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  • 1
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    Modest stabilization by most hydrogen-bonded side-chain interactions in membrane proteins (2008)
    Nature Publishing Group (NPG)
    Details
    Publication Date: 2008-05-27
    Description: Understanding the energetics of molecular interactions is fundamental to all of the central quests of structural biology including structure prediction and design, mapping evolutionary pathways, learning how mutations cause disease, drug design, and relating structure to function. Hydrogen-bonding is widely regarded as an important force in a membrane environment because of the low dielectric constant of membranes and a lack of competition from water. Indeed, polar residue substitutions are the most common disease-causing mutations in membrane proteins. Because of limited structural information and technical challenges, however, there have been few quantitative tests of hydrogen-bond strength in the context of large membrane proteins. Here we show, by using a double-mutant cycle analysis, that the average contribution of eight interhelical side-chain hydrogen-bonding interactions throughout bacteriorhodopsin is only 0.6 kcal mol(-1). In agreement with these experiments, we find that 4% of polar atoms in the non-polar core regions of membrane proteins have no hydrogen-bond partner and the lengths of buried hydrogen bonds in soluble proteins and membrane protein transmembrane regions are statistically identical. Our results indicate that most hydrogen-bond interactions in membrane proteins are only modestly stabilizing. Weak hydrogen-bonding should be reflected in considerations of membrane protein folding, dynamics, design, evolution and function.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2734483/" target="_blank"〉〈img src="https://static.pubmed.gov/portal/portal3rc.fcgi/4089621/img/3977009" border="0"〉〈/a〉   〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2734483/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Joh, Nathan Hyunjoong -- Min, Andrew -- Faham, Salem -- Whitelegge, Julian P -- Yang, Duan -- Woods, Virgil L -- Bowie, James U -- R01 CA081000/CA/NCI NIH HHS/ -- R01 CA081000-07/CA/NCI NIH HHS/ -- R01 CA081000-08/CA/NCI NIH HHS/ -- R01 CA081000-09/CA/NCI NIH HHS/ -- R01 GM063919/GM/NIGMS NIH HHS/ -- R01 GM063919-06/GM/NIGMS NIH HHS/ -- R01 GM063919-07/GM/NIGMS NIH HHS/ -- R01 GM063919-08/GM/NIGMS NIH HHS/ -- England -- Nature. 2008 Jun 26;453(7199):1266-70. doi: 10.1038/nature06977. Epub 2008 May 25.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Chemistry and Biochemistry, UCLA-DOE Center for Genomics and Proteomics, Molecular Biology Institute, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/18500332" target="_blank"〉PubMed〈/a〉
    Keywords: Bacteriorhodopsins/chemistry/genetics/metabolism ; Crystallography, X-Ray ; Deuterium Exchange Measurement ; Hydrogen Bonding ; Membrane Proteins/*chemistry/genetics/*metabolism ; Models, Molecular ; Mutation/genetics ; Protein Folding ; Solubility ; Thermodynamics
    Print ISSN: 0028-0836
    Electronic ISSN: 1476-4687
    Topics: Biology , Chemistry and Pharmacology , Medicine , Natural Sciences in General , Physics
    Published by Nature Publishing Group (NPG)
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  • 2
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    Structure of the human glucagon class B G-protein-coupled receptor (2013)
    Nature Publishing Group (NPG)
    Details
    Publication Date: 2013-07-19
    Description: Binding of the glucagon peptide to the glucagon receptor (GCGR) triggers the release of glucose from the liver during fasting; thus GCGR plays an important role in glucose homeostasis. Here we report the crystal structure of the seven transmembrane helical domain of human GCGR at 3.4 A resolution, complemented by extensive site-specific mutagenesis, and a hybrid model of glucagon bound to GCGR to understand the molecular recognition of the receptor for its native ligand. Beyond the shared seven transmembrane fold, the GCGR transmembrane domain deviates from class A G-protein-coupled receptors with a large ligand-binding pocket and the first transmembrane helix having a 'stalk' region that extends three alpha-helical turns above the plane of the membrane. The stalk positions the extracellular domain (~12 kilodaltons) relative to the membrane to form the glucagon-binding site that captures the peptide and facilitates the insertion of glucagon's amino terminus into the seven transmembrane domain.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3820480/" target="_blank"〉〈img src="https://static.pubmed.gov/portal/portal3rc.fcgi/4089621/img/3977009" border="0"〉〈/a〉   〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3820480/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Siu, Fai Yiu -- He, Min -- de Graaf, Chris -- Han, Gye Won -- Yang, Dehua -- Zhang, Zhiyun -- Zhou, Caihong -- Xu, Qingping -- Wacker, Daniel -- Joseph, Jeremiah S -- Liu, Wei -- Lau, Jesper -- Cherezov, Vadim -- Katritch, Vsevolod -- Wang, Ming-Wei -- Stevens, Raymond C -- F32 DK088392/DK/NIDDK NIH HHS/ -- P50 GM073197/GM/NIGMS NIH HHS/ -- P50GM073197/GM/NIGMS NIH HHS/ -- U54 GM094586/GM/NIGMS NIH HHS/ -- U54 GM094618/GM/NIGMS NIH HHS/ -- Y1-CO-1020/CO/NCI NIH HHS/ -- Y1-GM-1104/GM/NIGMS NIH HHS/ -- England -- Nature. 2013 Jul 25;499(7459):444-9. doi: 10.1038/nature12393. Epub 2013 Jul 17.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Integrative Structural and Computational Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, California 92037, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/23863937" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Binding Sites ; Cell Membrane/metabolism ; Crystallography, X-Ray ; Glucagon/chemistry/metabolism ; Humans ; Ligands ; Models, Molecular ; Molecular Sequence Data ; Mutagenesis, Site-Directed ; Protein Binding ; Protein Structure, Tertiary ; Receptors, CXCR4/chemistry/classification ; Receptors, Glucagon/*chemistry/*classification/genetics/metabolism
    Print ISSN: 0028-0836
    Electronic ISSN: 1476-4687
    Topics: Biology , Chemistry and Pharmacology , Medicine , Natural Sciences in General , Physics
    Published by Nature Publishing Group (NPG)
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  • 3
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    The crystal structure of Cpf1 in complex with CRISPR RNA (2016)
    Nature Publishing Group (NPG)
    Details
    Publication Date: 2016-04-21
    Description: The CRISPR-Cas systems, as exemplified by CRISPR-Cas9, are RNA-guided adaptive immune systems used by bacteria and archaea to defend against viral infection. The CRISPR-Cpf1 system, a new class 2 CRISPR-Cas system, mediates robust DNA interference in human cells. Although functionally conserved, Cpf1 and Cas9 differ in many aspects including their guide RNAs and substrate specificity. Here we report the 2.38 A crystal structure of the CRISPR RNA (crRNA)-bound Lachnospiraceae bacterium ND2006 Cpf1 (LbCpf1). LbCpf1 has a triangle-shaped architecture with a large positively charged channel at the centre. Recognized by the oligonucleotide-binding domain of LbCpf1, the crRNA adopts a highly distorted conformation stabilized by extensive intramolecular interactions and the (Mg(H2O)6)(2+) ion. The oligonucleotide-binding domain also harbours a looped-out helical domain that is important for LbCpf1 substrate binding. Binding of crRNA or crRNA lacking the guide sequence induces marked conformational changes but no oligomerization of LbCpf1. Our study reveals the crRNA recognition mechanism and provides insight into crRNA-guided substrate binding of LbCpf1, establishing a framework for engineering LbCpf1 to improve its efficiency and specificity for genome editing.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Dong, De -- Ren, Kuan -- Qiu, Xiaolin -- Zheng, Jianlin -- Guo, Minghui -- Guan, Xiaoyu -- Liu, Hongnan -- Li, Ningning -- Zhang, Bailing -- Yang, Daijun -- Ma, Chuang -- Wang, Shuo -- Wu, Dan -- Ma, Yunfeng -- Fan, Shilong -- Wang, Jiawei -- Gao, Ning -- Huang, Zhiwei -- England -- Nature. 2016 Apr 28;532(7600):522-6. doi: 10.1038/nature17944. Epub 2016 Apr 20.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉School of Life Science and Technology, Harbin Institute of Technology, Harbin 150080, China. ; Ministry of Education Key Laboratory of Protein Sciences, Center for Structural Biology, School of Life Sciences, Tsinghua University, Beijing 100084, China.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/27096363" target="_blank"〉PubMed〈/a〉
    Keywords: Bacterial Proteins/*chemistry/*metabolism ; CRISPR-Associated Proteins/*chemistry/*metabolism ; CRISPR-Cas Systems ; Clustered Regularly Interspaced Short Palindromic Repeats/*genetics ; Crystallography, X-Ray ; Firmicutes/*enzymology ; Genetic Engineering ; Models, Molecular ; Nucleic Acid Conformation ; Protein Binding ; Protein Structure, Tertiary ; RNA Stability ; RNA, Bacterial/*chemistry/genetics/*metabolism ; RNA, Guide/chemistry/genetics/metabolism ; Substrate Specificity
    Print ISSN: 0028-0836
    Electronic ISSN: 1476-4687
    Topics: Biology , Chemistry and Pharmacology , Medicine , Natural Sciences in General , Physics
    Published by Nature Publishing Group (NPG)
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  • 4
    Electronic Resource
    Electronic Resource
    Rheological studies of thermotropic liquid crystal copolyesters: P-hydroxybenzoic acid / 2-hydroxy-6-naphthoic acid (1989)
    Bognor Regis [u.a.] : Wiley-Blackwell
    Journal of Polymer Science Part B: Polymer Physics 27 (1989), S. 819-835 
    Details
    ISSN: 0887-6266
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Physics
    Notes: The rheological behavior of the thermotropic liquid crystal copolyesters composed of p-hydroxybenzoic acid and 2-hydroxy-6-naphthoic acid (indicated as HBA/HNA) is investigated for three different compositions: 75:25, 58:42, 30:70 (in mol%). The inherent viscosities are 9.2, 5.1, and 7.8 dl/g, respectively. Yield stress is observed for all three samples. This indicates the existence of crystallites in the melt which may be related to the shear thinning viscosity at low shear stress. Melt fracture, and a die swell ratio which increases with shear rate, are also observed at higher temperatures and at low shear stress for the two copolyesters having compositions 75:25 and 30:70. We have also estimated for 30HBA/70HNA at 335°C the entrance pressure loss, Δpent, and ΔPent/δw, where δw is the shear stress at the capillary wall. The large value of ΔPent/δw suggest that HBA/HNA is a highly elastic polymeric material. It is found that both ΔPent and ΔPent/δw increase with shear rate. However, the high elasticity does not account for the disappearance of melt fracture and contraction of die swell at high shear stress. This abnormal phenomenon is ascribed to the formation of a network of crystallites caused by blocky regions in the copolymer.
    Additional Material: 18 Ill.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/polb.1989.090270408
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  • 5
    Electronic Resource
    Electronic Resource
    Polarized Grazing Angle FTIR Study of Molecular Orientation and Bonding of Thioglycolates at the Metal Interface (1996)
    Chichester [u.a.] : Wiley-Blackwell
    Surface and Interface Analysis 24 (1996), S. 803-810 
    Details
    ISSN: 0142-2421
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Physics
    Notes: The mercaptoesters have been recognized as an effective coupling agent for bonding metals using acrylate and epoxy adhesives with enhanced bonding strength and improved durability. Here, we report the results of our investigation of the interaction of thioester coupling agents with a gold surface using a grazing angle FTIR (GA/FTIR) spectroscopic technique. We investigated the interaction of alkyl functional thioesters (octylthioglycolate, dodecyl-thioglycolate and stearylthioglycolate) coupling agents with the metal at the interface region. The formation of strong chemical bonding is proven to be the key feature of this application rather than wetting or hydrogen bonding for conventional adhesive applications. Based on our results we have concluded that the deposited layers exist as thioester bonded to the gold surface through the sulfur-metal bond and that the polarization results indicate that only those thioesters containing C12 and C18 hydrocarbon tail chains self-assemble readily and close pack on the surface. For dodecyl thioglycolate, the C12 alkyl chains are densely packed and oriented perpendicular to the substrate surface. For the stearyl thioglycolate, the C18 alkyl tail chains are also closely packed and oriented, but the chains appear to tilt from the normal surface. However, the carbonyl group of the C18 thioester appears to be parallel to the surface. For short-chain mercaptoesters, such as octyl thioglycolate, the alkyl chains do not self-assemble or orient on the gold surface. The molecular orientation of the coupling agent at the interface region has also been shown to play an important role in determining the interaction of the adhesive with the coupling agent layers. Results of the interfacial shear strength promotion on mild steel by the mercaptoester coupling agents are also reported.
    Additional Material: 10 Ill.
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  • 6
    Electronic Resource
    Electronic Resource
    Analysis of the polyolefin/trialkylamine primer interface (1993)
    Chichester [u.a.] : Wiley-Blackwell
    Surface and Interface Analysis 20 (1993), S. 407-415 
    Details
    ISSN: 0142-2421
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Physics
    Notes: Tertiary alkylamines of different chain lengths have been used as primers for adhesive bonding strength promotion for polyolefinic surfaces with cyanoacrylate (CA) adhesives. A combination of the construction of model polyolefin surfaces and advanced molecular-sensitive analysis tools has been employed for understanding the promoter/polyolefin interaction at the interface. Characterization of primer structure and interfacial properties has been carried out using grazing angle reflection-absorption Fourier transform infrared spectroscopy (GA/FTIR), ellipsometry, x-ray photoelectron spectroscopy (XPS) and contact angle titration using different pH probe liquids. Our work has focused on the design and construction of a model polyolefin surface using a new in situ polyethylene (PE) polymerization technique to form a controllable thickness (〈400 Å) of PE film on a reflective metal surface. The new technique of in situ PE polymerization is based on diazomethane chemistry. Both protonated and deuterated PE films have been successfully prepared. The results of spectroscopic investigations of these model deuterated and non-deuterated PE surfaces are disclosed. Molecular parameters that affect adhesion promotion have been studied. The parameters studied include molecular structure and alkyl chain length of tertiary alkylamines.
    Additional Material: 10 Ill.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/sia.740200513
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  • 7
    Electronic Resource
    Electronic Resource
    Interfacial analyses of copper corrosion by acrylic and methacrylic acids using XPS, auger and grazing angle FTIR spectroscopy (1995)
    Chichester [u.a.] : Wiley-Blackwell
    Surface and Interface Analysis 23 (1995), S. 276-288 
    Details
    ISSN: 0142-2421
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Physics
    Notes: We have observed that methacrylic acid (MA) is far more corrosive than acrylic acid (AA) on copper surfaces when copper was exposed to the vapor of these two acids at ambient temperature and environment. With the aid of modern surface-sensitive instrumentation, which included grazing angle Fourier transform infrared (FTIR), XPS, x-ray-induced Auger electron and SEM/energy-dispersive spectroscopies and white light stereo and metallurgical microscopy, we are reporting our results of an extensive study of the roles that MA and AA have in this unusual phenomenon of copper corrosion.By grazing angle FTIR analysis we demonstrated that copper carboxylate salt formation is very rapid upon short contact with the vapor of both acids, and the acids showed no evidence of polymerization. We have also demonstrated by XPS and x-ray-induced Auger electron spectroscopy that copper surfaces exposed to the MA vapor contains mainly Cu(II) species. However, the oxidation state of the copper exposed to AA vapor will depend on exposure time and environment. With limited exposure to the air, the copper surface remained shiny for up to 12 months test time. The spectrum obtained from the shiny area of the AA/Cu surface shows that it contains mainly Cu(I) mixed with some copper (II). When the spectrum was taken from a dull area of AA/Cu surfaces, the Cu(II) state was found to be predominant. These results strongly indicate that when the shiny AA/Cu surface changed to a dull color, the oxidation state of the copper also changed from +1 to +2. The molecular structure of the Cu(II)-AA salt is also believed to be altered.Both stereo microscopic and SEM/energy-dispersive spectroscopy techniques were also used to perform the visual and microanalysis of the surface texture and elemental compositions of the corroded surfaces, respectively. The presence of oxygen was also found to play an important role in the overall corrosion processes. The differences in molecular structure of copper carboxylate salts of different oxidation states are discussed and are believed to be responsible for this unusual phenomenon. We believe that this finding will provide a good explanation for the cause of drastic differences of copper corrosion by acrylic and methacrylic acids.
    Additional Material: 15 Ill.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/sia.740230503
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  • 8
    Electronic Resource
    Electronic Resource
    Recrystallization of HDPE in HDPE/iPP quenched films (1996)
    Weinheim : Wiley-Blackwell
    Acta Polymerica 47 (1996), S. 285-289 
    Details
    ISSN: 0323-7648
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Physics
    Notes: Epitaxial crystallization behavior of HDPE/iPP double layers under quenching and annealing conditions has been studied by means of transmission electron microscopy (TEM). The results obtained from bright field TEM observations indicate that in the as-quenched state the HDPE that is in direct contact with the surface of the oriented iPP substrate recrystallizes in the form of oriented crystallites dispersed on the iPP substrate. The electron diffraction results show that besides the two normally observed epitaxial orientations between HDPE and iPP, there is also a special orientation with [001]HDPE ‖ [001]iPP. The HDPE which is in contact with the clean surface of a glass slide crystallizes in small lamellae with random orientation. In the boundary region, the epitaxially crystallized HDPE small lamellae stop right on the boundary of the oriented iPP film. If the quenched samples are annealed at 128°C (below Tm of HDPE) for 2 h, the small HDPE crystals grow to thick lamellae in both areas. But only the epitaxial orientation of HDPE with [001]HDPE ‖ [101]iPP has been observed.
    Additional Material: 8 Ill.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/actp.1996.010470607
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  • 9
    Electronic Resource
    Electronic Resource
    Sorption and transport studies of water in KaptonRegistered trademark, E. I. du Pont de Nemours and Company. polymide. I (1985)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Applied Polymer Science 30 (1985), S. 1035-1047 
    Details
    ISSN: 0021-8995
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Mechanical Engineering, Materials Science, Production Engineering, Mining and Metallurgy, Traffic Engineering, Precision Mechanics , Physics
    Notes: Sorption isotherms and diffusion coefficients of water in a 0.3-mil Kapton polyimide film at 30, 45, and 60°C are reported. The data are well described by the dual mode sorption and transport models at low activities. At high penetrant activities, clustering of water is suggested by a Zimm-Lundberg analysis of the sorption data and the fact that the diffusion coefficient for water decreases with increasing external vapor activity. The effect of temperature on the diffusion coefficients at infinite dilution and the dual mode sorption parameters kD, b, and CH′ are presented and discussed. The magnitude of the activation energy of the diffusion coefficient at infinite dilution, 5.4 kcal/mol, is smaller than the corresponding activation energy in more flexible chain polymers, perhaps suggesting that rather small backbone motions are associated with diffusion of water through the Kapton matrix. The predictions for the isosteric enthalpy of sorption from the dual mode model are presented and compared with the values determined from graphical analysis of the sorption isotherms performed independently without reference to the dual mode sorption model.
    Additional Material: 7 Ill.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/app.1985.070300313
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  • 10
    Electronic Resource
    Electronic Resource
    The effects of morphology and hygrothermal aging on water sorption and transport in Kapton® polyimide (1986)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Applied Polymer Science 31 (1986), S. 1619-1629 
    Details
    ISSN: 0021-8995
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Mechanical Engineering, Materials Science, Production Engineering, Mining and Metallurgy, Traffic Engineering, Precision Mechanics , Physics
    Notes: A comparison of water sorption and diffusion behavior in 2 mil, as-received, Kapton= Trademark of E.I. Dupont de Nemours Inc. film, and in otherwise identical but hygrothermally aged samples, suggests chemical differences between the samples. These differences can be related to known polyimide chemistry and the specific history encountered by the samples. Although the sorption isotherms are similar for an as-received 0.3 mil sample studied earlier and for the as-received 2 mil samples studied here, the diffusion coefficient of water in the as-received 2 mil sample is approximately 300% larger than in the as-received 0.3 mil sample. This large effect is believed to be related to the presence of small, paracrystalline aggregates with large aspect ratios. Differences in orientation measured by birefringence for the two samples suggest that the barrier properties of Kapton® are strongly affected by the detailed morphological organization of the ordered aggregates. Comparison of the sorption isotherms for the as-received and hygrothermally aged 2-mil films suggests a significant increase in the hydrophillic nature of the aged film. This change is consistent with an apparent chemical reaction between water and uncyclized amic acid residues in the film. The tendency for water to cluster in as-received Kapton® is essentially eliminated by the chemical modification associated with hygrothermal aging. The hygrothermal aging produces a dramatic reduction in the water vapor diffusion coefficient at low vapor activities but a rather modest change at high activities.
    Additional Material: 5 Ill.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/app.1986.070310608
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