Pore Structure Characterizations of Shale Oil Reservoirs with Heat Treatment: A Case Study from Dongying Sag, Bohai Bay Basin, China.

Heat treatment plays a significant role in determining the petrophysical properties of shale reservoirs; however, the existing studies on the evolution of pore structures are still insufficient. This study conducts a series of tests, including Rock-Eval, low-temperature nitrogen adsorption-desorption, nuclear magnetic resonance (NMR) T2, and T1-T2 tests on samples from Shahejie Formation, Dongying Sag, Bohai Bay Basin. The tests aim to determine the changes in the shale pore structures under increasing heat treatments (ranging from 110 to 500 °C) and identify the factors that control pore structures. The results show that the gradual decomposition of organic matter leads to an eventual decrease in the total organic carbon (TOC) content. The decrease in TOC is more prominent when the temperature exceeds 300 °C. For shales with lower TOC contents (<2%), the Brunauer-Emmett-Teller specific surface area (BET SSA) first decreases, then increases, but eventually decreases again. However, the average pore diameter demonstrates an opposite trend when the temperature increases. In contrast, for organic-rich shales (TOC > 2%), the BET SSA increases at temperatures above 200 °C. The similarity between the D1 values implies that the complexity and heterogeneity of shale pore surface only undergo minor changes during heat treatment. Porosity shows an increasing trend, and the higher the contents of clay minerals and organic matter in shales are, the greater the change in porosity is. The NMR T2 spectra suggest that micropores (<0.1 µm) in shales first decrease and then increase, whereas the contents of meso- (0.1-1 µm) and macropores (>1 µm) increase, corresponding to the increase in free shale oil. Moreover, shale pore structures are primarily controlled by clay minerals and organic matter contents during heat treatments, with higher contents resulting in better pore structures. Overall, this study contributes to detailing the shale pore structure characteristics during the in situ conversion process (ICP).

Occurrence Characteristics of Water in Nano-Slit Pores under Different Solution Conditions: A Case Study on Kaolinite.

The presence of water in narrow pore spaces affects the occurrence and flow of methane, which in turn affects shale gas production. Therefore, studying the occurrence and distribution characteristics of water is of great significance to predict gas production. Based on molecular dynamics simulations, this study investigated the occurrence characteristics and influencing variables of liquid water in kaolinite nanopores in situ. Owing to its widespread distribution, kaolinite is the most prevalent clay mineral with two surfaces with different characteristics. Three systems of pure water, a CaCl2 solution, and a H2O/CH4 mixed phase were created at varied temperatures (80-120 °C) and pressures (70-120 MPa). The presence of gas and water in the nanopores was investigated thoroughly. The results showed that the adsorption of water on the Al-O octahedral surface of kaolinite was not affected by external conditions under in situ conditions, whereas the adsorption of water on the Si-O tetrahedral surface decreased with increasing temperature, but the change was small. When ions were present in the system, the water capacity decreased. Based on the aforementioned results, external conditions, such as temperature and pressure do not affect the basic state of water. However, if there are more than two fluid types in the system, the adsorption of water on the mineral surface is reduced owing to competitive adsorption. In addition, a CH4-H2O mixed system was simulated, in which methane molecules were distributed in clusters. There are two types of adsorptions in pores: gas-solid interactions and solid-liquid-gas interactions. CH4 molecules are thought to be clustered in water molecules because of the strong hydrogen bonding interactions among the water.

A quantum mechanics/molecular mechanics study on the hydrolysis mechanism of New Delhi metallo-ß-lactamase-1.

New Delhi metallo-ß-lactamase-1 (NDM-1) has emerged as a major global threat to human health for its rapid rate of dissemination and ability to make pathogenic microbes resistant to almost all known ß-lactam antibiotics. In addition, effective NDM-1 inhibitors have not been identified to date. In spite of the plethora of structural and kinetic data available, the accurate molecular characteristics of and details on the enzymatic reaction of NDM-1 hydrolyzing ß-lactam antibiotics remain incompletely understood. In this study, a combined computational approach including molecular docking, molecular dynamics simulations and quantum mechanics/molecular mechanics calculations was performed to characterize the catalytic mechanism of meropenem catalyzed by NDM-1. The quantum mechanics/molecular mechanics results indicate that the ionized D124 is beneficial to the cleavage of the C-N bond within the ß-lactam ring. Meanwhile, it is energetically favorable to form an intermediate if no water molecule coordinates to Zn2. Moreover, according to the molecular dynamics results, the conserved residue K211 plays a pivotal role in substrate binding and catalysis, which is quite consistent with previous mutagenesis data. Our study provides detailed insights into the catalytic mechanism of NDM-1 hydrolyzing meropenem ß-lactam antibiotics and offers clues for the discovery of new antibiotics against NDM-1 positive strains in clinical studies.

Structure-based computational study of the hydrolysis of New Delhi metallo-ß-lactmase-1.

New Delhi metallo-ß-lactmase-1 (NDM-1) is an enzyme that confers antibiotic resistance to bacteria and is thus a serious threat to human health. Almost all clinically available ß-lactam antibiotics can be hydrolyzed by NDM-1. To determine the mechanism behind the wide substrate diversity and strong catalytic ability of NDM-1, we explored the molecular interactions between NDM-1 and different ß-lactam antibiotics using computational methods. Molecular dynamics simulations and binding free energy calculations were performed on enzyme-substrate (ES) complex models of NDM-1-Meropenem, NDM-1-Nitrocefin, and NDM-1-Ampicillin constructed by molecular docking. Our computational results suggest that mutant residues Ile35 and Lys216, and active site loop L1 residues 65-73 in NDM-1 play crucial roles in substrate recognition and binding. The results of our study provide new insights into the mechanism behind the enhanced substrate binding and wider substrate spectrum of NDM-1 compared with its homologous enzymes CcrA and IMP-1. These insights may be useful in the discovery and design of specific and potent inhibitors against NDM-1.

Three silver iodides with zero and one-dimensional hybrid structures directed by conjugated organic templates: synthesis and theoretical study.

Under the direction of large conjugated organic cationic SDAs (structure-directing agents), three silver(I) iodides, (ipq)4(Ag2I6 x 2I2) (1), {[pql][Ag2I3]}n (2), [(npql)2(Ag4I6)]n (3) (ipq+ = N-(isopentyl)-quinolinium, pql+ = N-propyl-quinolinium, npql+ = N-(n-pentyl)-quinolinium) have been synthesized. 1 presents a zero-dimensional structure constituting of ipq+ cations, [Ag2I6]4- anions and molecular iodine. But 2 and 3 consist of one-dimensional coordination polymers that could be described as edge-sharing AgI4 tetrahedra. Electrostatic interactions between organic counter cations and inorganic moieties are present and contribute to the crystal packing. The structural differences between 1, 2 and 3 illustrate the influences of substituents of SDAs on the linkage modes of AgI4 tetrahedra. DFT calculations were carried out to reveal their electronic structures.

Multivalency iodine doped TiO2: preparation, characterization, theoretical studies, and visible-light photocatalysis.

Multivalency iodine (I(7)+/I(-)) doped TiO(2) were prepared via a combination of deposition-precipitation process and hydrothermal treatment. The as-prepared samples were characterized by X-ray diffraction, transmission electron microscopy, Brunauer-Emmett-Teller surface area, UV-vis diffuse reflectance spectra, X-ray photoelectron spectroscopy, surface photovoltage spectroscopy, and electric-field-induced surface photovoltage spectroscopy. The electronic structure calculations based on the density functional theory revealed that upon doping, new states that originated from the I atom of the IO(4) group are observed near the conduction-band bottom region of TiO(2), and the excitation from the valence band of TiO(2) to the surface IO(4-) is responsible for the visible-light response of the I-doped TiO(2). The as-prepared I-doped TiO(2) showed high efficiency for the photocatalytic decomposition of gaseous acetone under visible light irradiation (lambda > 420 nm). A possible mechanism for the photocatalysis on this multivalency iodine (I(7)+/I(-)) doped TiO(2) under visible light was also proposed.

A series of new copper iodobismuthates: structural relationships, optical band gaps affected by dimensionality, and distinct thermal stabilities.

Three new copper iodobismuthates, red tetranuclear [n-Bu(4)N][Cu(2)(CH(3)CN)(2)Bi(2)I(10)] (1), dark-red infinite linear [Et(4)N](2n)[Cu(2)Bi(2)I(10)](n) (2), and black polymeric ladderlike [Cu(CH(3)CN)(4)](2n)[Cu(2)Bi(2)I(10)](n) (3), crystallize from solutions of BiI3 and CuI in the presence of different cations. A regular structural relationship from 0-D (1) to 1-D linear anion chains (2) to 1-D ladderlike anion chains (3) is observed. The self-assembly of the basic building unit Cu(2)Bi(2)I(10) as altered by different cations is proposed to be the driving force for their formation. The optical band gaps exhibit a structure-related decrease from 1 to 2/3, in agreement with their color changes and the density functional theory (DFT) calculation results. The electronic structures and the relationship with corresponding monobismuth analogues and the Ag-Bi isotypes are discussed on the basis of DFT calculations. In spite of their structural similarities, the compounds are distinctive thermally: 2 is stable to 230 degrees C, 1 undergoes a solvent loss at 85 degrees C to form a new phase that is thermally stable to 230 degrees C, and 3 releases a solvent molecule and decomposes at 80 degrees C into BiI(3) and CuI. The essential reasons for these differences are discussed.

Spontaneous conversion between mutL and 6 bpDeltamutL in Salmonella typhimurium LT7: association with genome diversification and possible roles in bacterial adaptation.

Previously, we reported the phenomenon of genome diversification in Salmonella typhimurium LT7, i.e., individual strains derived from LT7 kept changing the genome structure by inversions, translocations, duplications, and mutations. To elucidate the genetic basis, we sequenced selected genes of the mismatch repair (MMR) system for correlations between MMR defects and genome diversification. We chose S. typhimurium LT7 mutants 8111F2 and 9052D1 for mut gene sequence analyses and found that both mutants had a deletion of one of three tandem 6-bp repeats, GCTGGC GCTGGC GCTGGC, within mutL, which was designated 6 bpDeltamutL. mutS and mutH genes were unchanged in the mutants analyzed. Some sublines of 8111F2 and 9052D1 spontaneously stopped the genome diversification process at certain stages during single-colony restreaking passages, and in these strains the 6 bpDeltamutL genotype also became wild-type mutL. We conclude that conversion between mutL and 6 bpDeltamutL occurs spontaneously and that transient defects of mutL facilitate genome diversification without leading to the accumulation of multiple detrimental genetic changes. Spontaneous conversion between mutL and 6 bpDeltamutL may be an important mechanism used by bacteria to regulate genetic stability in adaptation to changing environments.

Diverse genome structures of Salmonella paratyphi C.

BACKGROUND: Salmonella paratyphi C, like S. typhi, is adapted to humans and causes typhoid fever. Previously we reported different genome structures between two strains of S. paratyphi C, which suggests that S. paratyphi C might have a plastic genome (large DNA segments being organized in different orders or orientations on the genome). As many but not all host-adapted Salmonella pathogens have large genomic insertions as well as the supposedly resultant genomic rearrangements, bacterial genome plasticity presents an extraordinary evolutionary phenomenon. Events contributing to genomic plasticity, especially large insertions, may be associated with the formation of particular Salmonella pathogens. RESULTS: We constructed a high resolution genome map in S. paratyphi C strain RKS4594 and located four insertions totaling 176 kb (including the 90 kb SPI7) and seven deletions totaling 165 kb relative to S. typhimurium LT2. Two rearrangements were revealed, including an inversion of 1602 kb covering the ter region and the translocation of the 43 kb I-CeuI F fragment. The 23 wild type strains analyzed in this study exhibited diverse genome structures, mostly as a result of recombination between rrn genes. In at least two cases, the rearrangements involved recombination between genomic sites other than the rrn genes, possibly homologous genes in prophages. Two strains had a 20 kb deletion between rrlA and rrlB, which is a highly conservative region and no deletion has been reported in this region in any other Salmonella lineages. CONCLUSION: S. paratyphi C has diverse genome structures among different isolates, possibly as a result of large genomic insertions, e.g., SPI7. Although the Salmonella typhoid agents may not be more closely related among them than each of them to other Salmonella lineages, they may have evolved in similar ways, i.e., acquiring typhoid-associated genes followed by genome structure rearrangements. Comparison of multiple Salmonella typhoid agents at both single sequenced genome and population levels will facilitate the studies on the evolutionary process of typhoid pathogenesis, especially the identification of typhoid-associated genes.

Chemical anisotropies of carbon nanotubes and fullerenes caused by the curvature directivity.

The directional-curvature theory is developed as a rational basis for the strain energy and the chemical reactivity in single-walled carbon nanotubes (SWCNTs) and fullerenes. The directional curvature KD and its mean KM, derived from this theory, cover the overall curvatures of their bonds and atoms and break through the limitations of the pyramidalized-angle thetap approach, which is only available to atomic curvature. The directional-curvature theory demonstrates that KD and KM depend directly on the strain or reactive binding energies of the bonds and atoms and that there is approximate curvature conservation in SWCNTs and fullerenes. Application of this theory to addition reactions of various SWCNTs and fullerenes shows that the slope of the straight line between the strain or binding energies and KD is close to a constant, which helps clarify the puzzle as to why some functionalizations of C70 occur at the relatively flat midsection.

Silver iodobismuthates: syntheses, structures, properties, and theoretical studies of [Bi2Ag2I10 2-]n and [Bi4Ag2I16 2-]n.

Two novel silver iodobismuthates have been obtained: (Et4N)2n-[Bi2Ag2I10]n (1) with one-dimensional infinite chains built from bimetallic tetranuclear units and (Et4N)2n[Bi4Ag2I16]n (2) with a two-dimensional 44 grid assembly of the tetranuclear Bi4I16 subunits as nodes and Ag atoms as linkages. Their optical band gaps, 2.05 and 1.93 eV, fit nicely in a size correlation of the Bi/I subunit, which is further supported by the density functional theory studies.

Carbon nanotubes functionalized by NO2: coexistence of charge transfer and radical transfer.

The adsorption of NO(2) molecules on a series of zigzag (n,0) single-walled carbon nanotubes (SWNTs) (n = 6-12) have been investigated by first-principles methods. The results indicate that the tube diameter and the concentration of NO(2) gas determine the interactions between NO(2) molecules and the tube. The chemisorption of a single NO(2) is only possible for the tube with a small diameter (n < 10), while the second NO(2) molecule can be chemisorbed for all tubes studied here. The additions of more NO(2) molecules in different patterns have also been considered for a (8,0) tube, and the NO(2) groups prefer the pair arrangement with stronger binding energy. According to the results of band structure calculations, overall, the SWNT exhibits a p-type response upon exposure to NO(2) gas and the electron charge transfer is an important reason for explaining the enhancement of conductivity of the tube. Moreover, it is interesting that, accompanied by charge transfer, the chemisorption of NO(2) also leads to the radical transfer from the NO(2) group to the carbon atoms at the ortho and para sites of the six-membered ring. As a result, the SWNT possesses the radical characteristic, which facilitates the further functionalization of the tube wall.

Dissociative adsorption of carbon monoxide on Mo(110): first-principles theory.

The adsorption and dissociation of carbon monoxide on Mo (110) surface is studied with density functional theory. The results at different sites (atop, short bridge, long bridge, and hollow) are presented. The hollow site is found to be the most stable adsorption site for CO. The CO molecule is found to adsorb in end-on configurations (alpha states) at high coverage and inclined configurations (beta states) at low coverage. The dissociation activation energy from beta states is found to be approximately 1 eV lower than from alpha state. The adsorption of dissociation products, C and O, on Mo(110) has also been studied. The most stable adsorption site for C and O is long bridge and hollow site, respectively. The adsorption of C and O at low coverage is, in general, stronger than at high coverage, which is partly responsible for the high reactivity of CO dissociation at low coverage, since the binding energy of CO is not very sensitive to the coverage.

The cycloadditions of various substituted carbenes, silylenes, and germylenes onto the diamond (100) surface: a theoretical exploration.

The cycloadditions of 21 singlet substituted carbenes, silylenes, and germylenes onto the diamond (100) surface have been theoretically studied by means of density functional theory coupled with effective cluster models. The calculated reaction energies and reaction pathways have disclosed that the substituents play an important effect on the reaction profiles for the additions of carbenes, silylenes, and germylenes onto the diamond (100) surface. Our theoretical investigations illustrate that, irrespective of carbenes, silylenes, and germylenes, the cycloadditions of those with electropositive substituents (such as H and CH(3)) onto diamond (100) are much more favorable than those with electronegative and pi-donating substituents (such as F and NH(2)) both thermodynamically and kinetically. In broad perspective, we believe that a similar reactivity trend can also be extended to that of Si (100), Ge (100), fullerene, single-walled carbon nanotube, disilenes, digermenes, silenes, and germenes because all of these materials feature an analogous bonding motif.

Predicting facile epoxidation of the diamond (100) surface by dioxiranes and subsequent ring-opening reactions with nucleophiles.

By means of density functional theory coupled with effective cluster models, we have theoretically predicted the viability of epoxidation of the diamond (100) surface by organic dioxiranes. In addition, subsequent ring-opening reactions of the as-formed epoxide surface species with some nucleophiles, including water, ammonia, and alcohol, have also been explored. The facile epoxidation of diamond (100) by dioxiranes presents a new alternative for oxidation of the diamond (100) surface. More importantly, the as-formed epoxide-like surface species would be a useful springboard for further functionalizations of the diamond surface given the well-known abundant chemistry of organic epoxides. Therefore, this approach provides another new route to chemical functionalization of the diamond surface, which is potentially useful for leading to the improvement of diamond behavior and constructing new hybrid diamond-based materials for wide potential applications in many fields. In perspective, implications for other theoretical work are also discussed.

Structural characterizations and electronic properties of Ti-doped SnO2(110) surface: a first-principles study.

The Ti-doped SnO2(110) surface has been investigated by using first-principles method with a slab model. The geometrical optimizations and band-structure calculations have been performed for four possible doping models. Our results indicate that the substitution of Ti for sixfold-coordinated Sn atom at the top layer is most energetically favorable. Compared to the undoped surface, those Sn and O atoms located above Ti atom tend to move toward the bulk side. Besides the surface relaxations, the doping of Ti has significant influences on the electronic structures of SnO2(110) surface, including the value and position of minimum band gap, the components of valence and conduction bands, the distributions of the charge densities, and the work function of the surface. Furthermore, the effects introduced by the substitution of Ti atom observed in the experiments can be well explained when the sixfold-coordinated Sn atom at the first layer is replaced by Ti atom.

Organic functionalization of the Si (100) and Ge (100) surfaces by cycloadditions of carbenes and nitrenes: a theoretical prediction.

By means of density functional theory (B3LYP/6-31G*) coupled with effective cluster models, we predict that the well-known cycloaddition reactions of carbenes and nitrenes to alkenes in organic chemistry can be employed as a new type of surface reaction to organically functionalize the Si (100) and Ge (100) surfaces at low temperature. The well-established abundance of carbenes and nitrenes addition chemistry in organic chemistry provides versatile flexibility of functionalizing the surfaces of Si (100) and Ge (100), which can potentially impart new organic functionalities to the semiconductors surface for novel applications in a diversity of fields. Our predictions strongly advance the concept of using organic reactions to modify the solid surface in a controlled manner and quite intriguing chemistry can lie in the material featuring the analogous bonding motif. In further perspective, implications for other theoretical work, regarding disilenes, digermenes, silenes, and germenes that all feature the bonding motif similar to alkenes, are also discussed.

Functionalization of diamond (100) by organic cycloaddition reactions of nitrenes: a theoretical prediction.

[structure: see text] We predict the viability of organic cycloadditions of nitrenes onto the diamond (100) surface. This new type of surface reaction can be employed to functionalize diamond surface at low temperature, which might introduce new functionalities to the diamond surface for novel applications in a diversity of fields.

[Hepatitis B virus genotypes and alanine aminotransferase levels in HBeAg negative patients with chronic hepatitis B and liver cirrhosis].

OBJECTIVE: To investigate genotypes of the hepatitis B virus (HBV) and alanine aminotransferase (ALT) levels of HBeAg negative patients with chronic hepatitis B and liver cirrhosis. METHODS: HBV serological markers and ALT levels were detected in 62 patients with chronic hepatitis B and 41 cases with liver cirrhosis, using enzyme linked absorbent immunoassays and an enzyme method, respectively. A polymerase chain reaction of S region was used for HBV genotyping. RESULTS: Of the 62 patients with chronic hepatitis B, 21 (33.9%) were HBeAg negative, and 41 (66.1%) HBeAg positive. Among 41 cases with liver cirrhosis, 28 (68.3%) were HBeAg negative, and 13 (31.7%) HBeAg positive. Of these 62 patients with chronic hepatitis B, 53 (85.5%) were infected with HBV genotype C, and 9 (14.5%) with genotype B. Thirty-nine (95.1%) of the 41 patients with liver cirrhosis were infected with genotype C, and 2 (4.9%) with genotype B. The proportion of HBeAg negative chronic hepatitis B patients with ALT level > 40 U/L was lower than that of the HBeAg positive group (47.6% and 85.4%, respectively) (P < 0.01). The percentage of ALT levels > 40 U/L of the negative patients with liver cirrhosis was also lower as compared to that of the HBeAg positive patients, but there was no statistical difference between the two groups, because of the small sample size (P > 0.05). CONCLUSION: The proportion of HBeAg negative patients is high in the group of chronic hepatitis B and liver cirrhosis. These patients have relatively low ALT levels, and mainly have HBV genotype C infection.

Organic functionalization of diamond (100) by addition reactions of carbene, silylene, and germylene: a theoretical prediction.

We present a theoretical prediction of the facile cycloadditions of carbene, silylene, and germylene onto the diamond (100) surface, a new type of surface reaction that can be employed to functionalize diamond surface at low temperature. This finding renders the plausibility that the diamond surface can be chemically modified by the well-known carbene addition chemistry, which might introduce new functionalities to the diamond surface for novel applications in a diversity of fields.