Ab Inito Methods Research Articles

Automating the generation of detailed kinetic models for halocarbon combustion with the Reaction Mechanism Generator

Originally developed to predict the chemical kinetics of hydrocarbon combustion via automated generation of detailed reaction mechanisms, Reaction Mechanism Generator (RMG) contains extensive thermokinetic data for C,H,O chemisty, and has more recently been expanded to nitrogen and sulfur. In this work, we present the addition of halogen (fluorine, chlorine, and bromine) chemisty to RMG to enable automated generation of detailed kinetic models for halocarbon combustion. RMG’s existing reaction templates are updated to include halogens, and 11 new reactions families are created specific to halogen chemistry. Notably, kinetics for more than 1000 elementary reactions are calculated via ab inito methods and transition state theory, and these kinetic data are combined with kinetics from literature sources to train rate rule decision tree estimators. Additionally, halogen groups are added to RMG’s statistical mechanics database, enabling model generation with RMG’s pressure dependence module and automated computation of microcanonical rate constants for unimolecular networks. Halogen groups are also incorporated in RMG’s transport database to provide estimated parameters for the Lennard-Jones potential, important for transport-dependent simulations including laminar flame speeds. To demonstrate RMG’s capability for predicting halocarbon combustion, RMG is used to build a flame suppression model for 2-BTP (CH2=CBrCF3) in methane flames. The laminar flame speeds of RMG’s 2-BTP model show good agreement with a published model under a variety of reaction conditions. Automating the generation of detailed kinetic models for halocarbon combustion will facilitate the exploration of previously unexplored reaction pathways, thereby accelerating the development of greener refrigerants and suppressants, as well as advancing the field of automated mechanism generation.

Theoretical investigation of the spectroscopic properties of diatomic systems: ZnTe, ZnTe+, and ZnTe-

The Zinc telluride (ZnTe) system presents appealing optoelectronic properties used in radiology as well as in the detection of terahertz radiation (THz). In this work, we report a theoretical investigation of the ground and excited states of ZnTe and its ions ZnTe+ and ZnTe- using different ab inito methods. The potential energy curves (PEC) are computed using the CASSCF/LANL2DZ and MRCI/LANL2DZ methods. These curves allow inferring the different spectroscopic constants such as the internuclear distance (Re), the harmonic vibration frequency (ωe), the rotation constant (Be) and the dissociation energy (De). Our results indicate that the electronic states of ZnTe and its ions converge to several lower dissociation limits. The existence of unstable and crossings states is due to the presence of rotational and spin–orbit interactions. The results obtained are compared to the existing experimental data and have generally shown a reasonable agreement.

Tuned physical characteristics of PbSe binary compound: a DFT study

Physical features of transition metal (TM) doped lead selenide, Pb1-xCrxSe, Pb1-xCoxSe and Pb1-xNixSe (x=0% and 25%) have been investigated by ab-inito method. The exchange correlation energy is computed by generalized gradient approximation (GGA). A direct band gap (Eg) of 0.35 eV has been observed for PbSe. The analysis of spin-resolved electronic band structure (BS) and density of states (DOS) reveal the half-metallic ferromagnetic (HMF) character of doped compounds. In addition, the calculated magnetic moments (μB) of Pb1-xCrxSe, Pb1-xCoxSe and Pb1-xNixSe compounds are found to arise due to doped transition metals and confirmed by 3D spin-polaized iso-surface density plots. The optical features including optical conductivity (), absorption coefficient, extinction coefficient k, refractivity R, dielectric function and refractive index n() have been calculated to envisage the optical response of given materials. Further, the BoltzTrap code has been implemented to probe the thermoelectric characteristics in term of power factor (PF), Seebeck coefficient (S), thermal and electrical conductivity. The outcomes of calculations divulge that Pb1-xXxSe (X=Cr, Co, Ni) would be suitable candidates for both optoelectronics and thermoelectric applications.

A spectroscopic model for the low-lying electronic states of NO.

The rovibronic structure of A2Σ+, B2Π, and C2Π states of nitric oxide (NO) is studied with the aim of producing comprehensive line lists for its near ultraviolet spectrum. Empirical energy levels for the three electronic states are determined using a combination of the empirical measured active rotation-vibration energy level (MARVEL) procedure and ab initio calculations, and the available experimental data are critically evaluated. Ab initio methods that deal simultaneously with the Rydberg-like A2Σ+ and C2Π and the valence B2Π state are tested. Methods of modeling the sharp avoided crossing between the B2Π and C2Π states are tested. A rovibronic Hamiltonian matrix is constructed using the variational nuclear motion program Duo whose eigenvalues are fitted to the MARVEL. The matrix also includes coupling terms obtained from the refinement of the ab initio potential energy and spin-orbit coupling curves. Calculated and observed energy levels agree well with each other, validating the applicability of our method and providing a useful model for this open shell system.

TaF: a web platform for taxonomic profile-based fungal gene prediction.

The accurate prediction and annotation of gene structures from the genome sequence of an organism enable genome-wide functional analyses to obtain insight into the biological properties of an organism. We recently developed a highly accurate filamentous fungal gene prediction pipeline and web platform called TaF. TaF is a homology-based gene predictor employing large-scale taxonomic profiling to search for close relatives in genome queries. TaF pipeline consists of four processing steps; (1) taxonomic profiling to search for close relatives to query, (2) generation of hints for determining exon-intron boundaries from orthologous protein sequence data of the profiled species, (3) gene prediction by combination of ab inito and evidence-based prediction methods, and (4) homology search for gene models. TaF generates extrinsic evidence that suggests possible exon-intron boundaries based on orthologous protein sequence data, thus reducing false-positive predictions of gene structure based on distantly related orthologs data. In particular, the gene prediction method using taxonomic profiling shows very high accuracy, including high sensitivity and specificity for gene models, suggesting a new approach for homology-based gene prediction from newly sequenced or uncharacterized fungal genomes, with the potential to improve the quality of gene prediction. TaF will be a useful tool for fungal genome-wide analyses, including the identification of targeted genes associated with a trait, transcriptome profiling, comparative genomics, and evolutionary analysis.

First Principles Computational Study of Active and Stable Electrocatalysts for Oxygen Reduxtion and Evolution Reactions

Using first principle density functional theory calculations we show how to search highly active nonprecious catalysts for oxygen reduction reactions in acidic and alkaline media. It is clearly propose that both the activity and stability can be enhanced with novel computational design principles based on ab-inito methods. We also propose that a perovskite oxide with mixed oxidation states in transition metals is a good candidate for oxygen evolution reaction, which is key reaction in water splitting process storing energy in the fuels.

Externally predictive quantitative modeling of supercooled liquid vapor pressure of polychlorinated-naphthalenes through electron-correlation based quantum–mechanical descriptors

For predicting physico-chemical properties related to environmental fate of molecules, quantitative structure–property relationships (QSPRs) are valuable tools in environmental chemistry. For developing a QSPR, molecular descriptors computed through quantum–mechanical methods are generally employed. The accuracy of a quantum–mechanical method, however, rests on the amount of electron-correlation estimated by the method. In this work, single-descriptor QSPRs for supercooled liquid vapor pressure of chloronaphthalenes and polychlorinated-naphthalenes are developed using molecular descriptors based on the electron-correlation contribution of the quantum–mechanical descriptor. The quantum–mechanical descriptors for which the electron-correlation contribution is analyzed include total-energy, mean polarizability, dipole moment, frontier orbital (HOMO/LUMO) energy, and density-functional theory (DFT) based descriptors, namely, absolute electronegativity, chemical hardness, and electrophilicity index. A total of 40 single-descriptor QSPRs were developed using molecular descriptors computed with advanced semi-empirical (SE) methods, namely, RM1, PM7, and ab intio methods, namely, Hartree–Fock and DFT. The developed QSPRs are validated using state-of-the-art external validation procedures employing an external prediction set. From the comparison of external predictivity of the models, it is observed that the single-descriptor QSPRs developed using total energy and correlation energy are found to be far more robust and predictive than those developed using commonly employed descriptors such as HOMO/LUMO energy and dipole moment. The work proposes that if real external predictivity of a QSPR model is desired to be explored, particularly, in terms of intra-molecular interactions, correlation-energy serves as a more appropriate descriptor than the polarizability. However, for developing QSPRs, computationally inexpensive advanced SE methods such as PM7 can be more reliable than the expensive ab inito methods.

SAXS–WAXS studies of the low-resolution structure in solution of xylose/glucose isomerase from Streptomyces rubiginosus

The structure and conformation of molecule of xylose/glucose isomerase from Streptomyces rubiginosus in solution (at pH 6 and 7.6; with and without the substrate) has been studied by small- and wide-angle scattering of synchrotron radiation (SAXS–WAXS). On the basis of the SAXS–WAXS data, the low-resolution structure in solution has been reconstructed using ab inito methods. A comparison of the models of glucose isomerase shows only small differences between the model in solution and the crystal structure.

Synchrotron radiation small angle scattering studies of d(TTAGGG) 4 oligomer in solution

Telomeric DNA sequences play a crucial role in maintaining chromosome stability and integrity. In human chromosomes telomeres are composed of tandem (TTAGGG) n repeats. The structural parameters and low-resolution structure of a synthetic d(TTAGGG) 4 oligomer in solution has been studied in the absence and in the presence of potassium cations, with the use of the small angle scattering of synchrotron radiation. The radii of gyration R G, calculated for d(TTAGGG) 4 oligomer (in 10 mM Tris/HCl pH 7.3) was 1.42 nm, while R G, (in 10 mM Tris/HCl pH 7.3; 0.1 mM KCl) was 1.32 nm. The pair distance distribution function, P( r), yielded a maximum dimension of 4.55and 4.35 nm for solutions in the absence and the presence of potassium cations. On the basis of SAXS data, the low-resolution structure in solution has been reconstructed using ab inito methods.

The Gas-Phase Decomposition of CF3OH with Water: A Radical-Catalyzed Mechanism

CF(3)OH is an atmospheric sink for hydrofluorocarbons (HFCs) and hydrofluoroethers (HFEs). Several new mechanisms, including catalyzation via H(2)O and OH radical, for the decomposition of CF(3)OH into HF and CF(2)O are studied using ab inito methods. The present work demonstrates that the OH radical has a strong catalytic effect on the transition state for the decomposition of CF(3)OH. The barrier is found to be reduced from 45.9 kcal mol(-1) for the unimolecular decomposition to 11.0 kcal mol(-1) for decomposition including H(2)O and OH.

Hydrogen Bonding Interaction of Formic Acid‐, Formaldehyde‐, Formylfluoride‐Nitrosyl Hydride: Theoretical Study on the Geometries, Interaction Energies and Blue‐ or Red‐Shifted Hydrogen Bonds

AbstractThe hydrogen bonding interaction of formic acid‐, formaldehyde‐, formylfluoride‐nitrosyl hydride complexes was investigated by the density functional theory (DFT) and ab inito method in conjunction with 6‐311++G(2d,2p) basis set. The geometries, vibrational frequencies and interaction energies of the complexes were calculated by both standard and CP‐corrected methods respectively. Moreover, G3B3 method was employed to estimate the interaction energies. There are C–H···O, N–H···O, N–H···F blue‐shifted H‐bonds and red‐shifted O–H···O H‐bond in the complexes. Electron density redistribution and rehybridization contribute to the N–H and C–H blue shifts. All geometric reorganizations contribute to the N–H blue shifts and partial geometric reorganizations contribute to the C–H blue shifts. The geometric reorganizations of the complex C except (H(5)‐O(4)‐C(1) contribute to the O–H red shift. For the N–H blue shifts, the effect of r(N–O) variation on the N–H blue shifts is larger than that of (H‐N‐O variation. Rehybridization plays a dominant role in the degree of N–H blue shifts, whereas the electron density redistribution contributes more to the degree of C–H blue shifts than the other effects do.

Elastic and inelastic processes inH++C2H6collisions below the10−keVregime

Charge-transfer processes in collisions of ${\mathrm{H}}^{+}$ ions with ${\mathrm{C}}_{2}{\mathrm{H}}_{6}$ molecules are investigated theoretically below $10\text{\ensuremath{-}}\mathrm{keV}$ collision energies within a molecular representation. Converged total as well as differential cross sections are obtained in this energy range within a discrete basis of electronic states computed by ab inito methods. The present collision system suggests that the combination of the Demkov-type and Landau-Zener--type mechanisms primarily governs the scattering dynamics for the flux exit from the initial channel. The present charge-transfer cross sections determined are found to agree very well with all available experimental data below a few keV, but begin to deviate above $3\phantom{\rule{0.3em}{0ex}}\mathrm{keV}$, in which the present results slowly decrease, while measurements stay nearly constant. From the study of the electronic state calculation, we provide some information on fragmented species, which should help shed some light on the fragmentation mechanism and process of ${\mathrm{C}}_{2}{\mathrm{H}}_{6}^{+}$ ions produced after charge transfer. In addition, the vibrational effect of the initial target to charge transfer is examined.

Conformations and energetics of sulfur and selenium diimides.

The geometries and energetics of different conformations of sulfur and selenium diimides E(NR)(2) (E = S, Se; R = H, Me, (t)Bu, C(6)H(3)Me(2)-2,6, SiMe(3)) have been studied by using various ab initio and DFT molecular orbital techniques. The syn,syn conformation is found to be most stable for parent E(NH)(2), but in general, the preferred molecular conformation for substituted chalcogen diimides is syn,anti. In the case of E(NH)(2) the present calculations further confirm that syn,syn and syn,anti conformations lie energetically close to each other. From the three different theoretical methods used, B3PW91/6-31G proved to be the most suitable method for predicting the geometries of chalcogen diimides. The optimized geometrical parameters are in a good agreement with all available experimental data. While qualitative energy ordering of the different conformations is independent of the level of theory, the quantitative energy differences are dependent on the method used. The performance and reliability of higher level ab initio calculations and DFT methods using large basis sets were tested and compared with experimental information where available. All of the higher level ab inito methods give very similar results, but the use of large basis sets with the B3PW91 method does not increase the reliability of the results. The combination of CCSD(T)/cc-pVDZ with the B3PW91/6-31G-optimized geometries is found to be the method of choice to study energetic properties of chalcogen diimides.

Ab initio calculation of the torsional potential for 2-alkenylanthracene in the ground and excited states

Torsional potentials between the anthracene ring and alkene planes for two 2-alkenylanthracene derivatives both in the ground- and excited-states were calculated using ab inito method as a function of dihedral angle. Molecular geometries were optimized at the restricted Hartree–Fock level in the ground-state, whereas in the excited-state at the level of configuration interaction with single excitation. In the ground-state it is s- trans conformation that is more stable and more planar. While in the excited-state both are planar and the potential shape is more like symmetrical for 2-vinylanthracence, although somewhat distorted for 2-(2 ′ propenyl) anthracene. Stabilization energies, barrier energies, and barrier top frequencies of both ground- and excited-states were determind

A theoretical study of the low-lying electronic states of SC 3

A theoretical study of the excited electronic states of the SC 3 system has been carried out by means of density functional (B3LYP) and ab inito methods (QCI, MRCI, RHF-CC) in combination with relatively large basis sets. The structures of several singlet and triplet species are reported, together with their vibrational frequencies and infrared intensities. The electronic structures are analyzed by means of the natural bond orbital (NBO) method. The vertical electronic excitation energies and oscillator strengths of the ground state SCCC ( 1Σ +) have also been computed. The lowest-energy allowed transitions are X 1Σ + → C 1Π and X 1Σ + → D 1Σ + , and should have comparable intensities.

Ab Initio Study of Vibrational Anharmonic Coupling Effects in Oligo(para-phenylenes)

ABSTRACTIn this study we present a theoretical approach to simulate vibrational anharmonic coupling effects seen in the Raman spectra of oligo(para-phenylenes). Quantum chemical ab inito methods are applied to determine anharmonic force constants and energy corrections on the harmonic vibrational frequencies of the isolated molecules. Semiempirical methods are applied to compute Raman intensities of fundamentals and combination bands. This methodology is then used to characterize a previously unassigned Fermi resonance around 1600 cm-1. The evolution of this quantum mechanical resonance with oligomer length and planarity is compared to experimental data.

Oxygen absorption below and near the Herzberg I continuum. Ab initio calculation of the transitions probability from metastable states.

A number of unknown transitions below the Herzberg I band, A 3Σ u +← X 3Σ g −, have been studied by ab inito methods in the range 190–300 nm ( B 3Σ u −← b 1Σ g +, B 3Σ u −← a 1Δ g , 1 3Π u ← b 1Σ g + and 1 3Π u ← a 1Δ g ) and also in the visible ( B 3Σ u −← A 3Σ u +, 1 3Π g ← A 3Σ u + and 1 3Π g ← A′ 3Δ u ) and in the IR regions ( A 3Σ u +← c 1Σ u −). The singlet-triplet and singlet-singlet transitions from the metastable states of molecular oxygen were calculated by quadratic and linear response multiconfiguration self-consisted field (MCSCF) method, respectively. The larger active space and basis sets are used in comparison with previous calculations. A large value of the electric dipole B 3Σ u,0 −← b 1Σ g + transition moment (about 0.01 au) is confirmed. Absorbance in the range 192–231 nm could be determined by this B← b transition, since its cross-section exceeds the relatively intensive 1 1,3Π u ← b 1Σ g + continuous absorptions, which start to grow at ∼200 nm. At longer wavelengths the 1 3Π u ← b 1Σ g + continuum is about 20 times weaker than the B− b transition, but it is still more intensive than the A 3Σ u,1 +← b 1Σ g + continuum in the range 280–360 nm and than the A′ 3Δ u,3 ← a 1Δ g absorption band, 210–300 nm. Absorption from the a 1Δ g state is practically negligible. The magnetic dipole and quadrupole transition moments for the B 3Σ u −← A 3Σ u + and A 3Σ u,1 +← c 1Σ u − transitions have been recalculated with new wave functions. The B− A transition intensity is negligible. The A− c infra-red transition (2340 cm −1) has the same magnetic nature like the b− X transition and could be observed, in principle, ( f=1.5×10 −9). The allowed triplet-triplet transitions 1 3Π g ← A 3Σ u + and 1 3Π g ← A′ 3Δ u are shown to be important.

Structural and Conformational Dependence of Optical Rotation Angles

The ability to compute and to interpret optical rotation angles of chiral molecules is of great value in assigning relative and absolute stereochemistry. The molar rotations for an indoline and an azetidine, as well as for menthol and menthone, were calculated using ab inito methods and compared to the experimental values. In one case the calculated rotation angle allowed the assignment of the absolute configuration of a heterocycle of unknown stereochemistry. The critical importance of Boltzmann averaging of conformers for reliable prediction of the optical rotation angle was established. Comparisons between static-field and time-dependent methods were made pointing to the limits and validity of the methods as electronic resonance is approached. A protocol analogous to population analysis was used to analyze atomic contributions to the rotation angle in specific conformers. The combination of atomic contribution maps and conformational analysis may provide an indirect tool to assist in three-dimensional structure determination.

GEOMETRICAL OPTIMIZATIONS, NMR ANALYSES, AND NOVEL CRYSTAL STRUCTURES OF 3-OXA-7-BENZYL-7-AZABICYCLO[3.3.1]-NONAN-9-ONE AND 3-THIA-7-BENZYL-7-AZABICYCLO[3.3.1]-NONAN-9-ONE; STRUCTURAL ANALYSIS OF THE CORRESPONDING 3,7-DIHETERABICYCLO[3.3.l]NONANE HYDROPERCHLORATES

An investigation has been made of the structures of the title compounds via theoretical calculations, high resolution NMR analysis, and X-ray diffraction analysis. Conformational analyses of these compounds in the gas phase were performed using ab inito methods with GAUSSIAN 94. Single point calculations at the MP4/6-31G level for 3-oxa-7-azabicyclo[3.3.1]nonan-9-one revealed an energy difference of only ΔE = 1.497 kcal/mole between the chair-chair (CC) and boat-chair (BC) conformers. Full geometry optimization of the oxygen-containing ketone at the Hartree-Fock (HF) level using a 6-31G basis set indicated only a negligible variation in interatomic distances in the equilibrium geometry when the phenyl group was included in the calculation versus when the phenyl group was replaced by hydrogen. Full geometry optimization for the sulfur-containing ketone (phenyl replaced by a hydrogen) at the HF level using the 6-31G basis set again demonstrated that the BC form was slightly more stable than the CC form, identical to that found with the oxygen counterpart. Full geometry optimization of the two hydroperchlorates (phenyl replaced by hydrogen) resulted in the CC form being suggested as the more stable with H-bonding between the hydrogen on nitrogen and the respective heteroatom, a situation which likely enhances stability. Proton NMR analyses of both compounds using NOESY techniques strongly supported a predominance of the BC form in solution for the oxygen-containing ketone. Severe signal overlap in the sulfur ketone (even at 600 MHz) prevented in depth analysis of the structure. Using NOESY, DQCOSY, and HMBC techniques, NMR analyses of the corresponding hydroperchlorates implied CC forms for each in solution. The X-ray diffraction analysis of the oxygen-containing ketone revealed a CC in the solid state.

The Generalized Parameterization Procedure for Semiempirical MO Method and Calculation of ionization Potentials for the Fourth‐Period Element Molecules

AbstractThis study presents a set of the generalized parameters from a unique resource for the elements which are from the first‐period to the fourth‐period (H to Xe). In addition, these series of parameters are used to examine forty‐five compounds consisting of the fourth‐period elements and the second‐period transition metal elements. Herein, the major calculation theory applied is the s‐p‐d INDO MO method.To verify the reliability of the molecular calculations, similar calculations of the STO‐3G and STO‐3G* ab inito methods, along with the semiempirical PM3 and AM1 methods are also compared. Results in this study demonstrate that the s‐p‐d INDO MO computed with the generalized parameter is the best available method.