Atomically Thin Mesoporous In2O3–x/In2S3 Lateral Heterostructures Enabling Robust Broadband‐Light Photo‐Electrochemical Water Splitting

Atomically thin 2D heterostructures have opened new realms in electronic and optoelectronic devices. Herein, 2D lateral heterostructures of mesoporous In₂O_3–x/In₂S₃ atomic layers are synthesized through the in situ oxidation of In₂S₃ atomic layers by an oxygen plasma‐induced strategy. Based on experimental observations and theoretical calculations, the prolonged charge carrier lifetime and increased electron density reveal the efficient photoexcited carrier transport and separation in the In₂O_3–x/In₂S₃ layers by interfacial bonding at the atomic level. As expected, the synergistic structural and electronic modulations of the In₂O_3–x/In₂S₃ layers generate a photocurrent of 1.28 mA cm^?2 at 1.23 V versus a reversible hydrogen electrode, nearly 21 and 79 times higher than those of the In₂S₃ atomic layers and bulk counterpart, respectively. Due to the large surface area, abundant active sites, broadband‐light harvesting ability, and effective charge transport pathways, the In₂O_3–x/In₂S₃ layers build efficient pathways for photoexcited charge in the 2D semiconductive channels, expediting charge transport and kinetic processes and enhancing the robust broadband‐light photo‐electrochemical water splitting performance. This work paves new avenues for the exploration and design of atomically thin 2D lateral heterostructures toward robust photo‐electrochemical applications and solar energy utilization.     

A DFT study of adsorption and decomposition of hexahydro-1,3,5-trinitro-1,3,5-triazine on Mg(0001) surface

The adsorption and decomposition of hexogen (RDX) molecule on the Mg(0001) surface were investigated by the generalized gradient approximation (GGA) of density functional theory (DFT). The calculations employed a supercell (4?×?4?×?4) slab model and three-dimensional periodic boundary conditions. The strong attractive forces between RDX molecule and magnesium atoms induce the RDX’s N???O bond breaking. Subsequently, the dissociated oxygen atoms and radical fragment of RDX oxidize the Mg surface. The largest adsorption energy is ?2104.0 kJ mol^-1. We also investigated the decomposition mechanism of RDX molecule on the Mg(0001) surface. The activation energy for the dissociation step of configuration V4 is as small as 2.5 kJ mol^-1, while activation energies of other configurations are much larger, in the range of 964.9–1375.1 kJ mol^-1. Mg powder is more active than Al powder, and Mg powder performs better in increasing the combustion exothermicity of RDX as well.     

Fluorination of BC3 nanotubes: DFT studies

We have studied the adsorption of atomic and molecular fluorines on a BC₃ nanotube by using density functional calculations. It was found that the adsorption of atomic fluorine on a C atom of the tube surface is energetically more favorable than that on a B atom by about 0.97 eV. The adsorption of atomic fluorine on both C and B atoms significantly affects the electronic properties of the BC₃ tube. The HOMO-LUMO energy gap is considerably reduced from 2.37 to 1.50 and 1.14 eV upon atomic F adsorption on B and C atoms, respectively. Molecular fluorine energetically tends to be dissociated on B atoms of the tube surface. The associative and dissociative adsorption energies of F₂ were calculated to be about ?0.42 and ?4.79 eV, respectively. Electron emission density from BC₃ nanotube surface will be increased upon both atomic and molecular fluorine adsorptions due to work function decrement.     

Theoretical guidance and experimental confirmation on catalytic tendency of M-CeO2 (M = Zr,Mn, Ru or Cu) for NH3-SCR of NO

Abstract

Herein, we demonstrate that the degrees of catalytic performance of M-CeO₂-based catalysts (M=Mn, Cu, Ru or Zr) for an ammonia selective catalytic reduction (NH₃-SCR) of nitric-oxide (NO) can be estimated using three theoretical terms; (i) an oxygen vacancy formation energy of a catalyst, (ii) an adsorption energy of NO and (iii) an adsorption energy of NH₃. Those terms predict the trend of the catalytic performance as the order; Mn–CeO₂ > Cu–CeO₂ > Ru–CeO₂ > Zr–CeO₂ > CeO₂. To verify the theoretical prediction, the catalysts were synthesized and tested their performances on the NH₃-SCR of NO reaction. The normalized NO conversion rates at low temperatures (100–200 °C) were measured for Mn–CeO₂, Cu–CeO₂, Ru–CeO₂, Zr–CeO₂ and CeO₂ as 2.61–7.46, 1.30–6.82, 0.73–3.02, 0.81–3.31 and 1.55–2.33 mol s^?1 m^?2, respectively. In addition, a concept of a structure-activity relationship analysis shows a strong relationship between theoretical and experimental results. Consequently, an application of predicting the catalytic performance of catalysts from theoretical calculations prior the catalyst synthesis is useful in catalyst design and screening that can reduce time and cost.     

A new era of the prototropic tautomerism of the quercetin molecule: A QM/QTAIM computational advances

Abstract

In this study for the first time we have revealed and investigated in details 123 different prototropic tautomers of the most stable conformer of the quercetin molecule using quantum-mechanical calculations at the MP2/6-311++G(2df,pd)//B3LYP/6-311++G(d,p) level of QM theory. We have found that in the most energetically favorable prototropic tautomer mobile hydrogen atoms are localized at the О3, О3′, О4′, О5, and О7 exocyclic oxygen atoms. Molecular tautomers are in the range of the Gibbs free energies from 0.0 to 69.8?kcal·mol^?1, while zwitterionic ones – from 30.1 до 172.8?kcal·mol^?1 at normal conditions. It was also reliably established that the weakest point causing the decyclization of the molecule is its C ring – this reaction is launched by the transition of the proton from the C8H group to the endocyclic O1 oxygen atom. All prototropic tautomers, except two cases, are joined by the intramolecular cooperative specific interactions (from 1 to 5) – H-bonds and attractive van der Waals contacts, which have been revealed and characterized by QTAIM analysis.

Communicated by Ramaswamy H. Sarma     

Microbial Allyl Rearrangement and Resolution of Acetates of Unsaturated Cyclic Terpene Alchols by Pseudomonas sp. NOF-5 Strain

Microbial hydrolysis of the acetates of unsaturated cyclic terpene alcohols by Pseudomonas sp. NOF-5 isolated from soil was investigated. (±)-trans-Carveyl acetate ((±)-trans-3) was enantio-selectively hydrolyzed with NOF-5 strain to give ( – )-trans-carveol (( – )-trans-2 of 86.6% optical purity). However, the hydrolysis of (±)-cis-3 was less enantioselective, while (±)-piperitylacetate ((±)-6, a cis and trans mixture) was hydrolyzed to give the ( – )-trans- and ( – )-cis-piperitols (( – )- trans-5 and ( – )-cis-5) in a poor optical yield. In this case, other tert-alcohols, ( + )-trans- and ( – )- ds-2-p-menthen-1-ols ((±)-trans-7 and ( – )-cis-7), were also produced. Furthermore, microbial and enzymic allyl rearrangements of ( + )-trans-6 and ( – )-trans-verbenylacetate (( – )-trans-11) were studied. Biological treatment of (+)-trans-6 and ( – )-trans-11 with NOF-5 or its esterase gave (+)-trans- and (-)-cis-1 and ( + )-cis-3-pinen-2-ol (( + )-cis-12), respectively.     

Impact of Hydroxylation and Hydration on the Reactivity of α‐Fe2O3 (0001) and (102) Surfaces under Environmental and Electrochemical Conditions

Hematite (α‐Fe₂O₃) is widely used as a catalytic electrode material in photo‐electrochemical water oxidation, where its surface compositions and stabilities can strongly impact the redox reaction process. Here, its surface configurations in environmental or electrochemical conditions are assessed via density functional theory (DFT) calculations conducted at the Perdew, Burke, and Ernzerhof (PBE)+U level. The most energetically favorable surface domains of α‐Fe₂O₃ (0001) and (102) are predicted by constructing the surface phase diagrams in the framework of first‐principle thermodynamics. The relative surface stabilities are investigated as a function of partial pressures of oxygen and water, temperature, solution pH, and electrode potential not only for perfect bulk terminations but also for defect‐containing surfaces having various degrees of hydroxylation and hydration. In order to assess the impact on the redox reactions of the surface planes as well as of the extent of surface hydration/hydroxylation, the thermodynamics of the four‐step oxygen evolution reaction (OER) mechanism are examined in detail for different models of the α‐Fe₂O₃ (0001) and (102) surfaces. Importantly, the results underline that the nature of the surface termination and the degree of near‐surface hydroxylation give rise to significant variations in the OER overpotentials.     

Structure and adsorption properties of MoO3: insights from periodic density functional calculations

Structure and electronic properties of MoO₃ bulk and the (010) surface, as well as molecular adsorption of water on the (010) surface are investigated using periodic boundary density functional calculations. The bulk structure is calculated to be in good agreement with experiment. The structure and electronic properties of the (010) surface are confirmed to be very similar to those of the bulk. The terminal oxygen in both the bulk and the (010) surface is the least ionic among the three types of lattice oxygens. This study shows that the molecular adsorption of H₂O hardly takes place at the asymmetric and symmetric oxygens, but occurs at the terminal oxygen of the (010) surface. The results of the H₂O adsorption on the (010) at 1 and 0.5 monolayer coverages are interpreted based on charge-transfer interactions between the surface and H₂O species, and provide key information about the structural and energetic properties, in which each stable adsorption structure is suggested to orient on the surface via hydrogen bonding. These results also provide novel model systems for understanding the structure and adsorption states of MoO₃.     

Intensity of mineralization processes in mountain lakes in NW Slovenia

The potential and actual intensity of mineralization in sediments of fourteen mountain lakes and one subalpine lake in NW Slovenia have been measured. Potential mineralization was measured as the intensity of the electron transport system (ETS) activity of microzoobenthos and microbial communities and the actual mineralization as the oxygen consumption of respiration processes, both measured at a standard temperature of 20°C. The lakes are of different trophic levels and some exhibit seasonal anoxia. All but one are hardwater lakes. Two layers of sediment cores from the deepest point of the lakes were analysed: a surface layer and one below 15 cm. Significant differences among different lakes in their ETS activity and oxygen consumption in the surface and lower layers of sediment were observed. ETS activities and oxygen consumption rates were higher in the surface layers of all the lakes. From the three investigated deterministic factors (temperature, lake depth and total phosphorus in the water column) on sedimentary metabolism ETS activity in the surface layer correlated significantly with total phosphorus and lake depth, but oxygen consumption rate showed a significant correlation only with total phosphorus. The relationship between oxygen consumption and ETS activity was also investigated. ETS activities correlated with oxygen consumption rates according to the equation of logR = 0.421^* logETS + 0.898 (r=0.82; n=30; p<0.001). The R/ETS ratio was lower at the sediment surface than in the layers deeper than 15 cm. It is concluded that ETS activity and oxygen consumption are good indicators of the intensity of the metabolic activity and mineralization in lake sediments. As the characteristics of lakes and some environmental factors influence the ETS activity and the oxygen consumption differently, the same R/ETS ratio should not be used as conversion factor in calculations for different lakes.     

Benchmarking of ONIOM method for the study of NH<Subscript>3</Subscript> dissociation at open ends of BNNTs

The reliability of ONIOM approach have been examined in calculations of adsorption energies, transition structures, change of HOMO-LUMO energy gaps and equilibrium geometries of the interaction between NH₃ and N-enriched (A) or B-enriched (B) open ended boron nitride nanotubes. To these ends, four models of the A or B, with different inner and outer layers have been studied. In addition, various low-levels including, AM1, PM3, MNDO and UFF have been examined, applying B3LYP/6-31 G* in all high-levels. It was shown, that in the case of A, (choosing two atom layers of the tube open-end as inner layer) the results of ONIOM approach are in best agreement with those of the pure density functional theory (DFT) calculations, while their results significantly differ from those of DFT in the case of B in same conditions. All above and population analysis demonstrate that the ONIOM may be a reliable scheme in the study of weak interactions while it is a controversial approach and should be applied cautiously in the case of strong interactions. We also probed the effect of tube length and diameter on the consistency between ONIOM and DFT results, showing that this consistency is independent of the mentioned parameters.     

Quantifying CaCO3 Microprecipitates Within Developing Surface Mats of Marine Stromatolites Using GIS and Digital Image Analysis

The unique geochemical coupling of organic molecules and mineral CaCO₃ provides a fluorescence signature detectable using conventional confocal scanning laser microscopy (CSLM). The surface microbial mats of open-water marine stromatolites (Bahamas) exist in a continuum of states ranging from a Type 1 (i.e., nonlithifying) to Type 2 (i.e., lithified micritic laminae present) to Type 3 (i.e., fused grain layer). An approach was developed here, that utilizes geographical information systems (GIS) and digital image analysis, coupled with CSLM to estimate concentrations of calcium carbonate precipitates in developing marine stromatolites. We propose that the area occupied by particles within each image can be used to estimate concentrations of precipitates. Fluorescent polymeric microbeads and bacteria were used to calibrate the approach. We used this approach to demonstrate that CaCO₃ precipitates in lithifying layers were quantifiable and significantly different (p < 0.0001) from those in nonlithifying layers. The approach provided a useful tool for the unambiguous assessment of relative changes in microbial precipitates occurring over small ( μ m to mm) spatial scales, and that characterize the formation of lithified layers (micritic laminae) in open-water marine stromatolites.     

Adsorption and decomposition mechanism of hexogen (RDX) on Al(111) surface by periodic DFT calculations

The adsorption of hexogen (RDX) molecule on the Al(111) surface was investigated by the generalized gradient approximation (GGA) of density functional theory (DFT). The calculations employ a supercell (4×4×3) slab model and three-dimensional periodic boundary conditions. The strong attractive forces between RDX molecule and aluminum atoms induce the N?O and N?N bond breaking of the RDX. Subsequently, the dissociated oxygen atoms, NO₂ group and radical fragment of RDX oxidize the Al surface. The largest adsorption energy is ?835.7 kJ mol^–1. We also investigated the adsorption and decomposition mechanism of RDX molecule on the Al(111) surface. The activation energy for the dissociation steps of V4 configuration is as large as 353.1 kJ mol^–1, while activation energies of other configurations are much smaller, in the range of 70.5–202.9 kJ mol^–1. The N?O is even easier than the N?NO₂ bond to decompose on the Al(111) surface.     

Quinolinones Alkaloids with AChE Inhibitory Activity from Mangrove Endophytic Fungus Penicillium citrinum YX-002

Acetylcholinesterase (AChE) inhibitory activity-guided studies on the mangrove-derived endophytic fungus Penicillium citrinum YX-002 led to the isolation of nine secondary metabolites, including one new quinolinone derivative, quinolactone A ( 1 ), a pair of epimers quinolactacin C1 ( 2 ) and 3-epi-quinolactacin C1 ( 3 ), together with six known analogs ( 4 – 9 ). Their structures were elucidated based on extensive mass spectrometry (MS) and 1D/2D nuclear magnetic resonance (NMR) spectroscopic analyses, and compared with data in the literature. The absolute configurations of compounds 1 – 3 was determined by combination of electronic circular dichroism (ECD) calculations and X-Ray single crystal diffraction technique using CuK_α radiation. In bioassays, compounds 1 , 4 and 7 showed moderate AChE inhibitory activities with IC₅₀ values of 27.6, 19.4 and 11.2 μmol/L, respectively. The structure-activity relationships (SARs) analysis suggested that the existence of carbonyl group on C-3 and the oxygen atom on the five-membered ring were beneficial to the activity. Molecular docking results showed that compound 7 had a lower affinity interaction energy (−9.3 kcal/mol) with stronger interactions with different sites in AChE activities, which explained its higher activities.     

Ab initio Investigation of the Molecular Structure of Methyl Methoxymethyl Phosphonate,a Promising Nuclease-resistant Alternative of the Phosphodiester Linkage

Abstract

Conformational flexibility of the methyl methoxymethyl phosphonate anion (CH₃-O-PO₂- CH₂-O-CH₃)^?, a nuclease resistant alternative to the phosphodiester linkage in DNA, have been investigated by ab initio quantum mechanical calculations. The potential of backbone torsional degrees of freedom of methyl methoxymethyl phosphonate anion (MMP) was determined at the Hartree-Fock (HF) 3–21G* level using the adiabatic mapping technique. Energies, geometries, and effective atomic charges of different conformers were calculated at HF/6–31G* and MP2/6–31G* levels of theory. These were compared to the results obtained for dimethyl phosphate calculated at the same level. The impact on DNA structure from inserting a methylene group between phosphorus and oxygen of the nucleoside sugar moiety was examined via distance- and angle-constrained geometry optimizations. Due to its high flexibility, MMP has been shown to be compatible with both A and B forms of DNA.     

东海北部滨海湿地铁氧化细菌的分布及其对不同氧气穿透深度的响应

【目的】滨海湿地生态系统位于淡水与海水交互地带,含有高浓度Fe²⁺的地下水渗透到沉积物表层形成的湿地径流和周期性潮汐淹水形成的含氧-缺氧界面有利于铁氧化细菌介导的Fe²⁺的生物氧化过程发生。然而,目前缺乏对滨海湿地生态系统中铁氧化细菌类群的全面评估。【方法】以上海崇明西沙湿地公园及浙江舟山市朱家尖岛东沙沙滩两地共5处滨海湿地沉积物为研究对象,分析沉积物的氧气穿透深度等环境参数,并基于16S rRNA基因扩增子测序技术,全面解析不同滨海湿地生态系统中细菌与铁氧化细菌的群落组成与分布特征。【结果】与崇明西沙湿地相比,朱家尖岛东沙沙滩有更深的氧气穿透深度,达到10 mm以上。非度量多尺度分析(non-metric multidimensional scaling, NMDS)统计结果表明,细菌群落结构主要受到区域位置不同导致的环境条件差异的影响,而铁氧化细菌的群落结构则受到采样的区域位置和沉积物氧气穿透深度的共同影响。崇明西沙湿地和朱家尖岛东沙沙滩的优势细菌为蓝细菌门(Cyanobacteria)、γ-变形菌纲(Gammaproteobacteria)、拟杆菌门(Bacteroidetes)、α-变形菌纲(Alphaproteobacteria)和放线菌门(Actinobacteria);优势铁氧化细菌为嘉利翁氏菌属(Gallionella)、红细菌属(Rhodobacter)、Lepthothrix和Sideroxydans。【结论】通过对崇明西沙湿地和朱家尖岛东沙沙滩沉积物中栖息的铁氧化菌的调查发现,铁氧化细菌的群落组成与湿地沉积物类型导致的氧气穿透深度差异具有密切联系。     

Multipole electrostatic potential derived atomic charges in NDDO-methods with <Emphasis Type="Italic">spd</Emphasis>-basis sets

The recently introduced multipole approach for computing the molecular electrostatic potential (MEP) within the semiempirical neglect of diatomic differential overlap (NDDO) framework [Horn AHC, Lin Jr-H., Clark T (2005) Theor Chem Acc 114:159–168] has been used to obtain atomic charges of nearly ab initio quality by scaling the semiempirical MEP. The parameterization set comprised a total of 797 compounds and included not only the newly parameterized AM1* elements Al, Si, P, S, Cl, Ti, Zr, and Mo but also the standard AM1 elements H, C, N, O and F. For comparison, the ZDO-approximated MEP was also calculated analytically in the spd-basis. For the AM1*-optimized structures, single-point calculations at the B3LYP, HF and MP2 levels with the 6-31G(d) and LanL2DZP basis sets were performed to obtain the MEP. The regression analysis of all 12 combinations of semiempirical and ab initio MEP data yielded correlation coefficients of at least 0.99 in all cases. Scaling the analytical and multipole-derived semiempirical MEP by the regression coefficients yielded mean unsigned errors below 2.6 and 1.9 kcal mol⁻¹, respectively. Subsequently, for 22 drug molecules from the World Drug Index, atomic charges were computed according to the RESP procedure using XX/6-31G(d) (XX=B3LYP, HF, MP2) and scaled AM1* multipole MEP; the correlation coefficients obtained are 0.83, 0.85 and 0.83, respectively. Figure: Schematic representation of the atomic charge generation: The molecular electrostatic potential (MEP) is calculated using the AM1* Hamiltonian; then the semiempirical MEP is scaled to DFT or ab initio level, and atomic charges are generated subsequently by the restraint electrostatic potential (RESP) fit method. Electronic supplementary material Supplementary material is available in the online version of this article at and is accessible to authorized users. Proceedings of “Modeling Interactions in Biomolecules II”, Prague, September 5th–9th, 2005.     

2-Methylwyosine,a Nucleoside With Restricted Anti Conformation in the East Region Enforced by Nucleobase Moiety Modification: Synthesis and Conformational Analysis by NMR and Molecular Dynamics

GRAPHICAL ABSTRACT

We synthesized a new 2-methyl derivative of wyosine using a multistep procedure starting from guanosine. We examined different synthetic paths and optimized the conditions for each step. Based on MD calculations and analysis of the ³ J _HH and J _C1′H1′ of the ribose moiety, we discovered that the sugar part adopted conformation specific for the East region rarely occurring in solution. This unusual conformational preference is probably due to steric repulsions between the methyl group at position 2 and the 5′-CH₂OH group. We observed that N-glycosidic bond stability weakened 14-fold upon the introduction of the methyl group in position 2 compared with wyosine.     

Proteomic profile of the saliva and plasma protein layer adsorbed on Ti–Zr alloy: the effect of sandblasted and acid-etched surface treatment

Abstract

Titanium–zirconium (Ti–Zr) alloy has been widely used as a biomaterial for implant devices, and it is commonly treated by sandblasting followed by acid etching (SLA) to improve biological responses. Although protein adsorption is the first biological response, the effect of this SLA treatment on the proteomic profile of proteins adsorbed from saliva and blood plasma has not been tested. In this study, the proteomic profile was evaluated by liquid chromatography coupled with tandem mass spectrometry (LC–MS/MS). Streptococcus sanguinis was used to test whether the protein layer affects bacterial adhesion. SLA treatment affected the proteomic profile, showing exclusive proteins adsorbed from saliva (14) and plasma (3). However, both groups exhibited close patterns of intensity for common proteins, molecular functions and biological processes mediated by proteins. Interestingly, Ti–Zr_SLA showed higher bacterial adhesion (～1.9 fold over) for the surface coated with plasma proteins. Therefore, SLA treatment of Ti–Zr alloy changed the proteomic profile, which may affect bacterial adhesion.