DFT oligomer approach to vibrational spectra of poly(p-phenylenevinylene)

Experimental Raman and infrared spectra of poly(p-phenylenevinylene) have been analyzed on the basis of the normal coordinate calculations based on the density functional theory method at the B3LYP/cc-pVDZ level for a model oligomer. Vibrational modes corresponding to optically active modes of an infinite polymer chain have been selected from the calculated results. On the basis of these normal vibrations, the observed vibrational spectra of poly(p-phenylenevinylene) have been explained successfully. The angles between the calculated transition dipole moment vectors and the polymer axis for some infrared bands agree with those derived from observed infrared dichroic spectrum.     

Elucidation of a Sc(I) complex by DFT calculations and reactivity studies

Sc(BrMgL)(2)Br (L = (R(2)NCH(2)CH(2)NCMe)(2)CH, R = H) was studied by DFT methods leading to the conclusion that this diamagnetic formal scandium(I) system enjoys stabilization of its Sc-based filled d(yz)() orbital by a delta-acceptor linear combination of BrMgL ring orbitals. Investigation of the reactivity of Sc(BrMgL)(2)Br (L = (R(2)NCH(2)CH(2)NCMe)(2)CH, R = Et) with H(2)O.B(C(6)F(5))(3) and (HOCH(2))(2)CMe(2), respectively, led to decomposition, with LMgBr being isolated in the latter case.     

In vivo monitoring an important plant immune signaling molecule salicylic acid by rhodamine-engineered probes and their density functional theory (DFT) calculations

Monitoring the dynamic fluctuations of plant immune signaling molecules is particularly meaningful and challenging in crop protection. Herein, four rhodamine-functionalized probes (F₁-F₄) were designed and synthesized to attempt to selectively detect a plant hormone salicylic acid (SA). Screening results revealed that probe F₁ bearing a 4,5-dimethoxy-2-nitrobenzyl carbamate moiety was extremely sensitive and selective towards SA along with a conspicuous fluorescence “turn-on” manner. The Job’s plot experiment disclosed a 1:1 binding mode together with a binding constant of 1.34 × 10⁴ M^?1, indicating that an appreciable hydrogen bonding interaction happened between probe F₁ and SA, thereby leading to the spirolactam ring breakage and the succeeding fluorescence generation. Concentration-dependent titration assays offered an available linear relationship for quantifying SA (15–70 μM) and the detection limit of probe F₁ to SA was 1 μM. Density functional theory (DFT) calculations displayed that a smaller energy gap (ΔE_F1-Ⅱ = 498.89 kJ/mol) was obtained between its lowest unoccupied molecular orbital (LUMO) and highest occupied molecular orbital (HOMO), manifesting that probe F₁ was more reactive and sensitive than those of probes F₂-F₄ (ΔE = 567.07 ～ 601.74 kJ/mol) after adsorption with salicylic acid. Meanwhile, the possible monitoring mechanism was elucidated by ¹H NMR titration experiments, probe-SA DFT calculations, and HRMS. Finally, in vivo confocal imaging results found that probe F₁ could delicately and selectively monitor SA on the roots of cucumber. This study can motivate the intensive exploration of multitudinous fluorescent probes for direct SA monitoring in vivo.     

Synthesis of a new and versatile macrocyclic NADH model

A new macrocyclic NADH model 1 has been designed and synthesised. The new model consists of the same subunits as previously reported models. However, the present model is designed as such that the pyridine nitrogen of the nicotinamide units are not incorporated in the macrocyclic framework. Thus, properties such as solubility can easily be varied by alkylation with an appropriate agent. The macrocyclic framework was prepared in 7 steps. Methylation of the pyridine nitrogens followed by reduction gave the desired model. This model compound was found to reduce methyl benzoylformate stereoselectively in good yield with 48% enantiomeric excess.     

Molecular structure of the macrocyclic copper(II) chelate with 6,7,13,14-tetramethyl-3,10-dithio-1,2,4,5,8,9,11,12-octaazatetradecatetraene-1,5,7,11 according to quantum-chemical DFT calculations

The key parameters of the molecular structure of macrotetracyclic (NNNN)-coordinated chelate of Cu(II) with 6,7,13,14-tetramethyl-3,10-dithio-1,2,4,5,8,9,11,12-octaazatetradecatetraene-1,5,7,11 have been calculated by means of the DFT-based B3LYP6-31G(d) method in GAUSSIAN-09 software. The complex may be formed via self-assembly of Cu(II), thiocarbohydrazide, and diacetyl in the gelatin-immobilized matrix implants. The bond lengths, bond angles, and torsion angles are presented; it has been shown that the metal chelate and the chelating ligand are almost planar.     

DFT/electrostatic calculations of pK(a) values in cytochrome c oxidase

Using classical electrostatic calculations, earlier we examined the dependence of the protonation state of bovine cytochrome c oxidase (CcO) on its redox state. Based on these calculations, we have proposed a model of CcO proton pumping that involves His291, one of the Cu(B) histidine ligands, which was found to respond to redox changes of the enzyme Fe(a)(3)-Cu(B) catalytic center. In this work, we employ combined density functional and continuum electrostatic calculations to evaluate the pK(a)() values of His291 and Glu242, two key residues of the model. The pK(a) values are calculated for different redox states of the enzyme, and the influence of different factors on the pK(a)'s is analyzed in detail. The calculated pK(a)() values of Glu242 are between 9.4 and 12.0, depending on the redox state of the protein, which is in excellent agreement with recent experimental measurements. Assuming the reduced state of heme a(3), His291 of the oxidized Cu(B) center possesses a pK(a)() between 2.1 and 4.0, while His291 of the reduced Cu(B) center has a pK(a) above 17. The obtained results support the proposal that the His291 ligand of the Cu(B) center in CcO is a proton pump element.     

Organic probe molecule adsorption on extended Au(111) surface: a theoretical DFT study

Research on Chemical Intermediates - The cluster approach has been applied to mimic the interactions of probe trans-1,2-bis-(4-pyridyl) ethylene on a gold surface with the aim of discriminating the...     

Electron affinities of small uracil-water complexes: a comparison of benchmark CCSD(T) calculations with DFT

We present benchmark CCSD(T) calculations of the adiabatic electron affinities (AEA) and the vertical detachment energies (VDE) of the uracil molecule interacting with one to three water molecules. Calculations with rather large aug-cc-pVTZ basis set were only tractable when the space of virtual orbitals was reduced to about 60% of the full space employing the OVOS (Optimized Virtual Orbital Space) technique. Because of the microhydration, the valence-bound uracil anion is stabilized leading to gradually more positive values of both AEA and VDE with increasing number of participating water molecules. This agrees with experimental findings. Upon hydration by three water molecules, the electron affinity of uracil increased in comparison with AEA of the isolated molecule by about 250 up to 570 meV, depending on the geometry of the complex. CCSD(T) results confirm trends determined by DFT calculations of the microhydrated uracil and its anion, even if electron affinities of the free and hydrated uracil molecule are overestimated by DFT by up to 300 meV.     

A hexaaza macrocyclic ligand containing acetohydrazide pendants for Ln(III) complexation in aqueous solution. Solid-state and solution structures and DFT calculations

Lanthanide complexes of a hexaaza macrocyclic ligand containing acetohydrazide pendants (L) have been synthesised (Ln = La-Er, except Pm), and structural studies have been carried out both in the solid state and in aqueous solution. Attempts to isolate the complexes of the heaviest Ln(iii) ions (Ln = Tm-Lu) were unsuccessful. The crystal structures of the ligand and its lanthanum complex have been determined by single-crystal X-ray crystallography. The X-ray crystal structure of [La(L)](3+) shows the metal ion being ten-coordinate, with the acetohydrazide pendants situated alternatively above and below the plane of the macrocycle. The two five membered chelate rings formed by the ethylenediamine moieties adopt (deltadelta) [or (lambdalambda)] conformations. The [Ln(L)](3+) complexes have been characterised by means of density-functional theory (DFT) calculations (B3LYP model). The structures obtained from these theoretical calculations are in very good agreement with the experimental solution structures, as obtained from paramagnetic NMR measurements on the Ce(iii), Pr(III), Nd(III) and Eu(III) complexes. The complexes adopt in aqueous solution a D(2) structure with the ligand adopting a (deltadelta) [or (lambdalambda)] conformation.     

Triarylpyridines: a versatile small molecule scaffold for G-quadruplex recognition

The triarylpyridines are potent G-quadruplex ligands that are highly discriminating against duplex DNA and show promising selectivity between intramolecular quadruplexes.     

Computational modeling of polyoxotungstates by relativistic DFT calculations of (183)W NMR chemical shifts

The (183)W nuclear shielding in a variety of tungsten polyoxometalates (POM) (Lindqvist, Anderson, decatungstates, Keggin) of different shapes and charges has been modeled by DFT calculations that take into account relativistic effects, by means of the zero-order regular approximation (ZORA), and solvent effects, by the conductor-like screening model (COSMO) continuum method. The charge/surface area ratio (q/A) is proposed as an indicator of the charge density to which the solvation energies of all POMs are correlated in a satisfactory way. Among the various theoretical levels tested (ZORA scalar or spin-orbit, frozen-core or all-electron basis set, geometry optimization in the gas phase or in the continuum solvent, etc.), the best results are obtained when both geometry optimization in solvent and spin-orbit shielding are included (mean absolute error of delta=35 ppm). The quality of the computed chemical shifts depends systematically on the charge density as expressed by q/A; thus, POMs with low q/A ratios display the best agreement with experimental data. The performance of the method is such that computed values can aid the assignment of the (183)W NMR spectra of polyoxotungstates, as shown by the case of alpha-[PW(11)TiO(40)](5-), whose six signals are ranked computationally so as to almost reproduce the experimental ordering even though the signals are spaced by as little as 5 ppm.     

High basicity of phosphorus-proton affinity of tris-(tetramethylguanidinyl)phosphine and tris-(hexamethyltriaminophosphazenyl)phosphine by DFT calculations

It is shown by approximate but reliable DFT calculations that the title compounds represent very strong superbases in gas phase and MeCN. In particular, tris-(hexamethyltriaminophosphazenyl)phosphine has a proton affinity, PA, of 295.5 kcal mol(-1) and records a pKa(MeCN) of 50 +/- 1 units.     

Adsorption of 2,4,6-trinitrotoluene on Al(111) ultrathin film: periodic DFT calculations

The adsorption of 2,4,6-trinitrotoluene (TNT) molecule on the Al(111) ultrathin film were investigated by the generalized gradient approximation (GGA) of density functional theory (DFT). The calculations employ a supercell (4 × 4 × 2) model and three-dimensional periodic boundary conditions. The strong attractive forces between oxygen and aluminum atoms induce the N–O bond breaking of the TNT. Subsequently, the dissociated oxygen atoms and radical fragment of TNT oxidize the Al ultrathin film. The N–O bond of the o-NO₂ group is easier to rupture than that of the p-NO₂ group after the adsorption of the TNT molecule on the Al(111). Except for the breaking of the N–O bonds of the nitro group, other bonds of TNT molecule do not dissociate. The largest adsorption energy is −747.3 kJ/mol. The most of charge transfer is 3.42 e from the Al(111) to the fragment of TNT molecule. The aluminum ultrathin film is readily oxidized by the radical fragment of TNT, which is initiated by the dissociated O atoms from the nitro group.     

(Z)-(2-bromovinyl)-MIDA boronate: a readily accessible and highly versatile building block for small molecule synthesis

Iterative cross-coupling represents a potentially general approach for the simple, efficient, and flexible construction of a wide range of functional small molecules. In this context, (Z)-(2-bromovinyl)-N-methyliminodiacetic acid (MIDA) boronate is a very useful building block for small molecule synthesis. This compound can serve as a starting material for the preparation of a wide range of cis-alkene-containing MIDA boronates. This compound can also be used for the iterative cross-coupling-based synthesis of various cis-olefin-containing targets. Collectively, these results contribute to the expanding generality of the MIDA boronate platform.     

Synthesis,characterization and DFT calculations of a Re(V)-thiazolidine-2,4-dione complex

This article presents a combined experimental and computational study of a new oxorhenium(V) complex of thiazolidine-2,4-dione (HTDO). The complex has been synthesized by direct reaction of NH₄ReO₄ with thiazolidine-2,4-dione in the presence of Na₂S₂O₆ as a reducing agent. The complex [ReO(TDO)(H₂O)₃](S₂O₈) has been characterized by spectroscopy (FT-IR, NMR, UV-vis, mass), thermogravimetry, microanalysis, and HPL chromatography. The complex was geometrically optimized by DFT with B3LYP level of theory and satisfactory theoretical–experimental agreement was achieved for analysis of IR and NMR data of the complex. Additional information about binding between rhenium and oxo ligand in the complex has been obtained by NBO analysis. The antibacterial activity of the investigated complex has been tested and evaluated.     

Complexation of U(VI) with diphenyldithiophosphinic acid: spectroscopy,structure and DFT calculations

The complexation of U(VI) with diphenyldithiophosphinic acid (denoted as HL) in acetonitrile was studied by UV–Vis, FT-IR, crystallography and DFT calculations. UV–Vis absorption spectrophotometry implies that three successive complexes, UO₂L⁺, UO₂L₂, UO₂L₃^?, form in the solution. Significant ligand to metal charge transfer occurs from soft atom S to U(VI) in all the three complexes. A crystal of UO₂L₂ complex was successfully synthesized from the solution. In the crystal both the two ligands coordinate to U(VI) in bidentate form. DFT calculations confirm the formation of UO₂L₃^? complex and help illustrate the structures of all the U(VI) species in the solution.     

Examination of small molecule losses in 5‐methylpyranopelargonidin MS/MS CID spectra by DFT calculations

Pyranoanthocyanins are formed during food treatment and maturation (e.g. wine, juices), and they can be considered a natural alternative to artificial food colorants. Tandem mass spectrometry (MS/MS) is perhaps the most important technique in analysis of anthocyanin dyes. Knowledge of fragmentation pattern is a key aspect of their successful structural characterization. Polyphenolic compounds are known to lose small molecules during collision‐induced dissociation (CID) in MS/MS experiments. However, the specific positions where such losses occur preferentially are unknown. The aim of this communication is to investigate the energetically most preferred places for H₂O and CO losses during the fragmentation of 5‐methylpyranopelargonidin molecule by the means of computational chemistry (employing density functional theory) combined with CID MS/MS experiments and infrared multiphoton dissociation spectroscopy. Mechanisms responsible for the fragmentations were investigated, and optimal geometries and transition states were obtained. Cleavage of water as well as carbon monoxide occurs preferentially from the C‐ring of flavonoid skeleton. In the most stable structure of 5‐methylpyranopelargonidin, B‐ring was found to be tilted with respect to the rest of the molecule. Planarization effort of the parent molecule contributes both to its decarbonylation and dehydration. Copyright © 2014 John Wiley & Sons, Ltd.     

Chemistry of and on TiO2-anatase surfaces by DFT calculations: a partial review

We review recent theoretical studies of the surfaces and interfaces of the anatase polymorph of TiO₂. We discuss aspects of the surface structure, stability, and reactivity, as well as the growth and stability of anatase-supported oxide nanostructures of catalytic interest. Finally, we report on recent investigations of two-dimensional titania systems which appear to be closely related to anatase and which may have an important role during the growth of anatase nanoparticles.     

DFT calculations on the spin-crossover complex Fe(salen)(NO): a quest for the best functional

DFT calculations on the spin-crossover complex Fe(salen)(NO) provide a striking illustration of the comparative performance of different exchange-correlation functionals vis-à-vis the issue of transition metal spin state energetics. Thus, although the "classic" pure functionals PW91 and BLYP favor the S = 1/2 state by about 10 kcal/mol, relative to the S = 3/2 state, the hybrid functional B3LYP favors the latter state by nearly the same margin. In contrast, the newer pure functionals OLYP and OPBE, based on the OPTX exchange functional, as well as the B3LYP* hybrid functional (which has 15% Hartree-Fock exchange, compared with 20% for B3LYP) predict nearly isoenergetic S = 1/2 and 3/2 states, as required for a spin-crossover complex. Intriguingly, the OLYP and B3LYP* spin density profiles for the S = 1/2 state of Fe(salen)(NO) are substantially dissimilar.