Coupled Thermo-Hydro-Mechanical and Chemical Analysis of Expansive Clay Subjected to Heating and Hydration

A fully coupled formulation combining reactive transport and an existing thermo-hydro-mechanical (THM) code is presented. Special attention has been given to phenomena likely to be encountered in clay barriers used as part of containment systems of nuclear waste. The types of processes considered include hydrolysis, complex formation, oxidation/reduction reactions, acid/base reactions, precipitation/dissolution of minerals and cation exchange. Both kinetically-controlled and equilibrium-controlled reactions have been incorporated. The total analytical concentrations (including precipitated minerals) are adopted as basic transport variables and chemical equilibrium is achieved by minimizing Gibbs Free Energy. The formulation has been incorporated in a general purpose computer code capable of performing numerical analysis of engineering problems. A validation exercise concerning a laboratory experiment involving the heating and hydration of an expansive compacted clay is described.     

Thermal rearrangements of 2-vinylcyclopropylidene to cyclopentadiene and vinylallene: a theoretical investigation

In an attempt to clarify the favored rearrangement reaction of vinylcyclopropylidenes, the prototype thermal rearrangements of singlet 2-vinylcyclopropylidene (1) leading to 1,3cyclopentadiene (2) and 1,2,4-pentatriene (vinylallene) (3) were investigated by means of ab initio quantum-mechanical electronic-structure calculations. The B3LYP functional with the 6-31G(d) basis set was employed for geometry optimization of the equilibrium and transition-state structures relevant to the two reaction pathways and for computing their harmonic vibrational frequencies. Final energies were evaluated by single-point calculations at the CCSD(T) level of theory with the 6-311 + G(3df,2p) basis set. The rearrangement of s-cis 1 to 2 is found to occur by a three-step pathway. The first step involves the formation of a nonclassical carbene (5), which is an internal pi complex between the pi molecular orbital of the double bond and the empty p atomic orbital of the carbene carbon. In the second step, the nonplanar five-membered ring geometry of 5 flattens to reach the planar structure of 3-cyclopentenylidene (4). The last step is the 1,2-migration of a alpha-hydrogen atom to the carbene center in 4. The rate-determining step for the rearrangement of s-cis 1 to 2 is the formation of 5, with a predicted global deltaG++(220 K) of only 0.6 kcalmol(-1). The rearrangement of s-trans 1 to 2 requires an initial conversion of s-trans 1 to the s-cis conformer, with a predicted deltaG++(220 K) of 1.8 kcalmol(-1). The transition structure for the ring-opening of s-trans 1 into s-trans 3 (deltaG++(220 K)=4.7 kcalmol(-1)) is more energetic than that for the ring-opening of s-cis 1 into s-cis 3 (deltaG++(220 K)=2.5 kcalmol(-2)) due to larger repulsive nonbonded H...H interactions in the former transition structure. On the basis of these results, it is suggested that if the reaction of 1,1-dibromo-2-vinylcyclopropane with methyllithium at -78 degrees C leads to the initial formation of carbene 1, then the reaction should yield 2 as the main product together with small amounts of 3. This theoretical prediction nicely agrees with experimental findings.     

The 1,2,4-triazolyl cation: thermolytic and photolytic studies

The generation of the 1,2,4-triazolyl cation (1) has been attempted by the thermolysis and photolysis of 1-(1,2,4-triazol-4-yl)-2,4,6-trimethylpyridinium tetrafluoroborate (2) and the thermolysis of 1- and 4-diazonium-1,2,4-triazoles, using mainly mesitylene as the trapping agent. Thermolysis of 2 gave mostly 1,2,4-triazole, together with 3-(1,2,4-triazol-4-yl)-2,4,6-trimethylpyridine, 4-(1,2,4-triazol-4-ylmethyl)-2,6-dimethylpyridine, and 4-(2,4,6-trimethylbenzyl)-2,6-dimethylpyridine. Thermolysis of each of the diazonium salts in the presence of mesitylene again gave mainly triazole together with very low yields of 1-(1,2,4-triazol-1-yl)-2,4,6-trimethylbenzene and the corresponding -4-yl isomer in about the same ratio. On the other hand, photolysis of 2 in mesitylene gave mainly 1-(1,2,4-triazol-1-yl)-2,4,6-trimethylbenzene. A photoinduced electron transfer from mesitylene to 2 has been observed and preliminary laser flash photolyses of 2 and the corresponding 2,4,6-triphenylpyridinium salt have been carried out. The observed transients are explained as arising from the first excited states of the pyridinium salts rather than from 1. Ab initio MO calculations are reported and indicate that the predicted electronic ground-state of the triazolyl cation is a triplet state of B1 symmetry with five pi electrons, which corresponds to a diradical cation (1c). Possible mechanisms for the formation of the various products are proposed.     

Evaluation of MNDO calculated proton affinities

A large set of charged species arising mainly from protonation or deprotonation of hydrocarbons, alcohols, ethers, carboxylic acids, amines, imines, and nitriles has been studied by means of the semiempirical self-consistent-field (SCF ) molecular orbital (MO ) MNDO method. From the calculated heats of formation of such charged species and those of neutral molecules, MNDO -estimated proton affinities have been obtained and the results compared with experimental gas-phase proton affinities. If the small size anions and acetylides, for which the method predicts heats of formation too large, are ruled out, the mean absolute error in calculated proton affinities is ca. 7 kcal/mol for hydrocarbons (22 acid-base pairs) and ca. 8 kcal/mol for oxygen-containing compounds (25 acid-base pairs). For nitrogen-containing molecules it is necessary to discard, in addition, the values corresponding to the protonation of alkylamines and imines in order to achieve a reasonable mean absolute error of 7–8 kcal/mol.     

Theoretical study of the conformational energy hypersurface of cyclotrisarcosyl

The multidimensional Conformational Potential Energy Hypersurface (PEHS) of cyclotrisarcosyl was comprehensively investigated at the DFT (B3LYP/6-31G(d), B3LYP/6-31G(d,p) and B3LYP/6-311++G(d,p)), levels of theory. The equilibrium structures, their relative stability, and the Transition State (TS) structures involved in the conformational interconversion pathways were analyzed. Aug-cc-pVTZ//B3LYP/6-311++G(d,p) and MP2/6-31G(d)//B3LYP/6-311++G(d,p) single point calculations predict a symmetric cis-cis-cis crown conformation as the energetically preferred form for this compound, which is in agreement with the experimental data. The conformational interconversion between the global minimum and the twist form requires 20.88 kcal mol-1 at the MP2/6-31G(d)//B3LYP/6-311++G(d,p) level of theory. Our results allow us to form a concise idea about the internal intricacies of the PEHSs of this cyclic tripeptide, describing the conformations as well as the conformational interconversion processes in this hypersurface. In addition, a comparative analysis between the conformational behaviors of cyclotrisarcosyl with that previously reported for cyclotriglycine was carried out     

Some remarkable oxidations of 2,3,5,6-tetrachloro-p-phenylenediamine,and products therefrom

The oxidation of 2,3,5,6-tetrachloro-$\text{p}$-phenylenediamine with Cl₂ or Br₂ in CCl₄ containing I₂ affords unusual quinoniminium salts displaying remarkable chemical behaviour.     

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.     

Effects of CO<Subscript>2</Subscript> Compressibility on CO<Subscript>2</Subscript> Storage in Deep Saline Aquifers

The injection of supercritical CO₂ in deep saline aquifers leads to the formation of a CO₂ plume that tends to float above the formation brine. As pressure builds up, CO₂ properties, i.e. density and viscosity, can vary significantly. Current analytical solutions do not account for CO₂ compressibility. In this article, we investigate numerically and analytically the effect of this variability on the position of the interface between the CO₂-rich phase and the formation brine. We introduce a correction to account for CO₂ compressibility (density variations) and viscosity variations in current analytical solutions. We find that the error in the interface position caused by neglecting CO₂ compressibility is relatively small when viscous forces dominate. However, it can become significant when gravity forces dominate, which is likely to occur at late times of injection.     

Computational Model of the Complex between GR113808 and the 5-HT4 Receptor Guided by Site-Directed Mutagenesis and the Crystal Structure of Rhodopsin

A computational model of the transmembrane domain of the human 5-HT₄ receptor complexed with the GR113808 antagonist was constructed from the crystal structure of rhodopsin and the putative residues of the ligand-binding site, experimentally determined by site-directed mutagenesis. The recognition mode of GR113808 consist of: (i) the ionic interaction between the protonated amine and Asp^3.32; (ii) the hydrogen bond between the carbonylic oxygen and Ser^5.43; (iii) the hydrogen bond between the ether oxygen and Asn^6.55; (iv) the hydrogen bond between the C-H groups adjacent to the protonated piperidine nitrogen and the electrons of Phe^6.51; and (v) the - aromatic-aromatic interaction between the indole ring and Phe^6.52.This computational model offers structural indications about the role of Asp^3.32, Ser^5.43, Phe^6.51, Phe^6.52, and Asn^6.55 in the experimental binding affinities. Asp^3.32Asn mutation does not affect the binding of GR113808 because the loss of binding affinity from an ion pair to a charged hydrogen bond is compensated by the larger energetical penalty of Asp to disrupt its side chain environment in the ligand-free form, and the larger interaction between Phe^6.51 and the piperidine ring of the ligand in the mutant receptor. In the Phe^6.52Val mutant the indole ring of the ligand replaces the interaction with Phe^6.52 by a similarly intense interaction with Tyr^5.38, with no significant effect in the binding of GR113808. The mutation of Asn^6.55 to Leu replaces the hydrogen bond of the ether oxygen of the ligand from Asn^6.55 to Cys^5.42, with a decrease of binding affinity that approximately equals the free energy difference between the SHO and NHO hydrogen bonds.Because these residues are also present in the other members of the neurotransmitter family of G protein-coupled receptors, these findings will also serve for our understanding of the binding of related ligands to their cognate receptors.