Hydrogen splitting at a single phosphorus centre and its use for hydrogenation

Catalytic processes are largely dominated by transition-metal complexes. Main-group compounds that can mimic the behaviour of the transition-metal complexes are of great interest due to their potential to substitute or complement transition metals in catalysis. While a few main-group molecular centres were shown to activate dihydrogen via the oxidative addition process, catalytic hydrogenation using these species has remained challenging. Here we report the synthesis, isolation and full characterization of the geometrically constrained phosphenium cation with the 2,6-bis(o-carborano)pyridine pincer-type ligand. Notably, this cation can activate the H-H bond by oxidative addition to a single PIII cationic centre, producing a dihydrophosphonium cation. This phosphenium cation is also capable of catalysing hydrogenation reactions of C=C double bonds and fused aromatic systems, making it a main-group compound that can both activate H2 at a single molecular main-group centre and be used for catalytic hydrogenation. This finding shows the potential of main-group compounds, in particular phosphorus-based compounds, to serve as metallomimetic hydrogenation catalysts.

Computing the Differences between Asn-X and Gln-X Deamidation and Their Impact on Pharmaceutical and Physiological Proteins: A Theoretical Investigation Using Model Dipeptides

Protein deamidation is a degradation mechanism that significantly impacts both pharmaceutical and physiological proteins. Deamidation impacts two amino acids, Asn and Gln, where the net neutral residues are converted into their acidic forms. While there are multiple similarities between the reaction mechanisms of the two residues, the impact of Gln deamidation has been noted to be most significant on physiological proteins while Asn deamidation has been linked to both pharmaceutical and physiological proteins. For this purpose, we sought to analyze the thermochemical and kinetic properties of the different reactions of Gln deamidation relative to Asn deamidation. In this study, we mapped the deamidation of Gln-X dipeptides into Glu-X dipeptides using density functional theory (DFT). Full network mapping facilitated the prediction of reaction selectivity between the two primary pathways, as well as between the two products of Gln-X deamidation as a function of solvent dielectric. To achieve this analysis, we studied a total of 77 dipeptide reactions per solvent dielectric (308 total reactions). Modeled at a neutral pH and using quantum chemical and statistical thermodynamic methods, we computed the following values: enthalpy of reaction (ΔH_RXN), entropy (ΔS_RXN), Gibbs free energy of reaction (ΔG_RXN), activation energy (E_A), and the Arrhenius preexponential factor (log(A)) for each dipeptide. Additionally, using chemical reaction principles, we generated a database of computed rate coefficients for all possible N-terminus Gln-X deamidation reactions at a neutral pH, predicted the most likely deamidation reaction mechanism for each dipeptide reaction, analyzed our results against our prior study on Asn-X deamidation, and matched our results against qualitative trends previously noted by experimental literature.

Electronic structure of the ground and excited states of neutral and charged silicon hydrides, SiHx0/+/-, x = 1-4

The ground and excited electronic states of the titled species are investigated with multi-reference configuration interaction and diffuse basis sets. We found that in addition to the valence orbitals, the inclusion of the 4s, 4p, and especially 3d orbitals (although with minimal population) of silicon in the active space of the reference complete active space self-consistent field wavefunction are necessary for the proper convergence of the calculations. We also demonstrate that the aug-cc-pVTZ basis set provides quite accurate results compared to both larger basis sets and basis set limit results at a lower computational cost. The excited states involve excitations within the 3s and 3p orbitals of silicon (especially for the mono- and di-hydrides), followed by excitations from the Si-H bonding orbitals to either silicon valence or Rydberg (4s, 4p) orbitals. The number of electronic states per energy unit decrease as we add hydrogen atoms, and the first excited state of SiH₄ is at 9.0 eV and leads to SiH₃ + H. All species have stable ground state structures with all hydrogen atoms bound to silicon, except for SiH₄⁺ and SiH₄^-. The former dissociates to SiH₂⁺ + H₂, while the latter loses an electron or can dissociate forming H₂ as well.

Competitive Hydrogen Migration in Silicon Nitride Nanoclusters: Reaction Kinetics Generalized from Supervised Machine Learning

The rate coefficients for 52 hydrogen shift reactions for silicon nitrides containing up to 6 atoms of silicon and nitrogen have been calculated using the G3//B3LYP composite method and statistical thermodynamics. The overall reaction of substituted acyclic and cyclic silylenes to their respective silene and imine species by a 1,2-hydrogen shift reaction was sorted by three different types of H shift reactions using overall reaction thermodynamics: (1) endothermic H shift between N and Si:, (2) endothermic H shift between Si and Si:, and (3) exothermic H shift between Si and Si:. Endothermic H shift reactions between Si atoms have one dominant activation barrier where the exothermic H shift reaction between Si atoms has two barriers and a stable intermediate. The rate-determining step was determined to be from the intermediate to the substituted silene, and then kinetic parameters for the overall reaction were calculated for the two-step pathway. The single event pre-exponential factors, Ã, and activation energies, E_a, for the three different classes of hydrogen shift reactions of silicon nitrides were computed. The hydrogen shift reaction was explored for acyclic and cyclic monofunctional silicon nitrides, and the type of hydrogen shift reaction gives the most significant influence on the kinetic parameters. Using a supervised machine learning approach, the models for predicting the energy barrier of three different hydrogen shift reactions were generalized and suggested based on selected descriptors.

Deamidation reaction network mapping of pharmacologic and related proteins: impact of solvation dielectric on the degradation energetics of asparagine dipeptides

Asn-X deamidation pathways in the FV region of the monoclonal antibody (mAb).

Isolating key reaction energetics and thermodynamic properties during hardwood model lignin pyrolysis

Computational studies on the pyrolysis of lignin using electronic structure methods have been largely limited to dimeric or trimeric models. In the current work we have modeled a lignin oligomer consisting of 10 syringyl units linked through 9 β-O-4' bonds. A lignin model of this size is potentially more representative of the polymer in angiosperms; therefore, we used this representative model to examine the behavior of hardwood lignin during the initial steps of pyrolysis. Using this oligomer, the present work aims to determine if and how the reaction enthalpies of bond cleavage vary with positions within the chain. To accomplish this, we utilized a composite method using molecular mechanics based conformational sampling and quantum mechanically based density functional theory (DFT) calculations. Our key results show marked differences in bond dissociation enthalpies (BDE) with the position. In addition, we calculated standard thermodynamic properties, including enthalpy of formation, heat capacity, entropy, and Gibbs free energy for a wide range of temperatures from 25 K to 1000 K. The prediction of these thermodynamic properties and the reaction enthalpies will benefit further computational studies and cross-validation with pyrolysis experiments. Overall, the results demonstrate the utility of a better understanding of lignin pyrolysis for its effective valorization.

Silicon and Hydrogen Chemistry under Laboratory Conditions Mimicking the Atmosphere of Evolved Stars

Silicon is present in interstellar dust grains, meteorites and asteroids, and to date thirteen silicon-bearing molecules have been detected in the gas-phase towards late-type stars or molecular clouds, including silane and silane derivatives. In this work, we have experimentally studied the interaction between atomic silicon and hydrogen under physical conditions mimicking those at the atmosphere of evolved stars. We have found that the chemistry of Si, H and H₂ efficiently produces silane (SiH₄), disilane (Si₂H₆) and amorphous hydrogenated silicon (a-Si:H) grains. Silane has been definitely detected towards the carbon-rich star IRC+10216, while disilane has not been detected in space yet. Thus, based on our results, we propose that gas-phase reactions of atomic Si with H and H₂ are a plausible source of silane in C-rich AGBs, although its contribution to the total SiH₄ abundance may be low in comparison with the suggested formation route by catalytic reactions on the surface of dust grains. In addition, the produced a-Si:H dust analogs decompose into SiH₄ and Si₂H₆ at temperatures above 500 K, suggesting an additional mechanism of formation of these species in envelopes around evolved stars. We have also found that the exposure of these dust analogs to water vapor leads to the incorporation of oxygen into Si-O-Si and Si-OH groups at the expense of SiH moieties, which implies that, if this type of grains are present in the interstellar medium, they will be probably processed into silicates through the interaction with water ices covering the surface of dust grains.

Data-Driven Investigation of Monosilane and Ammonia Co-Pyrolysis to Silicon-Nitride-Based Ceramic Nanomaterials

With its high strength, high thermal stability, low density, and high electrical resistance, silicon-nitride-based ceramics have been widely used as gate insulating layers, oxidation masks, and passivation layers. Employing SiN nanomaterials in anode applications also improves rate performances and cycling stability of the lithium-ion batteries. However, a fundamental understanding of the SiN synthetic process remains elusive. SiN gas-phase synthesis can be tailored with a comprehensive understanding of the underlying thermodynamics. In comparison to the characterization data available for solid-state SiN materials, high-level theoretical studies on gas-phase materials possessing Si-N bonds and comprehensive investigation of the SiN chemistry, particularly for nanoclusters, are very uncommon. Thus, we performed a theoretical study of Si and SiN alloy acyclic hydrides and polycyclic clusters to predict electronic structures and thermochemistry using quantum chemical calculation and statistical thermodynamics. Electronic properties by way of highest and lowest occupied molecular orbital energy gap and natural bonding orbitals analysis were calculated to explore the influence of elemental composition and geometry on the stability. Our studies provide characteristic data of SiN species for a data-driven approach to map the design space for discovery of novel silicon-nitride-based ceramic materials for advanced electronic and coating applications.

Tuning Hydrogenated Silicon, Germanium, and SiGe Nanocluster Properties Using Theoretical Calculations and a Machine Learning Approach

There are limited studies available that predict the properties of hydrogenated silicon-germanium (SiGe) clusters. For this purpose, we conducted a computational study of 46 hydrogenated SiGe clusters (Si _xGe _yH _z, 1 < X + Y ≤ 6) to predict the structural, thermochemical, and electronic properties. The optimized geometries of the Si _xGe _yH _z clusters were investigated using quantum chemical calculations and statistical thermodynamics. The clusters contained 6 to 9 fused Si-Si, Ge-Ge, or Si-Ge bonds, i.e., bonds participating in more than one 3- to 4-membered rings, and different degrees of hydrogenation, i.e., the ratio of hydrogen to Si/Ge atoms varied depending on cluster size and degree of multifunctionality. Our studies have established trends in standard enthalpy of formation, standard entropy, and constant pressure heat capacity as a function of cluster composition and structure. A novel bond additivity correction model for SiGe chemistry was regressed from experimental data on seven acyclic Si/Ge/SiGe species to improve the accuracy of the standard enthalpy of formation predictions. Electronic properties were investigated by analysis of the HOMO-LUMO energy gap to study the effect of elemental composition on the electronic stability of Si _xGe _yH _z clusters. These properties will be discussed in the context of tailored nanomaterials design and generalized using a machine learning approach.

The role of multifunctional kinetics during early-stage silicon hydride pyrolysis: reactivity of Si2H2 isomers with SiH4 and Si2H6

Kinetic parameters for the dominant pathways during the addition of the four Si(2)H(2) isomers, i.e., trans-HSiSiH, SiSiH(2), Si(H)SiH, and Si(H(2))Si, to monosilane, SiH(4), and disilane, Si(2)H(6), have been calculated using G3//B3LYP, statistical thermodynamics, conventional and variational transition state theory, and internal rotation corrections. The direct addition products of the multifunctional Si(2)H(2) isomers were monofunctional substituted silylenes, hydrogen-bridged species, and silenes. During addition to monosilane and disilane, the SiSiH(2) isomer was found to be most reactive over the temperature range of 800 to 1200 K. Revised parameters for the Evans-Polanyi correlation and a representative pre-exponential factor for multifunctional silicon hydride addition and elimination reaction families under pyrolysis conditions were regressed from the reactions in this study. This revised kinetic correlation was found to capture the activation energies and rate coefficients better than the current literature methods.