a high energy C-P bond in phosphonopyruvate (PnPy). Mechanistic scrutiny of this unusual intramolecular O-to-C phosphoryl transfer began with the discovery of Ppm in 1988 and concluded in 2008 with computational evidence supporting a concerted phosphoryl transfer via a dissociative metaphosphate-like transition state. This mechanism deviates from the standard 'in-line attack' paradigm for enzymatic phosphoryl transfer that typically involves a phosphoryl-enzyme intermediate, but definitive evidence is sparse. Here we review the experimental evidence leading to our current mechanistic understanding and highlight the roles of previously underappreciated conserved active site residues. We then identify remaining opportunities to evaluate overlooked residues and unexamined substrates/inhibitors.

Atomically Dispersed CoN3 C1 -TeN1 C3 Diatomic Sites Anchored in N-Doped Carbon as Efficient Bifunctional Catalyst for Synergistic Electrocatalytic Hydrogen Evolution and Oxygen Reduction.

A encapsulation-adsorption-pyrolysis strategy for the construction of atomically dispersed Co-Te diatomic sites (DASs) that are anchored in N-doped carbon is reported as an efficient bifunctional catalyst for electrocatalytic hydrogen evolution reaction (HER) and oxygen reduction reaction (ORR). The as-constructed catalyst shows the stable CoN3 C1 -TeN1 C3 coordination structure before and after HER and ORR. The *OOH/*H intermediate species are captured by in situ Raman and in situ attenuated total reflectance-surface enhanced infrared absorption spectroscopy, indicating that the reactant O2 /H2 O molecule has a strong interaction with the Co site, revealing that Coδ+ is an effective active site. Theoretical calculations show that the Coδ+ has adsorption-activation function and the neighboring Teδ+ acts as an electron donor adjusting the electronic structure of Coδ+ , promoting the dissociation of H2 O molecules and the adsorption of H and oxygen-containing intermediates in HER and ORR. In the meanwhile, the nearest C atom around Co also profoundly affects the adsorption of H atoms. This results in the weakening of the OH adsorption and enhancement of H adsorption, as well as the more stable water molecule dissociation transition state, thus significantly boosting ORR and HER performance.

Theoretical investigation of CO2 conversion on corrugated g-C3N4 Surface decorated by single-atom of Fe, Co, and Pd

The conversion of CO2 molecules to useful fuels and value-added chemicals is important for protecting the atmosphere and developing a stable environment for humans. Therefore, the design of high-efficiency catalysts for CO2 adsorption, activation, and conversion has received considerable attention in recent decades. In this study, to investigate CO2 adsorption, activation, and dissociation on a decorated corrugated graphitic carbon nitride (g-C3N4) surface, we conducted density-functional theory (DFT) calculations. Owing to the synergetic effect between the metal and g-C3N4, the decoration of the surface enhances the catalytic activity of CO2 activation. The catalyst structures, CO2 adsorption configurations, and electronic properties for CO2 activation on a decorated g-C3N4 surface with dispersed transition metal single-atoms of Fe, Co, and Pd were investigated. The transition states for direct dissociation to form CO were obtained from the adsorbed CO2 to reveal the properties of activated carbon dioxide. Our calculations indicate that Fe@g-C3N4 and Co@g-C3N4 are good candidates for CO2 capture. Especially, the former exists a better catalytic activity for the CO2 activation. Additionally, DFT studies were combined with microkinetic simulations to comprehend the CO2 consumption and CO production reaction temperature on a single-atom decorated corrugated g-C3N4 surface.

A spin promotion effect in catalytic ammonia synthesis

The need for efficient ammonia synthesis is as urgent as ever. Over the past two decades, many attempts to find new catalysts for ammonia synthesis at mild conditions have been reported and, in particular, many new promoters of the catalytic rate have been introduced beyond the traditional K and Cs oxides. Herein, we provide an overview of recent experimental results for non-traditional promoters and develop a comprehensive model to explain how they work. The model has two components. First, we establish what is the most likely structure of the active sites in the presence of the different promoters. We then show that there are two effects dictating the catalytic activity. One is an electrostatic interaction between the adsorbed promoter and the N-N dissociation transition state. In addition, we identify a new promoter effect for magnetic catalysts giving rise to an anomalously large lowering of the activation energy opening the possibility of finding new ammonia synthesis catalysts.

Collision-induced dissociation of homodimeric and heterodimeric radical cations of 9-methylguanine and 9-methyl-8-oxoguanine: correlation between intra-base pair proton transfer originating from the N1-H at a Watson-Crick edge and non-statistical dissociation.

It has been shown previously in protonated, deprotonated and ionized guanine-cytosine base pairs that intra-base pair proton transfer from the N1-H at the Watson-Crick edge of guanine to the complementary nucleobase prompts non-statistical dissociation of the base-pair system, and the dissociation of a proton-transferred base-pair structure is kinetically more favored than that of the starting, conventional base-pair structure. However, the fundamental chemistry underlying this anomalous and intriguing kinetics has not been completely revealed, which warrants the examination of more base-pair systems in different structural contexts in order to derive a generalized base-pair structure-kinetics correlation. The purpose of the present work is to expand the investigation to the non-canonical homodimeric and heterodimeric radical cations of 9-methylguanine (9MG) and 9-methyl-8-oxoguanine (9MOG), i.e., [9MG·9MG]˙+, [9MOG·9MG]˙+ and [9MOG·9MOG]˙+. Experimentally, collision-induced dissociation tandem mass spectrometry coupled with an electrospray ionization (ESI) source was used for the formation of base-pair radical cations, followed by detection of dissociation product ions and cross sections in the collisions with Xe gas under single ion-molecule collision conditions and as a function of the center-of-mass collision energy. Computationally, density functional theory and coupled cluster theory were used to calculate and identify probable base-pair structures and intra-base pair proton transfer and hydrogen transfer reactions, followed by kinetics modeling to explore the properties of dissociation transition states and kinetic factors. The significance of this work is twofold: it provides insight into base-pair opening kinetics in three biologically-important, non-canonical systems upon oxidative and ionization damage; and it links non-statistical dissociation to intra-base pair proton-transfer originating from the N1-H at the Watson-Crick edge of 8-oxoguanine, enhancing understanding towards the base-pair fragmentation assisted by proton transfer.

Kinetic and Computational Analysis of CO Substitution in a Dinuclear Osmium Carbonyl Complex: Intersection between Dissociative and Dissociative-Interchange Mechanisms.

The mechanism for the CO substitution reaction involving the diosmium carbonyl sawhorse complex Os2(μ-O2CH)2(CO)6, which contains an Os-Os single bond, two axial CO ligands, and four equatorial CO ligands, was investigated experimentally and theoretically. Kinetic measurements show 13CO axial substitution proceeding by a dissociative reaction that is first-order in the complex and zero-order in 13CO but with an unexpectedly negative entropy of activation. The corresponding electronic structure calculations yield an enthalpy of activation for axial CO dissociation that is much larger than that determined by the kinetic experiments, but in agreement with the complex's stability with respect to CO loss. Additional calculations yield a dissociative interchange transition state whose free energy, enthalpy, and entropy of activation are in good agreement with those obtained from the kinetic measurements for the apparently dissociative substitution. These results point to an exchange reaction mechanism that is surprisingly close to the poorly understood transition from a dissociative mechanism with a CO-loss intermediate to a dissociative interchange mechanism with a transition state involving both the entering and the leaving COs. The key to explain these findings is provided by the vibrational analysis, which shows very low energy wagging motions for the axial COs. Thus, the incoming CO only displaces the outgoing CO when the complex has an outgoing CO near the wag's turning point. This dissociative interchange mechanism predicted by the calculation explains the unexpected combination of kinetics and stability characteristics. Kinetics reveals that the reaction is first-order in the Os dimer with a negative Eyring entropy, while a stability study shows that the Os dimer's decomposition rate is several orders of magnitude slower than CO exchange.

Characterization and development of new anti‐toxins targeting Clostridium difficile

Clostridium difficile is a bacterial pathogen that causes serious and potentially fatal inflammatory disease of the colon. One strategy for targeting C. difficile infection is to development treatments that target bacterial virulence. Anti-virulence strategies to treat C. difficile infection are attractive options to antibiotic therapy because the human microbiota is spared and damage to host tissue is minimized. The Tcd toxins, TcdA and TcdB, are the major virulence factors produced by C. difficile and mediate host cytotoxicity by glucosylating and inactivating Rho family GTPases using UDP-glucose as a glucosyl donor. Glucosylation of Rho GTPases leads to cell rounding and eventually cell death. We used kinetic isotope effects (KIEs) and transition state theory to solve the transition state structure of the glycosyltransferase domain of TcdB (TcdB-GTD). This permits the design of transition state analogues which are potent enzyme inhibitors. KIEs compare the chemical steps of enzymatic reaction rates with isotopically labeled substrates and unlabeled substrates and provide critical information on the catalytic mechanism, bond lengths and geometry at the transition state. KIE analysis on the glycohydrolase reaction of TcdB-GTD supported the formation of a late, dissociative glucocation-like transition state where positive charge develops on the anomeric carbon. Glucocationic transition states are best mimicked by cationic nitrogen groups at or near the anomeric carbon. Iminosugars contain a nitrogen atom in the sugar ring in place of oxygen and mimic glucocationic transition states. We tested iminosugars for inhibition of TcdB-GTD and TcdA-GTD. Isofagomine (Ki TcdB-GTD = 1.4 µM and Ki TcdA-GTD = 0.24 µM) and noeuromycin (Ki TcdB-GTD = 10.6 µM and Ki TcdA-GTD = 4.7 µM) were the most potent iminosugars identified. Isofagomine and noeuromycin were shown to exhibit an uncompetitive mechanism of inhibition suggesting that both iminosugars act by binding to the enzyme-UDP complex. Isothermal titration calorimetry experiments with TcdB-GTD supported this finding where isofagomine and noeuromycin could only bind to TcdB-GTD in the presence of UDP with Kd = 0.133 µM and Kd = 0.4 µM respectively. In addition, the X-ray crystal structure of TcdB-GTD in complex with either Isofagomine or noeuromycin with UDP revealed the formation of an ion-pair interaction between the cationic nitrogen atom of the iminosugar and the β-phosphate of UDP. Finally, we confirmed that isofagomine and noeuromycin could prevent Tcd toxin-induced cytotoxicity of IMR90 cells. Firstly, both iminosugars were able to prevent Tcd toxin-induced cell rounding as visualized by light microscopy. Secondly, Western blot analysis of Tcd toxin treated IMR90 cell lysates revealed that both isofagomine and noeuromycin could prevent glucosylation of Rac1 by Tcd toxin. Isofagomine and noeuromycin are effective in preventing Tcd toxin action. Transition state analogues against TcdA and TcdB have the potential to be used as treatments for C. difficile infections.

Structure, reactions, and electronic spectra of the rare gas cyanohydrides and isocyanohydrides, HRgCN and HRgNC (Rg = Xe or Rn)

The low-energy electronic excitations of HRgCN and HRgNC (Rg = Xe, Rn) were computed at the TDDFT level of theory, both in the gas phase and in xenon cluster. It was found that the most prominent peak in the spectra was due to the highest occupied molecular orbital (HOMO) to lowest unoccupied molecular orbital (LUMO) transition (∼6 eV for HRgCN and ∼4.5 eV for HRgNC). Cluster confinement brought about bathochromic shifts in the spectra and better agreement with experiment for HXeCN. The effects of spin–orbit coupling (SOC) in the heavier Rn systems were investigated: for HRnCN, SOC red-shifted the HOMO–LUMO peak, while it blue-shifted the HOMO–LUMO peak for HRnNC. Geometry optimizations were carried out for the HRgCN and HRgNC systems to locate minima and transition states for dissociation and isomerization. Effects of isotopic substitution on reaction rates were predicted. A new model core potentials basis set was introduced and effectiveness of several pseudopotential basis sets was studied.

Transition state structure of the reaction of homolytic dissociation of the C-N bond and competition between dif erent mechanisms of the primary act of gas-phase monomolecular decomposition of nitrobenzene

Various mechanisms of the primary act of gas-phase monomolecular thermal decomposition of nitrobenzene were studied theoretically. The following reactions were considered: radical decomposition with dissociation of the C-N bond, nitro-nitrite rearrangement to trans-phenyl nitrite and cis-phenyl nitrite, elimination of nitrous acid, as well as formation of 6(S)-7-oxa-8-azabicyclo[4.2.0]octa-1(8),2,4-triene 8-oxide were studied theoretically. Calculations were carried out for different temperatures using a number of density functional theory methods (B3LYP, wB97XD, CAM-B3LYP, MN12L, and PBE0) and basic sets (6-31G(d,p) and 6-31+G(2df,p)). The transition state of homolytic dissociation of the C-N bond was localized using the method of search for the structure corresponding to maximum value of the Gibbs free energy along the reaction coordinate. The structure thus found was used to evaluate the rate constants and the activation parameters at different temperatures. It was shown that not only radical decomposition, but also isomerization to trans-phenyl nitrite (at low temperatures) and cis-phenyl nitrite (at high temperatures) can contribute to the effective rate constant.