Development and applications in computational chemistry for inorganic catalysis

Abstract

A robust metadata database called the Collaborative Chemistry Database Tool (CCDBT) for massive amounts of computational chemistry raw data has been designed and implemented. It performs data synchronization and simultaneously extracts the meta data. The indexed meta data can be used for data analysis and data mining. A novel tree growth - hybrid genetic algorithm (TG-HGA) was developed to search the global minimum of small clusters. In the TG algorithm, the clusters grow from a small seed to the size of interest stepwise. New atoms are added to the smaller cluster from the previous step, by analogy to new leaves grown by a tree. The initial structures for the search for the global minimum of TiO_2 nanoclusters were generated by TG-HGA, and new low energy structures that have not been previously reported were found. Low energy isomers of Agn, n = 2 - 99, were studied at different computational level depending on the size of Agn. The geometries of Agn, n = 2 - 8, were optimized using density functional theory (DFT), and the energies were calculated at the CCSD(T)/CBS level. The Agn, n = 9 - 20, were initially generated by the TG-HGA builder with an EAM potential, and optimized using the DFT method. The relative energies and normalized atomization energies for the optimized structures were calculated at the CCSD(T) level with a small basis set. For larger Agn, 20 < n < 100, the low energy structures were generated using TG-HGA with an EAM potential, and the energies were calculated at the DFT level with a small basis set. A range of DFT functionals were benchmarked with the normalized atomization energies at the CCSD(T) level for the small Agn clusters. PW91 and ω-B97XD provided best results for predicting the normalized atomization energies. The normalized atomization energies for Agn start to converge slowly to the bulk at n = 55. At n = 99, the normalized atomization energy is predicted to be ~50 kcal/mol. The low energy isomers of the Irn(CO)m complexes (n=1, 2, 3, 4, and 6) were investigated using electronic structure methods at the density functional theory and coupled cluster (CCSD(T) theory levels. Ir4(CO)12 is predicted to be the most favored complex for reactions of Irn(CO)m with CO at low temperature, and Ir6(CO)16 is predicted to be formed above room temperature. Smaller Irn(CO)m clusters will nucleate to form Ir4(CO)12 spontaneously. Low-lying structures of the small iridum clusters Irn (n = 2 - 8) were optimized using DFT methods. Ir2 and Ir3 were also optimized using the CASSCF method. MRCI-SD (for Ir2) energies and CCSD(T) (for Ir2 and Ir3) energies of the leading configurations from the CASSCF calculations were done to predict the low-lying states. The normalized atomization energies for Irn (n = 2 - 8) were calculated at the CCSD(T) level up to the complete basis set (CBS) limit in some cases using the B3LYP optimized geometries. Inclusion of the spin orbit corrections in the normalized atomization energies for Irn is critical and will decrease the normalized atomization energies by ~ 15 kcal/mol for n ≥ 4. Several molecular models were used to characterize various binding sites of the metal complexes in the zeolites. The calculated structures and energies indicate a metal-oxygen (M(I)-O) coordination number of two for most of the supported complexes but a value of three when the ligands include C2H5 or H. The results characterizing various isomers of supported metal complexes incorporating hydrocarbon ligands indicate that some carbene and carbyne ligands could form. A set of ligand bond dissociation energies is reported to explain reactivity trends. The Pd-L ligand bond dissociation energies (BDEs) of cis- and trans-[L-Pd(PH3)2Cl]+ were predicted using coupled cluster CCSD(T) theory and a variety of density functional theory (DFT) functionals at the B3LYP optimized geometries. For cis-[L-Pd (PH3)2Cl]+ complexes, the Pd-L bond energies are 28 kcal/mol for CO; ~40 kcal/mol for AH3 (A = N, P, As, and Sb), norbornene, and CH3CN; and ~53 kcal/mol for CH3NC, pyrazole, pyridine, and tetrahydrothiophene at the CCSD(T) level. The benchmarks show that the dispersion-corrected hybrid, generalized gradient approximation, DFT functional ω-B97X-D is the best functional to use for this system. Use of the ω-B97X-D/aD functional gives predicted BDEs within 1 kcal/mol of the CCSD(T)/aug-cc-pVTZ BDEs for cis-[L-Pd(PH3)2Cl]+ and 1.5 kcal/mol for trans-[L-Pd(PH3)2Cl]+ . Lanthanide metal atoms, produced by laser ablation, were condensed with CH3F in excess Ar at 8 K. New infrared absorption bands are assigned to the first insertion CH3LnF and oxidative addition methylene lanthanide hydride fluoride CH2LnHF products on the basis of 13C and deuterium substitution and density functional theory calculations of the vibrational frequencies. For Ln = Eu and Yb only CH3LnF is observed. CH3LnF in the Ln formal +2 state is predicted to be more stable than CH2LnHF with the Ln in the formal +3 oxidation state. CH3-LnF forms a single bond between Ln and C and is a substituted methane. The calculated potential energy surface for the CH3F + La → CH3-LaF/CH2-LaHF shows a number of intermediates and transition states on multiple paths. The reaction mechanism involves the potential formation of LaF and LaHF intermediates.