Theoretical Design of Cage Structures with Unusual Linear P=O→Si Interactions

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.

For the first time, the structures and energies for the hydrogen bonding of a 1:1 complex formed between formamide and methanol molecules have been computed with various pure and hybrid density functional theory (DFT) and ab initio methods at varied basis set levels from 6‐31g to 6‐31+g(d,p). Five reasonable geometries on the potential energy surface of methanol and formamide system are considered and their relative stability is discussed. The infrared (IR) spectrum frequencies, IR intensities, and vibrational frequency shifts are reported. From the systematic studies, it is found that all the DFT methods selected here correctly compute the dimerization energies and geometries, with the B3P86 method predicting the hydrogen bond lengths relatively shorter and BPW91 yielding the interaction energies relatively lower. Finally, the solvent effects on the geometries of the formamide–methanol complexes have also been investigated using self‐consistent reaction field (SCRF) calculations with five different DFT methods at the 6‐31+g(d,p) basis set level. The results indicate that the polarity of the solvent has played an important role on the structures and relative stabilities of different isomers. Moreover, the basis set superposition error correction is critical to the interaction energies in the polar solvents. © 2003 Wiley Periodicals, Inc. Int J Quantum Chem, 2004

In this study, the molecular structure of Ketoprofen molecule, which is the drug active ingredient , was revealed by using the Density Functional Theory method and the Molecular Mechanical Force Field method. First of all, conformational space scanning in the Ketoprofen molecule was performed by the Molecular Mechanical Force Field method. The most stable structure of the ketoprofen molecule was found with the help of the Density Functional Theory method. The geometry parameters of the ketoprofen molecule and the Nuclear Magnetic Resonance parameters were calculated with the help of the Density Functional Theory method. Possible radicals were modeled using the most stable structure of the ketoprofen molecule. Electron Spin Resonance parameters of these possible radicals were calculated with the Density Functions Theory method. The calculated Electron Spin Resonance parameters were used in the JEOL IsoSimu/Fa Version 2.2.0 simulation program and theoretical Electron Spin Resonance spectra of possible radicals were obtained.

The 1,3-dipolar cycloaddition reactions of diazomethane with ethylene and formaldehyde as well as the nitrogen elimination reactions from the cycloadducts have been studied using density functional and conventional ab initio methods. The exothermicity of the reactions is underestimated by DFT methods with respect to CCSD(T) due to an overestimation of the C−N dissociation energy of diazomethane. For the cycloaddition reactions all methods lead to similar transition state geometries, and the potential energy barriers computed using DFT methods are similar to the CCSD(T) ones. On the other hand, for the nitrogen elimination reactions transition state geometries and energy barriers are more dependent on the level of calculation. The results obtained show that for the reaction between diazomethane and ethylene the pyrazoline intermediate is more stable than the reactants and that the Gibbs energy barrier for nitrogen elimination is larger than the barrier corresponding to its formation. On the contrary, for formaldehyde the kinetically most favorable cycloadduct, 1,2,3-oxadiazoline, is less stable than the reactants and has a lower barrier for nitrogen elimination.

The structure and intramolecular rearrangements of the model five-coordinate nickel PCP-pincer complex with the o-semiquinone ligand were studied by the density functional theory method at the B3LYP/6-311++G(d,p) level. The isomerization associated with swing vibrations of the o-semiquinone ligand can occur virtually barrierless (0.7 kcal mol−1). The dynamics of the coordination sphere determined by pendulum vibrations of the o-semiquinone ligand has the energy barriers of 4–5 kcal mol−1, which is in good agreement with experimental data. A comparison of the results of calculations with the ESR spectroscopic data revealed the dependence of the types and the energy characteristics of intramolecular rearrangements on the nature of substituents at the phosphorus atom.

The secondary alpha-deuterium, the secondary beta-deuterium, the chlorine leaving-group, the nucleophile secondary nitrogen, the nucleophile (12)C/(13)C carbon, and the (11)C/(14)C alpha-carbon kinetic isotope effects (KIEs) and activation parameters have been measured for the S(N)2 reaction between tetrabutylammonium cyanide and ethyl chloride in DMSO at 30 degrees C. Then, thirty-nine readily available different theoretical methods, both including and excluding solvent, were used to calculate the structure of the transition state, the activation energy, and the kinetic isotope effects for the reaction. A comparison of the experimental and theoretical results by using semiempirical, ab initio, and density functional theory methods has shown that the density functional methods are most successful in calculating the experimental isotope effects. With two exceptions, including solvent in the calculation does not improve the fit with the experimental KIEs. Finally, none of the transition states and force constants obtained from the theoretical methods was able to predict all six of the KIEs found by experiment. Moreover, none of the calculated transition structures, which are all early and loose, agree with the late (product-like) transition-state structure suggested by interpreting the experimental KIEs.

The geometries of NHn(CH3)3−n, NHn(CH3) (n = 0–3) and their corresponding coupling complexes [NHn(CH3)3−n···NHn(CH3) (n = 0–3)] were determined using density functional theory (DFT) and ab initio methods at the 6–311+G* basis set level, and the relative stability is predicted to decrease in the order H3N···NH > CH3H2N···NH2CH > (CH3)2HN···NH(CH3) > (CH3)3N···N(CH3) for the four stable encounter complexes. The inapplicability is also discussed for the DFT methods in predicting the dissociation energy curves especially with long contact distance in which the DFT methods give abnormal behavior for the dissociation of the complexes due to the ‘inverse symmetry breaking’ problem. The contact distance dependences of the activation energy, the coupling matrix element and the electron‐transfer (ET) rate were determined with the MP2/6–311+G* or MP2/6–31G* method. The results show that ET reactions occur chiefly only over a small range of contact distances where the favorable ones are 1.9 Å < RN—N < 4.0 Å for NH3···NH, 2.5 Å < RN—N < 5.0 Å for CH3H2N··· NH2CH, 2.1 Å < RN—N < 5.0 Å for (CH3)2HN···NH(CH3) and 3.2 Å < RN—N < 6.0 Å for (CH3)3N··· N(CH3) coupling systems. The most optimum contact distances for the above four coupling systems are 2.4, 3.0, 2.7 and 3.7 Å where the corresponding maximum ET rates are 2.53 × 105 s−1(H3N···NH), 1.16 × 103 s−1(CH3H2N···NH2CH), 7.55 × 10−3 s−1 [(CH3)2HN···NH(CH3)] and 2.25 × 10−4 s−1 [(CH3)3N··· N(CH3)], respectively, and the corresponding maximum ET rate order is H3N···NH > CH3H2N··· NH2CH > (CH3)2HN···NH(CH3) > (CH3)3N···N(CH3). Increasing substituents on the active N centers may significantly change the ET rate and other kinetic parameters. Copyright © 2004 John Wiley & Sons, Ltd.

Borondipyrromethene (BODIPY) dye possesses a bright and long wavelength emitting fluorescent character with a wide spectral range from visible to near infrared region. In the present work, the spectral properties of BODIPY dyes were analyzed using ab intio and density functional theory methods. The ground and excited state geometries of BODIPY and its substituted analogues in chloroform medium, were optimized using the density functional theory (DFT) and singly excited configuration interaction (CIS) methods. Based on the ground and excited state geometries, the absorption and emission spectra have been calculated using time-dependent density functional theory (TDDFT) method. The TDDFT calculations have been performed using hybrid exchange correlation functionals B3LYP and M06-HF and long-range separated functionals LC-BLYP, LC-BOP, LC-PBE, LC-PBE0 and CAM-B3LYP. The solvent phase calculations were carried out using polarizable continuum model (PCM). The TDDFT investigation reveals that the substitution of acceptor, donor–donor, donor–acceptor–donor and phenyl group in BODIPY dye influence the absorption and emission spectra significantly.

Rational design of fused-ring based non-fullerene acceptors for high performance organic solar cells

Binuclear hydride centers containing two Zr(IV) atoms are suggested as promising catalysts for the hydrogenolysis of alkanes under mild conditions (T < 450 K, p ∼ 1 atm). Reactions of model compounds L2(H)Zr(X)2Zr(H)L2 (X = H, L = OSi≡ (4a), X = L = OMe (4d)), L(H)Zr(O)2Zr(H)L (L = OSi≡ (4b), Cp(4c)) and (≡SiO)2(H)Zr-O-Zr(H)(OSi≡)2 (4e and 4f) with the propane molecule were studied using the density functional theory method. The results show that centers of the 4a, 4e, and 4f types and especially 4b are promising catalysts of the hydrogenolysis of alkanes due to a high degree of unsaturation of two Zr atoms and their sequential participation in the splitting of the C-C bond and hydrogenation of ethylene formed as a result of splitting.

The thermochemistry of organometallic complexes in solution and in the gas phase has been an area of increasing research interest. In this paper, the Fe–O and Fe–S homolytic bond dissociation energies [ΔHhomo(Fe–O)'s and ΔHhomo(Fe–S)'s] of two series of meta‐substituted phenoxydicarbonyl(η5‐cyclopentadienyl) iron [m‐G‐C6H4OFp (1)] and (meta‐substituted benzenethiolato)dicarbonyl(η5‐cyclopentadienyl) iron [m‐G‐C6H4SFp (2)] were studied using Hartree–Fock and density functional theory methods with large basis sets. In this study, Fp is (η5‐C5H5)Fe(CO)2, and G are NO2, CN, COMe, CO2Me, CF3, Br, Cl, F, H, Me, MeO, and NMe2. The results show that Tao–Perdew–Staroverov–Scuseria and Minnesota 2006 functionals can provide the best price/performance ratio and accurate predictions of ΔHhomo(Fe–O)'s and ΔHhomo(Fe–S)'s. The polar effects of the meta substituents show that the dominant role to the magnitudes of ΔΔHhomo(Fe–O)'s or ΔΔHhomo(Fe–S)'s. σα·, σc· values for meta substituents are all related to polar effects. Spin‐delocalization effects of the meta substituents in ΔΔHhomo(Fe–O)'s and ΔΔHhomo(Fe–S)'s are small but not necessarily zero. Molecular effects rather than ΔΔHhomo(Fe–O)'s and ΔΔHhomo(Fe–S)'s are more suitable indexes for the overall substituent effects on ΔHhomo(Fe–O)'s and ΔHhomo(Fe–S)'s. The meta substituent effects of meta‐electron‐withdrawing groups on the Fe–S bonds are much stronger than those on the Fe–O bonds. For meta‐electron‐donating groups, the meta substituent effects have the comparable magnitudes between series 1 and 2. ΔΔHhomo(Fe–O)'s (1) and ΔΔHhomo(Fe–S)'s (2) conform to the captodative principle. Insight from this work may help the design of more effective catalytic processes. Copyright © 2015 John Wiley &amp; Sons, Ltd.

Reactivity–selectivity principle in substituted cyclobutene ring opening computed with density functional theory methods

Graphene is an anode material that is expected to be a good alternative for graphite to increase the capacity and rate-capability of lithium-ion batteries. Graphene synthesis is always accompanied by defects in the structure. The most common defect in graphene is the divacancy (DV) defect. In this study, the effect of this defect on the adsorption of lithium was studied by density functional theory method, and also the doping effect of silicon and germanium atoms on the defective graphene structure was investigated. The bandgap energy of DV-defected graphene, which has an inverse relationship with electrical conductivity, is steady with the addition of germanium, but decreases with the addition of silicon. In all cases, along with lithium adsorption, the bandgap energy is increased, so that the germanium doped compound has the highest bandgap and the structure with no doped atom has the least bandgap. However, the difference in the minimum and maximum bandgap in structures is very low. The results show that the addition of silicon and germanium leads to stronger adsorption of lithium which means it is possible to raise the charge-discharge capacity of graphene through doping with elements while the material still has a high charge/discharge capability.

Galangin is a naturally occurring plant flavonoid with potential anticancer activity. In present work, the Becke three-parameter hybrid exchange functional method and the Lee-Yang-Parr correction functional methods were used to investigate the structural properties of galangin. The structure-activity relationship analysis has been performed to determine its antioxidant pharmacophore by using density functional theory method and quantum chemical calculations. The free radical scavenging activities of galangin were analyzed with the use of 2, 2-diphenyl-1-picrylhydrazyl and compared with Vitamin C as a control. Galangin decreased the cell proliferation rate in HCT-116 cells and showed concentration- and time-dependent response. Galangin significantly increase the inhibitory effect on HCT-116 clonogenicity and promotes cell cycle arrest at the G2/M or G1 phase, as confirmed by flow cytometry analysis.

Diazanaphthalenes (DAPs) are a broad class of N-heteroaromatic compounds with several technological and biological applications. Some of these applications are attributed to the ability of DAP molecules to form associated dimers through non-covalent interactions. A study of the types and strength of the interactions involved is crucial for understanding the preferred geometries and energetics of the dimers. In this study, the dimers of five DAPs are investigated by means of Møller–Plesset second order perturbation theory, hybrid meta-GGA [density functional theory methods (DFT): DFT/MPWB1K, DFT/M05-2X and DFT/M06-2X] and DFT dispersion-corrected (DFT-D/ωB97XD) methods to elucidate their dimers' preferred geometries, relative energies and nature of the interactions between monomer units. The results indicate that the monomer units of the dimers are held by either intermolecular hydrogen bonds or π…π stacking interactions, and that the preferred dimers are those in which the monomer units interact through π…π stacking interactions. A comparison across structures suggests that the position of the N atom in the ring has significant role in determining the relative energy and binding strength of the dimers. A comparison among the different methods utilised for the study indicates that DFT/M06-2X method provides binding energies that are close to those of DFT-CCSD(T) correction scheme and could therefore be considered as the best method for describing the binding properties of DAP dimers.