Energy decomposition in molecular complexes: implications for the treatment of polarization in molecular simulations

This study examines the contribution of electrostatic and polarization to the interaction energy in a variety of molecular complexes. The results obtained from the Kitaura-Morokuma (KM) energy decomposition analysis at the HF/6-31G(d) level indicate that, for intermolecular distances around the equilibrium geometries, the polarization energy can be determined as the addition of the polarization energies of interacting blocks, as the mixed polarization term is typically negligible. Comparison of KM and QM/MM results shows that the electrostatic energy determined in the KM method is underestimated (in absolute value) by QM/MM methods. The reason of such underestimation can be attributed to the simplified representation of treating the interaction between overlapping charge distribution by the interaction of a QM molecule with a set of point charges. Nevertheless, the polarization energies calculated by KM and QM/MM methods are in close agreement. Finally, a consistent, automated strategy to derive charge distributions that include implicitly polarization effects in pairwise, additive force fields is presented. The strategy relies in the simultaneous fitting of electrostatic and polarization energies computed by placing a suitable perturbing particle at selected points around the molecule. The suitability of these charges to describe molecular interactions is discussed.     

Characterisation of pitch by HPLC

Summary A new high performance liquid chromatography method for the characterisation of toluene-soluble fractions of pitches has been developed. Although a chromatographic system typical of size exclusion chromatography was used, results indicate that, for these structurally complex samples, separation does not follow the usual discrimination by molecular size. A differentiation between several classes of polyaromatic hydrocarbons is achieved instead. Data are reported on the analysis of individual standard polyaromatic hydrocarbons, showing that four different elution ranges can be observed: three ofcata-condensed compounds (Cata1, Cata2 and Cata3) and one ofperi-condensed compounds (Peri). Results are reported proving the capacity of this high performance liquid chromatography method to distinguish between pitches of different origin and nature. It is also effective for the study of the chemical reactions occurring during heat treatment.     

Thermal and photochemical rearrangement of bicyclo[3.1.0]hex-3-en-2-one to the ketonic tautomer of phenol. Computational evidence for the formation of a diradical rather than a zwitterionic intermediate

The ground state (S(0)) and lowest-energy triplet state (T(1)) potential energy surfaces (PESs) concerning the thermal and photochemical rearrangement of bicyclo[3.1.0]hex-3-en-2-one (8) to the ketonic tautomer of phenol (11) have been extensively explored using ab initio CASSCF and CASPT2 calculations with several basis sets. State T(1) is predicted to be a triplet pipi lying 66.5 kcal/mol above the energy of the S(0) state. On the S(0) PES, the rearrangement of 8 to 11 is predicted to occur via a two-step mechanism where the internal cyclopropane C-C bond is broken first through a high energy transition structure (TS1-S(0)()), leading to a singlet intermediate (10-S(0)()) lying 25.0 kcal/mol above the ground state of 8. Subsequently, this intermediate undergoes a 1,2-hydrogen shift to yield 11 by surmounting an energy barrier of only 2.7 kcal/mol at 0 K. The rate-determining step of the global rearrangement is the opening of the three-membered ring in 8, which involves an energy barrier of 41.2 kcal/mol at 0 K. This high energy barrier is consistent with the fact that the thermal rearrangement of umbellulone to thymol is carried out by heating at 280 degrees C. Regarding the photochemical rearangement, our results suggest that the most efficient route from the T(1) state of 8 to ground state 11 is the essentially barrierless cleavage of the internal cyclopropane C-C bond followed by radiationless decay to the S(0) state PES via intersystem crossing (ISC) at a crossing point (S(0)()/T(1)()-1) located at almost the same geometry as TS1-S(0)(), leading to the formation of 10-S(0)() and the subsequent low-barrier 1,2-hydrogen shift. The computed small spin-orbit coupling between the T(1) and S(0) PESs at S(0)()/T(1)()-1 (1.2 cm(-)(1)) suggests that the ISC between these PESs is the rate-determining step of the photochemical rearrangement 8 --> 11. Finally, computational evidence indicates that singlet intermediate 10-S(0)() should not be drawn as a zwitterion, but rather as a diradical having a polarized C=O bond.     

Quantitative vs. qualitative approaches to the electronic structure of solids

The usefulness of qualitative and quantitative theoretical approaches in solid state chemistry is discussed by considering three different types of problems: (a) the distribution of boron and carbon atoms in MB₂C₂ (M=Ca, La, etc.) phases, (b) the band structure and Fermi surface of low-dimensional transition metal oxides and bronzes, and (c) the correlation between the crystal and electronic structure of the ternary nitride Ca₂AuN.     

Michael additions of benzoins versus Michael-Stetter additions of aldehydes

Triethylamine catalyzed Michael additions of benzoins to chalcone can prevail over the expected Michael-Stetter additions when certain thiazolium ion conjugate bases - prepared $\text{in situ}$ from the pertinent thiazolium salts and triethylamine- are used as catalysts.     

LBGK method coupled to time splitting technique for solving reaction-diffusion processes in complex systems

A new approach to numerically solve a reaction-diffusion system is given, specifically developed for complex systems including many reacting/diffusing species with broad ranges of rate constants and diffusion coefficients, as well as complicated geometry of reacting interfaces. The approach combines a Lattice Boltzmann (LB) method with a splitting time technique. In the present work, the proposed approach is tested by focusing on the typical reaction process between a metal ion M and a ligand L, to form a complex ML with M being consumed at an electrode. The aim of the paper is to systematically study the convergence conditions of the associated numerical scheme. We find that the combination of LB with the time splitting method allows us to solve the problem for any value of association and dissociation rate constant of the reaction process. Also, the method can be extended to a mixture of ligands. We stress two main points: (1) the LB approach is particularly convenient for the flux computation of M and (2) the splitting time procedure is very well suited for reaction processes involving association-dissociation rate constants varying on many orders of magnitude.     

Analysis of conformational equilibria in aplidine using selective excitation 2D NMR spectroscopy and molecular mechanics/dynamics calculations

Aplidine (dehydrodidemnin B), a natural product with potent antitumor activity currently in multicenter phase II clinical trials, exists in DMSO as a mixture of four slowly interconverting conformations in a ratio of 47:33:13:7. NMR spectroscopy shows that these arise as a consequence of cis/trans isomerization about the NMe-Leu(7)-Pro(8) and Pro(8)-Pyr amide bonds of the molecule's side chain. Two major conformations account for 47% and 33% of the total population, a ratio of 60:40 between the two. They correspond to the cis- and trans-isomers, respectively, about the Pro(8)-Pyr amide bond. Two minor conformers arise as a consequence of similar isomerism about the Pro(8)-Pyr amide bond, but in structures in which the NMe-Leu(7)-Pro(8) amide bond is cis rather than trans. These account for approximately 13% and 7% of the total population, corresponding to a ratio of 65:35 cis/trans, respectively. Molecular dynamics simulations show that the three-dimensional structures of all four conformational isomers are similar in the macrocycle and that all are essentially unchanged with respect to the macrocycle of didemnin B. Significant differences in the conformation of the molecule's side chain are, however, observed between major and minor pairs. Analysis of hydrogen-bonding patterns shows that each major conformer exhibits a beta-turn like structure and is stabilized by hydrogen bonding between a different carbonyl group of the pyruvyl unit of the molecule's side chain and the NH of the Thr(6) residue. The minor isomers have a cis-amide bond between the NMe-Leu(7) and Pro(8) residues that obliges the side chain to adopt an extended disposition where hydrogen bonding to the macrocycle is absent. These results suggest that the ability of the molecule's side chain to adopt a beta-turn-like conformation may not be a prerequisite for biological activity in the didemnins and that conformations having an extended side-chain may play a role in the biological activity of aplidine.     

Fast solid-phase extraction-gas chromatography-mass spectrometry procedure for oil fingerprinting. Application to the Prestige oil spill

A rapid and simple fractionation procedure using solid-phase extraction (SPE) cartridges was developed for an accurate determination of aliphatic and polycyclic aromatic hydrocarbons in petroleum residues and further application in chemical fingerprinting of oil spills by gas chromatography-mass spectrometry (GC-MS). Among the adsorbents evaluated, SiO2/C3-CN exhibited the best selectivity, providing, by elution with n-hexane (4 ml) and n-hexane-CH2Cl2 (1:1) (5 ml), two well-resolved aliphatic and aromatic hydrocarbon fractions, with recoveries of 97 +/- 7.2 and 99.7 +/- 13.9%, respectively. The SPE fractionation procedure was compared with the conventional silica-alumina adsorption chromatography showing similar results but practical advantages in terms of reproducibility, analysis time, solvent reduction and cost. Moreover, is particularly suitable for routine analysis with a high sample throughput. The developed methodology was tested in the characterization of fuel-oil samples collected along the Spanish north-west coast, after the Prestige oil spill accident.     

Reactivity of pyrrole pigments. Part 9 MINDO/3 calculations on dipyrrolic partial models of bile pigments

The applicability of the MINDO/3 method is evaluated for calculations on dipyrrolic partial structures of bile pigments. It is shown that this method cannot be used for an accurate conformational analysis. However, when applying the frontier orbital model for reactivity parameters, a good picture of the HOMO and the LUMO distribution can be obtained in this type of molecules.

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Reaktivität von Pyrrolpigmenten, 9. Mitt. MINDO/3-Rechnungen von dipyrrolischen Partialmodellen von Gallenpigmenten

Zusammenfassung Es werden die Einsatzmöglichkeiten von MINDO/3 für den Fall dipyrrolischer Partialstrukturen der Gallenpigmente aufgezeigt. Die Methode ist für eine genaue Konformationsanalyse nicht geeignet. Unter Verwendung der Reaktionsparameter des Frontier-Orbital-Modells läßt sich jedoch ein gutes Bild der HOMO- und LUMO-Verteilung für diesen Verbindungstyp gewinnen.

     

Local aromaticity of [n]acenes, [n]phenacenes, and [n]helicenes (n = 1-9)

The local aromaticity of the six-membered rings in three series of benzenoid compounds, namely, the [n]acenes, [n]phenacenes, and [n]helicenes for n = 1-9, has been assessed by means of three probes of local aromaticity based on structural, magnetic, and electron delocalization properties. For [n]acenes our analysis shows that the more reactive inner rings are more aromatic than the outer rings. For [n]phenacenes, all indicators of aromaticity show that the external rings are the most aromatic. From the external to the central ring, the local aromaticity varies in a damped alternate way. The trends for the [n]helicene series are the same as those found for [n]phenacenes. Despite the departure from planarity in [n]helicenes, only a very slight loss of aromaticity is detected in [n]helicenes as compared to the corresponding [n]phenacenes. Finally, because of magnetic couplings between superimposed six-membered rings in the higher members of the [n]helicenes series, we have demonstrated that the NICS indicator of aromaticity artificially increases the local aromaticity of their most external rings.