Thermochemistry Calculations Research Articles

Mechanisms of Gas Phase Reactions in Germanium-Tin Chemical Vapor Deposition Processes Determined By in Situ Mass Spectrometric Investigation

Keywords: GeSn, Mass spectrometry, Residual gas analyzer (RGA), Chemical vapor deposition (CVD), gas phase reaction GeSn, an alloy in the group IV category, has garnered significant research interest. Its appeal lies in its compatibility with Si photonics platforms and its engineerable bandgap covering the mid-infrared (MIR) wavelengths[1]. These properties make GeSn a promising candidate for various applications, including high-speed optical communications, bio-medical sensing, and long-range light detection and ranging (LiDAR) systems. Chemical vapor deposition (CVD) was one of the main methods of synthesizing device-grade GeSn materials. However, the fundamental understanding of the growth mechanism is lacking. Our group has recently demonstrated the mass spectrometric method as an effective method for investigating chemical species generated by chemical reactions during CVD, where room temperature reactions between SnCl4 and GeH4 in the gas phase have been confirmed[2]. As extended research, this paper systematically studied the chemical reaction mechanisms for the GeSn CVD processes, emphasizing the gas phase reaction regime by sampling the reactant gases of SnCl4 and GeH4 using a residual gas analyzer (RGA). Reactions at room temperature, 100°C, 150°C, and 200°C with various gas partial pressure ratios (pSnCl 4 /pGeH 4 ) of 0.002, 0.005, 0.01 and 0.042 have been investigated. Figure 1 shows a set of representative mass spectra of the mixture gases of SnCl4 and GeH4 with different gas ratios at 100°C, where typical species of HxSnCl4-x and HxGeCl4-x are observed, indicating the reactions have taken place in the experimental conditions indicated in the figure.The resulting original mass spectra and derived fragmentation pattern data for the species generated from those reactions have been obtained compared to the National Institute of Standards and Technology (NIST) data of SnCl4 [3] and GeCl4 [4], respectively. Based on the analysis of the data, it is determined that gas phase reactions occurred in all scenarios investigated.Moreover, the reactions include both direct interactions between SnCl4 and GeH4, as well as the decomposition of GeH4 itself. The main products of the first type of reactions are the Tin hybrid of Sn, H3SnCl/SnCl, and the Germanium hybrid of H3GeCl/GeCl and H2GeCl2/GeCl2, respectively. The second type of reaction generates GeHx and hydrogens (H, H2, and H3 +), mainly occurring at the chamber surfaces. These products are the crucial intermediate species produced in the GeSn CVD process. Overall, the reactions exhibited a more pronounced response with increasing temperature. This agrees, at least qualitatively, with previous[2,5] data and the latest thermochemistry calculations using the Schrodinger software package, which employs the Jaguar program for molecular-orbital calculations [6]. It is based on the density functional theory (DFT) method, where the proposed chemical reactions were either exothermic or minimally endothermic reactions according to the calculations of ΔG(T)=ΔH-TΔS.The experimental and theoretical findings of this study offer valuable insights into the growth mechanism involved in GeSn CVD processes. Subsequent investigations will involve the incorporation of an RGA system into the CVD chamber during growth processes. This will facilitate a more comprehensive exploration of the chemical reaction mechanisms occurring throughout the entire process, encompassing both gas-phase and surface reactions. Acknowledgments The work is supported by the Air Force Office of Scientific Research (AFOSR) (Grant No.: FA9550-19-1-0341, FA9550-20-1-0168).

Density functional theory calculations of surface thermochemistry in Al/CuO thermite reaction

Density functional theory calculations of surface thermochemistry in Al/CuO thermite reaction

Interfacial adsorption of ionic liquids (ILs) on graphitic carbon nitride (g-C3N4) nanosheets: A DFT study

The adsorption of nine common ionic liquids (ILs) on two well-known structures of graphitic carbon nitride (g-C3N4) nanosheets, including Triazine-g-C3N4 and Heptazine-g-C3N4 has been investigated using density functional theory (DFT) method in gas phase and water solvent. The interactions between the ILs and the nanosheets are characterized by several techniques, such as quantum theory of atoms in molecules (QTAIM) analysis, noncovalent interaction (NCI) plots, and energy decomposition analysis (EDA) method. Interestingly, the obtained results showed that electrostatic interactions have the highest contributions to the interaction energies between the ILs and the surfaces, followed by dispersion interactions and orbital interactions (ΔEelec > ΔEdisp > ΔEorb) The most important Van der Waals (vdW) interactions between the ILs and the surfaces include π–π, CH…N, CH…π (CN), and CN…X (X = F, N, O) interactions. On the other hand, the adsorption of ILs is accompanied by charge transfer from the surfaces to the ILs. The calculated adsorption energy (Eads) showed that the [Bmim][PF6] IL has the highest adsorption affinity on the Triazine-g-C3N4 (−28.28 kcal/mol) and Heptazine-g-C3N4 (−26.68 kcal/mol) surfaces. Thermochemistry calculations showed that the Eads, ΔHads, and ΔGads values of IL@surface complexes decrease on moving from gas phase to water media. However, our results showed that the adsorption of ILs on the surfaces is still exothermic and proceeds spontaneously. Upon adsorption of ILs, a decrease in the HOMO–LUMO energy gap (Eg) is observed and is accompanied by an increase in the reactivity and electrophilic character of the surfaces. TD-DFT calculations showed that the weak adsorption of ILs leads to small red or blue shifts in the absorption bands of the Triazine-g-C3N4 and Heptazine-g-C3N4 surfaces. However, no significant changes are observed in the shape of the absorption spectra of the surfaces. Furthermore, the transition density matrix (TDM) heat maps of the IL@surface complexes showed that the electrons and holes are generally concentrated on the Triazine-g-C3N4 and Heptazine-g-C3N4 surfaces in the IL@surface complexes, signifying that the electronic transitions occur mainly on the surfaces.

Reply to Comment on "Benchmarking Basis Sets for Density Functional Theory Thermochemistry Calculations: Why Unpolarized Basis Sets and the Polarized 6-311G Family Should Be Avoided".

Reply to Comment on "Benchmarking Basis Sets for Density Functional Theory Thermochemistry Calculations: Why Unpolarized Basis Sets and the Polarized 6-311G Family Should Be Avoided".

Comment on "Benchmarking Basis Sets for Density Functional Theory Thermochemistry Calculations: Why Unpolarized Basis Sets and the Polarized 6-311G Family Should Be Avoided".

Comment on "Benchmarking Basis Sets for Density Functional Theory Thermochemistry Calculations: Why Unpolarized Basis Sets and the Polarized 6-311G Family Should Be Avoided".

Sustainable Aviation Fuel Molecules from (Hemi)Cellulose: Computational Insights into Synthesis Routes, Fuel Properties, and Process Chemistry Metrics.

Production of sustainable aviation fuels (SAFs) can significantly reduce the aviation industry's carbon footprint. Current pathways that produce SAFs in significant volumes from ethanol and fatty acids can be costly, have a relatively high carbon intensity (CI), and impose sustainability challenges. There is a need for a diversified approach to reduce costs and utilize more sustainable feedstocks effectively. Here, we map out catalytic synthesis routes to convert furanics derived from the (hemi)cellulosic biomass to alkanes and cycloalkanes using automated network generation with RING and semiempirical thermochemistry calculations. We find >100 energy-dense C8-C16 alkane and cycloalkane SAF candidates over 300 synthesis routes; the top three are 2-methyl heptane, ethyl cyclohexane, and propyl cyclohexane, although these are relatively short. The shortest, least endothermic process chemistry involves C-C coupling, oxygen removal, and hydrogen addition, with dehydracyclization of the heterocyclic oxygens in the furan ring being the most endothermic step. The global warming potential due to hydrogen use and byproduct CO2 is typically 0.7-1 kg CO2/kg SAF product; the least CO2 emitting routes entail making larger molecules with fewer ketonization, hydrogenation, and hydrodeoxygenation steps. The large number of SAF candidates highlights the rich potential of furanics as a source of SAF molecules. However, the structural dissimilarity between reactants and target products precludes pathways with fewer than six synthetic steps, thus necessitating intensified processes, integrating multiple reaction steps in multifunctional catalytic reactors.

Nano-Strand Formation via Gas Phase Reactions from Al-Co-Fe Reacted with CaF2-SiO2-Al2O3-MgO Flux at 1350 °C: SEM Study and Thermochemistry Calculations

The submerged arc welding (SAW) process is operated at high temperatures, up to 2500 °C, in the arc cavity formed by molten oxy-fluoride flux (slag). These high arc cavity temperatures and the complex interaction of gas–slag–metal reactions in a small space below the arc render the study of specific chemical interactions difficult. The importance of gas phase reactions in the arc cavity of the SAW process is well established. A low-temperature (1350 °C) experimental method was applied to simulate and study the vaporisation and re-condensation behaviour of the gas species emanating from oxy-fluoride flux. Energy dispersive X-ray spectroscopy (EDX) analyses and reaction thermochemistry calculations were combined to explain the role of Al as a de-oxidiser element in gas phase chemistry and, consequently, in nano-strand formation reactions. EDX element maps showed that the nano-strands contain elemental Ti only, and the nano-strand end-caps contain Co-Mn-Fe fluoride. This indicates a sequence of condensation reactions, as Ti in the gas phase is re-condensed first to form the nano-strands and the end-caps formed from subsequent re-condensation of Co-Mn-Fe fluorides. The nano-strand diameters are approximately 120 nm to 360 nm. The end-cap diameter typically matches the nano-strand diameter. Thermochemical calculations in terms of simple reactions confirm the likely formation of the nanofeatures from the gas phase species due to the Al displacement of metals from their metal fluoride gas species according to the reaction: yAl + xMFy ↔ xM + yAlFx. The gas–slag–metal equilibrium model shows that TiO2 in the flux is transformed into TiF3 gas. Formation of Ti nano-strands is possible via displacement of Ti from TiF3 by Al to form Al-fluoride gas.

The Effect of Composition and Temperature on the Hydrogen Reduction Behavior of Sintered Pellets of Bauxite Residue-Lime Mixtures

This study explores the isothermal hydrogen reduction of sintered pellets made of a mixture of bauxite residue and calcite with varying compositions at different reduction temperatures. Sintered pellets with varying compositions show three primary iron-containing oxide phases including brownmillerite, srebrodolskite, and fayalite; however, brownmillerite is the major phase in all the sintered pellets. The sintered pellets were reduced in a thermogravimetry furnace to establish instantaneous weight reduction with respect to time. Phases and microstructural analysis were carried out using X-ray diffraction and scanning electron microscopy, respectively. Mercury intrusion porosimeter and pycnometer were utilized to assess the porosity and density of the reduced pellets. Thermochemistry calculations were performed using the thermodynamics software FactSage 8.2. The reduction rate is most pronounced at a temperature of 1000 °C for all pellet compositions. It is intriguing to note that the rate of reduction shows minimal variance across pellets with different compositions; however, the higher calcite pellets exhibit a higher initial rate of reduction. Various kinetic models were examined to determine the activation energies for three different composition pellets, and the three-dimensional diffusion model has been well suited for this process. Close activation energies in the range of 84.6 to 94.8 kJ were obtained. A slightly higher activation energy was obtained for lower CaCO3 added pellets, and it was attributed to their reduced porosity and increased sintering, impeding the reaction kinetics. There were no significant differences in the formation of mayenite with varying the calcite amount; however, higher calcite pellets indicated more mayenite formation.Graphical

N-Bu4NI/K2S2O8-MEDIATED C-N COUPLING BETWEEN ALDEHYDES AND AMIDES.

n-Bu4NI/K2S2O8 mediated C-N coupling between aldehydes and amides is reported. A strong electronic effect is observed on the aromatic aldehyde substrates. The transformylation from aldehyde to amide takes place exclusively when an aromatic aldehyde bears electron-donating groups at either the ortho or para position of the formyl group, while the cross-dehydrogenative coupling dominates in the absence of these groups. Both the density functional theory (DFT) thermochemistry calculations and experimental data support the proposed single electron transfer mechanism with the formation of an acyl radical intermediate in the cross-dehydrogenative coupling. The n-Bu4NI/K2S2O8 mediated oxidative cyclization between 2-aminobenzamide and aldehydes is also reported, with four quinazolin-4(3H)-ones prepared in 65-99% yields.

Novel Solid Propellants Enabled Through In Situ Martian Perchlorates

With evidence for the native perchlorates existing in the Martian regolith, this paper examines the feasibility and performance of propellants formed from perchlorate salts reported to be present on Mars. Thermochemistry calculations indicate that the Martian perchlorate-based propellants provide less theoretical specific impulse than AP composite propellants but could still be viable propellants. Three propellants made from Martian perchlorates were manufactured and compared to a control propellant with AP as the oxidizer. Deflagration experiments were performed to obtain the burning rates as a function of pressure, with results comparable to AP baseline propellant. The propellant energy density was evaluated through bomb calorimetry. The propellant formulation with a similar perchlorate mixture to the distribution found in Martian soil was then subjected to thermal analysis, elemental analysis, and sensitivity testing to examine its combustion behavior and suitability for handling. Further characterization and development work would be needed to field these propellants, but initial conclusions indicate an in situ blend of calcium perchlorate and magnesium perchlorate could serve as a novel oxidizer for future safe, high-performing, and economical solid propellant rocket motors, offering an alternative to most current proposals for Martian ascent vehicle architectures.

Benchmarking Basis Sets for Density Functional Theory Thermochemistry Calculations: Why Unpolarized Basis Sets and the Polarized 6-311G Family Should Be Avoided.

Basis sets are a crucial but often largely overlooked choice in setting up quantum chemistry calculations. The choice of the basis set can be critical in determining the accuracy and calculation time of your quantum chemistry calculations. Clear recommendations based on thorough benchmarking are essential but not readily available currently. This study investigates the relative quality of basis sets for general properties by benchmarking basis set performance for a diverse set of 139 reactions (from the diet-150-GMTKN55 data set). In our analysis, we find the distributions of errors are often significantly non-Gaussian, meaning that the joint consideration of median errors, mean absolute errors, and outlier statistics is helpful to provide a holistic understanding of basis set performance. Our direct comparison of performance between most modern basis sets provides quantitative evidence for basis set recommendations that broadly align with the established understanding of basis set experts and is evident in the design of modern basis sets. For example, while zeta is a good measure of quality, it is not the only determining factor for an accurate calculation with unpolarized double- and triple-ζ basis sets (like 6-31G and 6-311G) having very poor performance. Appropriate use of polarization functions (e.g., 6-31G*) is essential to obtain the accuracy offered by double- or triple-ζ basis sets. In our study, the best performances for double- and triple-ζ basis sets are 6-31++G** and pcseg-2, respectively. However, the performances of singly polarized double-ζ and doubly polarized triple-ζ basis sets are quite similar with one key exception: the polarized 6-311G basis set family has poor parametrization, which means its performance is more like a double-ζ than a triple-ζ basis set. All versions of the 6-311G basis set family should be avoided entirely for valence chemistry calculations moving forward.

Short-range screened density matrix functional for proper descriptions of thermochemistry, thermochemical kinetics, nonbonded interactions, and singlet diradicals.

Common one-electron reduced density matrix (1-RDM) functionals that depend on Coulomb and exchange-only integrals tend to underestimate dynamic correlation, preventing reduced density matrix functional theory (RDMFT) from achieving comparable accuracy to density functional theory in main-group thermochemistry and thermochemical kinetics. The recently developed ωP22 functional introduces a semi-local density functional to screen the erroneous short-range portion of 1-RDM functionals without double-counting correlation, potentially providing a better treatment of dynamic correlation around equilibrium geometries. Herein, we systematically evaluate the performance of this functional model, which consists of two parameters, on main-group thermochemistry, thermochemical kinetics, nonbonded interactions, and more. Tests on atomization energies, vibrational frequencies, and reaction barriers reveal that the ωP22 functional model can reliably predict properties at equilibrium and slightly away from equilibrium geometries. In particular, it outperforms commonly used density functionals in the prediction of reaction barriers, nonbonded interactions, and singlet diradicals, thus enhancing the predictive power of RDMFT for routine calculations of thermochemistry and thermochemical kinetics around equilibrium geometries. Further development is needed in the future to refine short- and long-range approximations in the functional model in order to achieve an excellent description of properties both near and far from equilibrium geometries.

Self-assembly, structure and catalytic activity of Ni3 on TiO2: A triple-atom catalyst for hydrogen evolution

Triple-atom catalysts (TACs), structurally derived from single-atom catalysts (SACs) but beyond SACs in the active sites, have received increasing attention but are still in their infant stage. Using density functional theory, we study the self-assembly of the Ni3 trimer on TiO2 (Ni3/TiO2) by atom-by-atom deposition. Coordinatively unsaturated sites on the TiO2 surface are responsible for this self-assembly, resulting in different configurations of Ni3. According to the orientation relationship and lattice mismatch, an embryo of Ni crystal is thought to be born of triangle Ni3 trimer on TiO2. The hydrogen evolution reaction activity and mechanism of Ni3/TiO2 with different H coverages are evaluated using thermochemistry and kinetics calculations. Only at high H coverage would Ni3/TiO2 TACs exhibit a hydrogen production activity higher than that of Ni1/TiO2 SACs, indicating the matching relationship between multiple active sites and multi-step reaction intermediates for the active-site utilization. The quantum confinement effect throughout Nin/TiO2 (n = 1–3) is evidenced by the localization of metallic states of Nin. Our results not only open the possibility for synthesizing multimers on oxides by self-assembly, but also enrich the quantum control toolbox in few-atom catalysts by coordination modulation.

Molecular Geometries and Vibrational Contributions to Reaction Thermochemistry Are Surprisingly Insensitive to the Choice of Basis Sets.

Calculation of molecular geometries and harmonic vibrational frequencies are pre-requisites for thermochemistry calculations. Contrary to conventional wisdom, this paper demonstrates that quantum chemical predictions of the thermochemistry of many gas and solution phase chemical reactions appear to be very insensitive to the choice of basis sets. For a large test set of 80 diverse organic and transition-metal-containing reactions, variations in reaction free energy based on geometries and frequencies calculated using a variety of double and triple-zeta basis sets from the Pople, Jensen, Ahlrichs, and Dunning families are typically less than 4 kJ mol-1, especially when the quasiharmonic oscillator correction is applied to mitigate the effects of low-frequency modes. Our analysis indicates that for many organic molecules and their transition states, high-level revDSD-PBEP86-D4 and DLPNO-CCSD(T)/(aug-)cc-pVTZ single-point energies usually vary by less than 2 kJ mol-1 on density functional theory geometries optimized using basis sets ranging from 6-31+G(d) to aug-pcseg-2 and aug-cc-pVTZ. In cases where these single-point energies vary significantly, indicating sensitivity of molecular geometries to the choice of basis set, there is often substantial cancellation of errors when the reaction energy or barrier is calculated. The study concludes that the choice of basis set for molecular geometry and frequencies, particularly those considered in this study, is not critical for the accuracy of thermochemistry calculations in the gas or solution phase.

Novel organic molecule enabling a highly-stable and reversible sodium metal anode for room-temperature sodium-metal batteries

The cycle life of sodium metal batteries is hampered primarily by the unwarranted growth of sodium dendrites and their low Coulombic efficiency. Electrolyte additives can extend the cycle life by modifying the local interfacial electrochemistry of the metal anodes. Nevertheless, a high overpotential for deposition impeded the stripping/plating stability. We present 9-Fluorenone (9F), a novel electrolyte additive for highly stable and reversible sodium metal batteries. Even at a high current density of 20 mA cm−2, sodium deposition occurs seamlessly with this electrolyte additive. According to thermochemistry calculations, 9F molecules modulate the breakdown barrier and shield sodium-ion solvation shells from further decomposition, limiting the loss of metal anode and electrolyte inventory. As a result, a reversible stripping/plating of sodium can be accomplished for over 1200 h with a minimal overpotential of 25 mV. By combining metal sulfide cathodes, sodium metal anodes with ether-based electrolyte, and 9F additive molecules, we demonstrate the feasibility of developing a stable and long-lasting sodium‑sulfur battery that operates at room temperature and last >300 cycles.

Hydrogen storage in C6O6M6 (M = Li, Na): A DFT study

A density functional study of the electronic structures of C6O6M6 (M = Li, Na) clusters, as well as their potentials for dihydrogen storage, have been performed by two methods. Molecular dynamic simulations confirm that both clusters are thermodynamically stable. Calculations reveal that C6O6Li6/C6O6Na6 can adsorb up to 36/38H2 molecules with a gravimetric uptake capacity of 26.10/19.90 wt%, exceeding the goal (5.5 wt%) set by the US Department of Energy (DOE). The adsorption energies of H2 on C6O6Li6 and C6O6Na6 are in the range of 0.093–0.119 eV and 0.112–0.228 eV, respectively. The interactions of C6O6M6 (M = Li, Na) with H2 molecules are analyzed by a variety of electronic structure methods. Thermo-chemistry calculations indicate two H2 in C6O6Li6(H2)36 and fourteen H2 in C6O6Na6(H2)38 can be readily adsorbed at 77 K and desorbed at 298.15 K under atmospheric pressure, corresponding to the maximal reversible hydrogen storage densities are 2.11 wt% and 8.38 wt%, respectively. Higher pressure can improve the maximal reversible hydrogen storage abilities. Atom density matrix propagation (ADMP) molecular dynamic simulations indicate that H2 molecules are substantially and strongly bound at 77 K and get efficiently released at elevated temperature (300 K). The (C6O6M6)2 (M = Li, Na) dimers can also efficiently adsorb multiple H2 molecules with high gravimetric density and reversible average adsorption energy.

The effects of conformation and intermolecular hydrogen bonding on the structure and IR spectra of flutamide; a study based on the matrix isolation technique, ab initio and DFT calculations

In this study, stable conformers of flutamide referred to as an anticancer drug were searched through a relaxed potential energy surface scan carried out at the B3LYP/6-31G(d) level of theory. This was followed by geometry optimization and thermochemistry calculations performed with the HF-SCF, MP2, B3LYP methods and the 6-31G(d), 6–311++G(d,p), aug-cc-pvTZ basis sets for each of the determined minimum energy conformers. The results revealed that flutamide has at least five stable conformers and two of them provide the major contribution to the observed matrix isolation infrared (IR) spectra of the molecule. The effects of conformational variety and intermolecular hydrogen bonding interactions on the observed IR spectra of flutamide were interpreted in the light of the vibrational spectral data obtained for the most stable monomer and dimer forms of the molecule at the same levels of theory. Pulay’s “Scaled Quantum Mechanical-Force Field (SQM-FF)” method was used in the refinement of the calculated harmonic wavenumbers, IR intensities and potential energy distributions. This scaling method which proved its superiority to both anharmonic frequency calculations and other scaling methods helped us to correctly interpret the remarkable differences between the matrix IR spectra of flutamide in argon and the condensed phase IR spectra of the molecule in solvents such as KBr, H2O, D2O, ethanol and methanol.

Identification of Torsional Modes in Complex Molecules Using Redundant Internal Coordinates: The Multistructural Method with Torsional Anharmonicity with a Coupled Torsional Potential and Delocalized Torsions.

Identification of internal-rotation modes in the normal-mode analysis of complex molecules is important for accurately describing the thermodynamic properties and kinetics of complex molecules when it is necessary to treat the anharmonicity of torsions and the multiconformer anharmonicity caused by the internal rotations. However, identifying and distinguishing torsional modes are very challenging because they are coupled to one another. In this work, we present a new strategy to automatically identify torsional vibrations and separate them from the other vibrational modes. By combining a redundant-internal-coordinate auto-generation procedure with torsional projection techniques, we automate the procedure of identifying and separating the coupled torsions, and we show that we can obtain robust and consistent results with various reasonable definitions of redundant-internal-coordinate sets. This model has been implemented in a new development version of the MSTor program to reduce the user input needed for multistructural and torsional anharmonicity (MS-T) calculations. The new method is called multistructural and torsional anharmonicity with a coupled torsional potential and delocalized torsions ([MS-T(CD)]. As example applications, we consider MS-T(CD) calculations on three molecules (2-hexyl radical, n-propylbenzene, and 5-hydroperoxy-6-oxohexanoylperoxy radical) that have multiple rotors and that provide challenges to choosing good sets of nonredundant-internal coordinates, and we compare the performance of the new strategy to five other torsion identification methods. The new strategy is demonstrated to be efficient in separating the torsional and nontorsional elements in the Hessian matrix, as well as in providing reasonable projected nontorsional frequencies to be used for calculations of partition function and thermochemistry.

Fundamentals behind the specificity of Cysteinyl-tRNA synthetase: MD and QM/MM joint investigations.

Cysteinyl-tRNA synthetase (CysRS) catalyzes the aminoacylation reaction of cysteine to its cognate tRNACys in the first step of protein translation. It is found that CysRS is different from other aaRSs as it transfers cysteine without the need for an editing reaction, which is not applicable in the case of serine despite the similarity in their structures. Surprisingly, the reasons why CysRS has high amino acid specificity are not clear yet. In this research, the binding configurations of Cys-AMP and its near-cognate amino acid Ser-AMP with CysRS are compared by Molecular Dynamics (MD). The results reveal that CysRS screens the substrate Cys-AMP to a certain extent in the process of combination and recognition, thus providing a guarantee for the high selectivity of the next reaction. While Ser-AMP is in a folded state in CysRS. In the meanwhile, the interaction between Cys-AMP and Zn963 in CysRS is much stronger than Ser-AMP. The substrate-assisted aminoacylation mechanism in CysRS is also explored by Quantum Mechanics/Molecular Mechanics (QM/MM) modeling. According to the QM/MM potential energies, the energy barrier of TSCys-AMP is 91.75 kJ/mol, while that of TSSer-AMP is close to 150 kJ/mol. Based on thermochemistry calculations, it is found that the product of Cys-AMP is more stable than the reactant. In contrast, Ser-AMP has a reactant that is more stable than its product. As a result, it reflects that the specificity of CysRS originates from both the kinetic and thermodynamical perspectives of the reaction. Our investigations demonstrate comprehensively on how CysRS recognizes and catalyzes the substrate Cys-AMP, hoping to provide some guidance for researchers in this area.

Large-scale thermochemistry calculations for combustion models

Accurate thermochemical properties for chemical species are of vital importance in combustion chemistry research. Group additivity approaches are widely used to generate thermochemistry data used in chemical kinetic models, but this approach has limited accuracy. Following on previous studies by the combustion community, we performed electronic structure calculations to obtain reliable thermochemistry data for a large set of molecules taken from a well-established chemical kinetic model. The developed database consists of 1340 species that contain up to 18 and 5 carbon and oxygen atoms, respectively. The M06-2X/aug-cc-pVTZ level of theory was used for the geometry optimizations, vibrational frequency calculations, and dihedral angle scans. The potential energy of the different species was further refined with different composite methods, and the G3 method with the atomization reaction approach was selected to calculate the enthalpy of formation at 0 K. This information was then used in statistical thermodynamics calculations to obtain standard enthalpies of formation and entropy, as well as heat capacities at different temperatures. Our thermochemistry data exhibits good agreement with existing values in the literature, verifying the accuracy of our approach. Comparisons against group additivity (GA) method are also presented. The database of thermochemistry quantities developed in this study can be used to improve the training GA or machine learning models. The impact of the developed dataset is illustrated by examining the variation in ignition delay times using the updated thermochemistry values.