Automating the IRC Analysis within Eyringpy

To analyze the evolution of a chemical property along the reaction path, we have to extract all the necessary information from a set of electronic structure computations. However, this process is time-consuming and prone to human error. Here we introduce IRC-Analysis, a new extension in Eyringpy, to monitor the evolution of chemical properties along the intrinsic reaction coordinate, including complete reaction force analysis. IRC-Analysis collects the entire data set for each point on the reaction coordinate, eliminating human error in data capture and allowing the study of several chemical reactions in seconds, regardless of the complexity of the systems. Eyringpy has a simple input format, and no programming skills are required. A tracer has been included to visualize the evolution of a given chemical property along the reaction coordinate. Several properties can be analyzed at the same time. This version can analysis the evolution of bond distances and angles, Wiberg bond indices, natural charges, dipole moments, and orbital energies (and related properties).

Metal–metal bonding in deltahedral dimetallaboranes and trimetallaboranes: a density functional theory study

The skeletal bonding topology as well as the Re=Re distances and Wiberg bond indices in the experimentally knownoblatoclosodirhenaboranes Cp*2Re2Bn−2Hn−2(Cp*=η5Me5C5,n=8–12) suggest formal Re=Re double bonds through the center of a flattened Re2Bn−2deltahedron. Removal of a boron vertex from theseoblatoclosostructures leads tooblatonidostructures such as Cp2W2B5H9and Cp2W2B6H10. Similar removal of two boron vertices from the Cp2Re2Bn−2Hn−2(n=8–12) structures generatesoblatoarachnostructures such as Cp2Re2B4H8and Cp2Re2B7H11. Higher energy Cp2Re2Bn−2Hn−2(Cp=η5-C5H5,n=8–12) structures exhibitclosodeltahedral structures similar to the deltahedral borane dianions BnHn2−. The rhenium atoms in these structures are located at adjacent vertices with ultrashort Re≣Re distances similar to the formal quadruple bond found in Re2Cl82−by X-ray crystallography. Such surface Re≣Re quadruple bonds are found in the lowest energy PnRe2Bn−2Hn−2structures (Pn=η5,η5-pentalene) in which the pentalene ligand forces the rhenium atoms to occupy adjacent deltahedral vertices. The low-energy structures of the tritungstaboranes Cp3W3(H)Bn−3Hn−3(n=5–12), related to the experimentally known Cp*3W3(H)B8H8, have central W3Bn−3deltahedra with imbedded bonded W3triangles. Similar structures are found for the isoelectronic trirhenaboranes Cp3Re3Bn−3Hn−3. The metal atoms are located at degree 6 and 7 vertices in regions of relatively low surface curvature whereas the boron atoms are located at degree 3–5 vertices in regions of relatively high surface curvature. The five lowest-energy structures for the 11-vertex tritungstaborane Cp3W3(H)B8H8all have the same central W3B8deltahedron and differ only by the location of the “extra” hydrogen atom. The isosceles W3triangles in these structures have two long ~3.0 Å W–W edges through the inside of the deltahedron with the third shorter W–W edge of ~2.7 to ~2.8 Å corresponding to a surface deltahedral edge.

A theoretical study towards thermolysis process of thionesters and thiolesters

This paper focuses on the thermal elimination of alkenes from methyl alkyl thionacetates and thiolacetates. Three alkyl groups are calculated: ethyl, isopropyl and tert-butyl. Possible elimination mechanisms are considered, including six- and four-membered ring transition states for alkene elimination, four-membered ring isomerization and a possible five-membered ring decomposition. Theoretical calculations are performed with the MP2 method and the 6-31G* basis set. Wiberg bond indices are also summarized to monitor the reaction progress.

A computational study on the thermal decomposition of di(tri)thiocarbonates

Alkyl methyl di(tri)thiocarbonates can be thermally decomposed into alkenes. In this paper, theoretical calculations were used to calculate the thermal decomposition procedures. Six compounds, including ethyl, isopropyl and [Formula: see text] dithiocarbonate and trithiocarbonate, were examined. For each decomposition, nine possible paths were considered, including the paths leading to the desired alkene products, as well as rearrangement and elimination reactions. This calculation was performed with the MP2/6-31G(d) method. Wiberg bond indices were also calculated to further reveal the reaction progress.

Theoretical studies on structure, formation and nature of bond in a Disila-, Digerma- and distannacyclobutene ring

A theoretical study on the structure, formation and nature of E–E and C–E bonds (E[Formula: see text][Formula: see text][Formula: see text]Si, Ge, Sn) in catenated compounds of the group 14 elements including disila-, digerma- and distannacyclobutene ring formed from the reaction of 1-thiacyclohept-4-yne and E(NR)2SiR2 molecules [E[Formula: see text][Formula: see text][Formula: see text]Si, Ge, Sn, R[Formula: see text][Formula: see text][Formula: see text]t-Bu, H, F, Cl, Br] in 1:2 mole ratio has been investigated at the M06/def2-TZVPP level of theory. The results showed that the formation energy of the products of the reaction above with Si(NBr)2SiBr2 and Sn(NF)2SiF2 reactants has greatest and the smallest value, respectively. In agreement with the values of formation energies, both the calculated Wiberg bond indices (WBI) for E—E and C—E bonds and [Formula: see text](BCP) of E—E bond in the products of two above reactants have largest and smallest values, respectively. The nature of E—E bond in the products was also studied with atoms in molecules (AIM) and natural bond orbital (NBO) analyses. The data confirmed that the E—E bond is partly covalent. In addition, the nature of C—E bond was investigated with energy decomposition analysis (EDA) and it was shown that the covalent contribution is in the range 48–53% depending on the types of E atom and corresponding substituents.

Ab initio and DFT studies on the structures, binding energies and nature of bonds in X2Y3 metal clusters (X+ = Li+, Na+ and K+; ${\rm Y}_{3}^{2-} = {\rm Zn}_{3}^{2-}, {\rm Cd}_{3}^{2-}$ and ${\rm Hg}_{3}^{2-}$)

A comprehensive theoretical study on the structure and stability of linear and triangular isomers of anionic clusters of zinc, cadmium and mercury [Formula: see text] and their binding with one and two alkali metal cations ( X + = Li +, Na +, K +) has been investigated at the density functional (BP86 and B3LYP) and ab initio (MP2, MP4 and coupled cluster single and double (CCSD)) methods. The results showed that in all cases, the triangular geometry with D3h symmetry is more stable than linear one. The calculated values of interaction energies (IE) between [Formula: see text] anions and two X+ cations, Wiberg bond indices (WBI) and the electron densities at bond critical points (BCP), ρ(BCP), for Y–X bonds show that among all complexes investigated here at all levels of theory Zn 3 Li 2 and Hg 3 K 2 have the largest and the smallest values of IE, WBI and ρ(BCP), respectively. The natural charges of the atoms and WBI involved in the bonding as well as the global value of the charge transfer ΔQ from [Formula: see text] to X+ cation in X2Y3 clusters, evaluated through natural population analysis, confirmed that covalent contribution in Y–X bond formation increases from K + to Li +. Also the energy decomposition analyses (EDA) were used to detect the nature of interaction in the complexes. The results confirmed that the contribution of electrostatic interactions in present complexes is almost more than 70%.

Structures, Stabilities, and Electronic Properties for Rare-Earth Lanthanum Doped Gold Clusters

The structures, stabilities, and electronic properties of rare-earth lanthanum doped gold La2Aun (n = 1–9) and pure gold Aun (n ≤ 11) clusters have been investigated by using density functional theory. The optimized geometries show that the lowest energy structures of La2Aun clusters favour the 3D structure at n ≥ 3. The lanthanum atoms can strongly enhance the stabilities of gold clusters and tend to occupy the most highly coordinated position. By analysing the gap, vertical ionization potential, and chemical hardness, it is found that the La2Au6 isomer possesses higher stability for small-sized La2Aun clusters (n = 1–9). The charges in the La2Aun clusters transfer from La atoms to the Aun host. In addition, Wiberg bond indices analysis reveals that the intensity of different bonds of La2Aun clusters exhibits a sequence of La–La bond > La-Au bond > Au–Au bond.

Acyclic and cyclic nitrone cycloadditions to 1-cinnamoyl-1-piperidine: A DFT study

DFT studies have been carried out for the cycloaddition reactions of a cyclic nitrone, 1-pyrroline-1-oxide and an acyclic nitrone, C,N-diphenyl nitrone to an unsymmetrically disubstituted dipolarophile, 1-cinnamoyl-1-piperidine. These reactions proved to be opposite to each other with respect to the electron demand character predicted by the electronic chemical potentials, electrophilicities and charge transfer at the transition states. The regio- and stereoselectivities have been predicted from DFT based reactivity indices, interaction energy calculations using a perturbative orbital independent theoretical model and the activation parameters of the located transition states. Two different concepts have been used for the evaluation of interaction energies. The selectivities were found to be in conformity with the experimental findings. The time gaps between the formations of C – C and C – O bonds were evaluated from single trajectory simulations. The asynchronicity of bond formation process was analyzed from the wiberg bond indices, atom–atom overlap weighted NAO bond orders and the calculated asymmetry indices of the transition states.

Theoretical studies on the pyrolysis of (Thion)carbonates

MP2/6-31G(d) was employed to investigate the theoretical calculations on the pyrolysis of alkyl methyl (thion)carbonates, where alkyl groups referred to ethyl, isopropyl and t-butyl groups. Nine possible pathways were considered for the pyrolysis of alkyl methyl thioncarbonates, while only seven possible pathways were found to pyrolyze alkyl methyl carbonates. Both of them had three pathways to generate the desired alkene products. Not only thermal elimination pathways were calculated, other possible mechanisms, such as rearrangements and nucleophilic substitutions, were also considered. The progress of the reactions was also investigated by the calculation of Wiberg bond indices at MP2/6-31G(d) level.