Inversion using a new low-dimensional representation of complex binary geological media based on a deep neural network

Efficient and high-fidelity prior sampling and inversion for complex geological media is still a largely unsolved challenge. Here, we use a deep neural network of the variational autoencoder type to construct a parametric low-dimensional base model parameterization of complex binary geological media. For inversion purposes, it has the attractive feature that random draws from an uncorrelated standard normal distribution yield model realizations with spatial characteristics that are in agreement with the training set. In comparison with the most commonly used parametric representations in probabilistic inversion, we find that our dimensionality reduction (DR) approach outperforms principle component analysis (PCA), optimization-PCA (OPCA) and discrete cosine transform (DCT) DR techniques for unconditional geostatistical simulation of a channelized prior model. For the considered examples, important compression ratios (200 - 500) are achieved. Given that the construction of our parameterization requires a training set of several tens of thousands of prior model realizations, our DR approach is more suited for probabilistic (or deterministic) inversion than for unconditional (or point-conditioned) geostatistical simulation. Probabilistic inversions of 2D steady-state and 3D transient hydraulic tomography data are used to demonstrate the DR-based inversion. For the 2D case study, the performance is superior compared to current state-of-the-art multiple-point statistics inversion by sequential geostatistical resampling (SGR). Inversion results for the 3D application are also encouraging

Stille Cross-Coupling Reactions of Alkenylstannanes with Alkenyl Iodides Mediated by Copper(I) Thiophene-2-carboxylate: A Density Functional Study

The detailed reaction mechanism for the Stille cross-coupling reaction of vinylstannane with vinyl iodide mediated by copper(I) thiophene-2-carboxylate (CuTC) was studied with the aid of density functional theory (DFT) calculations. The results of the DFT calculations show that the reaction mechanism involves two major steps: (1) the transmetalation between (NMP)CuTC (NMP = N-methylpyrrolidone, a solvent molecule) and CH2CHSnMe3 to give the organocopper intermediate (NMP)Cu-CHCH2 and (2) a one-step process involving both oxidative addition of CH2CHI to (NMP)Cu-CHCH2 and reductive elimination of the coupling product CH2CH−CHCH2. We found that the overall barrier involves the effect of both steps. In this paper, we also examined the role of the thiophene-2-carboxylate ligand in the reaction and discussed the possibility of a catalytic version of the reaction

Theoretical Studies on the Reaction Mechanism of Platinum-Catalyzed Diboration of Allenes

The reaction mechanism of Pt(0)-catalyzed diboration reaction of allenes is investigated by the density functional method B3LYP. The overall reaction mechanism is examined. The electronic mechanisms of the allene insertion into the Pt−B bond are discussed in terms of the electron donation, back-donation, and d−π interaction. During allene insertion into the Pt−B bond, the internal carbon atom of allene is preferred over the terminal one due to the stronger electron back-donation and stronger charge transfer in the former case than that in the latter one. By using the monosubstituted allenes (CN, Ph, Me, and NH2), the influence of the substituents on the allene insertion into the Pt−B bond is analyzed. For CN, B−B bond addition to the terminal CC bond of allene is favored over the internal one, while for Ph, Me, and NH2, the internal one is preferred over the terminal one. This result can be explained by the influence of substituents on the charge transfer in the d−π interaction

Cu(I)/TF-BiphamPhos Catalyzed Reactions of Alkylidene Bisphosphates and Alkylidene Malonates with Azomethine Ylides: Michael Addition versus 1,3-Dipolar Cycloaddition

Cu­(I)/TF-BiphamPhos catalyzed reactions of alkylidene bisphosphates and alkylidene malonates with azomethine ylides have been investigated with the aid of density functional theory calculations at the B3LYP level. Michael addition and 1,3-dipolar cycloaddition were calculated. For reactions of alkylidene bisphosphates, the Michael addition pathway is both kinetically and thermodynamically more favorable than 1,3-dipolar cycloaddition. However, for reactions of alkylidene malonates, the 1,3-dipolar cycloaddition pathway is kinetically and thermodynamically more favorable than Michael addition. In the reactions of alkylidene bisphosphates, the significant repulsion between the two bulky phosphonate groups of the alkylidene bisphosphates and the phenyl substituent of the azomethine ylides suppresses 1,3-dipolar cycloaddition and favors Michael addition. In the reactions of alkylidene malonates the less bulky ester groups in the alkylidene malonates allow 1,3-dipolar cycloaddition to occur

DFT Studies on Copper-Catalyzed Arylation of Aromatic C–H Bonds

Cu-catalyzed arylation of aromatic C–H bonds with phenyl iodide has been investigated with the aid of density functional theory calculations at the B3LYP level. Both the neutral and anionic catalytic cycles have been examined by considering the neutral (phen)­Cu–OMe and anionic [MeO–Cu–OMe]⁻ complexes, respectively, as the active species. Various heterocycle and polyfluorobenzene substrates were studied. The relationship between the overall reaction barrier and the acidity of the cleaved C–H bond was studied in both the neutral and anionic catalytic cycles. Comparing the overall reaction barriers based on the neutral and anionic catalytic cycles, we were able to understand that some substrates prefer the anionic mechanism while others prefer the neutral mechanism. We also examined how different ligands influence the overall barriers in the neutral catalytic cycles by employing <i>N</i>,<i>N</i>′-dimethylethylenediamine (DMEDA) and <i>N</i>-methylpyrrolidine-2-carboxamide as the ligands

Tracking the Endocytic Pathway of Recombinant Protein Toxin Delivered by Multiwalled Carbon Nanotubes

The endocytic pathway of a recombinant protein toxin, ricin A-chain (RTA), delivered by multiwalled carbon nanotubes (MWCNTs) was tracked in HeLa cells by tagging RTA with enhanced green fluorescent protein (EGFP). EGFP−RTA was found to accumulate in the endosome and to be retrogradely transported to the endoplasmic reticulum, from which it translocated into the cytosol. Nuclear staining, Z-axis scanning with a laser scanning confocal microscope (LSCM), and transmission electron microscopy (TEM) indicated that the RTA exerted its toxic effects. Endocytosis-inhibiting tests with LSCM and flow cytometry showed that MWCNT−EGFP−RTA conjugates penetrated cells principally via clathrin-mediated endocytosis. These studies are beneficial to understanding the MWCNT-based intracellular drug delivery mechanism and provide guidelines for designing promising MWCNT-based vectors for targeting diagnostic or therapeutic compounds, not only to specific cells, but even to specific cellular compartments

Tracking the Endocytic Pathway of Recombinant Protein Toxin Delivered by Multiwalled Carbon Nanotubes

The endocytic pathway of a recombinant protein toxin, ricin A-chain (RTA), delivered by multiwalled carbon nanotubes (MWCNTs) was tracked in HeLa cells by tagging RTA with enhanced green fluorescent protein (EGFP). EGFP−RTA was found to accumulate in the endosome and to be retrogradely transported to the endoplasmic reticulum, from which it translocated into the cytosol. Nuclear staining, Z-axis scanning with a laser scanning confocal microscope (LSCM), and transmission electron microscopy (TEM) indicated that the RTA exerted its toxic effects. Endocytosis-inhibiting tests with LSCM and flow cytometry showed that MWCNT−EGFP−RTA conjugates penetrated cells principally via clathrin-mediated endocytosis. These studies are beneficial to understanding the MWCNT-based intracellular drug delivery mechanism and provide guidelines for designing promising MWCNT-based vectors for targeting diagnostic or therapeutic compounds, not only to specific cells, but even to specific cellular compartments

Mechanistic Insight into the Alcohol Oxidation Mediated by an Efficient Green [CuBr₂(2,2′-bipy)]-TEMPO Catalyst by Density Functional Method

Density functional theory (DFT) calculations have been performed to investigate the alcohol oxidation to acetaldehyde catalyzed by [CuBr2(2,2′-bipy)]-TEMPO (TEMPO stands for 2,2,6,6-tetramethylpiperidinyloxy; bipy stands for bipyridine). The total charge for the studied catalytic system is +1. The catalytic cycle consists of two parts, namely, alcohol oxidation and TEMPO regeneration. In alcohol oxidation, the reaction follows the Sheldon’s mechanism for the proposed two mechanisms, i.e., Semmelhack’s mechanism and Sheldon’s mechanism. The water participation plays minor role in the H atom abstraction step. In TEMPO regeneration, the proposed three paths are competitive in energy. By comparing with experimental observation, it is found that the path, in which alcohol provides the proton to TEMPO− to produce TEMPOH followed by the oxidation of TEMPOH directly to TEMPO by O2, is favored. In TEMPO regeneration, CH3CN acts as the ligand to stabilize the CuI species during the catalytic cycle

Tracking the Endocytic Pathway of Recombinant Protein Toxin Delivered by Multiwalled Carbon Nanotubes

The endocytic pathway of a recombinant protein toxin, ricin A-chain (RTA), delivered by multiwalled carbon nanotubes (MWCNTs) was tracked in HeLa cells by tagging RTA with enhanced green fluorescent protein (EGFP). EGFP−RTA was found to accumulate in the endosome and to be retrogradely transported to the endoplasmic reticulum, from which it translocated into the cytosol. Nuclear staining, Z-axis scanning with a laser scanning confocal microscope (LSCM), and transmission electron microscopy (TEM) indicated that the RTA exerted its toxic effects. Endocytosis-inhibiting tests with LSCM and flow cytometry showed that MWCNT−EGFP−RTA conjugates penetrated cells principally via clathrin-mediated endocytosis. These studies are beneficial to understanding the MWCNT-based intracellular drug delivery mechanism and provide guidelines for designing promising MWCNT-based vectors for targeting diagnostic or therapeutic compounds, not only to specific cells, but even to specific cellular compartments

Regioselective Bis-Selenation of Allenes Catalyzed by Palladium Complexes: A Theoretical Study

The reaction mechanism of Pd(0)-catalyzed allene bis-selenation reactions is investigated by using density functional methods. The overall reaction mechanism has been examined. It is found that with the bulkier PMe3 ligand, the rate-determining step is the reductive elimination process, while allene insertion and reductive elimination processes are competitive for the rate-determining step with the PH3 ligand, indicating the importance of the ligand effect. For both cis and trans palladium complexes, allene insertion into the Pd−Se bond of the trans palladium complex using the internal carbon atom attached to the selenyl group is preferred among the four pathways of allene insertion processes. The formation of σ-allyl and π-allyl palladium complexes is favored over that of the σ-vinyl palladium species. By using methylallene, the regioselectivity of monosubstituted allene insertion into the Pd−Se bond is analyzed. In addition, the influence of carbon monoxide on allene bis-selenation is studied by comparing the relevant transition states. It is found that carbon monoxide prefers to activate the Pd−C bond of the σ-vinyl palladium complex generated from allene insertion into the Pd−Se bond