Geometry Optimization Calculations Research Articles

Three-Body Dispersion Corrections to the Spherical Atom Model: The PFD-3B Density Functional.

The performance of the isotropic spherical atom model can be significantly enhanced through combination with anisotropic three-body dispersion interactions to give the new PFD-3B density functional, which reduces the mean absolute deviation (MAD) relative to CCSD(T)/CBS benchmark energies from 0.78 to 0.19 kcal/mol for the S22 test set. Comparison with the extended S22 × 5 test set in the figure indicates that this accuracy is maintained through large variations in geometry. The performance of the PFD-3B functional over the S22 × 5 test set is superior to any of the functionals previously applied to this set. Over the S22 set of examples, the MADs from the CCSD(T)/CBS values for Re, De, and ωe, are 0.032 Å, 0.21 kcal/mol, and 6 cm-1, respectively. Over a comparable set of 26 examples containing second and third row atoms, the MADs from the CCSD(T)/CBS values for Re, De, and ωe, are 0.033 Å, 0.19 kcal/mol, and 5 cm-1, respectively. If used to optimize the geometry of the 48 examples, on average the PFD-3B functional introduces an error of only 0.042 kcal/mol in CCSD(T) single-point energies. This small error combines with the reported analytical first and second derivatives to makes the PFD-3B functional an attractive model for geometry optimization and zero-point energy calculations.

(Invited) Approaches to Understanding and Predicting the Stability of Liquid Electrolytes and the Early Formation of the Solid-Liquid Electrolyte Interphase

Electrolytes with improved stability have the potential to transform the current state-of-the-art Li-ion architectures and enable future technologies such as multivalent systems (e.g., Mg2+, Ca2+ and Zn2+), as well as Li-S and Li-O2 conversion systems. A remaining challenge in the pursuit of rational design of novel and optimized electrolytes is understanding and ultimately predicting the reaction cascade responsible for the creation of a functional liquid-anode solid-electrolyte interface (SEI). We here present an overview of the challenge, coupled with several examples of systems where minority as well as majority speciation of the electrolyte is imperative to understand the origin of the electrochemical window. Furthermore, to address the complexity of the resulting reaction cascade once these species start to decompose, we advocate the need for data-driven approach coupled with a high-throughput quantum chemistry computational infrastructure. To this end, we have constructed a chemical reaction network with tens of thousands of elementary reactions which allow for bond breaking/formation as well as oxidation/reduction reactions. The reaction energetics are obtained from our computational framework which automate geometry optimization and vibrational frequency calculations for molecules, including radical, charged, metal-coordinated, and solvated species. To analyze possible reaction pathways, we apply a graph representation to our network, leveraging an iterative reweighting strategy that solves for all prerequisite branching such that traditional pathfinding algorithms correctly capture coordinated pathways. Machine-learning algorithms operating on bond-formation and breaking energetics aid in rapid evaluation of highly reactive processes. We show that without any apriori chemical intuition, our automated framework can recover favorable reaction paths to form key SEI components, which have been carefully identified over the past two decades. This data-driven approach and infrastructure show promise to accelerate the understanding of chemical reactivity in complex environments, in the aid of novel electrolyte design.

Structural Characterization of the Solution Chemistry of Zirconium(IV) Desferrioxamine: A Coordination Sphere Completed by Hydroxides.

Positron emission tomography (PET) using radiolabeled, monoclonal antibodies has become an effective, noninvasive method for tumor detection and is a critical component of targeted radionuclide therapy. Metal ion chelator and bacterial siderophore desferrioxamine (DFO) is the gold standard compound for incorporation of zirconium-89 in radiotracers for PET imaging because it is thought to form a stable chelate with [89Zr]Zr4+. However, DFO may not bind zirconium-89 tightly in vivo, with free zirconium-89 reportedly liberated into the bones of experimental mouse models. Although high bone uptake has not been observed to date in humans, this potential instability has been proposed to be related to the unsaturated coordination sphere of [89Zr]Zr-DFO, which is thought to consist of the 3 hydroxamate groups of DFO and 1 or 2 water molecules. In this study, we have used a combination of X-ray absorption spectroscopy and density functional theory (DFT) geometry optimization calculations to further probe the coordination chemistry of this complex in solution. We find the extended X-ray absorption fine structure (EXAFS) curve fitting of an aqueous solution of Zr(IV)-DFO to be consistent with an 8-coordinate Zr with oxygen ligands. DFT calculations suggest that the most energetically favorable Zr(IV) coordination environment in DFO likely consists of the 3 hydroxamate ligands from DFO, each with bidentate coordination, and 2 hydroxide ligands. Further EXAFS curve fitting provides additional support for this model. Therefore, we propose that the coordination sphere of Zr(IV)-DFO is most likely completed by 2 hydroxide ligands rather than 2 water molecules, forming Zr(DFO)(OH)2.

PTCDA adsorption on CaF2 thin films.

Thin insulating films are commonly employed for the electronic decoupling of molecules as they enable a preservation of the intrinsic molecular electronic functionality. Here, the molecular properties of 3,4,9,10-perylene tetracarboxylic dianhydride (PTCDA) adsorbed on insulating CaF2 thin films that were grown on Si(111) surfaces are studied. Scanning tunnelling microscopy is used to compare the properties of PTCDA molecules adsorbed on a partly CaF1-covered Si(111) surface with deposition on thicker CaF2/CaF1/Si(111) films. The identification of mostly single molecules on the CaF1/Si(111) interface layer is explained by the presence of atomic-size defects within this layer. Geometry-optimisation calculations using density functional theory reveal a geometry on CaF2(111) of nearly flat-lying PTCDA molecules with two oxygen atoms displaced towards calcium surface ions. This geometry is in agreement with the experimental observations.

De novo generation of optically active small organic molecules using Monte Carlo tree search combined with recurrent neural network.

Optically active small organic molecules are computationally designed using the ChemTS python library developed by Tsuda and collaborators, which utilizes a combined Monte Carlo tree search (MCTS) and recurrent neural network model. Geometry optimization and excited-state calculations are performed for each generated molecule, following which the excitation energy and dissymmetry factors are computed to evaluate the score function in the MCTS process. Using this procedure, molecules not contained in existing databases are generated. Molecules having either high dissymmetry factors or high transition dipole strengths can be generated depending on the choice of the score function. In a single trajectory with 100,000 trials, mutually similar high-scoring molecules are generated frequently after the initial 15,000-20,000 trials. This indicates that it is better to sample high-scoring molecules from several trajectories having a modest number of trials each than from a single trajectory having a large number of trials.

A minimum quantum chemistry CCSD(T)/CBS dataset of dimeric interaction energies for small organic functional groups.

We have performed a quantum chemistry study on the bonding patterns and interaction energies for 31 dimers of small organic functional groups (dubbed the SOFG-31 dataset), including the alkane-alkene-alkyne (6 + 4 + 4 = 14, AAA) groups, alcohol-aldehyde-ketone (4 + 4 + 3 = 11, AAK) groups, and carboxylic acid-amide (3 + 3 = 6, CAA) groups. The basis set superposition error corrected super-molecule approach using the second order Møller-Plesset perturbation theory (MP2) with the Dunning's aug-cc-pVXZ (X = D, T, Q) basis sets has been employed in the geometry optimization and energy calculations. To calibrate the MP2 calculated interaction energies for these dimeric complexes, we perform single-point calculations with the coupled cluster with single, double, and perturbative triple excitations method at the complete basis set limit [CCSD(T)/CBS] using the well-tested extrapolation methods. In order to gain more physical insights, we also perform a parallel series of energy decomposition calculations based on the symmetry adapted perturbation theory (SAPT). The collection of these CCSD(T)/CBS interaction energy values can serve as a minimum quantum chemistry dataset for testing or training less accurate but more efficient calculation methods. As an application, we further propose a segmental SAPT model based on chemically recognizable segments in a specific functional group. These model interactions can be used to construct coarse-grained force fields for larger molecular systems.

Kinetic investigation of the reaction of ethylperoxy radicals with ethanol

AbstractThe thermodynamic and kinetic investigation for the reaction of ethylperoxy radical (CH3CH2OO•) with ethanol (CH3CH2OH) was studied computationally with variational transition state theory. The geometry optimization calculations showed that both the reactants have two conformers. The energetics and thermodynamic properties were calculated using the G4 composite method. The results showed that the abstraction of H atom from the ─CH2─ site is most feasible, when compared to the other pathways, since it has the lowest energy barrier. The rate coefficient calculations for the title reaction were carried out using the multistructural canonical variational transition state theory with small curvature tunneling corrections in the temperature range of 400‐1500 K. The results showed a similar trend to that of the energetics in which the abstraction of the H atom from the ─CH2─ site has a larger rate coefficient, when compared to other reaction pathways. The reactivity trend towards the H atom abstraction by ethylperoxy radicals varies as ─CH2 > ─CH3 > ─OH. The contributions from the ground‐state conformers of both the reactants were included into the total kinetics using the Boltzmann probability distribution. The obtained temperature‐dependent expression for the studied reaction is ktotal = 1.51 × 10−32 T6.3 exp(−3691/T) cm3 molecule−1 s−1.

Characteristics of multidentate schiff base ligand and its complexes using cyclic voltammetry, fluorescence, antimicrobial behavior and DFT-calculations

The electrochemical behavior of a series of the metal complexes [Fe(III), Ni(II), Ru(III),Pd(II) and Hf(IV)]derived from the Schiff base ligand(E)-5-((phenyl(-pyridin-2-yl) methylene) amino) pyrimidine-2,4(1H, 3H)‑dione(H2L) which was previously prepared from condensation of 5-aminouracil and 2-benzoylpyridine was studied by using cyclic voltammetric technique. The Schiff base ligand H2L and its metal complexes exhibited quasi- reversible oxidation- reduction with three electron transfer and it was suggested that their reactions on the platinum surface electrode are not purely diffusion controlled but also under adsorption control. The redox reactive sites of the H2L and its complexes were located via the geometry optimization and frequency calculations using density functional theory (DFT) at the B3LYP/LanL2DZ level of theory. In addition, the Schiff base ligand and its metal complexes exhibit fluorescent properties. The antimicrobial activity of the Schiff base ligand H2L and its metal complexes was tested against Gram-positive bacteria (Staphylococcus aureus and Bacillus cereus(, Gram-negative bacteria (E. coli and Pseudomonas aeruginosa) and fungal strain (Aspergillus niger) by using agar well-diffusion method. The microbial testes of the ligand (H2L) and its metal complexes exhibited good inhibition efficiency to prevent growth of bacteria.

Optical properties, structural, and DFT studies of Pd(II) complexes with 1‐phenyl‐1H‐tetrazol‐5‐thiol, X‐ray crystal structure of [Pd(κ1‐S‐ptt)2(κ2‐dppe)] complex

Seven tetrazole‐thione complexes, [Pd2(κ2‐ptt)4](1), trans‐[Pd(k1‐S‐ptt)2(PPh3)2] (2), trans‐[Pd(k1‐S‐ptt)2(SPPh3)2] (3), trans‐[Pd(k1‐S‐ptt)2(OPPh3)2] (4), [Pd(k1‐N‐ptt)2(k2‐dppe)] (5a), [Pd(k1‐S‐ptt)2(k2‐dppe)] (5b), [Pd(k1‐S‐ptt)2(k2‐dppeS2)] (6), and [Pd(k1‐S‐ptt)2(k2‐dppeO2)] (7), were prepared from 1‐phenyl‐1H‐tetrazole‐5‐thiol (Hptt), with substituted phosphines. These complexes were investigated by CHNS analysis; infrared (IR), nuclear magnetic resonance (NMR) (1H and 31P), and ultraviolet–visible (UV–Vis) spectroscopy; and single‐crystal X‐ray data for 5b. In Complex 1, the ptt− ligand adopted μ2‐ k‐N, k‐S bridging mode to afford a dimeric complex, whereas in Complexes 2–4, 6, and 7, the ptt− was covalently coordinated via sulfur atom of the thiol group as a solo product. In contrast, in Complex 5, the ptt− ligand was bonded in a monodentate fashion through a deprotonated tetrazole ring nitrogen atom in isomer 5a or via a thiolato sulfur atom in isomer 5b. These linkage isomers were clearly shown in the 31P‐{1H} NMR. To explain the adoption of the ligand binding modes in Complexes 5a and 5b, geometry optimization calculations were carried out on two isomers. Very small differences of all molecular parameters were found between 5a and 5b isomers. This confirms the reason for obtaining two isomers. Also, theoretical studies are made for all compounds, and excellent agreement is obtained with experimental data. The direct band gap (Eg) values are equal to 2.88, 2.85, and 2.45 eV for Complexes 1, 2, and 4, respectively, revealing a semiconductor nature. The inhibition activity of Complexes 1–3, 5, and 8 were evaluated versus the growth of four types of bacteria in vitro. The complexes showed a good activity compared with free ligand and a standard antibiotic.

Synthesis, characterization, investigation of mesomorphic properties and DFT studies of a new 2,5-(dimethoxy)-2-[[(4-(dodecyloxy)phenyl)imino]methyl]benzene): a material liquid crystal for optoelectronics

In this article, synthesis, characterization and mesomorphic properties of a new calamitic liquid crystal, 2,5-(dimethoxy)-2-[[(4-(dodecyloxy)phenyl)imino]methyl]benzene) (DDPIMB) are described. The phase transition temperatures of the DDPIMB mesomorphic compound have been carried out by differential scanning calorimetry and optical polarizing microscopy. Geometry optimization calculations have been made for the two possible isomers as cis and trans of DDPIMB using the DFT/B3LYP/6-311++G(d,p) level of theory. According to the theoretical calculation results, trans isomerism was found more stable than cis isomerism. Therefore, all theoretical calculations were made for the trans-isomer and compared to the observed results. Vibrational assignments of the observed infrared spectra of title compound were carried out based on the calculated potential energy distributions (PEDs). The electronic properties of the DDPIMB were shown on the TD-DFT/B3LYP level. The optical behavior of the liquid crystal DDPIMB was determined through basic optical parameters, nonlinear optics (NLO) properties and dipole moments. Moreover, frontier molecular orbitals and molecular electrostatic potential (MEP) were determined to define the chemical activity of the headline molecule. The obtained results showed that this liquid crystal is a candidate material that can be used in NLO, optics and optoelectronic technology.

Basis Set Effects in Density Functional Theory Calculation of Muoniated Cytosine Nucleobase

The Density Functional Theory method was employed to investigate the electronic structure and muonium hyperfine interaction of muonium trapped near carbon atom labelled as '5' in cytosine nucleobase. Eighteen different basis sets in combination with B3LYP functional were examined in geometry optimization calculations on the muoniated radical. There are significant quantitative differences in the calculated total energy. The employment of basis set that does not include polarization function produces an optimized structure with high total energy. The 6-311++G(d,p) basis set yielded the lowest total energy as compared to other basis sets. The bond order of muonium trapped at C5 atom is in the range of 0.841 to 0.862. The 6-31G basis set produced the muonium Fermi contact coupling constant that is the closest to the experimental value.

Chemical reactivity descriptors as a tool of prediction in the synthesis of sandwich type polyoxometalate organic–inorganic hybrid compounds

In the present study a predictive model aimed at the selection of organic ligands for the successful synthesis of Cobalt sandwich-type polyoxometalate (Co-STPs) organic–inorganic hybrid compounds in aqueous solution, has been introduced. The computations were performed using Gaussian09 and the results have been evaluated by the graphic interface program, GaussView05. Geometry optimization and frequency calculations have been performed at B3LYP level with 6-311G basis set. Dipole moment was recalled from optimization results and reactivity descriptors were calculated via Fukui function using atomic charges and frontier orbitals energies. Firstly the organic molecules with dipole moments more than water are filtered.Then, ligands with less electronegativity, hardness, global electrophilicity and energy bond gap and more softness, global softness and chemical potential found to be promoters for substitution reaction on the cobalt atoms. From the local reactivity descriptors, it is concluded when the fk+, Sk+, ωk+ >fk-, Sk-, ωk- and ωk+ is greater than Sk+, the ligand will undergo substitution reaction.2-Aminobenzimidazole (ABI), 4-nitroaniline (PNA), imidazole and pyridine were evolved in synthesis reaction to test the predicted results for a major product. Applying obtained rules from local Fukui descriptors has predicted ABI and PNA will engage in a substitution reaction, which indeed occurred and resulted in two new thermodynamic controlled and purple colored organic–inorganic hybrid sandwich type polyoxometalates, (PNA)2Na12[Co4(PW9O34)2] and (ABI)2Na12[Co4(PW9O34)2]. These hybrids were characterized by infrared spectroscopy, ICP-MS, TGA-DSC and EDX. Imidazole and pyridine were failed to perform substitution reaction and led to yellow disfavored kinetic controlled products.

A DFT Study of N2O Homogeneous and Heterogeneous Reduction Reaction by the Carbon Monoxide

ABSTRACT The mechanism of N2O homogeneous and heterogeneous reactions with CO were investigated using density functional theory (DFT). The M06-2X method with the 6–311 G(d) basis set were adopted for geometry optimization and energy calculations of each configuration (reactants, intermediates, transition states and products). Thermodynamic and kinetic analyzes were also conducted to study the influence of temperature on the reaction process. Calculation results showed that there are two channels for the homogeneous reaction between N2O and CO. In addition, the heterogeneous reduction reaction of N2O and CO has two possible reaction pathways due to the different adsorption configurations of CO on char surface. From thermodynamic analysis, the enthalpy difference (ΔH) and Gibbs free energy difference (ΔG) of the homogeneous and heterogeneous reactions are both negative, which indicates that the reaction of N2O and CO is an exothermic process and can take place spontaneously. For the both homogeneous and heterogeneous reactions between N2O and CO, the equilibrium constant of the N2O and CO reaction is always higher than 105 at 800 ~ 1800 K, suggesting that the reaction can be carried out completely. From the kinetic analysis, activation energy of the heterogeneous reaction (137.26 kJ/mol) is much lower than that of the homogeneous reactions (224.53 kJ/mol and 215.89 kJ/mol), which indicates that the reduction reaction of N2O with CO is more likely to take place on char surface. The calculation results explain the reaction mechanism of N2O and CO, which can provide a theoretical foundation for N2O emission.

Ab-initio Calculations of the Structural, Electronic and Optical Properties of (Cdse)2 Clusters

The distinctive properties of cadmium selenide (CdSe) semiconductor situated it in a multitudinous number of applications. Although (CdSe)2 cluster has more than one isomer, the previous studies concentrated merely on one isomer. The goal of this study was to determine the various stable geometric structure isomers of (CdSe)2 clusters; also, structural, electronic, and optical properties of the stable isomers are investigated using density functional theory (DFT). First, geometry optimization calculations of the possible geometric isomers were carried out using the BroydenFletcher-Goldfarb-Shanno minimization (BFGS) algorithm. Total ground-state energy calculations showed that all the converged isomers have a high probability of existing in any experiment, relying on the implemented experimental technique. Twenty initial possible geometric structures were investigated, in which eleven isomers were converged. However, all of them are relaxed in the 2D planar geometry. The results showed that eleven possible stable isomers were disclosed, where the final structures of the converged isomers produced six different structures; three of them were not detected before. The rhombus structure was ascertained to be the most stable isomer followed by the trapezoidal structure of (CdSe)2. The isomers’ Cd-Se bond length are 2.50-2.74 A, and the average Cd-Se-Cd, Se-Cd-Se angles were 64.5o-123o and 56.3o-114.2o, respectively. Furthermore, the bond angles show that the selenium atom lone-pairs electrons are responsible for shifting the isomers’ structure from the linearity. The total ground-state energy differences were 0.00-1.82 eV. The calculated highest occupied molecular orbital (HOMO), and the lowest unoccupied molecular orbital (LUMO) gap of the isomers implied that the gap depends on the symmetrical geometry of the isomer. Furthermore, it was evident that the most stable isomers are accompanied with larger gaps. The HOMO-LUMO graphs demonstrated that HOMO orbitals were localized around the selenium atom, while LUMO orbitals were distributed around both cadmium and selenium atoms. The calculated absorption spectrum was unique for each isomer. The absorption edges for the isomers are ranging from 2.53 to 3.73 eV. The results show that the obtained absorption spectra peaks’ values (nm) are smaller compared to CdSe experimental results. (CdSe)2 clusters are very active that they straightforwardly react to produce larger clusters. Finally, the results of this study corroborate with previous computational studies.

ELSI — An open infrastructure for electronic structure solvers

Routine applications of electronic structure theory to molecules and periodic systems need to compute the electron density from given Hamiltonian and, in case of non-orthogonal basis sets, overlap matrices. System sizes can range from few to thousands or, in some examples, millions of atoms. Different discretization schemes (basis sets) and different system geometries (finite non-periodic vs. infinite periodic boundary conditions) yield matrices with different structures. The ELectronic Structure Infrastructure (ELSI) project provides an open-source software interface to facilitate the implementation and optimal use of high-performance solver libraries covering cubic scaling eigensolvers, linear scaling density-matrix-based algorithms, and other reduced scaling methods in between. In this paper, we present recent improvements and developments inside ELSI, mainly covering (1) new solvers connected to the interface, (2) matrix layout and communication adapted for parallel calculations of periodic and/or spin-polarized systems, (3) routines for density matrix extrapolation in geometry optimization and molecular dynamics calculations, and (4) general utilities such as parallel matrix I/O and JSON output. The ELSI interface has been integrated into four electronic structure code projects (DFTB+, DGDFT, FHI-aims, SIESTA), allowing us to rigorously benchmark the performance of the solvers on an equal footing. Based on results of a systematic set of large-scale benchmarks performed with Kohn–Sham density-functional theory and density-functional tight-binding theory, we identify factors that strongly affect the efficiency of the solvers, and propose a decision layer that assists with the solver selection process. Finally, we describe a reverse communication interface encoding matrix-free iterative solver strategies that are amenable, e.g., for use with planewave basis sets. Program summaryProgram title: ELSI InterfaceCPC Library link to program files:http://dx.doi.org/10.17632/473mbbznrs.1Licensing provisions: BSD 3-clauseProgramming language: Fortran 2003, with interface to C/C++External routines/libraries: BLACS, BLAS, BSEPACK (optional), EigenExa (optional), ELPA, FortJSON, LAPACK, libOMM, MPI, MAGMA (optional), MUMPS (optional), NTPoly, ParMETIS (optional), PETSc (optional), PEXSI, PT-SCOTCH (optional), ScaLAPACK, SLEPc (optional), SuperLU_DISTNature of problem: Solving the electronic structure from given Hamiltonian and overlap matrices in electronic structure calculations.Solution method: ELSI provides a unified software interface to facilitate the use of various electronic structure solvers including cubic scaling dense eigensolvers, linear scaling density matrix methods, and other approaches.

Synthesis, spectroscopic properties, crystal structures, DFT studies, and the antibacterial and enzyme inhibitory properties of a complex of Co(II) 3,5-difluorobenzoate with 3-pyridinol

A new complex, [Co(DFB)2(3-Pyr)2(H2O)2] (where DFB = 3,5-difluorobenzoate, 3-Pyr = 3-pyridinol), is synthesized and characterized using different techniques (elemental analysis, Fourier transform infrared spectroscopy, and single-crystal X-ray diffraction). Looking at the crystal structure of the complexes, the cobalt atom is coordinated by two nitrogen atoms from two 3-Pyr ligands, two carboxylate oxygen atoms from two DFB anions, and two oxygen atoms from two water molecules. The complex has distorted octahedral geometry around the cobalt atom center complex and crystallizes in the P21/n space group (monoclinic system). Geometry optimization, frequency analysis, and energy quantum chemical calculations on the complex are performed by Density Functional Theory [B3LYP/6-31G (d,p) basis set] to predict the molecular properties. The novel complex is tested against the metabolic isoenzymes human carbonic anhydrases I and II. The novel complex shows Ki values of 317.26 ± 23.25 µM against hCA I and 255.41 ± 48.05 µM against hCA II; the IC50 values for these isoenzymes are 274.37 and 204.33 µM.

Resonance Raman investigation of dithionite‐reduced cobalamin

AbstractAbsorption (Abs) and resonance Raman (rR) spectroscopy along with density functional theory (DFT) have been applied to investigate the derivatives of vitamin B12 (or cobalamins = Cbls). Cbls are cobalt‐containing corrin complexes, vibrations of which can be probed using rR spectroscopy. The oxidation state of Co ion in Cbls can range between Co3+, Co2+, and Co1+, and axially, cobalt can be coordinated by variety of ligands. Recent spectroscopic study revealed that Co2+Cbl reduced by dithionite (DTH) exhibited a unique property distinct from other Co2+Cbls. Accordingly, in this study, rR spectra of Co2+Cbls reduced by DTH were compared with these reduced by dithiothreitol (DTT). The DTT‐reduced Cbl gave ordinary rR spectrum at pH 3 and 8. On the other hand, the DTH‐reduced Cbl gave different rR spectra at pH 3 and 8 and contained a new rR band at 987 cm−1, which is absent with the DTT‐reduced one. The α and γ Abs bands of DTH‐reduced Cbls were also shifted to shorter wavelengths and exhibited broadening. To understand these rR spectra, geometry optimization and frequency calculations using DFT have been carried out for different structural models of Cbls and compared with experiment. Based on current spectroscopic studies and computation, we deduced that the DTH‐reduced Cbl has SO2‐. radical anion at an axial coordination position of Co2+ and that the ππ* transition of corrin ring is partially mixed with π bond of SO2‐. radical anion, giving rise to the S=O stretching rR band in resonance with the γ Abs band.

Electronic and optical properties of stanane and armchair stanane nanoribbons

In this study, we performed a density functional theory based investigation of the structural, electronic, and optical properties of a stanane, fully hydrogenated stanene SnH, and armchair stanane nanoribbons ASnHNRs. Our full geometry optimization calculations show stanane has 0.84 A buckled height and the buckled structure is preserved in ASnHNRs. The optimized lattice parameter of stanane, Sn–Sn, and Sn–H bond length are 4.58 A, 2.75A, and 1.73 A, respectively. Electronic structure calculations show that stanane is a moderate-band-gap semiconductor with a direct band gap of 1.2 eV and ASnHNRs are wide-band-gap semiconductors. The band gap of ASnHNRs decreases as the ribbons width increases. We investigated the optical properties for two directions of polarization. For perpendicular-polarized light, the imaginary part of dielectric function $$\varepsilon _2(\omega )$$ of stanane peaks between 5 and 10 eV; while for the parallel-polarized light, the peaks are seen in a wide range of energy. According to the results, stanane is a good absorptive matter, especially for visible regions of the electromagnetic spectrum. The presence of anisotropy with respect to the type of light polarization is observed in ASnHNRs also. In these structures, the main peak of $$\varepsilon _2(\omega )$$ is located at 3.4 eV for parallel- and in 6–8 eV for perpendicular-polarized light.

Temperature Dependent Stabilities of the C32 and K@C32, Ca@C32 and Sc@C32 Endohedral Metallofullerene Isomeric Set

Abstract Since their discovery in 1985, Fullerenes have been an intriguing subject due to their structure and varying stabilities and potential use in medical and energy research. In this article, we present the temperature dependent thermodynamic stabilities of the C32, K@C32, Ca@C32, and Sc@C32 isomeric sets as computed at temperatures ranging from 298 K to 6000 K, using Density Functional Theory (B3LYP/6-31G(d)) for geometry optimization and frequency calculations. In all four cases, the D3 isomer (number 6 by Fowler's algorithm) was found to be the most stable throughout the temperature range.

Systematic description of molecular deformations with Cremer-Pople puckering and deformation coordinates utilizing analytic derivatives: Applied to cycloheptane, cyclooctane, and cyclo[18]carbon.

The conformational properties of ring compounds such as cycloalkanes determine to a large extent their stability and reactivity. Therefore, the investigation of conformational processes such as ring inversion and/or ring pseudorotation has attracted a lot of attention over the past decades. An in-depth conformational analysis of ring compounds requires mapping the relevant parts of the conformational energy surface at stationary and also at non-stationary points. However, the latter is not feasible by a description of the ring with Cartesian or internal coordinates. We provide in this work, a solution to this problem by introducing a new coordinate system based on the Cremer-Pople puckering and deformation coordinates. Furthermore, analytic first- and second-order derivatives of puckering and deformation coordinates, i.e., B-matrices and D-tensors, were developed simplifying geometry optimization and frequency calculations. The new coordinate system is applied to map the potential energy surfaces and reaction paths of cycloheptane (C7H14), cyclooctane (C8H16), and cyclo[18]carbon (C18) at the quantum chemical level and to determine for the first time all stationary points of these ring compounds in a systematic way.