DFT study on the isomerization in vitamin B6

Isomerization and tautomerism reactions of the active form of vitamin B6, pyridoxal phosphate, are studied at B3LYP level of theory using 6-311++G(2df,p) basis set in gas and aqueous phases. Twenty-three transition state (TS) structures for vitamin B6 isomerization are optimized, including 13 TS structures for O–H and C–C rotations, 8 TS structures for imine–enamine tautomerism, and 2 TS structures for keto–enol tautomerism. Activation energy (E _a), imaginary frequency (υ), and Gibbs free energy of activation (ΔG ^#) for the isomerization reactions are calculated. The activation energies of the imine–enamine tautomerism are in the range of 190–280 kJ/mol and of O–H and C–C rotations are mainly less than 60 kJ/mol. Also, our calculation shows that the imine forms of B6 are mainly more stable than the enamine forms. Effect of microhydration on the TS structures and activation energies is also investigated. It is found that the presence of water molecules catalyzes only the imine–enamine tautomerism.     

Insights into the reaction mechanism between propadienylidene and ethylene: a DFT study

The reaction mechanism between propadienylidene and ethylene has been systematically investigated employing the B3LYP/6-311++G** and MP2/cc-pVTZ levels of theory to better understand the reactivity of propadienylidene with unsaturated hydrocarbons. Geometry optimization, vibrational analysis, and energy property for the involved stationary points on the potential energy surface have been calculated. Two important initial reaction complexes characterized by three- and four-membered ring structures have been located firstly. After that, three different products possessing three-, four-, and five-membered ring characters have been obtained through three reaction pathways. In the first reaction pathway, a three-membered ring alkyne compound has been obtained. As for the second reaction pathway, it is a diffusion-controlled reaction, resulting in the formation of the four-membered ring conjugated diene compound. A five-membered conjugated diene compound has been obtained in the third reaction pathway, which is the most stable product in the available products thermodynamically. On the other hand, the second reaction pathway is the most favorable reaction to proceed kinetically.     

Dynamic nature of the intramolecular electronic coupling mediated by a solvent molecule: a computational study

We present a combined Molecular Dynamics/Quantum Chemical study of the solvent-mediated electronic coupling between an electron donor and acceptor in a C-clamp molecule. We characterize the coupling fluctuations due to the solvent motion for different solvents (acetonitrile, benzene, 1,3-diisopropyl-benzene) for the charge separation and the charge recombination processes. The time scale for solvent-induced coupling fluctuation is approximately 0.1 ps. The effect of these fluctuations on the observed rate is discussed using a recently developed theoretical model. We show that, while the microscopic charge transfer process is very complicated and its computational modeling very subtle, the macroscopic phenomenology can be captured by the standard models. Analyzing the contribution to the coupling given by different solvent orbitals, we find that many solvent orbitals mediate the electron transfer and that paths through different solvent orbitals can interfere constructively or destructively. A relatively small subset of substrate-solvent configurations dominate contributions to solvent-mediated coupling. This subset of configurations is related to the electronic structure of the C-clamp molecule.     

Copper cation interactions with biologically essential types of ligands: a computational DFT study

This work presents a systematic theoretical study on Cu(I) and Cu(II) cations in variable hydrogen sulfide-aqua-ammine ligand fields. These ligands model the biologically most common environment for Cu ions. Molecular structures of the complexes were optimized at the density functional theory (DFT) level. Subsequent thorough energy analyses revealed the following trends: (i) The ammine complexes are the most stable, followed by those containing the aqua and hydrogen sulfide ligands, which are characterized by similar stabilization energies. (ii) The most preferred Cu(I) coordination number is 2 in ammine or aqua ligand fields. A qualitatively different binding picture was obtained for complexes with H(2)S ligands where the 4-coordination is favored. (iii) The 4- and 5-coordinated structures belong to the most stable complexes for Cu(II), regardless of the ligand types. Vertical and adiabatic ionization potentials of Cu(I) complexes were calculated. Charge distribution (using the natural population analysis (NPA) method) and molecular orbital analyses were performed to elucidate the nature of bonding in the examined systems. The results provide in-depth insight into the Cu-binding properties and can be, among others, used for the calibration of bioinorganic force fields.     

A DFT investigation on interactions between lignin and ionic liquids

The interactions of the lignin model, the lignin oligomer with degree of polymerization n = 2, with 1-butyl-3-methylimidazolium chloride ionic liquid were investigated through DFT calculations in detail. Computational results revealed that lignin dissolution in ionic liquids should be a result of the joint interactions of lignin with anion and cation of ionic liquid, and the formation of ion pair weakens the interactions between lignin and ionic liquid components. Unlike the dominant H-bonds within the lignin–anion interactions, the lignin–cation interactions involve a combination of hydrogen bond and π-stacking. These results would provide mechanistic insights and suggestions for lignocellulosic dissolution in ionic liquids.     

DFT study on cooperativity in the interactions of hydrazoic acid clusters

Density functional theory at the B3LYP level with the 6‐311G** basis set is performed to calculate the systems consisting of up to four hydrazoic acid molecules. The dimers are found to exhibit cyclic and chain structures with N … H contacts at ca. 2.1–2.7 Å. However, there are only cyclic structures with N … H contacts at ca. 2.0–2.3 Å and 2.0–2.1 Å in the trimer and tetramer, respectively. Hydrogen bond distances in the trimer and tetramer are shorter than those in the cyclic dimer as a result of the stronger interaction between molecules. The contribution of cooperative effect to the interaction energy is significant. After the correction of the basis set superposition error and zero‐point energy, the binding energies are ?10.69, ?29.34, and ?54.26 kJ·mol^?1 for the most stable dimer, trimer, and tetramer, respectively. The calculated IR shifts for N? H stretching mode increase with the size of the cluster growths, reaching more than 200 cm^?1 in the tetramer. For the most stable clusters, the transition from the monomer to dimer, dimer to trimer, and trimer to tetramer involve changes of ?14.40, ?25.68, and ?31.88 kJ·mol^?1 for the enthalpies at 298.15 K and 1atm, respectively. We also perform Mulliken populations analysis and find the Mulliken populations on intermolecular N … H increasing in the sequence of the dimer, trimer, and tetramer. © 2003 Wiley Periodicals, Inc. Int J Quantum Chem 94: 279–286, 2003     

Theoretical study of interactions between 1-alkyl-3-methyimidazolium tetrafluoroborate and dibenzothiophene: DFT,NBO, and AIM analysis

Density functional theory is employed to study the interaction energies between dibenzothiophene (DBT) and 1-alkyl-3-methylimidazolium tetrafluoroborate ([C _n mim]⁺[BF₄]^?). The structures of DBT, 1-ethyl-3-methylimidazolium tetrafluoroborate ([C₂mim]⁺[BF₄]^?), 1-butyl-3-methylimidazolium tetrafluoroborate ([C4mim]+[BF₄]?), 1-hexyl-3-methylimidazolium tetrafluoroborate ([C₆mim]⁺[BF₄]^?), 1-octyl-3-methylimidazolium tetrafluoroborate ([C₈mim]⁺[BF₄]^?), [C₂mim]⁺[BF₄]^?–DBT, [C₄mim]⁺[BF₄]^?–DBT, [C₆mim]⁺[BF₄]^?–DBT and [C₈mim]⁺[BF₄]^?–DBT systems are optimized systematically at the B3LYP/6-31G(d,p) level, and the most stable geometries are obtained by NBO and AIM analyses. The results indicate that DBT and imidazolium rings of ionic liquids are parallel to each other. It is found that the [BF₄]^? anion prefers to be located close to a C1–H9 proton ring in the vicinity of the imidazolium ring and the most stable gas-phase structure of [C _n mim]⁺[BF₄]^? has four hydrogen bonds between [C _n mim]+ and [BF₄]?. There are hydrogen bonding interactions, π–π and C–H–π interactions between [C₈mim]⁺[BF₄]^? and DBT, which is confirmed by NBO and AIM analyses. The calculated interaction energies for the studied ionic liquids can be used to interpret a better extracting ability of [C₈mim]⁺[BF₄]^? to remove DBT, due to stronger interactions between [C₈mim]⁺[BF₄]^? and DBT, in agreement with the experimental results of dibenzothiophene extraction by [C _n mim]⁺[BF₄]^?.     

Interaction of porphine and its metal complexes with C60 fullerene: a DFT study

We performed DFT calculations (BLYP general-gradient approximation in conjunction with a double numerical basis set) for the interaction of free porphine ligand and a number of its metal complexes with C60 molecule to analyze how the nature of a central metal ion influences the geometry and electronic characteristics (electrostatic potential and spin density distribution and highest-occupied molecular orbital (HOMO) and lowest-unoccupied molecular orbital (LUMO) structure). We found that the presence of a central metal ion is crucial for a strong interaction. The energy of interaction between H2P and C60 is -0.3 kcal mol(-1) only, whereas the formation energies for the metal complexes vary from -27.3 kcal mol(-1) for MnClP.C60 to -45.8 kcal mol(-1) for MnP.C60. As a rule, the formation energy correlates with the separations between porphinate and fullerene molecules; the Mn and Fe complexes exhibit the closest approach of ca. 2.2 A between the metal ion and carbon atoms of C60. In most porphine-C60 complexes studied, the two closest contacts of central metal ion or H are those with carbon atoms of the (6,6) bond; VOP.C60 is the only exception, where the closest V...C contacts involve the (5,6) bond. The macrocycle geometry changes, and the magnitude of the effect depends on the central atom, being especially dramatic for Mn, MnCl, and Fe complexes. The shape of LUMOs in most complexes with C60 is not affected notably as compared to the LUMO of the isolated C60 molecule. In the case of Fe, the HOMO extends from the central atom to two opposite pyrrol rings. At the same time, the HOMO-LUMO gap energy decreases drastically in most cases, by ca. 20-30 kcal mol(-1). For electrostatic potential distribution, we systematically observed that the negative lobe contacting C60 shrinks, whereas the opposite one becomes notably bigger. In the case of paramagnetic complexes of VO, Mn, FeCl, Co, and Cu, spin density distribution was analyzed as well.     

Ruthenium-mediated C–C coupling reactions of alkynes – mechanistic investigations based on DFT calculations

This article describes the highlights of the reactions of the substitutionally labile neutral pseudo 14VE complexes RuCp(COD)Cl (COD = 1,5-cyclooctadiene) and the cationic complexes [RuCp(CH₃CN)₂ L]⁺ with alkynes. The ligand L is a co-ligand, whose nature turns out to be critical to the reaction’s outcome being tertiary phosphines (PR ₃ ) and the N-heterocyclic carbene 1,3-bis(2,6-diisopropylphenyl)imidazol-2-ylidene (IPr). A crucial role in all reactions reported is the intermediacy of electrophilic ruthenacyclopentatriene complexes, an entity featuring a biscarbene functionality. While with RuCp(COD)Cl the catalytic cylcotrimerization of alkynes is achieved, [RuCp(CH₃CN)₂(L)]⁺ complexes are catalytically inactive for this process. These compounds undergo selective head-to-tail coupling of two alkynes. However, addition of a third alkyne is precluded due to an unusual migratory insertion of the PR ₃ and the N-heterocyclic carbene, respectively, into the Ru–C carbon double bond of a ruthenacyclopentatriene intermediate to afford stable allyl carbenes. With parent acetylene, on the other hand, an unusual C–C coupling process takes place involving three acetylene molecules and migration of the NHC ligand to give formal [2 + 2 + 1] cycloaddition products. Conceivable mechanisms for all these reactions are established by means of DFT/B3LYP calculations. Correspondence: Karl Kirchner, Institute of Applied Synthetic Chemistry, Vienna University of Technology, Getreidemarkt 9, A-1060 Vienna, Austria.     

Hydrazine trapping ability of Si12C12 fullerene-like nanoclusters: a DFT study

Structural Chemistry - In this study, the nondissociative hydrazine (N2H4) adsorption on the surface of Si12C12 nanoclusters have been investigated using density functional theory at...     

Microsolvation of glycine: a DFT study

PBE1PBE/6-311+G(d,p) computations exploring the microsolvation of neutral and zwitterionic glycine are reported. A broad configuration search was performed to identify the lowest energy clusters of glycine with one to seven water molecules. The structures of the clusters are analyzed on the basis of the hydrogen-bonding network established between the water molecules and between water and glycine. Neutral glycine is favored when associated with zero to six water molecules, but with seven water molecules the two structures are isoenergetic.     

Dispersion interactions in oligomerization of metal diketonates: a DFT evaluation

The structures of the oligomers of Co(II), Ni(II), Cu(II) and Zn(II) β-diketonates and their stability with respect to dissociation into the monomeric components were studied with the use of density functional theory [DFT B3LYP/6-311++G(d,p)] method taking additionally into account corrections for dispersion interactions in CAM and D3BJ approximations. The calculated geometries of the oligomers well match those experimentally determined, but stabilization energies obtained at the B3LYP-CAM and B3LYP-D3BJ approximations are significantly overestimated.     

DFT study of the mechanism of benzocyclobutene formation by palladium-catalysed C(sp3)-H activation: role of the nature of the base and the phosphine

DFT(B3PW91) calculations of the mechanism of the intramolecular C(sp(3))-H arylation of 2-bromo-tert-butylbenzene to form benzocyclobutene catalysed by Pd(PR(3)) (R = Me, (t)Bu) and a base (acetate, bicarbonate, carbonate) show that the preferred mechanism is highly dependent on the nature of the phosphine and the base used in the calculations. With the experimental reagents (P(t)Bu(3) and carbonate) the rate-determining step is C-H activation with the base coordinated trans to the C-H bond. An agostic interaction of a geminal C-H bond with respect to the bond to be cleaved induces a lowering of the activation barrier.     

N,N-Dimethylaminopropylsilane: a case study on the nature of weak intramolecular Si...N interactions

N,N-Dimethylaminopropylsilane H(3)Si(CH(2))(3)NMe(2) was synthesised by the reaction of (MeO)(3)Si(CH(2))(3)NMe(2) with lithium aluminium hydride. Its solid-state structure was determined by X-ray diffraction, which revealed a five-membered ring with an SiN distance of 2.712(2) A. Investigation of the structure by gas-phase electron diffraction (GED), ab initio and density functional calculations and IR spectroscopy revealed that the situation in the gas phase is more complicated, with at least four conformers present in appreciable quantities. Infrared spectra indicated a possible SiN interaction in the Si-H stretching region (2000-2200 cm(-1)), as the approach of the nitrogen atom in the five-membered ring weakens the bond to the hydrogen atom in the trans position. Simulated gas-phase IR spectra generated from ab initio calculations (MP2/TZVPP) exhibited good agreement with the experimental spectrum. A method is proposed by which the fraction of the conformer with a five-membered ring can be determined by a least-squares fit of the calculated to experimental absorption intensities. The abundance of this conformer was determined as 23.7(6) %, in good agreement with the GED value of 24(6) %. The equilibrium SiN distance predicted by theory for the gas-phase structure was highly variable, ranging from 2.73 (MP2) to 3.15 A (HF). The value obtained by GED is 2.91(4) A, which could be confirmed by a scan of the potential-energy surface at the DF-LCCSD[T] level of theory. The nature of the weak dative bond in H(3)Si(CH(2))(3)NMe(2) can be described in terms of attractive inter-electronic correlation forces (dispersion) and is also interpreted in terms of the topology of the electron density.     

Hydroxyl-functionalized polyaniline nanospheres: tracing molecular interactions at the nanosurface via vitamin C sensing

Here, we report a synthesis of novel polyaniline nanospheres bearing mono- and bishydroxyl functional groups to trace the molecular interactions at the nanosurfaces through vitamin C sensing. Two new aniline monomers were synthesized via a tailor-made approach and polymerized to produce soluble and uniform polyaniline nanospheres. The structures of the monomers and polymers were characterized by NMR, FT-IR, and MS techniques, and the morphology of the nanomaterials was analyzed by SEM and TEM. The mechanistic aspects of the nanomaterial formations were analyzed by FT-IR and dynamic light scattering techniques. These studies revealed that the hydroxyl-functionalized monomers have strong hydrogen bonding at the monomer level and form spherical aggregates in water, which are templates for the polyaniline nanospheres 600 +/- 100 nm in size. A controlled synthesis was also carried out using aniline hydrochloride as an unsubstituted counterpart, which yields polyaniline nanofibers. WXRD analysis confirmed the presence of a sharp peak at lower angle at 2theta = 7.3 degrees ( d-spacing of 13.4 A) in hydroxyl-substituted nanospheres with respect to enhancement of solid-state ordered crystalline domains, whereas unsubstituted nanofibers were found to be highly amorphous. Vitamin C was employed as an analyte to trace the molecular interaction at the nanosphere surface and study the influence of nanosurface functionalization on the sensing ability of biomolecules. The bishydroxyl-functionalized polyaniline nanospheres were found to show efficient molecular interactions toward vitamin C, whereas nanospheres with a monohydroxyl group or unsubstituted nanofibers failed as sensing materials. In a nut shell, in the present investigation, for the first time, we have proved the importance of surface functionalization of polyaniline nanomaterial, exclusively nanospheres, using hydroxyl groups for studying the molecular interactions at the nanosurfaces with biomolecules such as vitamin C.     

A DFT study of the ambiphilic nature of arylpalladium species in intramolecular cyclization reactions

The remarkable structure-dependent reactivity observed in the cyclization of (2-haloanilino)-ketones with Pd-catalysts has been studied computationally within the density functional theory framework. The experimental reaction products ratio may be explained through the formation of a common palladaaminocyclobutane intermediate which can undergo a nucleophilic addition reaction and/or an enolate α-arilation process. The evolution of this metallacycle to the final products depends on two factors, the length of the tether joining the amino and the carbonyl groups, and the electronic nature of the substituent directly attached to the nitrogen atom. Thus, shorter chains (2 CH(2)) facilitate the nucleophic addition reaction by approximating the reactive aryl and Pd-coordinated carbonyl groups whereas longer chains (3 CH(2)) favor the enolate α-arylation proccess. For electron-withdrawing groups attached to the aniline nitrogen atom, the nucleophilic addition pathway becomes slightly disfavored, mainly due to the electron-withdrawing effect of the CO(2)Me group which avoids the delocation of the LP in the π-system, thus decreasing the nucleophilicity of the reactive arylic carbon atom. In contrast, the enolate α-arylation reaction is facilitated by the CO(2)Me group. This is translated into a small computed barrier energy difference of these competitive reaction pathways which should lead to a mixture of reaction products as experimentally found.     

Regioselective control of the nickel-mediated coupling of acetylene and carbon dioxide - A DFT study

The nickel-mediated coupling of asymmetric alkynes with carbon dioxide is known to be highly regioselective with respect to the formation of nickelacycle intermediates and α,β-unsaturated carboxylic acid products. Using density functional theory (DFT), we have investigated the effect that parameters such as acetylene-substituent, ancillary ligand and solvent have on the potential energy surface of the nickelacycle coupling reaction. 3-R-substituted nickelacycles are the thermodynamically preferred product in all cases surveyed, however, the transition structure characterised by the attack of CO₂ on the alkyne carbon distal from the R-group is generally lower in energy, making the 2-R-substituted nickelacycle the kinetically favoured product. Ligating the zerovalent nickel species with the diazabicyclo[5.4.0]undec-7-ene (DBU) ancillary ligand in preference to 2,2′-bipyridine (BIPY) leads to lower activation energies for the coupling reaction and products that are less susceptible to steric bulk in the 2-position of the nickelacycle. Solvation with dimethylformamide (DMF) has the advantage of lowering the activation barrier for the coupling reaction when compared to tetrahydrofuran (THF).