Excited state substituent constants: to Hammett or not?

In this study, an answer has been sought to several questions: Can substituents’ impact on the electronic properties of molecules in the excited singlet states be summed up by a set of substituent constants? Are the well known, ground state Hammett σ constants practical for this purpose? To answer these questions, the potentials and charges on atoms of the functional groups in two classes of compounds, p-substituted benzoic acids and p-substituted nitrosobenzenes, were regressed against σ_p. It appeared that all correlations found in the ground state of the molecules also hold in the excited state, with lower correlation coefficients in the latter. An attempt has also been made to find a molecular characteristic which could be useful in a comparison of the acidic properties of benzoic acids (in gas phase) in the first excited and ground states.     

To be,or not to be…Electrochemist?

Journal of Solid State Electrochemistry -     

New cyanine dyes or not? Theoretical insights for model chains

The quest of organic dyes presenting improved electronic features has been extremely active during the last decades, as new structures are necessary to build novel materials such as dye-sensitized solar cells, nonlinear optics commutators, or molecular photochromic switches. Cyanine derivatives occupy a key spot in that scene, as they present intense absorption bands and tunable colors, even when a relatively short π-conjugated path is used. This behavior has often been interpreted as a consequence of a negligible bond length alternation. Recently, Thorley et al. have designed and characterized new cationic compounds that possess the cyanine electronic features, though presenting sizable bond length alternation (Angew. Chem. Int. Ed.2008, 47, 7095-7098). In this contribution, I investigate, with quantum mechanical tools, the size dependence of these properties in model symmetric dyes displaying Thorley's patterns. Extended chains are simulated in order to obtain insights into the chain length convergence, and the results are compared to those obtained at the same level of theory for classical cyanine architectures. This theoretical work is a step toward the rational development of more efficient π-conjugated compounds.     

Vinylphosphirane-phospholene rearrangements: pericyclic [1,3]-sigmatropic shifts or not?

The conversion of "free" and Cr(CO)(5)-complexed 2-vinylphosphiranes into 3-phospholenes via [1,3]-sigmatropic shifts was studied with density functional theory and compared with the corresponding hydrocarbon system, that is, the vinylcyclopropane-cyclopentene rearrangement. All three systems behave similarly with subtle but important differences. No intermediate was found on any of the potential energy surfaces. 2-Vinylphosphiranes have smaller rearrangement barriers than vinylcyclopropane, and those carrying the Cr(CO)(5) group have still smaller ones. The rearrangement of both anti- and syn-2-vinylphosphiranes occurs in a concerted pericyclic manner with inversion of configuration at the migrating phosphorus, requiring, respectively, 29.3 and 36.7 kcal/mol, much in contrast to the 44.6 kcal/mol demanding diradical-like process for the hydrocarbon analogue. Epimerization at the phosphorus center (syn right arrow over left arrow anti) requires approximately 32.0 kcal/mol and occurs in a single step, reflecting a diradical-like ring opening-ring closure process that can occur in both a clockwise and counterclockwise fashion. Complexation of the phosphorus center by Cr(CO)(5) results in the substantial stabilization of reagents and products and further reduces the barriers for rearrangement. The anti isomer has the lowest barrier for the [1,3]-shift (DeltaE = 20.5 kcal/mol), which is slightly less than that needed for P-epimerization and for conversion of the syn isomer, both of which are nonpericyclic processes. When a P-phenyl group is introduced, the diradical-like conversion of the syn isomer is favored over the anti isomer, in agreement with experimental reports. The influence of torquoselectivity is discussed for the rearrangements of these structures with their heavy substituents. The origin of the stabilization rendered by the Cr(CO)(5) group and its influence on the [1,3]-conversion are also analyzed. The DFT activation energies for the diradical-like [1,3]-sigmatropic shifts were verified with a multireference method.     

Theoretical and computational studies of organometallic reactions: successful or not?

Theoretical and computational methods are powerful in studying transition metal complexes. Our theoretical studies of C–H σ‐bond activation of benzene by Pd(II)–formate complex and that of methane by Ti(IV)‐imido complex successfully disclosed that these reactions are understood to undergo heterolytic σ‐bond activation and the driving force is the formation of strong O–H and N–H bonds in the former and the latter, respectively. Orbital interactions are considerably different from those of σ‐bond activation by oxidative addition. The transmetallation, which is a key process in the cross‐coupling reaction, is understood to be heterolytic σ‐bond activation. Our theoretical study clarified how to accelerate this transmetallation. Also, we wish to discuss weak points in theoretical and computational studies of large systems including transition metal elements, such as the necessity to incorporate solvation effect and to present quantitatively correct numerical results. The importance of solvation effects is discussed in the oxidative addition of methyliodide to Pt(II) complex which occurs in a way similar to an S_N2 substitution. To apply the CCSD(T) (coupled cluster singles and doubles with perturbative triples correction) method, which is the gold standard of electronic structure theory, to large system, we need to reduce the size of the system by employing a small model. But, such modeling induces neglects of electronic and steric effects of substitutents which are replaced in the small model. Frontier‐orbital‐consistent quantum‐capping potential (FOC‐QCP) was recently proposed by our group to incorporate the electronic effects of the substituents neglected in the modeling. The CCSD(T) calculation with the FOC‐QCP was successfully applied to large systems including transition metal elements. © 2010 The Japan Chemical Journal Forum and Wiley Periodicals, Inc. Chem Rec 10: 000–000; 2010: Published online in Wiley InterScience ( www.interscience.wiley.com ) DOI 10.1002/tcr.200900019     

Crystal structures of 2-chloropyridine and 2-fluoropyridine: Isostructural crystal packing or not?

Structural Chemistry - In order to investigate how halogen substituents influence the crystal packing of 2-halogenpyridines, the crystal structure of 2-chloropyridine was determined and the crystal...     

To D or not to D? On estimating the microenvironment polarity of biomolecular cavities

Knowledge of the local polarity of specific cavities in biopolymers can facilitate the design of selective low MW ligands that impact the structure and function of macromolecules. The most common tools for interrogating local polarity are fluorescent probes that are sensitive to their microenvironment. Researchers often evaluate and express this local polarity using dielectric constants, a parameter that reflects an inherent bulk property. A more appropriate expression should take into account solvent-solute interactions at the molecular level. Reevaluation of commonly used fluorophores illustrates the improved correlation between observed Stokes shift changes and E(T)(30) values as compared to the corresponding dielectric constants.     

Why 11-cis-retinal? Why not 7-cis-, 9-cis-, or 13-cis-retinal in the eye?

One of the basic and unresolved puzzles in the chemistry of vision concerns the natural selection of 11-cis-retinal as the light-sensing chromophore in visual pigments. A detailed computational examination of the structure, stability, energetics, and spectroscopy of 7-cis-, 9-cis-, 11-cis-, and 13-cis-retinal isomers in vertebrate (bovine, monkey) and invertebrate (squid) visual pigments was carried out using a hybrid quantum mechanics/molecular mechanics (QM/MM) method. The results show that the electrostatic interaction between retinal and opsin dominates the natural selection of 11-cis-retinal over other cis isomers in the dark state. In all of the pigments, 9-cis-retinal was found to be only slightly higher in energy than 11-cis-retinal, which provides strong evidence for the presence of 9-cis-rhodopsin in nature. 7-cis-Retinal is suggested to be an "upside-down" version of the all-trans isomer because the structural rearrangements observed for 7-cis-rhodopsin from squid were found to be very similar to those for squid bathorhodopsin. The progressive red shift in the calculated absorption wavelength (λ(max)) (431, 456, 490, and 508 nm for the 7-cis-, 9-cis-, 11-cis-, and 13-cis-retinal isomers) is due to the decrease in bond length alternation of the retinal.     

Why orbitals do not exist?

In this paper we will address the problem of the existence of orbitals by analyzing the relationship between molecular chemistry and quantum mechanics. In particular, we will consider the concept of orbital in the light of the arguments that deny its referring character. On this basis, we will conclude that the claim that orbitals do not exist relies on a metaphysical reductionism which, if consistently sustained, would lead to consequences clashing with the effective practice of science in its different branches.     

Reactivity of coordinatively unsaturated iron complexes towards carbon monoxide: to bind or not to bind?

An overview of the reactivity of coordinatively unsaturated iron complexes (in most cases Fe(II)) towards carbon monoxide is presented. Unsaturated iron complexes are known with coordination numbers (CN) of two to five adopting linear or slightly bent (CN = 2), trigonal (CN = 3), tetrahedral, square planar or trigonal pyramidal (CN = 4), and square-pyramidal or trigonal-bipyramidal geometries (CN = 5), respectively. The binding of CO depends strongly on the number and the nature of co-ligands (overall ligand field strength), the charge of the complex, the complex geometry, and the spin state of the unsaturated metal center. In many cases, CO addition to high-spin iron complexes takes place with concomitant spin state changes forming compounds in the lowest possible spin state, i.e., with S = 0. In several other cases, however, the addition of CO is reversible or is even totally rejected altogether for either thermodynamic or kinetic reasons. In the case of the latter such reactions are termed "spin-blocked" or "spin forbidden".     

Specialist or generalist?

Analytical and Bioanalytical Chemistry -     

Is there an unambigous answer to the question: Whether the aging program exists or not?

The article discusses up-to-date viewpoints on the reasons of aging in respect to their compliance with the concepts of programmed or stochastic aging.     

A future for nuclear analytical techniques? Why not?

The choices of universities and national research institutions in supporting scientific research are increasingly justified on the basis of, amongst others, the relevance that has to be reflected by external, preferably sustainable funding of the research programs. Many traditional fields of application such as environmental sciences do not offer a promising outlook in this respect. As a consequence, university research reactors face closure because of reallocations of university funds to more contemporary sciences such as molecular biology and nanotechnology. Therefore, laboratories operating nuclear analytical techniques (NAA, (TR)XRF, and PIXE) need to use their creativity in finding ways for participation in, for example, nanotechnology, cancer research, or genomics. This requires an open mind in terms of the opportunities, strengths, and weaknesses of the techniques, and a departure of technique-oriented research towards problem-oriented research in which other nuclear techniques can be used. The unique features of radiotracers, nuclear imaging, and nuclear beam techniques are discussed in view of the new areas mentioned above. Some examples of opportunities for nuclear analytical techniques in the above-mentioned fields are given.     

The 1,2,3-tridehydrobenzene triradical: 2B or not 2B? The answer is 2A!

The molecular and electronic structure of 1,2,3-tridehydrobenzene was investigated by a variety of computational methods. The two lowest electronic states of the triradical are the (2)B(2) and (2)A(1) doublet states characterized by different interactions of the unpaired electrons. Vertically, the two states are well separated in energy-by 4.9 and 1.4 eV, respectively. However, due to different bonding patterns, their equilibrium structures are very different and, adiabatically, the two states are nearly degenerate. The adiabatic energy gap between the (2)B(2) and (2)A(1) states is estimated to be 0.7-2.1 kcal/mol, in favor of the (2)A(1) state. Harmonic vibrational frequencies and anharmonic corrections were calculated for both states. Comparison with the three experimentally observed IR transitions supports the assignment of the (2)A(1) ground state for the triradical with a weakly bonding distance of 1.67-1.69 A between the meta radical centers.     

Heterometallic coordination polymers incorporating dipyrrin based heteroleptic copper and cobalt complexes: to Ag-π or not?

Using ligands based on either an acetylacetonate or a dipyrrin moiety appended with pyridyl groups, a series of novel heteroleptic copper(II) and cobalt(III) complexes combining both chelate units such as (acacpy(2))Cu(dpm-py) and (acacpy(2))Co(dpm-py)(2) (acacpy(2) = 1,3-bis(4-pyridyl)-1,3-propanedionate; dpm-py = 5-(4-pyridyl)dipyrrin) have been prepared and fully characterized. These two complexes were obtained upon reaction of dpm-py with the (acacpy(2))M homoleptic species (M = Cu(II), Co(II)). In the solid state, the (acacpy(2))Cu(dpm-py) complex behaves as a self-complementary metallatecton and leads to the formation of a 1D coordination polymer (CP) through the coordination of a peripheral pyridyl group to the copper centre. Contrastingly, the octahedral (acacpy(2))Co(dpm-py)(2) complex featuring a coordinatively saturated Co(III) centre crystallizes as an isolated mononuclear species. In order to generate heterometallic CPs, both complexes have been used as metallatectons upon their combination with different silver(I) salts. Upon reaction of (acacpy(2))Cu(dpm-py) with Ag(BF(4)) or Ag(TfO), 2- and 3-D heterometallic networks were obtained, respectively. In both cases, sheet type arrangements resulting from the binding of Ag(+) cations by three peripheral pyridyl groups were observed. These 2D sheets are further interconnected through Ag-π interactions with the pyrrolic rings. Under the same conditions, the combination of (acacpy(2))Co(dpm-py)(2) with Ag(TfO) leads to two networks differing by their connectivity patterns and dimensionality. Interestingly, whereas no Ag-π interactions were observed for the 2D network, a combination of coordination bonding with the pyridyl moieties and Ag-π interactions was detected for the 1D architecture.