Aliphatic Side Chains Research Articles

Multiscale Simulation of Carbonate-Based Electrolytes for Li-Ion Battery

Organic electrodes have been extensively studied for their application as cathode materials for Li-ion battery due to their relatively inexpensive synthesis, earth-abundant precursors, and their high-rate capabilities. In our previous studies, we developed hybrid machine learning-density functional theory protocols to predict and analyze the redox potentials for novel organic moieties. Although the prediction of the electrochemical activity is critical for the design of high energy density cathodes, one of the most detrimental challenges facing the practical application of organic electrode materials is their dissolution by liquid electrolytes. Therefore, it is necessary to investigate several avenues to curb this undesirable dissolution by the electrolyte. In this fundamental study, we investigate novel carbonate-based solid-polymer electrolytes (SPE) using MD simulations and compare their performance to their conventional liquid carbonate electrolyte counterparts. Specifically, we characterize how the nanophase morphology of the amorphous polycarbonate systems is affected by modulating the composition of the carbonate side chains, while comparing them with their liquid electrolyte counterparts such as dimethyl carbonate and ethylene carbonate. Moreover, our study will elucidate how the morphology and thermodynamic properties, such as glass transition temperature, are affected by using aliphatic vs aromatic carbonate side chains, mixing of the side chain types, as well as by adjusting the length of the spacer carbon chain between the carbonate groups and the main chain. Therefore, this investigation can provide valuable insight regarding the optimal polymeric composition and mixture to achieve a morphology that is desirable for enhanced ion transport, while also inhibiting the disintegration of the organic cathode by the electrolyte.

Synthesis and Characterization of Derivatives of the Antifungal Peptoid RMG8-8.

Cryptococcal meningitis, caused by the fungal pathogen Cryptococcus neoformans, is a devastating disease with a mortality rate of over 80%. Due to the increasing prevalence of resistance to antifungals and the high mammalian toxicity of current treatments, the development of new antifungal therapies is vital. In an effort to improve the biological properties of a previously discovered antifungal peptoid, termed RMG8-8, an iterative structure–activity relationship study was conducted. This three-round study sought to optimize the structure of RMG8-8 by focusing on three main structural components: the lipophilic tail, aliphatic side chains, and aromatic side chains. In addition to antifungal testing against C. neoformans, cytotoxicity testing was also performed on all derivatives against human liver cells, and select promising compounds were tested for hemolytic activity against human red blood cells. A number of derivatives containing unique aliphatic or aromatic side chains had antifungal activity similar to RMG8-8 (MIC = 1.56 μg/mL), but all of these compounds were more toxic than RMG8-8. While no derivative was improved across all biological tests, modest improvements were made to the hemolytic activity with compound 9, containing isobutyl side chains in positions 2 and 5, compared to RMG8-8 (HC10 = 130 and 75 μg/mL, respectively). While this study did not yield a dramatically optimized RMG8-8 derivative, this result was not totally unexpected given the remarkable selectivity of this compound from discovery. Nonetheless, this study is an important step in the development of RMG8-8 as a viable antifungal therapeutic.

Influence of coal structure change caused by different pretreatment methods on Shengli lignite pyrolysis

Coal pyrolysis is one of the methods of clean and efficient utilization of coal. Coal has a complex structure, which has an important influence on its pyrolysis characteristics. In order to further explore the structure–activity relationship between the structure and pyrolysis characteristics of coal, the structure of coal can be artificially changed to investigate the influence of structural changes on its pyrolysis characteristics. In this study, hydrothermal pretreatment (HTP) and solvent swelling pretreatment (SSP) were used to artificially change the structure of Shengli (SL) lignite. The influence of each pretreatment on the physicochemical structure was analysed by Fourier-transform infrared (FT-IR), X-ray diffraction (XRD), and X-ray photoelectron spectroscopy (XPS). The evolution of functional groups and the pyrolysis characteristics of the SL/pretreated coal were investigated by using an in-situ FT-IR device and a fluidised bed reactor, respectively. The results showed: HTP could remove some oxygen-containing functional groups and aliphatic side chains, hydrolyze ether bonds and generate phenolic hydroxyl groups, thus destroying the cross-linking structure, promote the release of aromatic CC, the yield of pyrolysis tar increased from 9.4% to 10.6%, and the content of light tar increases from 43.1% to 49.1%. SSP mainly weakening the cross-linking structure by destroying hydrogen bonds and dissolving part of oxygen-containing functional groups, which reduces the pyrolysis activation energy of oxygen-containing functional groups and aliphatic groups, promotes the generation of tar. Accordingly, the yield of tar increases from 9.4% to 11.1%, and the content of light tar increases from 43.1 % to 49.8%. In particular, this research work reveals the structure–activity relationship between the structural changes of coal and the pyrolysis characteristics, which provides a theoretical basis for the directional pyrolysis of lignite.

Analysis of 1-Aroyl-3-[3-chloro-2-methylphenyl] Thiourea Hybrids as Potent Urease Inhibitors: Synthesis, Biochemical Evaluation and Computational Approach.

Urease is an amidohydrolase enzyme that is responsible for fatal morbidities in the human body, such as catheter encrustation, encephalopathy, peptic ulcers, hepatic coma, kidney stone formation, and many others. In recent years, scientists have devoted considerable efforts to the quest for efficient urease inhibitors. In the pharmaceutical chemistry, the thiourea skeleton plays a vital role. Thus, the present work focused on the development and discovery of novel urease inhibitors and reported the synthesis of a set of 1-aroyl-3-[3-chloro-2-methylphenyl] thiourea hybrids with aliphatic and aromatic side chains 4a–j. The compounds were characterized by different analytical techniques including FT-IR, 1H-NMR, and 13C-NMR, and were evaluated for in-vitro enzyme inhibitory activity against jack bean urease (JBU), where they were found to be potent anti-urease inhibitors and the inhibitory activity IC50 was found in the range of 0.0019 ± 0.0011 to 0.0532 ± 0.9951 μM as compared to the standard thiourea (IC50 = 4.7455 ± 0.0545 μM). Other studies included density functional theory (DFT), antioxidant radical scavenging assay, physicochemical properties (ADMET properties), molecular docking and molecular dynamics simulations. All compounds were found to be more active than the standard, with compound 4i exhibiting the greatest JBU enzyme inhibition (IC50 value of 0.0019 ± 0.0011 µM). The kinetics of enzyme inhibition revealed that compound 4i exhibited non-competitive inhibition with a Ki value of 0.0003 µM. The correlation between DFT experiments with a modest HOMO-LUMO energy gap and biological data was optimal. These recently identified urease enzyme inhibitors may serve as a starting point for future research and development.

Multi-spectroscopic characterization of bitumen and its polarity-based fractions

• Insights on H/C-ratio, aromatic systems and average molecular sizes are obtained. • NMR reveals varying chain lengths of aliphatic substituents throughout the fractions. • Characteristic NMR shifts in the resins suggest presence of some esters or amides. • 31 P NMR after derivatization, shows minor amounts of alcohols and carboxylic acids. Bitumen contains a complex mixture of molecules, ranging from simple linear alkanes to complex polyaromatic systems. Used in road construction, those structures are permanently influenced by atmospheric processes, which result in oxidation, degradation, loss of volatiles and structural rearrangements. In order to understand those molecular changes, a profound description of the unaltered system is needed. In this study, structural and chemical peculiarities of bitumen and its polarity-based fractions were analysed using nuclear magnetic resonance (NMR) techniques in combination with infrared/fluorescence spectroscopy and elemental analysis. The bitumen sample was separated into saturates, aromatics, resins and asphaltenes. Elemental analysis provided insights into variations of heteroatom content and hydrogen-carbon ratio among the fractions. Fluorescence spectroscopy showed an increase in the aromatic condensation degree with rising polarity. The combination of heteronuclear single quantum coherence (HSQC) and elemental analysis facilitated the assessment of length and branching extent of aliphatic side chains, throughout the fractions. Another 2D NMR technique, heteronuclear multiple bond coherence (HMBC) found evidence for minor contributions of carboxylic esters or amides within the resins. Hydroxyl and amino groups were analysed by 31 P NMR after derivatization, revealing minor amounts of alcohols, amides and carboxylic acids in the most polar fractions. Additionally, diffusion ordered spectroscopy was carried out to obtain estimations on average molecular sizes and weights. Applying in-depth NMR analysis to bitumen and combining it with complementary analytical techniques, this study provides a unique basis for future ageing studies and demonstrates how multi-spectroscopy can give new insights into bitumen structure and chemistry.

Bio-solubilization of Yunnan lignite by Penicillium ortum MJ51 and characterization of its products

In this study, a newly discovered fungal strain Penicillium ortum MJ51 was isolated from lignite collected from a coal mine in Yunnan Province, China. The strain was then utilized to convert solid Yunnan lignite to liquid value-added chemicals. It solubilized 36.4% of the raw lignite and 82.0% of lignite pretreated with nitric acid within 8 days. The extracellular metabolites and enzymes secreted by MJ51 were detected dynamically, along with an analysis of the organic element composition, Fourier-transform infrared spectroscopy, and gas chromatography-mass spectrometry of the raw lignite, pretreated lignite, and their bio-solubilized residues and soluble fractions. The results suggested that extracellular metabolites including alkaline substances and surfactants, secreted by MJ51 were the primary contributors to the depolymerization of lignite, because the lignite-solubilization ability of MJ51 was correlated with pH and surface tension of the culture. Moreover, extracellular enzymes, such as lignin peroxidase and esterase, secreted by MJ51 participated in the degradation of lignite despite their poor activity. Furthermore, MJ51 could introduce CO into the structure of raw lignite in the same way as HNO3. Under the associated action of extracellular alkaline substances, surfactants, and enzymes, the hydrogen bond in coal was rebuilt, the complex aromatic skeletons were opened, and the attached long aliphatic side chain was cut off. The pretreated lignite could be thoroughly degraded by MJ51 than raw lignite as it had a lower degree of aromatic condensation, shorter aliphatic side chain and more carbonyl groups. The soluble bio-solubilized fractions of lignite contained aliphatic and aromatic compounds, and their derivatives.

EPR Investigations to Study the Impact of Mito-Metformin on the Mitochondrial Function of Prostate Cancer Cells.

Background: Mito-metformin10 (MM10), synthesized by attaching a triphenylphosphonium cationic moiety via a 10-carbon aliphatic side chain to metformin, is a mitochondria-targeted analog of metformin that was recently demonstrated to alter mitochondrial function and proliferation in pancreatic ductal adenocarcinoma. Here, we hypothesized that this compound may decrease the oxygen consumption rate (OCR) in prostate cancer cells, increase the level of mitochondrial ROS, alleviate tumor hypoxia, and radiosensitize tumors. Methods: OCR and mitochondrial superoxide production were assessed by EPR (9 GHz) in vitro in PC-3 and DU-145 prostate cancer cells. Reduced and oxidized glutathione were assessed before and after MM10 exposure. Tumor oxygenation was measured in vivo using 1 GHz EPR oximetry in PC-3 tumor model. Tumors were irradiated at the time of maximal reoxygenation. Results: 24-hours exposure to MM10 significantly decreased the OCR of PC-3 and DU-145 cancer cells. An increase in mitochondrial superoxide levels was observed in PC-3 but not in DU-145 cancer cells, an observation consistent with the differences observed in glutathione levels in both cancer cell lines. In vivo, the tumor oxygenation significantly increased in the PC-3 model (daily injection of 2 mg/kg MM10) 48 and 72 h after initiation of the treatment. Despite the significant effect on tumor hypoxia, MM10 combined to irradiation did not increase the tumor growth delay compared to the irradiation alone. Conclusions: MM10 altered the OCR in prostate cancer cells. The effect of MM10 on the superoxide level was dependent on the antioxidant capacity of cell line. In vivo, MM10 alleviated tumor hypoxia, yet without consequence in terms of response to irradiation.

Self-assembling Peptides with Internal Ionizable Unnatural Amino Acids: A General Approach to pH-responsive Peptide Materials.

Self-assembled peptides are an emerging family of biomaterials that show great promise for a range of biomedical and biotechnological applications. Introducing and tuning the pH-responsiveness of the assembly is highly desirable for improving their biological activities. Inspired by proteins with internal ionizable residues, we report a simple but effective approach to constructing pH-responsive peptide assembly containing unnatural ionic amino acids with an aliphatic tertiary amine side chain. Through a combined experimental and computational investigation, we demonstrate that these residues can be accommodated and stabilized within the internal hydrophobic compartment of the peptide assembly. The hydrophobic microenvironment shifts their pKa significantly from a basic pH typically found for free amines to a more biologically relevant pH in the weakly acidic range. The pH-induced ionization and ionization-dependent self-assembly and disassembly are thoroughly investigated and correlated with the biological activity of the assembly. This new approach has unique advantages in tuning the pH-responsiveness of self-assembled peptides across a large pH range in a complex biological environment. We anticipate the ionizable amino acids developed here can be widely applicable to the synthesis and self-assembly of many amphiphilic peptides with endowed pH-responsive properties to enhance their biological activities toward applications ranging from targeted therapeutic delivery to proton transport.

Catalytic conversion of asphaltenes to BTXN using metal-loaded modified HZSM-5

HZSM-5 zeolites with Si/Al ratios of 20, 35, 50 and 65 were prepared by the directing crystallization process of silicalite-1 seeds. The influence of Si/Al ratios on the production of benzene, toluene, xylene and naphthalene (BTXN) originated from asphaltenes catalytic pyrolysis was explored by adopting Py-GC/MS. Modified Z5-50 zeolites were prepared by various metal ions (Ni 2+ , Mo 6+ , Fe 3+ , and Co 2+ ) with different loading rates (3% (mass), 5% (mass), 7% (mass), and 9% (mass)) and the physical and chemical properties of these zeolites were characterized by XRD, SEM, ICP-OES, XPS, NH 3 -TPD, FTIR, Py-IR and N 2 adsorption−desorption isotherm. In addition, they were employed to catalyze the conversion of asphaltenes pyrolysis production to BTXN using Py-GC/MS. Results show that the highest relative content of aromatics has been obtained over HZSM-5 with Si/Al ratio of 50 (Z5-50), reaching 61.87%. Besides, the loading of Ni, Mo, Fe, and Co on Z5-50 leads to an increase of acid strength and provides new active sites. The relative content of BTXN increases by 3.17% over 3Ni-Z5, which may be ascribed to that Ni promoted the conversion of polycyclic aromatic hydrocarbons (PAHs) to monocyclic aromatics due to the cracking of aliphatic side chains of PAHs and the decrease of phenolic activation energy. While under the catalysis of 5Mo-Z5, the relative content of aromatics and BTXN augmented by 5.75% and 4.02%, respectively. In addition, the highest relative content of aromatics reaches 70.09% when the loading rate of Fe was 7% (mass), and the relative content of BTXN increases from 25.87% to 29.42%. The results demonstrate that the active sites provided by different metal species expressed diverse effects on BTXN. Although the Brønsted/Lewis acid ratios of HZSM-5 modified by metal decreased, the acid strength and the relative content of BTXN both increased, which illustrated that there is a synergistic catalysis with the Brønsted acid sites and Lewis acid sites provided by metal species. In general, the performance of the catalyst is affected by the pore structure, acidity and metal active sites. Moreover, the possible formation mechanism of BTXN derived from asphaltenes catalytic pyrolysis was proposed on the basis of structural features and catalytic performances of a series of zeolites.

Recombinant Extracellular Cholesterol Oxidase from Nocardioides simplex.

Cholesterol oxidase is a highly demanded enzyme used in medicine, pharmacy, agriculture, chemistry, and biotechnology. It catalyzes oxidation of 3β-hydroxy-5-ene- to 3-keto-4-ene- steroids with the formation of hydrogen peroxide. Here, we expressed 6xHis-tagged mature form of the extracellular cholesterol oxidase (ChO) from the actinobacterium Nocardioides simplex VKM Ac-2033D (55.6 kDa) in Escherichia coli cells. The recombinant enzyme (ChONs) was purified using affinity chromatography. ChONs proved to be functional towards cholesterol, cholestanol, phytosterol, pregnenolone, and dehydroepiandrosterone. Its activity depended on the structure and length of the aliphatic side chain at C17 atom of the steroid nucleus and was lower with pregnenolone and dehydroepiandrosterone. The enzyme was active in a pH range of 5.25÷6.5 with the pH optimum at 6.0. Kinetic assays and storage stability tests demonstrated that the characteristics of ChONs were generally comparable with or superior to those of commercial ChO from Streptomyces hygroscopicus (ChOSh). The results contribute to the knowledge on microbial ChOs and evidence that ChO from N. simplex VKM Ac-2033D is a promising agent for further applications.

Differences in Macromolecular Structure Evolution during the Pyrolysis of Vitrinite and Inertinite Based on In Situ FTIR and XRD Measurements

An accurate understanding of molecular structure evolution during pyrolysis is essential for the clean utilization of coal. In this study, middle-rank coal was taken as the research subject, and vitrinite and inertinite samples were stripped from coal using a hand picking and sink–float separation process. In situ Fourier transform infrared (FTIR) spectroscopy and in situ X-ray diffraction (XRD) were performed to compare the macromolecular structure changes between vitrinite and inertinite during pyrolysis. The results show that the aromaticity (I), the polycondensation degree of aromatic rings (DOC), the average lateral sizes (La) of basic structure unit (BSU), and the stacking heights (Lc) of BSU in both vitrinite and inertinite during pyrolysis increase continuously with increasing temperature. The values of these parameters for inertinite are higher than those of vitrinite, suggesting that the aromatization degree of inertinite has always been higher than that of vitrinite. In situ FTIR spectroscopy shows that the macromolecular structure evolution of vitrinite and inertinite could be divided into three stages based on temperature: 30–200 °C, 200–300 °C, and 300–500 °C. The content of C–O–C, aromatic C=O, O–H groups, and aromatic ring C=C gradually decreases, while that of the CH2 in aliphatic hydrocarbons increases between 30 °C and 200 °C. The 200–300 °C stage is mainly filled by the synergistic effects of aliphatic and aromatic groups. The content of aliphatic groups, C–O–C groups, aromatic C=O, and aromatic ring C=C of both vitrinite and inertinite decreases greatly. The 300–500 °C stage is dominated by the aromatization and condensation of macromolecules. The substituents of the aromatic system gradually detach, leading to an increase in I and DOC. From 30 °C to 1000 °C, in situ XRD results reveal a difference in macromolecular structural evolution between vitrinite and inertinite. The arrangement of aromatic layers in vitrinite tends to be ordered during pyrolysis, whereas there are no significant changes in the inertinite. However, the aromatic layers of inertinite are always more compact than that of vitrinite. In addition, the aliphatic side chains of inertinite are more stable than that of vitrinite during the pyrolysis process.

Bile acid-based advanced drug delivery systems, bilosomes and micelles as novel carriers for therapeutics.

Diabetes mellitus affects almost half a billion patients worldwide and results from either destruction of β-cells responsible for insulin secretion or increased tissue resistance to insulin stimulation and the reduction of glycemic control. Novel drug delivery systems can improve treatment efficacy in diabetic patients. The low aqueous solubility of most oral antidiabetic drugs decreases drug bioavailability; therefore, there is a demand for the use of novel methods to overcome this issue. The application of bile acids mixed micelles and bilosomes can provide an enhancement in drug efficacy. Bile acids are amphiphilic steroidal molecules that contain a saturated tetracyclic hydrocarbon cyclopentanoperhydrophenanthrene ring, and consist of three 6-membered rings and a 5-membered ring, a short aliphatic side chain, and a tough steroid nucleus. This review offers a comprehensive and informative data focusing on the great potential of bile acid, their salts, and their derivatives for the development of new antidiabetic drug delivery system.

Crystallizable Aliphatic Chains Enhanced Covalent Adaptable Networks: Fast Reprocessing and Improved Performance.

Covalent adaptable networks (CANs) exhibit recyclability such as reprocessing, but it's a challenge to address the contradiction between reprocessing rate and performance. Here, pendent aliphatic chain anhydride monoesters are innovatively introduced into epoxy CANs based on transesterification, which efficiently accelerates the reprocessing without sacrificing thermal and mechanical properties. The transesterification rate is raised on account of the flexible aliphatic chain-promoted segment movement and dynamic transfer auto-catalysis. When the carbon number reflecting the length of the pendent chain is 12, the epoxy CAN exhibits the fastest stress relaxation or reprocessing. Computation via molecular dynamics simulation demonstrates that the increased segmental mobility from the pendent aliphatic chains contributes to enhanced reprocessability. Interestingly, the crystallization of the pendent aliphatic chains maintains or even improves the thermal and mechanical properties. Thus, introducing a flexible and crystallizable aliphatic side chain is an innovative and efficient approach to accelerate dynamic reactions and network arrangement while improving performance.

Structural Basis of Pyridostatin and Its Derivatives Specifically Binding to G-Quadruplexes.

The nucleic acid G-quadruplex (G4) has emerged as a promising therapeutic target for a variety of diseases such as cancer and neurodegenerative disease. Among small-molecule G4-binders, pyridostatin (PDS) and its derivatives (e.g., PyPDS) exhibit high specificity to G4s, but the structural basis for their specific recognition of G4s remains unknown. Here, we presented two solution structures of PyPDS and PDS with a quadruplex-duplex hybrid. The structures indicate that the rigid aromatic rings of PyPDS/PDS linked by flexible amide bonds match adaptively with G-tetrad planes, enhancing π-π stacking and achieving specific recognition of G4s. The aliphatic amine side chains of PyPDS/PDS adjust conformation to interact with the phosphate backbone via hydrogen bonding and electrostatic interactions, increasing affinity for G4s. Moreover, the N-H of PyPDS/PDS amide bonds interacts with two O6s of G-tetrad guanines via hydrogen bonding, achieving a further increase in affinity for G4s, which is different from most G4 ligands. Our findings reveal from structural perspectives that the rational assembly of rigid and flexible structural units in a ligand can synergistically improve the selectivity and affinity for G4s through spatial selective and adaptive matching.

Dramatic Decrease of Vitamin K2 Subtype Menaquinone-7 in COVID-19 Patients.

(1) Background: Vitamin K (VK) is a fat-soluble compound with a common chemical structure, a 2-methyl-1,4-naphthoquinone ring, and a variable aliphatic side-chain. VK is involved in the synthesis of blood-clotting proteins, bone stability, anti-oxidative, and immune inflammatory-modulatory functions. Vitamin K also activates protein S, which acts as an antioxidant and anti-inflammatory. The fact that cytokine overproduction, oxidative stress, and disturbed microcirculation by thrombogenicity play a central role in severe COVID-19 prompted us to analyze this vitamin. (2) Methods: We analyzed by a validated liquid-chromatography tandem mass-spectrometry method serum vitamin K1, MK4, MK7, and VK epoxide levels in 104 healthy controls, 77 patients with non-COVID-19 pneumonia, and 135 hospitalized COVID-19 patients with potentially fatal outcomes admitted to our University Hospital between April and November 2020. We included the quotient between VK and triglyceride (TG, nmol/mmol/L) values in the analyses with respect to the TG transporter function for all VK subtypes. Additionally, we assessed anthropometric, routine laboratory, and clinical data from the laboratory and hospital information systems. (3) Results: The COVID-19 patients had significantly lower MK7 levels than non-COVID-19 pneumonia patients and healthy controls. COVID-19 and non-COVID-19 pneumonia patients had significantly lower vitamin K1 and significantly higher MK4 compared to healthy controls, but did not differ significantly from each other. Between COVID-19 non-survivors (n = 30) and survivors (n = 105) no significant differences were seen in all vitamin K subtypes, despite the fact that non-survivors had higher peak concentrations of IL-6, CRP, d-dimer, and higher oxygen needs, respectively. (4) Conclusions: The present data identified significantly decreased vitamin K1, K2 (MK7), and increased MK4 levels in patients with COVID-19 compared to healthy controls. Vitamin K2 (MK7) was lowest in COVID-19 patients irrespective of potentially fatal courses, indicating consumption of this VK subtype by COVID-19 immanent effects, most probably inflammatory and oxidative stress factors.

Conformational Dynamics Allows Sampling of an “Active-like” State by Oncogenic K-Ras-GDP

Mutations in K-Ras GTPase replacing Gly12 with either Asp or Val are common in cancer. These mutations decelerate intrinsic and catalyzed GTP hydrolysis, leading to accumulation of K-Ras-GTP in cells. Signaling cascades initiated by K-Ras-GTP promote cell proliferation, survival, and invasion. Despite functional differences between the most frequent G12D mutation and the most aggressive and chemotherapy resistant G12V mutation, their long-suspected distinct structural features remain elusive. Using NMR, X-ray structures, and computational methods, we found that oncogenic mutants of K-Ras4B, the predominant splice variant of K-Ras, exhibit distinct conformational dynamics when GDP-bound, visiting the “active-like” conformational state similar to the one observed in GTP-bound K-Ras. This behavior distinguishes G12V from wild type and G12D K-Ras4B-GDP. The likely reason is interactions between the aliphatic sidechain of V12 and the Switch II region of K-Ras4BG12V-GDP, which are distinct in K-Ras4BG12D-GDP. In the X-ray structures, crystal contacts reduce the dynamics of the sidechain at position 12 by stabilizing the Switch I region of the protein. This explains why structural differences between G12V and G12D K-Ras have yet not been reported. Together, our results suggest a previously unknown mechanism of K-Ras activation. This mechanism relies on conformational dynamics caused by specific oncogenic mutations in the GDP-bound state. Our findings also imply that the therapeutic strategies decreasing the level of K-Ras-GTP by interfering with nucleotide exchange or by expediting GTP hydrolysis may work differently in different oncogenic mutants.

Comprehensive evaluation of polycyclic aromatic units in three liquefaction-derived heavy fractions from Zhunnan lignite

The structural characteristics of polycyclic aromatic units in three liquefaction-derived heavy fractions from Zhunnan lignite, including thermal dissolution (TD) in cyclohexane (HF C ), ethanolysis (HF E ), and two-step sequential TD in cyclohexane-ethanol (HF CE ), were investigated in depth. Combining multiple destructive tools, the intrinsic correlation among dissociated/degraded fragments and organic macromolecular networks, involving the types of alkyl side chain, methylene bridged bond, heteroatom, and aromatic nucleus, was also constructed. The results indicate that HF C with a smaller average molecular weight may be rich in -OH, >C-O-, and >C O units, while HF CE has higher aromaticity. In addition, abundant arenes and arenols were detected in the volatiles released from HF C flash pyrolysis, but macro/ultramolecular groups dominated in HF E and HF CE . Obviously, the differences in thermochemical reactions further confirmed that the component distribution of volatiles is mainly related to the direct gasification of small/medium molecules and the cleavage of weak/moderate strength covalent bonds. The analyses with quadrupole exactive orbitrap mass spectrometer and ruthenium ion-catalyzed oxidation show that HF C also contains abundant oxynitrides, while HF CE may be dominated by cata -condensed aromatics and polyaryl units, followed by few peri -condensed aromatics, long-chain saturated rings, aromatic rings with longer aliphatic side chains, and polymethylene linkage units. Comprehensive evaluation of these difficult-to-detect parts is beneficial to the resource and diversified utilization of such special soluble portions with potential environmental hazards. • HFCE has the highest aromaticity, while HFC is rich in O-containing FGs. • HFC also contains abundant >C-O- moieties and oxynitrides. • HFCE may be dominated by cata-condensed aromatics and polyaryl units. • The inner link among degraded fragments and organic structures was revealed.

The influence of alkyl substitution on the in vitro metabolism and mutagenicity of benzo[a]pyrene

In recent years concerns over consumer exposure to mineral oil aromatic hydrocarbons (MOAH), especially those containing alkylated polycyclic aromatic hydrocarbons (PAHs), have emerged. This is especially due to the fact that some PAHs are known to be genotoxic and carcinogenic upon metabolic activation. However, available toxicological data on PAHs mainly relate to non-substituted PAHs with limited data on alkyl substituted PAHs. Therefore, the aim of the present study was to characterize in more detail the effect of alkyl substitution on the metabolism and mutagenicity of benzo[a]pyrene (B[a]P), a PAH known to be genotoxic and carcinogenic. To this end, the oxidative metabolism and mutagenicity of B[a]P and a series of its alkyl substituted analogues were quantified using in vitro microsomal incubations and the Ames test. The results obtained reveal that upon alkylation the metabolic oxidation shifts to the aliphatic side chain at the expense of aromatic ring oxidation. The overall metabolism, including metabolism via aromatic ring oxidation resulting potentially in bioactivation, was substantially reduced with elongation of the alkyl side chain, with metabolism of B[a]P with an alkyl substituent of >6 C atoms being seriously hampered. In the Ames test upon metabolic activation, the methyl substitution of B[a]P resulted in an increase or decrease of the mutagenic potency depending on the substitution position. The relevant pathways for mutagenicity of the selected monomethyl substituted B[a]P may involve the formation of a 7,8-dihydrodiol-9,10-epoxide, a 4,5-oxide and/or a benzylic alcohol as an oxidative side chain metabolite which subsequently may give rise to an unstable and reactive sulfate ester conjugate. It is concluded that alkylation of B[a]P does not systematically reduce its mutagenicity in spite of the metabolic shift from aromatic to side chain oxidation.

Effect of different functional groups on CH4 adsorption heat and surface free energy of vitrinite during coalification

Here vitrinite of various coal ranks was collected to study the characteristics of initial isosteric heat of adsorption (Qst0) and surface free energy (Δσ) by the isothermal methane-adsorbing at various temperatures on dry basis. The surface area of demineralized dry samples was examined for the calculation of Qst0 and Δσ, and the macromolecular structures of dry vitrinite samples were determined using Fourier transform infrared spectroscopy and 13C nuclear magnetic resonance experiments. The Qst0 shows no obvious correlations with oxygen-containing groups, however, there is a positive correlation between the alcoholic hydroxyl group (R–OH) and maximal surface free energy (Δσmax), indicating that the decreasing in R–OH content with the increasing coal rank can reduce adsorption capacity. Qst0 decrease as the amount of nonprotonated aromatic carbon attached to phenolic (including phenoxy or phenol groups) increases, indicating that phenoxy or phenol group loss with maturation is beneficial to increasing Qst0. As the degree of coal metamorphism increases, the aliphatic side chains gradually decline, inducing Qst0 initially decreases and then increases. For aromatic groups, with increases of aromatic carbons, aromatic bridgehead carbons, and ratio of aromatic CC to aromatic CH, Qst0 initially decreases and then increases.

Electron-Induced Decomposition of Different Silver(I) Complexes: Implications for the Design of Precursors for Focused Electron Beam Induced Deposition.

Focused electron beam induced deposition (FEBID) is a versatile tool to produce nanostructures through electron-induced decomposition of metal-containing precursor molecules. However, the metal content of the resulting materials is often low. Using different Ag(I) complexes, this study shows that the precursor performance depends critically on the molecular structure. This includes Ag(I) 2,2-dimethylbutanoate, which yields high Ag contents in FEBID, as well as similar aliphatic Ag(I) carboxylates, aromatic Ag(I) benzoate, and the acetylide Ag(I) 3,3-dimethylbutynyl. The compounds were sublimated on inert surfaces and their electron-induced decomposition was monitored by electron-stimulated desorption (ESD) experiments in ultrahigh vacuum and by reflection−absorption infrared spectroscopy (RAIRS). The results reveal that Ag(I) carboxylates with aliphatic side chains are particularly favourable for FEBID. Following electron impact ionization, they fragment by loss of volatile CO2. The remaining alkyl radical converts to a stable and equally volatile alkene. The lower decomposition efficiency of Ag(I) benzoate and Ag(I) 3,3-dimethylbutynyl is explained by calculated average local ionization energies (ALIE) which reveal that ionization from the unsaturated carbon units competes with ionization from the coordinate bond to Ag. This can stabilise the ionized complex with respect to fragmentation. This insight provides guidance with respect to the design of novel FEBID precursors.