A QTAIM-based energy partitioning for understanding the physical origin of conformational preferences: Application to the Z effect in O=C-X-R and related units

A quantum theory of atoms in molecules-based energy partitioning was carried out for Z and E conformers of a series of O=C-X-R containing compounds. The results obtained for the simplest compound (formic acid) indicate that the attraction of the electron density within carbonyl oxygen by the nucleus of the acid hydrogen is the most important energy term for Z preference. This conclusion can be extended (mutatis mutandis) to larger carboxylic acids, esters, sulfur derivatives, secondary amides, and carbonyl isocyanates, and even explains the sequence of relative conformational energies in the HCXOH series (X = O, S, Se). In contrast, although the hyperconjugative model has been traditionally employed to explain this preference, we observe it is incompatible with: (i) relative values of diverse QTAIM atomic populations for the Z / E conformational equilibrium; (ii) conformational energies in the HCXOH series. © 2012 Wiley Periodicals, Inc.     

Capillary Rise in Granitic Rocks: Interpretation of Kinetics on the Basis of Pore Structure

The capillary transport of water into granitic rocks has been interpreted on the basis of the structure of its porous network. An effective pore radius has been calculated from a three-sized single-pore model proposed by F. A. L. Dullien, El-Sayed, and V. K. Batra (J. Colloid Interface Sci. 60, 497, 1977) Considering the porous network of granites as consisting of fissures grouped in two size types, macro- and microfissures, an effective radius was found from the characteristic radii for each type and the average of these two values. Good agreement between the effective radius calculated and the radius estimated using a capillary rate value measured experimentally provides a suitable basis for identifying interrelationships between the pore structure and moisture capillary rise. In fact, it is possible to predict the process rate from only two characteristic pore sizes, corresponding to the radii of macrofissures and microfissures. The abnormally low rate of capillary rise observed in one of the granites studied could be easily interpreted as due to the involvement exclusively of the macrofissures of its porous network in capillary transport. Copyright 2000 Academic Press.     

The dynamic mechanical response of fiber-reinforced beams to large transverse loads

The paper describes the results of experiments on fiber-reinforced metal beams which have been subjected to dynamic transverse loading. The beams were fabricated by embedding sets of parallel steel wires in a matrix of lead-tin alloy, and were clamped at one end. The transverse dynamic loading was applied to the tip of the beam so that the problem was one of the transverse deformation of a composite cantilever. Two separate techniques were employed to load the specimens, one being to hit the end with a fast moving hammer in a “Hyge” Shock Testing Machine; the other was to detonate an explosive charge in contact with a small projectile close to the tip. The deformations were monitored by a number of different experimental techniques and the final plastic transverse deflection of the tip as well as the final position of the plastic wave front were compared with the theoretical predictions of Spencer, Jones and their co-workers. The agreement was found to be very satisfactory. In making these comparisons strain rate effects in the lead-tin matrix metal had to be allowed for and this was done with the help of a separate set of tests.     

Ultrafast proton transfer to solvent: molecularity and intermediates from solvation- and diffusion-controlled regimes

Photoinduced proton transfer (PT) from cations 6-hydroxyquinolinium (6HQc) and 6-hydroxy-1-methylquinolinium (6MQc) to water and alcohols, and solvation of the zwitterionic conjugate base 1-methylquinolinium-6-olate (6MQz) were studied with stationary and transient absorption spectroscopy and by quantum chemical calculations. Transient emission spectra from 6MQz in acetonitrile and protic solvents shift dynamically to the red without changing their shape and intensity. The shift matches the solvation correlation function C(t) either measured with known solvatochromic probes coumarin 343 and coumarin 153 or derived from infrared/dielectric-loss data on neat solvents. This indicates that 6MQz monitors the solvation dynamics and that no intramolecular electron transfer occurs on a subpicosecond or longer time scale. The PT dynamics S(t) from 6HQc and 6MQc closely follows C(t), being initially 2-3 times slower. This allows for the conclusion that PT is controlled by solvation, with a barrier of 2 kJ/mol. In water, a pre-condition of this ultrafast reaction seems to be hydrogen-bonding between the negatively charged oxygen and two water molecules, resulting in a complex 6HQc:H2O:H2O. The complex is stable due to a high (47 kJ/mol) bonding energy between 6HQc and a water molecule. In acetonitrile, the reaction equilibrium is strongly shifted to the cation. There an intermediate PT state was detected, which may be ascribed to the cationic form 6HQc:H2O due to residual water impurities. In water-acetonitrile mixtures, the ultrafast solvent-controlled PT is followed by a diffusion-controlled reaction; the measured rate kD approximately 1010 s-1 M-1 is characteristic for simple bimolecular diffusion. The dependence of the short-time PT signal on water concentration can be fitted with a Poisson distribution of water molecules around the cation. Altogether, the short-time and long-time behaviors provide strong evidence that diffusion of only one water molecule is sufficient to detach the proton. Subsequent solvent stabilization of the products completes the PT reaction.     

Atoms in molecules interpretation of the anomeric effect in the O--C--O unit

The conformational preferences of two model compounds for the O--CH2--O anomeric unit: methanediol and dimethoxymethane analyzed within the framework of the QTAIM theory provide a new interpretation of the anomeric effect. The characteristic stabilization of the gauche conformers of these compounds is accompanied by a progressive reduction of the electron population of the hydrogens of the central methylene as the number of their gauche interactions to lone pairs rises. The electron population removed from these atoms during the conformational change is gained in the gauche conformers by atoms of larger atomic number, which results in a more negative molecular energy. Also, the variations displayed by atomic populations and the QTAIM delocalization indexes are not keeping in line with the hyperconjugative model of the anomeric effect.     

Interaction between explosive and analyte layers in explosive matrix-assisted plasma desorption mass spectrometry

An HMX/insulin two-layer system was chosen as a model for further investigation of the matrix properties of explosive materials for protein analytes in plasma desorption mass spectrometry. The dependencies of the molecular ion yield and average charge state as a function of the analyte thickness were studied. An increase in the charge state of multiply protonated molecular species was confirmed as the major matrix effect, with the average charge state z at the smallest thickness studied being higher than in matrix-assisted laser desorption/ionization and closer to the value obtained in electrospray ionization under standard acidic conditions. Observed charge state distributions are significantly narrower than the corresponding Poisson distributions, which suggests that the protonation of insulin is limited in plasma desorption by the number of basic sites in the molecule, similar to electrospray ionization. Both the curve displaying total molecular ion yield and the one showing the total charge (proton) yield as a function of the insulin thickness have maxima at a thickness different from an insulin monolayer. These observations diminish the significance of a matrix/analyte interface mechanism for the explosive matrix assistance. Instead, a mechanism related to the chemical energy release during conversion of the explosive after the ion impact is proposed. As additional mechanisms, enhanced protonation of the analyte through collisions with products of the explosive decay is considered, as well as electron scavenging by other products, which leads to a higher survival probability of positively charged protein molecular ions. Copyright 1999 John Wiley & Sons, Ltd.     

Quantum embedding for material chemistry based on domain separation and open subsystems

This perspective considers two theories we recently proposed to perform quantum embedding calculations for chemical systems: domain-separated density functional theory (DS-DFT) and locally coupled open subsystems (LCOS). The development includes both the fundamentals of each theory as well as potential applications, some technical aspects, and related challenges. DS-DFT is suited to study intramolecular effects, where one can apply a high level of theory (based on DFT or wave function theory) to a region of interest inside a molecule or solid and lower level theory elsewhere, with smooth switching between the regions. LCOS, in contrast, is a fragment-based embedding, which offers computational advantages to study intermolecular behavior such as electron hopping, spin-environment interaction, and charge-transfer excitations. However, both theories can exchange roles when appropriate. In addition, these theories allow for control of computational scaling of their algorithms. We explore paths to determine the charge-transfer operator used in LCOS, and suggest an auxiliary energy minimization that can provide a practical estimate to this operator. We also briefly discuss how to implement density fitting techniques in domain separation, and how domain separation can be used for pure wave function-based embedding.     

Wave scattering effects in elastic percolation models

The study of the propagation of waves in randomly diluted models is presented. Porosity (crack-like) models are simulated by constructing typical elastic percolation networks with random microscopic heterogeneities in order to resemble rock media. Central and bond-bending forces (Born Hamiltonian) models are considered. For each experimental case, the elastic energy of the system is relaxed in equilibrium and then the model is excited by a pulse source in order to produce wave propagation. First, a review is presented of the well established velocity-porosity relationship from rock physics, which shows a linear trend from small porosities up to the critical porosity (percolation threshold) where the rocks fall apart. From the wave propagation analysis a general trend is observed for the attenuation of waves, from the small to the large porosity models, suggesting multiple scattering effects similar to those reported from effective-medium approximations of wave scattering due to random heterogeneities. Finally, the results are compared with those obtained from laboratory experiments on dry rocks with different porosities and different applied stress regimes.