6-31G Level Of Theory Research Articles

DFT Calculations, Pro-Apoptotic Effects, and Anti-Infective Investigations of Alkaloids Isolated from the Stem Bark Extract of Enantia chlorantha

Fractionation of the stem bark of Enantia chlorantha Oliv yields three alkaloids, palmatine (1), jatrorrhizine (2), columbamine (3), and β-Sitosterol (4). In this investigation, density functional theory (DFT) calculations were carried out to evaluate the electronic structure and properties of 1–4 by DFT-B3LYP/6-31G level of theory using Gaussian 09 software. The highest occupied molecular orbital (HOMO), lowest unoccupied molecular orbital (LUMO), HOMO-LUMO energy difference (band gap), hardness (η), softness (S), dipole moment (μ), electronegativity (χ), hydrophobicity (logP), topological surface area (TPSA), and energy gap (Eg) were calculated. The in vitro cytotoxicity of the compounds was investigated against MCF-7 and HCT116 cancer cell lines using Wi-38 cells as a control. The compounds inhibited the proliferation of the MCF-7 and HCT116 cell lines and induced apoptosis via upregulation of caspase-3, Bax, PARP cleavage, and downregulation of Bcl-2. DFT analyses revealed that compounds 1 and 3 have smaller energy gaps, 0.072 and 0.071eV, respectively, with the highest dipole moments; hence, these compounds are more chemically reactive and exhibit better modulation of caspase-3 enzyme and inhibitory activities of the MCF-3 and HCT116 cell lines. The antimicrobial and antiparasitic evaluation of 1–4 showed moderate efficacy against the bacterial strains and moderate antiparasitic activity against Cichlidogyrus tilapia.

Theoretical and kinetic study of the H-atom abstraction reactions by Ḣ atom from alkyl cyclohexanes.

Reaction kinetics of hydrogen atom abstraction from six alkyl cyclohexanes, methyl cyclohexane (MCH), ethyl cyclohexane (ECH), n-propyl cyclohexane (nPCH), iso-propyl cyclohexane (iPCH), sec-butyl cyclohexane (sBCH) and iso-butyl cyclohexane (iBCH), by the Ḣ atom are systematically studied in this work. The M06-2X method combined with the 6-311++G(d,p) basis set is used to perform geometry optimization, frequency analysis and zero-point energy calculations for all species. The intrinsic reaction coordinate (IRC) calculations are performed to confirm the transition states connecting the reactants and products correctly. One-dimensional hindered rotors are used to treat the low frequency torsional models with potentials scanned at the M06-2X/6-31G level of theory. Electronic single-point energy calculations for all reactants, transition states, and products are performed at the QCISD(T)/CBS level of theory. High-pressure limiting rate constants of 39 reaction channels are obtained using conventional transition state theory with asymmetric Eckart tunneling corrections in the temperature range 298.15-2000 K. Reaction rate rules for H-atom abstraction by the Ḣ atom from alkyl cyclohexanes on primary, secondary and tertiary carbon sites on both the side chain and ring are provided. The obtained rate constants are given by the Arrhenius expression in the temperature range 500-2000 K, which can be used for the combustion kinetics model development for alkyl cyclohexanes.

Theoretical investigation on isomerization and decomposition reactions of pentanol radicals-part II: linear pentanol isomers.

High-level ab initio calculations are conducted for studying the kinetics of three linear pentanol radicals generated through H-atom abstraction reactions. The species involved are optimized using the M06-2X/6-311++G(d,p) level of theory, while a relaxed scan at the M06-2X/6-31g level of theory with 10° increments is used for the hindrance potential for low-frequency torsional modes. Single-point energies for all stationary points are obtained through the QCISD(T) and MP2 methods in combination with cc-pVDZ, cc-pVTZ, and cc-pVQZ basis sets, which can be extrapolated to the complete basis set (CBS) limit. The rate constants and branching ratios for isomerization and decomposition reactions are computed over a temperature range of 250-2000 K and a pressure range of 0.01-100 atm. Isomerization reactions are dominant at low temperatures, while decomposition reactions are more dominant at high temperatures. The branching ratio of the isomerization reaction exhibits a slight decrease with increasing pressure, while the trend for decomposition reactions depends on the type of the breaking bond. Based on the calculations for five branched pentanol radicals in part I, kinetics of linear and branched pentanol radicals are compared in this work and the results reveal that, for the same kind of β-scission reaction at similar positions of linear and branched pentanol radicals, the rate constants of branched ones are faster than those of linear ones at low temperatures. The hydroxyl group adjacent to the breaking bond can increase the β-scission reaction rate constants, while the effect can be ignored when the hydroxyl group is not adjacent to the breaking bond. Moreover, compared to when the hydroxyl group is located in the middle of the carbon chain, its positioning at the chain's end yields a more noticeable impact on the products and rate constants of C-O bond and O-H bond β-scission reactions. Besides, when incorporating calculated rate constants into the CRECK model, the updated mechanism shows a better performance for ignition delay times of 1-pentanol in the NTC range but exhibits lower reactivity at higher temperatures. The simulation of speciation profiles also shows better agreement with the experimental data obtained using a flow reactor.

Kinetic Properties Study of H Atom Abstraction by CH3Ȯ2 Radicals from Fuel Molecules with Different Functional Groups.

The detailed kinetic properties of hydrogen atom abstraction by methylperoxy (CH3Ȯ2) radicals from alkanes, alkenes, dienes, alkynes, ethers, and ketones are systematically studied in this work. Geometry optimization, frequency analysis, and zero-point energy corrections were performed for all species at the M06-2X/6-311++G(d,p) level of theory. The intrinsic reaction coordinate calculation was consistently performed to ensure that the transition state connects the correct reactants and products, and one-dimensional hindered rotor scanning results were performed at the M06-2X/6-31G level of theory. The single-point energies of all reactants, transition states, and products were obtained at the QCISD(T)/CBS level of theory. High-pressure-limit rate constants of 61 reaction channels were calculated using conventional transition state theory with asymmetric Eckart tunneling corrections over the temperature range of 298.15-2000 K. Reaction rate rules for H atom abstraction by CH3Ȯ2 radicals from fuel molecules with different functional groups are constructed, which can be used in the development of combustion models of these fuels and fuel types. In addition, the influence of the functional groups on the internal rotation of the hindered rotor is also discussed.

Theoretical investigation on isomerization and decomposition reactions of pentanol radicals-part I: branched pentanol isomers.

Theoretical investigations on the kinetics of decomposition and isomerization reactions for five types of branched pentanol radicals are carried out in this work. The M06-2X/6-311++G(d,p) level of theory was used to optimize the geometries of all reactants, transition states, and products, while the hindrance potentials for the lower frequency modes in all of the species were obtained through a relaxed scan with an increment of 10° at the M06-2X/6-31G level of theory. Single-point energies of all species were determined at the QCISD(T)/cc-pVDZ, TZ level of theories with basis set corrections from MP2/cc-pVDZ, TZ, QZ methods. The RRKM/master equation was solved to calculate the pressure- and temperature-dependent rate coefficients for all channels in the pressure range of 0.01-100 atm over 250-2000 K. Pressure and temperature-dependent branching fractions of key species produced from pentanol radicals show that most of the pentanol radical isomers tend to isomerize to alkoxy radicals via a six-membered-ring or five-membered-ring transition state at low temperatures, producing ketones or aldehydes. At higher temperatures, the β-scission reactions are the main reaction channels for the consumption of pentanol radicals. A weak pressure dependence has been found for all isomerization reactions, and it becomes more and more important as pressure increases. The pressure dependence trends are different for the β-scission reactions of different branched pentanol radicals. In part I, the results for branched pentanol radical isomers are presented in detail, while in part II the results for linear pentanol radical isomers will be discussed.

Triphenylamine based donor-acceptor-donor type small molecules for organic solar cells

To ascertain geometry optimization, chemical reactivity, electronic absorption spectra, charge transport rate, transition density matrix (TDM), and density of states (DOS) properties, four novel Donor-Acceptor-Donor (D-A-D) type small molecules have been investigated through DFT and TD-SCF at selected hybrid CAM-B3LYP functional. Amongst all molecules,F2shows maximum λ value with chlorobenzene solvent (λmax = 526 nm) while F3 possess the lowest energy band gap (4.35 eV) and surpassed in exhibiting the best photovoltaic properties and conversion efficiency due to presence of strong electron-withdrawing acceptor moiety. Moreover, the results imply that the newly designed moieties (F1-F4) proved defter in executing low reorganization energies, low binding energies, higher dipole moment, and comparable frontier molecular orbitals regarding modelR. In conclusion designed molecule parameters were calculated using functional CAM-B3LYP/6-31G level of theory as a useful tactic in the quest for achieving good photovoltaic applications.

Transportation of single wall carbon nanotube (SWCNT) through the cell membrane

Carbon nanotubes (CNTs) are very common in medical research and are being highly studied in the fields of biosensing methods for disease treatment and efficient drug delivery and health monitoring. The transportation of open-end Single wall carbon nanotube (SWCNT) through the cell membrane widely investigated because of many advantages. In our recent study, extensive quantum mechanical (QM) calculation of electronic structure of open-end of SWCNT and transportation of single wall carbon nanotube through the cell membrane have been administered in vacuum media using GAUSSIAN 98 software. Our results manifested that the interaction of open-end of SWCNT has minimum value of energy interaction and then most structural stability in vacuum. We assayed effects of vacuum on transportation of SWCNT through the cell membrane with using B1LYP and Hartree Fock (HF) methods at STO-3G, 3-21G, 6-31G levels of theory. Also, we demonstrated the total atomic charges of dense region calculated STO-3G, 3-21G and 6-31G basis sets in vacuum with HF method. The calculated values showed negative charge at this site. The O and S atoms at interaction site produced negative charge because they have high electron affinity. Key words: Single wall carbon nanotube (SWCNT), quantum mechanical (QM), STO-3G, 3-21G and 6-31G basis.

Polaron binding energy in polymers: poly[methyl(phenyl)silylene

This paper presents a theoretical approach to the evaluation of polaron binding energy in polymers. Quantum chemical calculations were performed on a model polymer, poly[methyl(phenyl)silylene], employing the B3LYP and CAM-B3LYP method. The polaron binding energy consists of two terms: the molecular deformation energy and electron-phonon term. Its value was found to be about 0.23 eV at the CAM-B3LYP/6-31G level of theory.

Ab initio investigation of doping-enhanced electronic and vibrational second hyperpolarizability of polyacetylene chains

The effect of charging on the longitudinal second hyperpolarizability of polyacetylene (PA) chains containing up to nearly 70 carbon atoms has been investigated ab initio by characterizing chains with and without an explicit alkali atom (Li, Na, K) as dopant. Whereas charging dramatically enhances the static electronic and vibrational hyperpolarizabilities, γLe(0) and γLv, of an isolated chain at intermediate chain lengths, the presence of an alkali atom counterion substantially reduces this effect. As the size of the alkali atom increases, most properties, including the hyperpolarizabilities, approach those of the isolated chain. Detailed analysis shows that the behavior of γLe(0) is most simply explained in terms of a reduced electrostatic pinning potential due to increased distance between chain and counterion. At all chain lengths studied γLe(0) of PA is enhanced by alkali doping. For chains containing 50 carbon atoms (NC=50), the increase due to K doping is about 9×107 a.u., which more than doubles the value for an undoped chain of similar length. The normalized quantity γLe(0)/NC exhibits a maximum for the isolated soliton (at about NC=61) that is over four times that of the infinite undoped (and unbent) chain. When the alkali dopant is taken into account this maximum diminishes considerably and shifts to larger NC than we have considered. In comparison with the maximum for the undoped species (at NC=∞) there is a small enhancement of γLe(0)/NC for K doping, but none for either Li or Na doping at the coupled-perturbed Hartree–Fock (CPHF)/6-31G level of theory. Intermediate length isolated chains bearing a charged soliton show order of magnitude increases in γv for the degenerate four-wave mixing (DFWM) and, especially, electric field-induced second harmonic generation (dc-SHG) processes compared to undoped PA. As in the case of γLe(0) this enhancement persists, but is significantly reduced when the dopant atom is included. Vibrational anharmonicity, which contributes only to the dc Kerr effect at our level of treatment, is much more important in the doped than undoped species.

Electron beam induced degradation of poly(perfluoroethers) and poly(olefin sulfones)

G values are reported for a variety of poly(perfluorinated ethers) when exposed in a vacuum system to a 25-kV electron beam. The G values for polymer decomposition ranged from 0.1 to 1.2 depending upon the polymer structure and irradiation temperature and were generally higher for polymers containing perfluoromethylene oxide comonomer units compared to perfluoroethylene oxide and perfluoropropylene oxide units. Activation energies for polymer decomposition were obtained from temperature-dependent electron beam irradiation studies using specular reflectance infrared spectroscopy. Values of about 1 kcal/mol are obtained for the poly(perfluoroethers) and 6.8 kcal/mol for poly(2-methylpentane 1-sulfone), respectively. The [beta]-scissioning reaction in poly(perfluorinated ether) radicals which leads to evolution of COF[sub 2] were investigated using ab initio calculations at the 6-31G level of theory. The calculations predict a [Delta]H at room temperature of [approx]1.2 kcal/mol. Alternative chain scissioning pathways are investigated also. 22 refs., 8 figs., 4 tabs.