Infrared Crystallography: Structural Refinement through Spectroscopy

A method for determining the orientation of individual bonds within complex macromolecules from polarized IR measurements on oriented single crystals is described. At present, X-ray diffraction is the principal technique used to define the global structure and orientation of macromolecules in the crystalline state. However, resolution limitations and conformational disorder limit the accuracy of the resulting structural model. A quantitative understanding of protein function often requires a more precise description of structural features at a localized active site. Polarized IR measurements of internal stretching bands of N−3, CN−, OCN−, and SCN− bound at the ferric heme iron of single crystals of myoglobin are presented. A synthesis of such measurements on different crystal forms leads to an N−3 orientation consistent with IR measurements on both P21 and P212121 crystals, but significantly different from the orientation reported in X-ray crystal structures. Subtle structural changes between these two crystal forms of the CN− complex may account for small differences in the stretching frequency and orientation of the C–N bond.

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Structural characterization of the N-terminal part of the MERS-CoV nucleocapsid by X-ray diffraction and small-angle X-ray scattering

Acta Crystallographica Section D Structural Biology ◽

10.1107/s2059798315024328 ◽

2016 ◽

Vol 72 (2) ◽

pp. 192-202 ◽

Cited By ~ 12

Author(s):

Nicolas Papageorgiou ◽

Julie Lichière ◽

Amal Baklouti ◽

François Ferron ◽

Marion Sévajol ◽

...

Keyword(s):

Structural Model ◽

Structural Features ◽

Terminal Region ◽

X Ray Diffraction ◽

Terminal Part ◽

Multifunctional Protein ◽

X Ray ◽

N Protein ◽

Intrinsically Disordered ◽

X Ray Scattering

The N protein of coronaviruses is a multifunctional protein that is organized into several domains. The N-terminal part is composed of an intrinsically disordered region (IDR) followed by a structured domain called the N-terminal domain (NTD). In this study, the structure determination of the N-terminal region of the MERS-CoV N proteinviaX-ray diffraction measurements is reported at a resolution of 2.4 Å. Since the first 30 amino acids were not resolved by X-ray diffraction, the structural study was completed by a SAXS experiment to propose a structural model including the IDR. This model presents the N-terminal region of the MERS-CoV as a monomer that displays structural features in common with other coronavirus NTDs.

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Structural Refinement and Density Functional Theory Study of Synthetic Ge-Akaganéite (β-FeOOH)

Crystals ◽

10.3390/cryst10040239 ◽

2020 ◽

Vol 10 (4) ◽

pp. 239

Author(s):

Donghoon Chung ◽

Changyun Park ◽

Woohyun Choi ◽

Yungoo Song

Keyword(s):

Density Functional Theory ◽

Density Functional ◽

Structural Model ◽

Dispersion Correction ◽

Chemical Formula ◽

Structural Refinement ◽

X Ray Diffraction ◽

Functional Theory ◽

X Ray ◽

Twisted Cube

In this study, we propose a revised structural model for highly ordered synthetic Ge-akaganéite, a stable analogue of tunnel-type Fe-oxyhydroxide, based on the Rietveld refinement of synchrotron X-ray diffraction data and density functional theory with dispersion correction (DFT-D) calculations. In the proposed crystal structure of Ge-akaganéite, Ge is found not only in the tunnel sites as GeO(OH)3− tetrahedra, but also 4/5 of total Ge atoms are in the octahedral sites substituting 1/10 of Fe. In addition, the tunnel structures are stabilized by the presence of hydrogen bonds between the framework OH and Cl− species, forming a twisted cube structure and the GeO(OH)3− tetrahedra corner oxygen, forming a conjugation bond. The chemical formula of the synthetic Ge-akaganéite was determined to be (Fe7.2Ge0.8)O8.8(OH)7.2Cl0.8(Ge(OH)4)0.2.

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AlkalineEarthMetal-Hydride-Iodide Compounds: Syntheses andCrystal Structures of Sr2H3I and Ba5H2I3.9(2)O2

Zeitschrift für Naturforschung B ◽

10.1515/znb-2011-0104 ◽

2011 ◽

Vol 66 (1) ◽

pp. 21-26

Author(s):

Olaf Reckeweg ◽

Francis J. DiSalvo

Keyword(s):

Single Crystal ◽

Single Crystals ◽

Structural Model ◽

Structure Type ◽

Lattice Parameters ◽

Molar Ratio ◽

X Ray Diffraction ◽

Space Group ◽

X Ray ◽

New Compounds

Single crystals of Sr2H3I andBa5H2I3.9(2)O2 were obtained by reacting Sr or Ba, respectively, with dried and sublimed NH4I in a 4 : 1 molar ratio in silica-jacketed Nb ampoules for 13 h at 1200 K. The crystal structures of the new compounds have been determined by means of single-crystal X-ray diffraction. Sr2H3I crystallizes in a stuffed anti-CdI2 structure isotypic to Ba2H3Cl in the space group P3m1 (no. 164) with the lattice parameters a = 426.0(1) and c = 774.9(2) pm, while Ba5H2I3.9(2)O2 crystallizes in a new structure type in the space group Cmcm (no. 63) with the lattice parameters a = 1721.0(2), b = 1452.5(2) and c = 639.03(9) pm. The structural results for Sr2H3I are corroborated by EUTAX calculations. For the disordered compound Ba5H2I3.9(2)O2, EUTAX calculations on an approximated, ordered structural model were used to find possible insights into the disorder

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Investigation of the crystal structure of a low water content hydrous olivine to 29.9 GPa: A high-pressure single-crystal X-ray diffraction study

American Mineralogist ◽

10.2138/am-2020-7444 ◽

2020 ◽

Vol 105 (12) ◽

pp. 1857-1865

Author(s):

Jingui Xu ◽

Dawei Fan ◽

Dongzhou Zhang ◽

Bo Li ◽

Wenge Zhou ◽

...

Keyword(s):

High Pressure ◽

Equation Of State ◽

Single Crystal ◽

Water Content ◽

Structural Changes ◽

Volume Data ◽

Structural Refinement ◽

X Ray Diffraction ◽

X Ray ◽

Water Contents

Abstract Olivine is the most abundant mineral in the Earth's upper mantle and subducting slabs. Studying the structural evolution and equation of state of olivine at high-pressure is of fundamental importance in constraining the composition and structure of these regions. Hydrogen can be incorporated into olivine and significantly influence its physical and chemical properties. Previous infrared and Raman spectroscopic studies indicated that local structural changes occur in Mg-rich hydrous olivine (Fo ≥ 95; 4883–9000 ppmw water) at high-pressure. Since water contents of natural olivine are commonly <1000 ppmw, it is inevitable to investigate the effects of such water contents on the equation of state (EoS) and structure of olivine at high-pressure. Here we synthesized a low water content hydrous olivine (Fo95; 1538 ppmw water) at low SiO2 activity and identified that the incorporated hydrogens are predominantly associated with the Si sites. We performed high-pressure single-crystal X-ray diffraction experiments on this olivine to 29.9 GPa. A third-order Birch-Murnaghan equation of state (BM3 EoS) was fit to the pressure-volume data, yielding the following EoS parameters: VT0 = 290.182(1) Å3, KT0 = 130.8(9) GPa, and K′T0 = 4.16(8). The KT0 is consistent with those of anhydrous Mg-rich olivine, which indicates that such low water content has negligible effects on the bulk modulus of olivine. Furthermore, we carried out the structural refinement of this hydrous olivine as a function of pressure to 29.9 GPa. The results indicate that, similar to the anhydrous olivine, the compression of the M1-O and M2-O bonds are comparable, which are larger than that of the Si-O bonds. The compression of M1-O and M2-O bonds of this hydrous olivine are comparable with those of anhydrous olivine, while the Si-O1 and Si-O2 bonds in the hydrous olivine are more compressible than those in the anhydrous olivine. Therefore, this study suggests that low water content has negligible effects on the EoS of olivine, though the incorporation of water softens the Si-O1 and Si-O2 bond.

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Investigation of the catalytic triad of arylamine N-acetyltransferases: essential residues required for acetyl transfer to arylamines

Biochemical Journal ◽

10.1042/bj20050277 ◽

2005 ◽

Vol 390 (1) ◽

pp. 115-123 ◽

Cited By ~ 41

Author(s):

James Sandy ◽

Adeel Mushtaq ◽

Simon J. Holton ◽

Pamela Schartau ◽

Martin E. M. Noble ◽

...

Keyword(s):

Mycobacterium Smegmatis ◽

Structural Model ◽

Sequence Data ◽

Structural Features ◽

Catalytic Triad ◽

Site Directed Mutagenesis ◽

X Ray ◽

X Ray Crystallography ◽

Acetyl Transfer ◽

Insight Into

The NATs (arylamine N-acetyltransferases) are a well documented family of enzymes found in both prokaryotes and eukaryotes. NATs are responsible for the acetylation of a range of arylamine, arylhydrazine and hydrazine compounds. We present here an investigation into the catalytic triad of residues (Cys-His-Asp) and other structural features of NATs using a variety of methods, including site-directed mutagenesis, X-ray crystallography and bioinformatics analysis, in order to investigate whether each of the residues of the catalytic triad is essential for catalytic activity. The catalytic triad of residues, Cys-His-Asp, is a well defined motif present in several families of enzymes. We mutated each of the catalytic residues in turn to investigate the role they play in catalysis. We also mutated a key residue, Gly126, implicated in acetyl-CoA binding, to examine the effects on acetylation activity. In addition, we have solved the structure of a C70Q mutant of Mycobacterium smegmatis NAT to a resolution of 1.45 Å (where 1 Å=0.1 nm). This structure confirms that the mutated protein is correctly folded, and provides a structural model for an acetylated NAT intermediate. Our bioinformatics investigation analysed the extent of sequence conservation between all eukaryotic and prokaryotic NAT enzymes for which sequence data are available. This revealed several new sequences, not yet reported, of NAT paralogues. Together, these studies have provided insight into the fundamental core of NAT enzymes, and the regions where sequence differences account for the functional diversity of this family. We have confirmed that each of the three residues of the triad is essential for acetylation activity.

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Дипольное упорядочение и ионная проводимость в NASICON-подобных структурах типа Na-=SUB=-3-=/SUB=-Fe-=SUB=-2-=/SUB=-(PO-=SUB=-4-=/SUB=-)-=SUB=-3-=/SUB=-

Физика твердого тела ◽

10.21883/ftt.2020.08.49605.012 ◽

2020 ◽

Vol 62 (8) ◽

pp. 1216

Author(s):

А.С. Ногай ◽

А.А. Ногай ◽

С.Ю. Стефанович ◽

Ж.М. Солиходжа ◽

Д.Е. Ускенбаев

Keyword(s):

Phase Transitions ◽

Ionic Conductivity ◽

Single Crystals ◽

Hot Pressing ◽

Structural Changes ◽

Structural Features ◽

Polymorphic Transformations ◽

Relaxation Polarization ◽

Dipole Ordering

Abstract The problems of the structural features, the dielectric and conducting properties of Na_3Fe_2(PO_4)_3 polycrystals prepared by hot pressing have been studied. The Na_3Fe_2(PO_4)_3 polycrystals in the α and β phases are shown to have higher conducting properties than the α and β phases of the single crystals grown by the solution–melt method. The regularities of the appearance of the dipole ordering, the ionic and superionic conductivities related to phase transitions and structural changes in the {[Fe_2(PO_4)_3]^3–}_3∞ rhombohedral crystalline frame during polymorphic transformations are refined. The problems of the relaxation polarization in the α and β phases of Na_3Fe_2(PO_4)_3 are discussed. A model for explaining the dipole ordering and the ionic conductivity in Na_3Fe_2(PO_4)_3 is proposed.

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Azide und Cyanamide – ähnlich und doch anders/Azides and Cyanamides – Similar and Yet Different

Zeitschrift für Naturforschung B ◽

10.1515/znb-2003-1111 ◽

2003 ◽

Vol 58 (11) ◽

pp. 1097-1104 ◽

Cited By ~ 48

Author(s):

Olaf Reckeweg ◽

Arndt Simon

Keyword(s):

Ir Spectroscopy ◽

Single Crystals ◽

Crystal Structures ◽

Spectroscopic Data ◽

Structural Features ◽

X Ray Diffraction ◽

X Ray ◽

First Time ◽

Raman And Ir Spectroscopy

Abstract The crystal structures of LiN3*H2O (P63/mcm (No. 193), Z = 6; 924.01(13); 560.06(7) pm); NH4N3 (Pmna (No. 53), Z =4; a=889.78(18), b=380,67(8), c=867.35(17) pm); Ca(N3)2 (Fddd (No. 70), Z = 8; a=595.4(2), b=1103.6(5), c=1133.1(6) pm), Sr(N3)2 (Fddd (No. 70), Z =8; a= 612.02(9), b = 1154.60(18), c = 1182.62(15) pm); Ba(N3)2 (P21/m (No. 11), Z = 2; a = 544.8(1), b = 439.9(1), c = 961.3(2) pm, β = 99.64(3)°) and TlN3 (I4/mcm (No. 140), Z = 2; 618.96(9); 732.71(15) pm) have been either determined for the first time or redetermined by X-ray diffraction on single crystals. The afore mentioned compounds, AN3 (A = Na, K, Rb, Cs), M(N3)2 · 2.5 H2O (M = Mg, Zn) and the cyanamides Li2CN2, CdCN2 and CuCN2 were investigated by Raman and IR spectroscopy (KBr technique). Structural features and spectroscopic data of azides and cyanamides from this work and from literature are listed and compared.

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Growth and Optical Properties of the Whole System of Li(Mn1-x,Nix)PO4 (0 ≤ x ≤ 0.5) Single Crystals

Materials ◽

10.3390/ma14237233 ◽

2021 ◽

Vol 14 (23) ◽

pp. 7233

Author(s):

Benyan Xu ◽

Zhenyou Li ◽

Kunpeng Wang ◽

Jianxiu Zhang ◽

Lanju Liang ◽

...

Keyword(s):

Single Crystals ◽

Second Harmonic ◽

Diffraction Method ◽

Physical Property ◽

Laser Generation ◽

Structural Refinement ◽

Zone Method ◽

X Ray ◽

First Time

A series of single crystals of Li(Mn1-x,Nix)PO4 (x = 0.00, 0.01, 0.02, 0.03, 0.04, 0.05, 0.06, 0.08, 0.10, 0.15, 0.20, and 0.50) have been grown to large sizes up to 5 mm in diameter and 120 mm in length using the floating zone method for the first time. The comprehensive characterizations of the as-grown crystals were performed before further physical property measurements. The composition of the grown crystals was determined by energy-dispersive X-ray spectroscopy. The crystal structures were characterized by the X-ray powder diffraction method with a GSAS fitting for structural refinement, which reveals a high phase purity of the as-obtained crystals. The polarized microscopic images and Laue patterns prove the excellent quality of the single crystals. Oriented cuboids with sizes of 2.7 × 3.8 × 2.1 mm3 along the a, b, and c crystalline directions were cut and polished for further anisotropic magnetic and transparent measurements. We also first proposed a new potential application in the non-linear optical (NLO) and laser generation application for LiMPO4 (M = transition metal) materials. The optical and laser properties, such as the absorption spectra and the second harmonic generation (SHG), have been investigated and have furthermore confirmed the good quality of the as-grown single crystals.

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The growth of decagonal Al–Co–Ni single crystals as a function of chemical composition

Journal of Materials Research ◽

10.1557/jmr.1997.0303 ◽

1997 ◽

Vol 12 (9) ◽

pp. 2274-2280 ◽

Cited By ~ 12

Author(s):

B. Zhang ◽

M. Estermann ◽

W. Steurer

Keyword(s):

Single Crystals ◽

Structural Changes ◽

Ternary Systems ◽

X Ray Diffraction ◽

X Ray ◽

Decagonal Phase ◽

Different Types ◽

Diffraction Patterns ◽

The Stability ◽

Diagram Analysis

Decaprismatic single crystals taken from a series of alloys of nominal compositions within Al65–77Co3–22Ni3–22 have been studied by means of x-ray diffraction techniques. The substitution of Co by Ni in increasing amounts changes the (pseudo)decagonal diffraction patterns drastically and indicates structural changes which range from a single-crystalline approximant via orientationally ordered nanodomain structures and quasiperiodic phases with different types of ordering phenomena, to a basic decagonal phase. A quantum phase diagram analysis shows a clear separation of the stability regions of the ternary systems described in this study and other decagonal phases.

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Transmission electron microscopy of hexadecyltrimethylammonium-exchanged smectite

Clay Minerals ◽

10.1180/0009855023730044 ◽

2002 ◽

Vol 37 (3) ◽

pp. 465-471 ◽

Cited By ~ 7

Author(s):

Seung Yeop Lee ◽

Soo Jin Kim

Keyword(s):

Electron Microscopy ◽

Transmission Electron Microscopy ◽

Structural Changes ◽

Structural Features ◽

Morphological Features ◽

X Ray Diffraction ◽

X Ray ◽

Morphological Heterogeneity ◽

Transmission Electron ◽

Lattice Distortions

AbstractThe morphological and structural changes in smectite caused by hexadecyltrimethylammonium (HDTMA) treatment were studied using X-ray diffraction (XRD) and transmission electron microscopy (TEM). The HDTMA-exchanged smectite shows not only morphological features such as irregular, wavy surface with curled edges, but also structural features such as large d-spacings (20 – 26 Å ) and lattice distortions. The surface morphological heterogeneity is assumed to be related to the inhomogeneous intercalation of HDTMA cations into the interlayer of smectite.

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