Efficient Basis Sets for Core-Excited States Motivated by Slater’s Rules

X-ray photoemission spectroscopy is a commonly applied characterization technique that probes the local chemistry of atoms in molecules and materials via the photoexcitation of electrons from atomic core orbitals. These...

Density Functional Theory (DFT) Investigation of The Oxidative Degradation of NaAsO2 Via Hydroxyl Radical

Arsenic is an environmentally ubiquitous health hazard due to its toxicity combined with its natural abundance and heavy industrial applications. Due to its role in cardiovascular disease, neurotoxicity, and various cancers, it is important to understand environmental fate of arsenic-containing compounds to take steps towards remediation. Sodium arsenite (NaAsO2) is one such compound that has been used worldwide as an herbicide, rodenticide, and insecticide. It is also toxic by ingestion, inhalation, and skin absorption. In aqueous environments arsenite (As(III))-containing compounds can be oxidized to the less-toxic arsenate (As(V)) form. We have investigated the oxidation of sodium arsenite in water solution at the density functional theory level using the Minnesota 06 hybrid (M06-2X) functional and Pople basis sets (6-31G(d,p) and 6-311G(d,p)) with polarizable continuum model (PCM) solvation approach. Our computational results indicate that the oxidation mechanism of NaAsO2 by hydroxyl radical proceeds via sequential addition reactions where sodium arsenite (III) converts to sodium arsenate (V) via an arsenic (IV) intermediate.

Oxane dendrimers of tetravalent elements as models for their dioxide polymorphs

Oxides of tetravalent elements are well known to have a lot of crystalline modifications. For example, most of silica polymorphs are characterized by tetrahedral coordination environment of silicon atoms. On the contrary, crystals of stishovite and of some silicate minerals have their silicon atoms in octahedral coordination spheres. It has been found experimentally that the phase transitions between silica polymorphs accompanied by a rearrangement of silica-oxygen tetrahedrons into octahedra require an energy income (preference energy) of 54 kJ/mol. When increasing the atomic mass of the oxide forming element, the former decreases extremely and for tin dioxide is equal to -59 kJ/mol. These values can be reproduced in a theoretical way, within the frameworks of modern quantum chemical methods and periodic models. High disperse silica nanoparticles (as well as those for other oxides) have only the nearest order of atomic stationing, so that theoretical approaches developed for crystals cannot be applied to small particles. These particles can be transformed into stishovite form under hydrothermal conditions. Such a process can be simulated within cluster approximation by use of molecular models. This work is devoted to quantum chemical simulation of formation of the fragments with hexa-coordinated atoms of silicon and of its analogs in the structure of oxane dendrimers. A row of high symmetry models was examined containing two, three, five, and seventeen atoms of silicon and of germanium, titanium and tin, terminated with hydroxyl groups. These structures can be rearranged into another ones including oxide forming atoms with elevated (equal to 5 or 6) coordination number, so mimicking the rutile-like structure. Such models let it possible to fulfill the procedure of transformation without rupturing siloxane bonds, so remaining within a deformation approach. Another advantage is the exclusion of the basis set superposition error due to use of molecular models of the same total formula for all the coordination states. All calculations were carried out by Hartree-Fock and density functional theory methods with the all-electron (3-21G*) and valent (SBKJC) basis sets by means of the GAMESS program. Models of various size have been examined, in particular, disiloxane (HO)3Si-O-Si(OH)3 witch can be transformed into a self-coordinated form where one of silicon atoms becomes a five-coordinated; trisiloxane (HO)3Si-O-Si(OH)2-O-Si(OH)3 can be rearranged into symmetric isomer with one hexa-coordinated silicon atom. Pentasiloxane with neo-structure of [(HO)3Si-O]4Si forms three coordination structures, the most stable of them mimicking the stishovite crystal; it contains one 6-coordinated and two 5-coordinated silicon atoms. Siloxane containing 17 silicon atoms has a super-neo-structure of {[(HO)3Si-O]3Si-O}4Si; it includes seven six-coordinated and four five-coordinated silicon atoms. Relative models for silicon analogs have been also examined. When analyzing a dependence of the energy differences between open and coordinated oxane structures on the number of atoms of the oxide forming element in the cluster, one can jump to the conclusion that the specific value of this characteristic monotonously decreases with the increase in the number of atoms of the molecular model, so becoming close to the experimental data.

31P Transversal Relaxation Times and Metabolite Concentrations in the Human Brain at 9.4T

A method to estimate phosphorus (31P) transversal relaxation times (T2) of coupled spin systems is demonstrated. Additionally, intracellular and extracellular pH (pHext, pHint) and relaxation corrected metabolite concentrations are reported. Echo time (TE) series of 31P metabolite spectra were acquired using STEAM localization. Spectra were fitted using LCModel with accurately modeled Vespa basis sets accounting for J−evolution of the coupled spin systems. T2s were estimated by fitting a single exponential two−parameter model across the TE series. Fitted inorganic phosphate frequencies were used to calculate pH, and relaxation times were used to determine the brain metabolite concentrations. The method was demonstrated in the healthy human brain at a field strength of 9.4T. T2 relaxation times of ATP and NAD are the shortest between 8 ms and 20 ms, followed by T2s of inorganic phosphate between 25 ms and 50 ms, and PCr with a T2 of 100 ms. Phosphomonoesters and −diesters have the longest T2s of about 130 ms. Measured T2s are comparable to literature values and fit in a decreasing trend with increasing field strengths. Calculated pHs and metabolite concentrations are also comparable to literature values

Comprehensive Basis-Set Testing of Extended Symmetry-Adapted Perturbation Theory and Assessment of Mixed-Basis Combinations to Reduce Cost

Hybrid or "extended" symmetry-adapted perturbation theory (XSAPT) replaces traditional SAPT's treatment of dispersion with better-performing alternatives, while at the same time extending two-body (dimer) SAPT to a many-body treatment of polarization using a self-consistent charge-embedding procedure. The present work presents a systematic study of how XSAPT interaction energies and energy components converge with respect to the choice of Gaussian basis set. Although errors can be reduced in a systematic way using correlation-consistent basis sets, similar performance at lower cost is obtained using Karlsruhe basis sets, and we introduce new versions with limited augmentation (diffuse functions) that are even more efficient. Pople-style basis sets, which are even more efficient, often afford good results if a large number of polarization functions are included. The dispersion models used in XSAPT afford much faster basis-set convergence as compared to the perturbative description of dispersion in conventional SAPT, meaning that "compromise" basis sets (such as jun-cc-pVDZ) are no longer required and benchmark-quality results can be obtained using basis sets of triple-zeta quality. The use of diffuse functions proves to be essential, especially for the description of hydrogen bonds. The "delta(Hartree-Fock)" correction that accounts for high-order induction can be performed in double-zeta basis sets without significant loss of accuracy, leading to a mixed-basis approach that offers 4x speedup over the existing (cubic-scaling) XSAPT approach.

NH Stretching Frequencies of Intramolecularly Hydrogen-Bonded Systems: An Experimental and Theoretical Study

The vibrational NH stretching transitions in secondary amines with intramolecular NH···O hydrogen bonds were investigated by experimental and theoretical methods, considering a large number of compounds and covering a wide range of stretching wavenumbers. The assignment of the NH stretching transitions in the experimental IR spectra was, in several instances, supported by measurement of the corresponding ND wavenumbers and by correlation with the observed NH proton chemical shifts. The observed wavenumbers were correlated with theoretical wavenumbers predicted with B3LYP density functional theory, using the basis sets 6-311++G(d,p) and 6-31G(d) and considering the harmonic as well as the anharmonic VPT2 approximation. Excellent correlations were established between observed wavenumbers and calculated harmonic values. However, the correlations were non-linear, in contrast to the results of previous investigations of the corresponding OH···O systems. The anharmonic VPT2 wavenumbers were found to be linearly related to the corresponding harmonic values. The results provide correlation equations for the prediction of NH stretching bands on the basis of standard B3LYP/6-311++G(d,p) and B3LYP/6-31G(d) harmonic analyses, with standard deviations close to 38 cm−1. This is significant because the full anharmonic VPT2 analysis tends to be impractical for large molecules, requiring orders of magnitude more computing time than the harmonic analysis.

Benchmarking Density Functionals, Basis Sets, and Solvent Models in Predicting Thermodynamic Hydricities of Organic Hydrides

Many renewable energy technologies, such as hydrogen gas synthesis and carbon dioxide reduction, rely on chemical reactions involving hydride anions. When selecting molecules to be used in such applications, an important quantity to consider is the thermodynamic hydricity, which is the free energy required for a species to donate a hydride anion. Theoretical calculations of thermodynamic hydricity depend on several parameters, mainly the density functional, basis set, and solvent model. In order to assess the effects of the above three parameters, we carry out hydricity calculations for a set of molecules with known experimental hydricity values, generate linear �fits, and compare the R-squared, root-mean-squared error, and Akaike Information Criterion across different combinations of density functionals, basis sets, and solvent models. Based on these results we are able to quantify the accuracy of theoretical predictions of hydricity and recommend the parameters with the best compromise between accuracy and computational cost.

Theoretical Study of Solvent Effects on the Electronic and Thermodynamic Properties of Tetrathiafulvalene (TTF) Molecule Based on DFT

Tetrathiafulvalene () is an organosulfur compound used in the production of molecular devices such as switches, sensors, nonlinear optical devices and rectifiers. In this work, a theoretical study on the effects of solvent on TTF molecule was investigated and reported based on Density Functional Theory (DFT) as implemented in Gaussian 03 package using B3LYP/6-31++G(d,p) basis set. Different solvents were introduced as a bridge to investigate their effects on the electronic structure. The HUMO, LUMO, energy gap, global chemical index, thermodynamic properties, NLO and DOS analysis of the TTF molecule in order to determine the reactivity and stability of the molecule were obtained. The results obtained showed that the solvents have effects on the electronic and non-linear-optical properties of the molecule. The optimized bond length revealed that the molecule has strong bond in gas phase with smallest bond length of about 1.0834Å than in the rest of the solvents. It was observed that the molecule is more stable in acetonitrile with HOMO-LUMO gap and chemical hardness of 3.6373eV and 1.8187eV respectively. This indicates that the energy gap and chemical hardness of TTF molecule increases with the increase in polarity and dielectric constant of the solvents. The computed results agreed with the results in the literature. The thermodynamics and NLO properties calculation also indicated that TTF molecule has highest value of specific heat capacity (Cv), total dipole moment () and first order hyperpolarizability () in acetonitrile, while acetone has the highest value of entropy and toluene has a slightly higher value of zero point vibrational energy (ZPVE) than the rest of the solvents. The results show that careful selection of the solvents and basis sets can tune the frontier molecular orbital energy gap of the molecule and can be used for molecular device applications.

Evaluating Fast Methods for Static Polarizabilities on Extended Conjugated Oligomers

Given the importance of accurate polarizability calculations to many chemical applications, coupled with the need for efficiency when calculating the properties of sets of molecules or large oligomers, we present a benchmark study examining possible calculation methods for polarizable materials. We first investigate the accuracy of highly-efficient semi-empirical tight-binding method GFN2-xTB, and the popular D4 dispersion model, comparing its predicted additive polarizabilities to ωB97X-D results for a subset of PubChemQC and a compiled benchmark set of molecules spanning polarizabilities from approximately 3-600 Å^3, with a few compounds in the range of approximately 1200-1400 Å^3. Although we find GFN2 to have large errors with polarizability calculations, on large oligomers it would appear a quadratic correction factor can remedy this. We also compare the accuracy of DFT polarizability calculations run using basis sets of varying size and level of augmentation, determining that a non-augmented basis set may be used for highly polarizable species in conjunction with a linear correction factor to achieve accuracy extremely close to that of aug-cc-pVTZ.

Spectroscopic constants and anharmonic force field of dithioformic acid and its isomers: a theoretical study

The potential astronomical interest dithioformic acid (trans-HC(=S)SH) exists five isomers and has received considerable attention of astronomical observation in recent years. The different positions of H atoms of five isomers lead to diverse point groups, dipole moments, and spectroscopic constants. The anharmonic force field and spectroscopic constants of them are calculated using CCSD(T) and B3LYP employing correlation consistent basis sets. Molecular structures, dipole moments, rotational constants, and fundamental frequencies of trans-HC(=S)SH are compared with the available experimental data. The B3LYP/Gen=5 and CCSD(T)/Gen=Q results can reproduce them well. Molecular structures, dipole moments, relative energies, spectroscopic constants of cis-HC(=S)SH and dithiohydroxy carbene (DTHC) are also calculated. The new data obtained in this study are expected to guide the future high resolution experimental work and to assist astronomical search for CH2S2.