17,356 results match your criteria network hydrogen


A Comprehensive mechanism for 5-carboxylcytosine induced transcriptional pausing revealed by Markov state models.

J Biol Chem 2021 May 12:100735. Epub 2021 May 12.

Department of Chemistry, State Key Laboratory of Molecular Neuroscience, The Hong Kong University of Science and Technology, Kowloon, Hong Kong; Hong Kong Center for Neurodegenerative Diseases, Hong Kong Science Park, Hong Kong. Electronic address:

RNA polymerase II (Pol II) surveils the genome, pausing as it encounters DNA lesions and base modifications and initiating signals for DNA repair among other important regulatory events. Recent work suggests that Pol II pauses at 5-carboxycytosine (5caC), an epigenetic modification of cytosine, due to a specific hydrogen bond between the carboxyl group of 5caC and a specific residue in fork loop 3 of Pol II. This hydrogen bond compromises productive NTP binding and slows down elongation. Read More

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Protein Cold Denaturation in Implicit Solvent Simulations: A Transfer Free Energy Approach.

J Phys Chem B 2021 May 14. Epub 2021 May 14.

Department of Chemistry and Biochemistry, University of California, Santa Barbara, California 93106, United States.

Proteins are stable over a narrow temperature range, with hot and cold denaturation occurring outside of this window, both of which adversely affect protein function. While hot unfolding is entropically driven, cold denaturation, on the other hand, results from a more favorable free energy associated with the interaction of water with apolar groups at low temperature. Because of the key role of water in this latter process, capturing cold denaturation using implicit solvent models is challenging. Read More

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Fiber-optic time-frequency transfer in gigabit ethernet networks over urban fiber links.

Opt Express 2021 Apr;29(8):11693-11701

We demonstrate a new optical pulse amplitude modulation (PAM) scheme where joint ultrastable time-frequency and gigabit ethernet data transfer with the same laser wavelength is realized. Time transmission is compatible with the White Rabbit (WR) based on gigabit ethernet networks, and frequency transmission is achieved by using 100MHz radio frequency (RF) modulation and the round-trip compensation methods. The laser is on-off keying (OOK) modulated by the WR signal, the RF and WR signal are modulated by optical PAM in a Mach-Zehnder interferometer modulator (MZM), and the local and remote site are connected by 96km urban fiber in Shanghai. Read More

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Arginine multivalency stabilizes protein/RNA condensates.

Protein Sci 2021 May 12. Epub 2021 May 12.

Centre de Biochimie Structurale (CBS), INSERM, CNRS, Université de Montpellier, Montpellier, France.

Biomolecular condensates assembled through liquid-liquid phase separation (LLPS) of proteins and RNAs are currently recognized to play an important role in cellular organization. Their assembly depends on the formation of a network of transient, multivalent interactions between flexible scaffold biomolecules. Understanding how protein and RNA sequences determine these interactions and ultimately regulate the phase separation is an open key challenge. Read More

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Critical Interactions Between the SARS-CoV-2 Spike Glycoprotein and the Human ACE2 Receptor.

J Phys Chem B 2021 May 12. Epub 2021 May 12.

Department of Mechanical Engineering, Istanbul Technical University (ITU), 34437 Istanbul, Turkey.

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infects human cells by binding its spike (S) glycoproteins to angiotensin-converting enzyme 2 (ACE2) receptors and causes the coronavirus disease 2019 (COVID-19). Therapeutic approaches to prevent SARS-CoV-2 infection are mostly focused on blocking S-ACE2 binding, but critical residues that stabilize this interaction are not well understood. By performing all-atom molecular dynamics (MD) simulations, we identified an extended network of salt bridges, hydrophobic and electrostatic interactions, and hydrogen bonds between the receptor-binding domain (RBD) of the S protein and ACE2. Read More

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Aqueous TMAO solution under high hydrostatic pressure.

Phys Chem Chem Phys 2021 May 11. Epub 2021 May 11.

Lehrstuhl für Physikalische Chemie II, Ruhr-Universität Bochum, 44780 Bochum, Germany.

Trimethylamine N-oxide (TMAO) is a well known osmolyte in nature, which is used by deep sea fish to stabilize proteins against High Hydrostatic Pressure (HHP). We present a combined ab initio molecular dynamics, force field molecular dynamics, and THz absorption study of TMAO in water up to 12 kbar to decipher its solvation properties upon extreme compression. On the hydrophilic oxygen side of TMAO, AIMD simulations at 1 bar and 10 kbar predict a change of the coordination number from a dominating TMAO·(H2O)3 complex at ambient conditions towards an increased population of a TMAO·(H2O)4 complex at HHP conditions. Read More

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Two 6/10-connected CuS cluster-based organic frameworks: crystal structure and proton conduction.

Dalton Trans 2021 May 10. Epub 2021 May 10.

Qinzhou Key Laboratory for Development and Application of High Performance Functional Materials, College of Petroleum and Chemical Engineering, Beibu Gulf University, Qinzhou 535011, People's Republic of China.

Nowadays, although the exploration of proton conductive materials has ranged from traditional sulfonated polymers to novel crystalline solid materials such as MOFs, COFs, and HOFs, research on crystalline cluster-based organic framework materials is very limited. Here, a pair of homologues Cu(i)-based organic framework containing a Cu12S6 cluster, [Cu12(MES)6(H2O)3]n (1) and {[Cu12(MPS)6(H2O)4]·6H2O}n (2) (H2MES = 2-mercaptoethanesulfonate acid and H2MPS = 2-mercaptoethanesulfonate acid), were hydrothermally synthesized under the same conditions and fully investigated for their proton conduction. Their structures were characterized by means of single-crystal X-ray diffraction, elemental analysis, thermogravimetric analyses, and PXRD measurements. Read More

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Selective cyclohexene oxidation to allylic compounds over a Cu-triazole framework homolytic activation of hydrogen peroxide.

Dalton Trans 2021 May 10. Epub 2021 May 10.

School of Energy Science and Engineering, Vidyasirimedhi Institute of Science and Technology, Wangchan, Rayong 21210, Thailand. and Research Network of NANOTEC-VISTEC on Nanotechnology for Energy, Vidyasirimedhi Institute of Science and Technology, Wangchan, Rayong 21210, Thailand.

Utilization of metal-organic frameworks as heterogeneous catalysts is crucial owing to their abundant catalytic sites and well-defined porous structures. Highly robust [Cu3(trz)3(μ3-OH)(OH)2(H2O)4]·2H2O (trz = 1,2,4-triazole) was employed as a catalyst for liquid-phase cyclohexene oxidation with hydrogen peroxide (H2O2). Possessing the porous structure together with Lewis acid attributes from the triangular [Cu3(trz)3(μ3-OH)] center, selective oxidation of cyclohexene to allylic products gives a molar yield of 31% with 87% selectivity. Read More

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identification of RBD subdomain of spike protein from Pro-Thr for applications in vaccine development against SARS-CoV2.

J Mol Struct 2021 Sep 30;1240:130534. Epub 2021 Apr 30.

Li Ka Shing Applied Virology Institute, Department of Medical Microbiology and Immunology, University of Alberta, Edmonton, AB, Canada.

The three-dimensional hybrid structures of coronavirus spike proteins including the C-terminal sequence and receptor binding motif (RBM) was remodeled and energy minimized. Further, protein-protein docking show that Receptor Binding Domain (RBD) of SARS-CoV 2 Lys-Pro bind on the surface of ACE2 receptor near N-terminal helices to form host-pathogen attachment. In this binding interface, SARS-CoV 2 shows a tight network of hydrogen bonds than other spike proteins from BtRsRaTG13-CoV, SARS-CoV, BtRsBeta-CoV, BtRsCoV-related, Pangolin-CoV (PCoV), human-CoV (hCoV), MERS-CoV (MCoV), Avian-CoV (ACoV) and PEDV1-CoV. Read More

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September 2021

Green additive to upgrade biochar from spent coffee grounds by torrefaction for pollution mitigation.

Environ Pollut 2021 Apr 28;285:117244. Epub 2021 Apr 28.

School of Chemical Engineering, Universiti Sains Malaysia, Engineering Campus, Seri Ampangan, Nibong Tebal, 14300, Pulau Pinang, Malaysia.

A green approach using hydrogen peroxide (HO) to intensify the fuel properties of spent coffee grounds (SCGs) through torrefaction is developed in this study to minimize environmental pollution. Meanwhile, a neural network (NN) is used to minimize bulk density at different combinations of operating conditions to show the accurate and reliable model of NN (R = 0.9994). Read More

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Investigation on the impact of different proportions of components in formulations on stability of a moisture sensitive drug.

Int J Pharm 2021 May 6:120690. Epub 2021 May 6.

GEA-NUS Pharmaceutical Processing Research Laboratory, Department of Pharmacy, National University of Singapore, 18 Science Drive 4, Singapore 117543, Singapore. Electronic address:

Physicochemical and mechanical properties of tablets are largely dictated by formulation compositions. Different excipients possess different tableting and moisture sorption behaviors. Therefore, this study was designed to elucidate the relative influence of the proportion of components in formulations on tablet properties. Read More

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Proton exit pathways surrounding the oxygen evolving complex of photosystem II.

Biochim Biophys Acta Bioenerg 2021 May 5;1862(8):148446. Epub 2021 May 5.

Department of Chemistry, The Graduate Center, City University of New York, New York, NY 10016, United States; Department of Physics, City College of New York, NY 10031, United States; Department of Physics, The Graduate Center of the City University of New York, New York, NY 10016, United States. Electronic address:

Photosystem II allows water to be the primary electron source for the photosynthetic electron transfer chain. Water is oxidized to dioxygen at the Oxygen Evolving Complex (OEC), a MnCaO inorganic core embedded on the lumenal side of PSII. Water-filled channels surrounding the OEC must bring in substrate water molecules, remove the product protons to the lumen, and may transport the product oxygen. Read More

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Photocuring Three-Dimensional Printing of Thermoplastic Polymers Enabled by Hydrogen Bonds.

ACS Appl Mater Interfaces 2021 May 7. Epub 2021 May 7.

College of Transportation and Civil Engineering, Fujian Agriculture and Forestry University, Fuzhou 350108, P. R. China.

The advent of 3D printing has led to a new era of highly customized products. Printing reprocessable thermoplastic polymers is limited to slow printing techniques such as fused deposition modeling. Photocuring 3D printing is a high-speed 3D printing technique suitable for photocurable thermosetting resins because the cross-linked 3D network could achieve rapid solid-liquid separation during printing. Read More

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Molecular Dynamics Studies of Therapeutic Liquid Mixtures and Their Binding to Mycobacteria.

Front Pharmacol 2021 20;12:626735. Epub 2021 Apr 20.

Red Glead Discovery AB, Lund, Sweden.

Tuberculosis is an highly contagious disease still considered by the WHO as one of most infectious diseases worldwide. The therapeutic approach, used to prevent and treat tuberculosis targets the complex, comprises a combination of drugs administrated for long periods of time, which, in many cases, could cause several adverse effects and, consequently, low compliance of the patient to the treatment and drug-resistance. Therefore, therapeutic liquid mixtures formulated with anti-tuberculosis drugs and/or adjuvants in tuberculosis therapy are an interesting approach to prevent toxic effects and resistance to anti-tuberculosis drugs. Read More

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Cannabidiol Protects Human Skin Keratinocytes from Hydrogen-Peroxide-Induced Oxidative Stress via Modulation of the Caspase-1-IL-1β Axis.

J Nat Prod 2021 May 6. Epub 2021 May 6.

Bioactive Botanical Research Laboratory, Department of Biomedical and Pharmaceutical Sciences, College of Pharmacy, University of Rhode Island, Kingston, Rhode Island 02881, United States.

Preclinical and clinical studies support cannabidiol (CBD)'s antioxidant and anti-inflammatory effects, which are linked to its skin protective effects, but there have been limited mechanistic studies reported. Herein we evaluated CBD's protective effects against hydrogen peroxide (HO)-induced oxidative stress in human keratinocyte HaCaT cells and explored its possible mechanism(s) of action. CBD (10 μM) protected HaCaT cells by alleviating HO (200 μM)-induced cytotoxicity (by 11. Read More

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Structural investigation of -[2-(4-fluoro-3-phen-oxy-benzo-yl)hydrazinecarbo-thio-yl]benzamide and -[2-(4-fluoro-3-phen-oxy-benzo-yl)hydrazinecarbo-thio-yl]-4-meth-oxy-benzamide.

Acta Crystallogr E Crystallogr Commun 2021 Mar 19;77(Pt 3):277-281. Epub 2021 Feb 19.

Rallis India Ltd, Bangalore 560091, Karnataka, India.

The compound -[2-(4-fluoro-3-phen-oxy-benzo-yl)hydrazinecarbo-thio-yl]benzamide, CHFNOS, crystallizes in the monoclinic centrosymmetric space group 2/ and its mol-ecular conformation is stabilized an intra-molecular N-H⋯O hydrogen bond. The corresponding -meth-oxy derivative, namely, -[2-(4-fluoro-3-phen-oxy-benzo-yl)hydrazinecarbo-thio-yl]-4-meth-oxy-benzamide, CHFNOS, crystallizes in the monoclinic centrosymmetric space group 2/. The supra-molecular network mainly comprises N-H⋯O, N-H⋯S and C-H⋯O hydrogen bonds, which contribute towards the formation of the crystal structures for the two mol-ecules. Read More

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Threefold helical assembly hy-droxy hydrogen bonds: the 2:1 co-crystal of bi-cyclo-[3.3.0]octane--3,-7-diol and bi-cyclo-[3.3.0]octane--3,-7-diol.

Acta Crystallogr E Crystallogr Commun 2021 Mar 19;77(Pt 3):270-276. Epub 2021 Feb 19.

School of Chemistry, University of New South Wales, UNSW Sydney NSW 2052, Australia.

Reduction of bi-cyclo-[3.3.0]octane-3,7-dione yields a mixture of the -3,-7-diol and -3, -7-diol (CHO) isomers ( and ). Read More

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Crystal structure and Hirshfeld surface analysis of ()-3-hy-droxy-2-{[(3a,6,7a)-2-(4-methyl-phenyl-sulfon-yl)-2,3,3a,6,7,7a-hexa-hydro-3a,6-ep-oxy-1-isoindol-6-yl]meth-yl}isoindolin-1-one.

Acta Crystallogr E Crystallogr Commun 2021 Mar 16;77(Pt 3):260-265. Epub 2021 Feb 16.

Department of Chemistry, M.M.A.M.C (Tribhuvan University), Biratnagar, Nepal.

The title compound, CHNOS, crystallizes with two independent mol-ecules ( and ) in the asymmetric unit. In the central ring systems of both mol-ecules, the tetra-hydro-furan rings adopt envelope conformations, the pyrrolidine rings adopt a twisted-envelope conformation and the six-membered ring is in a boat conformation. In mol-ecules and , the nine-membered groups attached to the central ring system are essentially planar (r. Read More

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Tribarium dicitrate penta-hydrate, [Ba(CHO)(HO)]·HO.

Authors:
James A Kaduk

Acta Crystallogr E Crystallogr Commun 2021 Mar 12;77(Pt 3):251-254. Epub 2021 Feb 12.

Department of Physics, North Central College, 131 S. Loomis St., Naperville IL 60540 , USA.

The crystal structure of tribarium dicitrate penta-hydrate, [Ba(CHO)(HO)]·HO, has been solved and refined using synchrotron X-ray powder diffraction data, and optimized using density functional techniques. The BaO and BaO coordination polyhedra share edges and corners to form a three-dimensional network. All of the active hydrogen atoms act as donors in O-H⋯O hydrogen bonds. Read More

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Crystal structure and Hirshfeld surface analysis of ethyl 2-[9-(2-hy-droxy-phen-yl)-3,3,6,6-tetra-methyl-1,8-dioxo-2,3,4,4a,5,6,7,8a,9,9a,10,10a-dodeca-hydro-acridin-10-yl]acetate.

Acta Crystallogr E Crystallogr Commun 2021 Mar 12;77(Pt 3):247-250. Epub 2021 Feb 12.

Faculty of Science, Department of Bio Chemistry, Beni Suef University, Beni Suef, Egypt.

In the title compound, CHNO, a 3,3,6,6-tetra-methyl-tetra-hydro-acridine-1,8-dione ring system carries an ethyl acetate substituent on the acridine N atom and an -hy-droxy-phenyl ring on the central methine C atom of the di-hydro-pyridine ring. The benzene ring is inclined to the acridine ring system at an angle of 80.45 (7)° and this conformation is stabilized by an intra-molecular O-H⋯O hydrogen bond between the hy-droxy substituent on the benzene ring and one of the carbonyl groups of the acridinedione unit. Read More

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Crystal structures of two hydrazide derivatives of mefenamic acid, 3-(2,3-di-methyl-anilino)-'-[()-(furan-2-yl)methyl-idene]benzohydrazide and '-[()-benzyl-idene]-2-(2,3-di-methyl-anilino)benzo-hydrazide.

Acta Crystallogr E Crystallogr Commun 2021 Mar 12;77(Pt 3):242-246. Epub 2021 Feb 12.

Department of Chemistry, Faculty of Science, Sana'a University, Sana'a, Yemen.

The conformation about the central benzene ring in the mol-ecule of (I), CHNO, is partially determined by an intra-molecular N-H⋯O hydrogen bond. In the crystal, chains parallel to the axis are generated by inter-molecular N-H⋯O hydrogen bonds with the chains assembled into a three-dimensional network structure by inter-molecular C-H⋯O hydrogen bonds and C-H⋯π(ring) inter-actions. The mol-ecule of (II), CHNO, differs from (I) only in the substituent at the hydrazide N atom where a phenyl-methyl-ene moiety for (II) is present instead of a furan-methyl-ene moiety for (I). Read More

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Crystal structure of a methanol solvate of a macrocycle bearing two flexible side-arms.

Acta Crystallogr E Crystallogr Commun 2021 Mar 5;77(Pt 3):233-236. Epub 2021 Feb 5.

Technische Universität Bergakademie Freiberg, Leipziger Str. 29, D-09596 Freiberg/Sachsen, Germany.

Di--butyl ,'-{[13,15,28,30,31,33-hexa-ethyl-3,10,18,25,32,34-hexa-aza-penta-cyclo-[25.3.1. Read More

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A hierarchical clustering method of hydrogen bond networks in liquid water undergoing shear flow.

Sci Rep 2021 May 5;11(1):9542. Epub 2021 May 5.

State Key Laboratory of Hydro-Science and Engineering, Department of Hydraulic Engineering, Tsinghua University, Beijing, 100084, China.

Many properties of water, such as turbulent flow, are closely related to water clusters, whereas how water clusters form and transform in bulk water remains unclear. A hierarchical clustering method is introduced to search out water clusters in hydrogen bonded network based on modified Louvain algorithm of graph community. Hydrogen bonds, rings and fragments are considered as 1st-, 2nd-, and 3rd-level structures, respectively. Read More

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Cold Gas-Dynamic Spray for Catalyzation of Plastically Deformed Mg-Strips with Ni Powder.

Nanomaterials (Basel) 2021 Apr 29;11(5). Epub 2021 Apr 29.

Nanotechnology and Applications Program, Energy and Building Research Center, Kuwait Institute for Scientific Research, Safat 13109, Kuwait.

Magnesium hydride (MgH) has received significant attention due to its potential applications as solid-state hydrogen storage media for useful fuel cell applications. Even though MgH possesses several attractive hydrogen storage properties, it cannot be utilized in fuel cell applications due to its high thermal stability and poor hydrogen uptake/release kinetics. High-energy ball milling, and mechanically-induced cold-rolling processes are the most common techniques to introduce severe plastic deformation and lattice imperfection in the Mg/MgH. Read More

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Bioinspired Crowding Inhibits Explosive Ice Growth in Antifreeze Protein Solutions.

Biomacromolecules 2021 May 4. Epub 2021 May 4.

Key Laboratory of Green Printing, Beijing National Laboratory for Molecular Science, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, People's Republic of China.

Antifreeze (glyco)proteins (AF(G)Ps) are naturally evolved ice inhibitors incomparable to any man-made materials, thus, they are gaining intensive interest for cryopreservation and beyond. AF(G)Ps depress the freezing temperature () noncolligatively below the melting temperature (), generating a thermal hysteresis (TH) gap, within which the ice growth is arrested. However, the ice crystals have been reported to undergo a retaliatory and explosive growth beyond the TH gap, which is lethal to living organisms. Read More

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Protective effects of hydrogen gas inhalation on radiation-induced bone marrow damage in cancer patients: a retrospective observational study.

Med Gas Res 2021 Jul-Sep;11(3):104-109

Faculty of Environment and Information Studies, Keio University, Fujisawa, Japan.

Although intensity-modulated radiation therapy (IMRT) has been developed as an alternative to conventional radiotherapy, reducing bone marrow damage is limited. Thus, a novel technology is needed to further mitigate IMRT-induced bone marrow damage. Molecular hydrogen (H) was recently reported as a preventive and therapeutic antioxidant that selectively scavenges hydroxyl radical (·OH) and peroxynitrite (ONOO). Read More

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Improving gelling properties of diluted whole hen eggs with sodium chloride and sodium tripolyphosphate: Study on intermolecular forces, water state and microstructure.

Food Chem 2021 Apr 20;358:129823. Epub 2021 Apr 20.

State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu 214122, China; School of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu 214122, China. Electronic address:

Individual and synergistic effects of sodium chloride (NaCl) and sodium tripolyphosphate (STPP) on the physicochemical and gelling properties of highly diluted liquid whole eggs were studied. Results showed that NaCl and STPP acted differently whereby NaCl addition increased the surface hydrophobicity of the egg proteins and STPP addition increased the protein solubility and the negative surface charge. When combined together, these changes led to a significant increase in a number of intermolecular forces after heat treatment, including hydrophobic interactions, disulfide bonds, and hydrogen bonds, contributing to the best structure and texture of the whole egg gels enriched with binary salts. Read More

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Interaction between A-type/B-type starch granules and gluten in dough during mixing.

Food Chem 2021 Apr 20;358:129870. Epub 2021 Apr 20.

College of Food Science and Engineering, Henan University of Technology, Zhengzhou 450001, PR China.

To explore the interaction between A/B starch and gluten, the rheological and structural properties of starch-gluten dough with varied A/B starch ratios during mixing were investigated. The G' and G″ values of under- and overdeveloped dough with an A/B starch ratio of 5:5 were higher than those of dough with other ratios and decreased as the A/B starch ratio increased in optimized dough. B starch enhanced extension resistance and dough firmness. Read More

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First-Principles Simulations of CuCl in High-Temperature Water Vapor.

J Phys Chem B 2021 May 3;125(18):4794-4807. Epub 2021 May 3.

Chemistry Division, Los Alamos National Laboratory, Los Alamos, New Mexico 87545, United States.

Experimental data suggest that the solubility of copper in high-temperature water vapor is controlled by the formation of hydrated clusters of the form CuCl(HO), where the average number of water molecules in the cluster generally increases with increasing density [Migdisov, A. A.; et al. Read More

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Simultaneously Toughening and Stiffening Elastomers with Octuple Hydrogen Bonding.

Adv Mater 2021 May 3:e2008523. Epub 2021 May 3.

NTNU Nanomechanical Lab, Department of Structural Engineering, Norwegian University of Science and Technology (NTNU), Trondheim, 7491, Norway.

Current synthetic elastomers suffer from the well-known trade-off between toughness and stiffness. By a combination of multiscale experiments and atomistic simulations, a transparent unfilled elastomer with simultaneously enhanced toughness and stiffness is demonstrated. The designed elastomer comprises homogeneous networks with ultrastrong, reversible, and sacrificial octuple hydrogen bonding (HB), which evenly distribute the stress to each polymer chain during loading, thus enhancing stretchability and delaying fracture. Read More

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