Predictive coupled-cluster isomer orderings for some Sin{}_nCm{}_m (m,n≤12m, n\le 12) clusters; A pragmatic comparison between DFT and complete basis limit coupled-cluster benchmarks

The accurate determination of the preferred ${\rm Si}_{12}{\rm C}_{12}$ isomer is important to guide experimental efforts directed towards synthesizing SiC nano-wires and related polymer structures which are anticipated to be highly efficient exciton materials for opto-electronic devices. In order to definitively identify preferred isomeric structures for silicon carbon nano-clusters, highly accurate geometries, energies and harmonic zero point energies have been computed using coupled-cluster theory with systematic extrapolation to the complete basis limit for set of silicon carbon clusters ranging in size from SiC$_3$ to ${\rm Si}_{12}{\rm C}_{12}$. It is found that post-MBPT(2) correlation energy plays a significant role in obtaining converged relative isomer energies, suggesting that predictions using low rung density functional methods will not have adequate accuracy. Utilizing the best composite coupled-cluster energy that is still computationally feasible, entailing a 3-4 SCF and CCSD extrapolation with triple-$\zeta$ (T) correlation, the {\it closo} ${\rm Si}_{12}{\rm C}_{12}$ isomer is identified to be the preferred isomer in support of previous calculations [J. Chem. Phys. 2015, 142, 034303]. Additionally we have investigated more pragmatic approaches to obtaining accurate silicon carbide isomer energies, including the use of frozen natural orbital coupled-cluster theory and several rungs of standard and double-hybrid density functional theory. Frozen natural orbitals as a way to compute post MBPT(2) correlation energy is found to be an excellent balance between efficiency and accuracy

Valence and Charge-transfer Optical Properties for Some Si\u3csub\u3en\u3c/sub\u3eC\u3csub\u3em\u3c/sub\u3e (m, n ≤ 12) Clusters: Comparing TD-DFT, Complete-basis-limit EOMCC, and Benchmarks from Spectroscopy

Accurate optical characterization of the closo-Si12C12 molecule is important to guide experimental efforts toward the synthesis of nano-wires, cyclic nano-arrays, and related array structures, which are anticipated to be robust and efficient exciton materials for opto-electronic devices. Working toward calibrated methods for the description of closo-Si12C12 oligomers, various electronic structure approaches are evaluated for their ability to reproduce measured optical transitions of the SiC2, Si2Cn (n = 1–3), and Si3Cn (n = 1, 2) clusters reported earlier by Steglich and Maier [Astrophys. J. 801, 119 (2015)]. Complete-basis-limit equation-of-motion coupled-cluster (EOMCC) results are presented and a comparison is made between perturbative and renormalized non-iterative triples corrections. The effect of adding a renormalized correction for quadruples is also tested. Benchmark test sets derived from both measurement and high-level EOMCC calculations are then used to evaluate the performance of a variety of density functionals within the time-dependent density functional theory (TD-DFT) framework. The best-performing functionals are subsequently applied to predict valence TD-DFT excitation energies for the lowest-energy isomers of SinC and Sin−1C7−n (n = 4–6). TD-DFT approaches are then applied to the SinCn (n = 4–12) clusters and unique spectroscopic signatures of closo-Si12C12 are discussed. Finally, various long-range corrected density functionals, including those from the CAM-QTP family, are applied to a charge-transfer excitation in a cyclic (Si4C4)4 oligomer. Approaches for gauging the extent of charge-transfer character are also tested and EOMCC results are used to benchmark functionals and make recommendations

Kinetics of the Reactions of Ozone with Halogen Atoms in the Stratosphere

It is well established that reaction cycles involving inorganic halogens contribute to the depletion of ozone in the atmosphere. Here, the kinetics of O3 with halogen atoms (Cl, Br, and I) were investigated between 180 and 400 K, expanding the temperature range relative to prior studies. Canonical variational transition state theory including small curvature tunneling correction (CVT/SCT) were considered, following the construction of the potential energy surfaces. MRCI + Q/aug-ano-pVTZ//MP2/aug-cc-pV(T + d)Z and MRCI + Q/aug-ano-RCC-VTZP//MP2/aug-cc-pV(T + d)Z levels of theory were used to calculate the kinetic parameters. Calculated rate coefficients were used to fit the Arrhenius equations, which are obtained to be k1 = (3.48 ± 0.4) × 10−11 exp[(−301 ± 64)/T] cm3 molecule−1 s−1, k2 = (3.54 ± 0.2) × 10−11 exp[(−990 ± 35)/T] cm3 molecule−1 s−1 and k3 = (1.47 ± 0.1) × 10−11 exp[(−720 ± 42)/T] cm3 molecule−1 s−1 for the reactions of O3 with Cl, Br, and I atoms, respectively. The obtained rate coefficients for the reactions of O3 with halogen atoms using CVT/SCT are compared to the latest recommended rate coefficients by the NASA/JPL and IUPAC evaluations. The reactivity trends and pathways of these reactions are discussed

Revealing the critical role of radical-involved pathways in high temperature cyclopentanone pyrolysis

Cyclopentanone (CPO) is a promising biofuel for spark-ignition engines due to its ring strain and high auto-ignition resistance. Understanding CPO decomposition is crucial for building a high-temperature combustion model. Here we present a comprehensive kinetic model for high-temperature pyrolysis of CPO with verified results from high-pressure shock tube (HPST) measurements. The time-histories of carbon monoxide (CO), ethylene (C₂H₄), and CPO absorbances over the temperature range of 1156–1416 K and pressure range of 8.53–10.06 atm were measured during current experiments. A corresponding detailed kinetic model was generated using the Reaction Mechanism Generator (RMG) with dominant unimolecular/radical-involved decomposition pathways from either previous studies or quantum calculations within the current work. The obtained model containing 821 species and 79,859 reactions exhibited a good agreement with the experimental results. In this study, the absorbance ratio between C₂H₄ and CO was used as an important factor to validate models and to prove that radical-involved bimolecular pathways were as significant as unimolecular decomposition of CPO. The rate of production (ROP) analysis showed H radicals play a major role in the decomposition, and the whole decomposition process could be divided into three stages based on the H radical concentration. The insights from present work can be used to generate a better CPO combustion model and help evaluate CPO as an advanced biofuel.Department of Energy (Grant DE-EE007982

The Venom of Spectacled Cobra (Elapidae: Naja naja): In Vitro Study from Distinct Geographical Origins in Sri Lanka

Several countries residing envenomation due to Naja naja had revealed a disparity in the venom composition according to their geographic location and Sri Lankan cobra still lacks the evidence to support this. Therefore, the current study was focused on addressing relationship between the histopathological changes according to geographic variation of Sri Lankan N. naja venom. The histopathological changes in vital organs and muscle tissues following intramuscular administration of venom of N. naja were studied using BALB/c mice. The median lethal dose of venom of N. naja in the present study was determined to be 0.55, 0.66, 0.68, 0.62, and 0.7 mg/kg for North (NRP), Central (CRP), Western, Southern, and Sabaragamuwa Regional Population venoms, respectively. Histopathological changes were observed in different levels in vital organs and muscle tissues of mice. NRP accompanied significantly higher infiltration of inflammatory and necrotic cells into skeletal muscle and CRP venom demonstrated high level of cardiotoxic effects comparing to other regions. This study revealed a certain extent of variations in the pathological effects of N. naja venom samples according to their geographical distribution

Regio-selectivity prediction with a machine-learned reaction representation and on-the-fly quantum mechanical descriptors

© The Royal Society of Chemistry 2021. Accurate and rapid evaluation of whether substrates can undergo the desired the transformation is crucial and challenging for both human knowledge and computer predictions. Despite the potential of machine learning in predicting chemical reactivity such as selectivity, popular feature engineering and learning methods are either time-consuming or data-hungry. We introduce a new method that combines machine-learned reaction representation with selected quantum mechanical descriptors to predict regio-selectivity in general substitution reactions. We construct a reactivity descriptor database based onab initiocalculations of 130k organic molecules, and train a multi-task constrained model to calculate demanded descriptors on-the-fly. The proposed platform enhances the inter/extra-polated performance for regio-selectivity predictions and enables learning from small datasets with just hundreds of examples. Furthermore, the proposed protocol is demonstrated to be generally applicable to a diverse range of chemical spaces. For three general types of substitution reactions (aromatic C-H functionalization, aromatic C-X substitution, and other substitution reactions) curated from a commercial database, the fusion model achieves 89.7%, 96.7%, and 97.2% top-1 accuracy in predicting the major outcome, respectively, each using 5000 training reactions. Using predicted descriptors, the fusion model is end-to-end, and requires approximately only 70 ms per reaction to predict the selectivity from reaction SMILES strings

Towards Accurate Quantum Mechanical Thermochemistry: (1) Extensible Implementation and Comparison of Bond Additivity Corrections and Isodesmic Reactions

Obtaining accurate enthalpies of formation of chemical species, Hf, often requires empirical corrections that connect the results of quantum mechanical (QM) calculations with the experimental enthalpies of elements in their standard state. One approach is to use atomization energy corrections (AECs) followed by bond additivity corrections (BACs), such as those defined by Petersson et al. or Anantharaman and Melius. Another approach is to utilize isodesmic reactions (IDRs) as shown by Buerger et al. We implement both approaches in Arkane, an open-source software that can calculate species thermochemistry using results from various QM software packages. In this work, we collect 421 reference species from the literature to derive Hf corrections, and fit AECs and BACs for 15 commonly used model chemistries. We find that both types of BACs yield similar accuracy, although Anantharaman and Melius-type BACs appear to generalize better. Furthermore, BACs tend to achieve better accuracy than IDRs for commonly used model chemistries, and IDRs can be less robust because of the sensitivity to the chosen reference species and reactions. Overall, Anantharaman and Melius-type BACs are our recommended approach for achieving accurate QM corrections for enthalpies