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At least 631 records · Page 35

Crystal structure of the CueO mutants at Glu506, the key amino acid located in the proton transfer pathway for dioxygen reduction

Highlights: •Proton transfer pathway in the four-electron reduction of dioxygen by CueO. •Compensatory hydrogen bond network comprised of only water molecules in the Glu to Ala mutant. •Shutdown of the hydrogen bond network by the Glu to Ile mutation. •X-ray crystal structures of the CueO mutants with the modified proton transport pathway. -- Abstract: Glu506 involved in the hydrogen bond network leading from solvent waters to the trinuclear copper center in a multicopper oxidase, CueO plays a crucial role to transport protons in the four-electron reduction of dioxygen to water. We performed X-ray crystal structure analyses of the Glu506Ala and Glu506Ile mutants, showing the formation of a compensatory proton transport pathway with only water molecules and a disruption of the hydrogen bond network due to the bulky side chain, respectively. We discuss the efficiency of proton transport through the hydrogen bond network based on the present results and our previous modification of the proton transport pathway by the Glu506 to Gln mutation, which have allowed us to trap and characterize the reaction intermediates.

60 APPLIED LIFE SCIENCES↗

Synthesis and Crystal Structure of the Zintl Phases Na2CaCdSb2, Na2SrCdSb2 and Na2EuCdSb2

This work details the synthesis and the crystal structures of the quaternary Zintl phases Na2CaCdSb2, Na2SrCdSb2 and Na2EuCdSb2. They are isostructural and their noncentrosymmetric structure is with the space group Pmc21 (Pearson code oP12). All structural work is carried out via single-crystal X-ray diffraction methods. The structure features [CdSb2]4– layers of corner-shared CdSb4 tetrahedra, which are stacked along the b-crystallographic axis and are separated by cations. The results from the structure refinements suggest that in addition to full cation ordering, which is typical for this structure, there also exists a possibility for an accommodation of a small degree of cation disorder.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Report on the sixth blind test of organic crystal structure prediction methods

The sixth blind test of organic crystal structure prediction (CSP) methods has been held, with five target systems: a small nearly rigid molecule, a polymorphic former drug candidate, a chloride salt hydrate, a co-crystal and a bulky flexible molecule. This blind test has seen substantial growth in the number of participants, with the broad range of prediction methods giving a unique insight into the state of the art in the field. Significant progress has been seen in treating flexible molecules, usage of hierarchical approaches to ranking structures, the application of density-functional approximations, and the establishment of new workflows and `best practices' for performing CSP calculations. All of the targets, apart from a single potentially disordered Z ' = 2 polymorph of the drug candidate, were predicted by at least one submission. Despite many remaining challenges, it is clear that CSP methods are becoming more applicable to a wider range of real systems, including salts, hydrates and larger flexible molecules. The results also highlight the potential for CSP calculations to complement and augment experimental studies of organic solid forms.

Chemistry↗

Development of a scalar-based geometric parameterization approach for the crystal structure landscape of dithienylethene-based crystalline solids

Dithienylethenes (DTEs) are a promising class of organic photoswitches that can be used to create crystalline solids with properties controlled by light. However, the ability of DTEs to adopt multiple conformations, only one of which is photoactive, complicates the rational design of these materials. Herein, the synthesis and structural characterization of 19 crystalline solids containing a single DTE molecule are described. A novel D – D analysis of the molecular geometries obtained from rotational potential energy surface calculations and the ensemble of experimental structures were used to construct a crystal landscape for DTE. Of the 19 crystal structures, 17 contained photoinactive DTE rotamers and only 2 were photoactive. These results highlight the challenges associated with the design of these materials. Overall, the D – D analysis described herein provides rapid, effective and intuitive means of linking the molecular structure to photoactivity that could be applied more broadly to afford a general strategy for producing photoactive diarylethene-based crystalline solids.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

The Crystal Structure of the RNA-Dependent RNA Polymerase from Human Rhinovirus: A Dual Function Target for Common Cold Antiviral Therapy

Human rhinoviruses (HRV), the predominant members of the Picornaviridae family of positive-strand RNA viruses, are the major causative agents of the common cold. Given the lack of effective treatments for rhinoviral infections, virally encoded proteins have become attractive therapeutic targets. The HRV genome encodes an RNA-dependent RNA polymerase (RdRp) denoted 3D{sup pol}, which is responsible for replicating the viral genome and for synthesizing a protein primer used in the replication. Here the crystal structures for three viral serotypes (1B, 14, and 16) of HRV 3D{sup pol} have been determined. The three structures are very similar to one another, and to the closely related poliovirus (PV) 3D{sup pol} enzyme. Because the reported PV crystal structure shows significant disorder, HRV 3D{sup pol} provides the first complete view of a picornaviral RdRp. The folding topology of HRV 3D{sup pol} also resembles that of RdRps from hepatitis C virus (HCV) and rabbit hemorrhagic disease virus (RHDV) despite very low sequence homology.

36 MATERIALS SCIENCE↗

Crystal structure of the FLT3 kinase domain bound to the inhibitor quizartinib (AC220)

More than 30% of acute myeloid leukemia (AML) patients possess activating mutations in the receptor tyrosine kinase FMS-like tyrosine kinase 3 or FLT3. A small-molecule inhibitor of FLT3 (known as quizartinib or AC220) that is currently in clinical trials appears promising for the treatment of AML. Here, we report the co-crystal structure of the kinase domain of FLT3 in complex with quizartinib. FLT3 with quizartinib bound adopts an “Abl-like” inactive conformation with the activation loop stabilized in the “DFG-out” orientation and folded back onto the kinase domain. This conformation is similar to that observed for the uncomplexed intracellular domain of FLT3 as well as for related receptor tyrosine kinases, except for a localized induced fit in the activation loop. The co-crystal structure reveals the interactions between quizartinib and the active site of FLT3 that are key for achieving its high potency against both wild-type FLT3 as well as a FLT3 variant observed in many AML patients. This co-complex further provides a structural rationale for quizartinib-resistance mutations.

59 BASIC BIOLOGICAL SCIENCES↗

New CeMgCo{sub 4} and Ce{sub 2}MgCo{sub 9} compounds: Hydrogenation properties and crystal structure of hydrides

Two new ternary intermetallic compounds, CeMgCo{sub 4} (C15b pseudo-Laves phase, MgCu{sub 4}Sn type) and Ce{sub 2}MgCo{sub 9} (substitution derivative of PuNi{sub 3} type) were synthesized by mechanical alloying method. The structural and hydrogenation properties of these compounds were studied by X-ray diffraction and Pressure-Composition-Temperature measurements. Both compounds absorb hydrogen at room temperature and pressures below 10 MPa forming hydrides with maximum compositions CeMgCo{sub 4}H{sub 6} and Ce{sub 2}MgCo{sub 9}H{sub 12}. Single plateau behavior was observed in P-C isotherm during hydrogen absorption/desorption by Ce{sub 2}MgCo{sub 9} alloy. The CeMgCo{sub 4}-H{sub 2} system is characterized by the presence of two absorption/desorption plateaus corresponding to formation of {beta}-CeMgCo{sub 4}H{sub 4} and {gamma}-CeMgCo{sub 4}H{sub 6} hydride phases. The structure of {beta}-hydride CeMgCo{sub 4}H(D){sub 4} was determined from X-ray and neutron powder diffraction data. In this structure initial cubic symmetry of CeMgCo{sub 4} is preserved and hydrogen atoms fill only one type of interstitial sites, triangular MgCo{sub 2} faces. These positions are occupied by 70% and form octahedron around Mg atom with Mg-D bond distances 1.84 A. - Graphical abstract: Crystal structure of the {beta}-CeMgCo{sub 4}D{sub 4.2} deuteride. Octahedra of D-sites around Mg atoms are shown. Highlights: Black-Right-Pointing-Pointer Two new ternary compounds have been synthesized in the Ce-Mg-Co system. Black-Right-Pointing-Pointer Below 100 bar H{sub 2} CeMgCo{sub 4} and Ce{sub 2}MgCo{sub 9} reversibly absorb hydrogen at room temperature. Black-Right-Pointing-Pointer Crystal structure of cubic CeMgCo{sub 4}D{sub 4.2} deuteride has been determined.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Comparison of NMR and crystal structures highlights conformational isomerism in protein active sites

The JCSG has recently developed a protocol for systematic comparisons of highquality crystal and NMR structures of proteins. In this paper, the extent to which this approach can provide function-related information on the two functionally annotated proteins TM1081, a Thermotoga maritima anti- factor antagonist, and A2LD1 (gi:13879369), a mouse -glutamylamine cyclotransferase, is explored. The NMR structures of the two proteins have been determined in solution at 313 and 298 K, respectively, using the current JCSG protocol based on the software package UNIO for extensive automation. The corresponding crystal structures were solved by the JCSG at 100 K and 1.6 Å resolution and at 100 K and 1.9 Å resolution, respectively. The NMR and crystal structures of the two proteins share the same overall molecular architectures. However, the precision of the structure determination along the amino-acid sequence varies over a significantly wider range in the NMR structures than in the crystal structures. Thereby, in each of the two NMR structures about 65% of the residues have displacements below the average and in both proteins the less well ordered residues include large parts of the active sites, in addition to some highly solvent-exposed surface areas. Whereas the latter show increased disorder in the crystal and in solution, the active-site regions display increased displacements only in the NMR structures, where they undergo local conformational exchange on the millisecond time scale that appears to be frozen in the crystals. These observations suggest that a search for molecular regions showing increased structural disorder and slow dynamic processes in solution while being well ordered in the corresponding crystal structure might be a valid initial step in the challenge of identifying putative active sites in functionally unannotated proteins with known three-dimensional structure.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Phase equilibria in the La–Mg–Ge system at 500 °C and crystal structure of the new ternary compounds La{sub 11}Mg{sub 2}Ge{sub 7} and LaMg{sub 3−x}Ge{sub 2}

The whole 500 °C isothermal section of the La–Mg–Ge ternary system was constructed. The existence and crystal structure of three ternary compounds were confirmed: La{sub 2+x}Mg{sub 1−x}Ge{sub 2} (τ{sub 2}, P4/mbm, tP10–Mo{sub 2}FeB{sub 2}, 0≤x≤0.25), La{sub 4}Mg{sub 5}Ge{sub 6} (τ{sub 3}, Cmc2{sub 1}, oS60–Gd{sub 4}Zn{sub 5}Ge{sub 6}) and La{sub 4}Mg{sub 7}Ge{sub 6} (τ{sub 4}, C2/m, mS34, own structure type). Five novel compounds were identified and structurally characterized: La{sub 11}Mg{sub 2}Ge{sub 7} (τ{sub 1}, P4{sub 2}/ncm, tP88-8, own structure type, a=1.21338(5), c=1.57802(6) nm), LaMg{sub 3−x}Ge{sub 2} (τ{sub 5}, P3{sup ¯}1c, hP34-0.44, own structure type, x=0.407(5), a=0.78408(4), c=1.45257(7) nm), La{sub 6}Mg{sub 23}Ge (τ{sub 6}, Fm3{sup ¯}m, cF120–Zr{sub 6}Zn{sub 23}Si, a=1.46694(6) nm), La{sub 4}MgGe{sub 10−x} (τ{sub 7}, x=0.37(1), C2/m, mS60-1.46, own structure type, a=0.88403(8), b=0.86756(8), c=1.7709(2) nm, β=97.16°(1) and La{sub 2}MgGe{sub 6} (τ{sub 8}, Cmce, oS72–Ce{sub 2}(Ga{sub 0.1}Ge{sub 0.9}){sub 7}, a=0.8989(2), b=0.8517(2), c=2.1064(3) nm). Disordering phenomena were revealed in several La–Mg–Ge phases in terms of partially occupied sites. The crystal structures of La{sub 11}Mg{sub 2}Ge{sub 7} and LaMg{sub 3−x}Ge{sub 2} are discussed in details. The latter is a √3a×√3a×2c superstructure of the LaLi{sub 3}Sb{sub 2} structure type; the symmetry reduction scheme is shown in the Bärnighausen formalism terms. - Graphical abstract: La–Mg–Ge isothermal section at 500 °C and group–subgroup relation between the LaLi{sub 3}Sb{sub 2} (parent type) and LaMg{sub 3−x}Ge{sub 2} (derivative) structures. - Highlights: • Novel La−Mg−Ge compounds structure determination from X-ray single crystal data. • Disordering phenomena as common features of the studied germanides. • Bärnighausen formalism as a useful tool for accurate structure determination. • Full isothermal section of the La–Mg–Ge ternary system at 500 °C.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

The crystal structure of HIV CRF07 B′/C gp41 reveals a hyper-mutant site in the middle of HR2 heptad repeat

HIV CRF07 B′/C is a strain circulating mainly in northwest region of China. The gp41 region of CRF07 is derived from a clade C virus. In order to compare the difference of CRF07 gp41 with that of typical clade B virus, we solved the crystal structure of the core region of CRF07 gp41. Compared with clade B gp41, CRF07 gp41 evolved more basic and hydrophilic residues on its helix bundle surface. Based on sequence alignment, a hyper-mutant cluster located in the middle of HR2 heptads repeat was identified. The mutational study of these residues revealed that this site is important in HIV mediated cell–cell fusion and plays critical roles in conformational changes during viral invasion. - Highlights: • We solved the crystal structure of HIV CRF07 gp41 core region. • A hyper-mutant cluster in the middle of HR2 heptads repeat was identified. • The hyper-mutant site is important in HIV-cell fusion. • The model will help to understand the HIV fusion process.

60 APPLIED LIFE SCIENCES↗

Design of HIV-1 Protease Inhibitors with C3-Substituted Hexahydrocyclopentafuranyl Urethanes as P2-Ligands: Synthesis, Biological Evaluation, and Protein-Ligand X-ray Crystal Structure

We report the design, synthesis, biological evaluation, and the X-ray crystal structure of a novel inhibitor bound to the HIV-1 protease. Various C3-functionalized cyclopentanyltetrahydrofurans (Cp-THF) were designed to interact with the flap Gly48 carbonyl or amide NH in the S2-subsite of the HIV-1 protease. We investigated the potential of those functionalized ligands in combination with hydroxyethylsulfonamide isosteres. Inhibitor 26 containing a 3-(R)-hydroxyl group on the Cp-THF core displayed the most potent enzyme inhibitory and antiviral activity. Our studies revealed a preference for the 3-(R)-configuration over the corresponding 3-(S)-derivative. Inhibitor 26 exhibited potent activity against a panel of multidrug-resistant HIV-1 variants. A high resolution X-ray structure of 26-bound HIV-1 protease revealed important molecular insight into the ligand-binding site interactions.

59 BASIC BIOLOGICAL SCIENCES↗

Synthesis, crystal structure and magnetic properties of Li{sub 0.44}Eu{sub 3}[B{sub 3}N{sub 6}]

Li{sub 0.44}Eu{sub 3}[B{sub 3}N{sub 6}] was synthesized from the metathesis reaction of Li{sub 3}[BN{sub 2}] and EuCl{sub 3} at 850 °C. Li{sub 0.44}Eu{sub 3}[B{sub 3}N{sub 6}] crystallizes in the trigonal space group R3{sup ¯}c (No. 167) with a=12.0225(2) Å, c=6.8556(2) Å and Z=6. In the crystal structure, isolated, planar cyclic [B{sub 3}N{sub 6}]{sup 9−} units are charge-balanced by the mixed-valence Eu{sup 3+}/Eu{sup 2+} and Li{sup +} cations. Li{sup +} occupies partially (44%) the Wyckoff site 6b and is sandwiched between the [B{sub 3}N{sub 6}]{sup 9−} anions. Mössbauer spectroscopy results show the resonance lines of Eu{sup 2+} and Eu{sup 3+}, respectively, indicating the heterogeneous mixed valency of the Eu atoms. X-Band ESR investigations between 5 and 300 K reveal an intense signal over the whole temperature range originating from Eu{sup 2+}. Magnetic susceptibility measurements indicate a Curie–Weiss behavior with an experimental effective magnetic moment of μ{sub eff}=8.28 μ{sub B} per formula unit. - Graphical abstract: Single crystals of Li{sub 0.44}Eu{sub 3}[B{sub 3}N{sub 6}] was obtained from the metathesis reaction of Li{sub 3}[BN{sub 2}] and EuCl{sub 3.}{sup 151}Eu Mössbauer, ESR and magnetic susceptibility measurements reveal the heterogeneous mixed valency of the Eu atoms. Display Omitted - Highlights: • Single crystals of Li{sub 0.44}Eu{sub 3}[B{sub 3}N{sub 6}] was obtained from the metathesis reaction of Li{sub 3}[BN{sub 2}] and EuCl{sub 3} at 850 °C. • Crystal structure is built up by isolated, planar cyclic [B{sub 3}N{sub 6}]{sup 9−} units which are surrounded by mixed valence Eu{sup 3+}/Eu{sup 2+}. • Li{sup +} occupies partially (44%) the site 6b and is sandwiched between the [B{sub 3}N{sub 6}]{sup 9−} anions. • The {sup 151}Eu Mössbauer spectroscopy, electron spin resonance spectroscopy and magnetic susceptibility measurements confirm the heterogeneous mixed valency of Eu.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Enhancement of photoluminescence properties and modification of crystal structures of Si{sub 3}N{sub 4} doping Li{sub 2}Sr{sub 0.995}SiO{sub 4}:0.005Eu{sup 2+} phosphors

Highlights: • Si{sub 3}N{sub 4} modified Li{sub 2}Sr{sub 0.995}SiO{sub 4}:0.005Eu{sup 2+} phosphors were prepared. • The luminescence intensity of Li{sub 2}Sr{sub 0.995}SiO{sub 4}:Eu{sup 2+} was enhanced by doping Si{sub 3}N{sub 4}. • The fluorescence decay times and thermal stability were enhanced by doping Si{sub 3}N{sub 4}. - Abstract: Si{sub 3}N{sub 4} modified Li{sub 2}Sr{sub 0.995}SiO{sub 4}:0.005Eu{sup 2+} (Li{sub 2}Sr{sub 0.995}SiO{sub 4−3x/2}N{sub x}:0.005Eu{sup 2+}) phosphors were synthesized with the conventional solid-state reaction in the reduced atmosphere. The crystal structure and vibrational modes were analyzed by X-ray diffraction, Raman scattering spectroscopy and Rietveld crystal structure refinement. Photoluminescence (PL) and photoluminescence excitation (PLE) spectra showed that Li{sub 2}Sr{sub 0.995}SiO{sub 4−3x/2}N{sub x}:0.005Eu{sup 2+} powder exhibited a broad yellow emission band centered at 560 nm under the excitation of 460 nm visible light, due to the 4f{sup 6}5d{sup 1} → 4f{sup 7} transition of Eu{sup 2+}. The partial nitridation of Li{sub 2}Sr{sub 0.995}SiO{sub 4−3x/2}N{sub x}:0.005Eu{sup 2+} (x = 0.01) phosphors led to a large enhancement in the luminescence intensity, as much as 190%. At the same time, the fluorescence decay behavior curves further showed that the photoluminescence efficiencies of Li{sub 2}Sr{sub 0.995}SiO{sub 4−3x/2}N{sub x}:0.005Eu{sup 2+} phosphors were enhanced by addition of Si{sub 3}N{sub 4}. The temperature quenching characteristics confirmed that the oxynitride based Li{sub 2}Sr{sub 0.995}SiO{sub 4−3x/2}N{sub x}:0.005Eu{sup 2+} showed slightly higher stability. It is implied that Li{sub 2}Sr{sub 0.995}SiO{sub 4−3x/2}N{sub x}:0.005Eu{sup 2+} phosphors had a possible potential application on white LEDs to match blue light chips.

36 MATERIALS SCIENCE↗

Crystal structure of citalopram hydrobromide, C 20 H 22 FN 2 OBr

The crystal structure of citalopram hydrobromide has been solved and refined using synchrotron X-ray powder diffraction data, and optimized using density functional theory techniques. Citalopram hydrobromide crystallizes in space group P 2 1 / c (#14) with a = 10.766 45(6), b = 33.070 86(16), c = 10.892 85(5) Å, β = 90.8518(3)°, V = 3878.03(4) Å 3 , and Z = 8. N–H∙∙∙Br hydrogen bonds are important to the structure, but the crystal energy is dominated by van der Waals attraction. The powder pattern was submitted to International Centre for Diffraction Data for inclusion in the Powder Diffraction File™.

Celexa↗

Crystal structures of the reverse transcriptase-associated ribonuclease H domain of xenotropic murine leukemia-virus related virus

The ribonuclease H (RNase H) domain of retroviral reverse transcriptase (RT) plays a critical role in the life cycle by degrading the RNA strands of DNA/RNA hybrids. In addition, RNase H activity is required to precisely remove the RNA primers from nascent (-) and (+) strand DNA. We report here three crystal structures of the RNase H domain of xenotropic murine leukemia virus-related virus (XMRV) RT, namely (i) the previously identified construct from which helix C was deleted, (ii) the intact domain, and (iii) the intact domain complexed with an active site {alpha}-hydroxytropolone inhibitor. Enzymatic assays showed that the intact RNase H domain retained catalytic activity, whereas the variant lacking helix C was only marginally active, corroborating the importance of this helix for enzymatic activity. Modeling of the enzyme-substrate complex elucidated the essential role of helix C in binding a DNA/RNA hybrid and its likely mode of recognition. The crystal structure of the RNase H domain complexed with {beta}-thujaplicinol clearly showed that coordination by two divalent cations mediates recognition of the inhibitor.

59 BASIC BIOLOGICAL SCIENCES↗

X-ray Crystal Structures of Monomeric and Dimeric Peptide Inhibitors in Complex with the Human Neonatal Fc Receptor, FcRn

The neonatal Fc receptor, FcRn, is responsible for the long half-life of IgG molecules in vivo and is a potential therapeutic target for the treatment of autoimmune diseases. A family of peptides comprising the consensus motif GHFGGXY, where X is preferably a hydrophobic amino acid, was shown previously to inhibit the human IgG:human FcRn protein-protein interaction (Mezo, A. R., McDonnell, K. A., Tan Hehir, C. A., Low, S. C., Palombella, V. J., Stattel, J. M., Kamphaus, G. D., Fraley, C., Zhang, Y., Dumont, J. A., and Bitonti, A. J. (2008) Proc. Natl. Acad. Sci. U.S.A., 105, 2337-2342). Herein, the x-ray crystal structure of a representative monomeric peptide in complex with human FcRn was solved to 2.6 {angstrom} resolution. The structure shows that the peptide binds to human FcRn at the same general binding site as does the Fc domain of IgG. The data correlate well with structure-activity relationship data relating to how the peptide family binds to human FcRn. In addition, the x-ray crystal structure of a representative dimeric peptide in complex with human FcRn shows how the bivalent ligand can bridge two FcRn molecules, which may be relevant to the mechanism by which the dimeric peptides inhibit FcRn and increase IgG catabolism in vivo. Modeling of the peptide:FcRn structure as compared with available structural data on Fc and FcRn suggest that the His-6 and Phe-7 (peptide) partially mimic the interaction of His-310 and Ile-253 (Fc) in binding to FcRn, but using a different backbone topology.

36 MATERIALS SCIENCE↗

Bulk moduli and high pressure crystal structure of U 3 Si 2

Bulk moduli are vital parameters to assess the mechanical performance of materials including nuclear fuels. Yet, little experimental data exist for U 3 S i2 , a potential accident-tolerant nuclear fuel, whose bulk modulus has only been measured by resonant ultrasonic spectroscopy (RUS). In addition, the knowledge for high-pressure structural behavior and phase equilibrium of U 3 Si 2 is largely lacking. Here we reviewed pressure dependence of the crystal structure of U 3 Si 2 using high-energy synchrotron X-ray diffraction coupled with Rietveld analysis. The pressurization was achieved using a diamond anvil cell (DAC) which provides quasi-hydrostatic pressures up to 37.6 GPa. Crystal structural variation and equations of state of U 3 Si 2 were obtained, and its bulk modulus, a- and c-axial moduli were derived to be 107.11 +/- 5.65 GPa, 82.87 +/- 4.78 GPa and 194.52 +/- 12.03 GPa, respectively. The determined elastic parameters are compared with those obtained by RUS and nanoindentation. (C) 2019 Elsevier B.V. All rights reserved.

36 MATERIALS SCIENCE↗