Richard E. Marsh

An investigation of the structure of silk fibroin

Abstract An investigation based on new X-ray diffraction data, including quantitative spectrometric measurements of X-ray intensities, has led to the derivation of the fundamental structural features of silk fibroin. The structure consists of extended polypeptide chains bonded together by lateral N—H…O hydrogen bonds to form antiparallel-chain pleated sheets. The sequence-G-X-G-X-G-X-in which G represents glycyl and X alanyl or seryl residues predominates throughout the structure, so that adjacent sheets pack together at distances of about 3.5 and 5.7 A. Longer inter-sheet distances are explained by the presence in the structure of the larger amino-acid residues, such as tyrosine.

The crystal structure of guanosine dihydrate and inosine dihydrate

Crystals of the dihydrates of guanosine (C_(10)H_(13)N_5O_5) and inosine (C_(10)H_(12)N_4O_5) are nearly isostructural. They are monoclinic, space group P2_1, with cell dimensions ɑ = 17·518, b = 11 ·502, c = 6·658 A, β = 98·17° (guanosine) and ɑ = 17·573, b =11·278, c=6-654 A, β = 98·23° (inosine). There are two nucleoside molecules and four water molecules per asymmetric unit. Data were collected on an automated diffractometer; the structures were solved by Patterson and trial-and-error methods and refined to R indices of about 0·035. The structure features hydrogen bonding between purine bases to form ribbons parallel to b and parallel stacking of purine bases along c; the separation between adjacent rings within a stack is 3·3 A. The conformations about the glycosidic C-N bond and the puckerings of the sugar rings arc quite different for the two molecules in the asymmetric unit.

The perils of Cc revisited

The space groups of 98 structures originally reported in Cc are revised. In 75 cases the revised space group is C2/c and the revision entails adding a center of symmetry, usually leading to large changes in bond lengths and angles. In the remaining 23 cases, where the revised space group is Fdd2, R3c or (in one case) I4c2, the lattice type is changed but no center is added; in these cases the molecular dimensions are effectively unchanged.

Some thoughts on choosing the correct space group

Some problems that may lead to incorrect assignments of space group are identified and discussed, and some suggestions for avoiding these problems are made. Along the way, about four dozen structures listed in the Cambridge Structural Database are identified as having, almost surely, been described in space groups of unnecessarily low symmetry.

Some 60 new space-group corrections

Some 60 examples of crystal structures are presented which can be better described in space groups of higher symmetry than used in the original publications. These are divided into three categories: (A) incorrect Laue group (33 examples), (B) omission of a center of symmetry (22 examples), (C) omission of a center of symmetry coupled with a failure to recognize systematic absences (nine examples). Category A errors do not lead to significant errors in molecular geometry, but these do accompany the two other types of error. There are 19 of the current set of examples which have publication dates of 1996 or later. Critical scrutiny on the part of authors, editors and referees is needed to eliminate such errors in order not to impair the role of crystal structure analysis as the chemical court of last resort.

Peri interactions: an X-ray crystallographic study of the structure of 1,8-bis(dimethylaminonaphthalene)

Crystals of 1,8-bis(dimethylamino)naphthalene, C_(14)H_(18)N_2, are orthorhombic, space group P2_12_12_1, with ɑ= 12•855 (1), b= 10•110 (1), c=9•664 (1)A and Z=4. A complete structure determination, including refinement of the positions of the hydrogen atoms, led to an R index of 0-053 and a goodness-off-it of 2.02 for 1477 reflections. The molecule adopts a conformation in which one carbon atom of each of the dimethylamino groups is eclipsed with respect to the naphthalene ring. Hindrance between the dimethylamino groups and/or resonance interactions between the dimethylamino groups and the aromatic ring are sufficiently great to distort the ring in several ways, the most conspicuous being a sizable increase in the non-bonded C(1)••• C(8) distance (2.56 A) compared to the C(4)••• C(5) distance (2•44 A) and a twisting of the naphthalene ring into a considerably nonplanar conformation.

The Cation H13O6+: A Short, Symmetric Hydrogen Bond

The H_(13)O_6+ ion has been found to exist as a discrete entity, forming when the cage compound [(C_9H_(18)_3(NH)_2Cl]+Cl is crystallized from hydrochloric acid solution. The aquo-cation H_(13)O_6 has crystallographic symmetry 2/m (C_(2h)). The central bond O••H••O is symmetric, with a length of 2.39 ± 0.02 angstroms; the four outer hydrogen bonds are asymmetric, with a length of 2.52 ± 0.01 angstroms. The cage compound consists of a chloride ion encapsulated within a triply bridged diammonium species, with hydrogen bond distances N(H)••Cl of 3.10 ± 0.01 angstroms.

Interatomic distances and atomic valences in NaZn13

The crystal structure of NaZn_(13) and of several homologous compounds AB_(13) was reported by Ketelaar and by Zintl & Hauke to be based on space group O_h^6-Fm3c, with 8 :Na in 8(a): ¼, ¼:, ¼; ... ; 8 Zn_I in 8(b): 0, 0, 0; .... ; and 96 Zn_(II) in 96(i): 0, y, z; ... . Approximate values were reported for the parameters a_0, y, and z; for NaZn_(13) Zintl & Hauke reported 12.27 A, 0.178, and 0.122 for these three parameters. Each Zn_I is surrounded by twelve Zn_(II) at the vertices of a nearly regular icosahedron, and each Na by twenty-four Zn_(II) at the vertices of a snub cube. Our interest in the structure was largely concerned with the valences of the two different kinds of Zn atoms, it being presumptive that Zn_I has a larger valence than Zn_(II) because its icosahedral coordination requires it to be smaller than Zn_(II). Lines on new powder photographs of NaZn_(13) were measured and the intensities were estimated visually with as much precision as possible. Least-squares treatments were employed in order to obtain the best possible values for the three parameters; the values obtained are a_0 = 12.2836 ± 0.0003A, y = 0.1806 ± 0.0003, and z = 0.1192 ± 0.0003. The uncertainties given are calculated standard deviations. Analysis of the interatomic distances yields a selfconsistent interpretation in which Zn_I is assumed to be quinquevalent and Zn_(II) quadrivalent, while Na may have a valence of unity or one as high as 1¼, the excess over unity being suggested by the interatomic distances and being, if real, presumably a consequence of electron transfer. A valence electron number of approximately 432 per unit cell is obtained, which is in good agreement with the value 428.48 predicted on the basis of a filled Brillouin polyhedron defined by the forms {444}, {640}, and {800}.

Space group Cc: an update

A recent survey of the Cambridge Structural Database, CSD [Allen (2002). Acta Cryst. B58, 380-388], shows that the percentage of incorrect assignments of the space group Cc has remained at about 10% since the last survey in 1997.

Use of software to search for higher symmetry: space group C2

From a search of the October 2000 release of the Cambridge Structural Database we find coordinate data for approximately 1500 entries under space group No. 5: C2 or, occasionally, A2, I2 or B112. Software designed to detect cases of missed higher symmetry identified 144 entries for detailed inspection. Of these, 50 should, we believe, be revised to space groups of higher symmetry. The most common revision is to space group C2/m, which entails adding a center of inversion and usually results in important changes in bond lengths and angles.