Kenneth N. Trueblood

Base pairing in DNA.

On the basis of recent structural information which extends somewhat the range of possible dimensions for bases and base pairs, five new geometrically acceptable hydrogen-bonded base pairs which might be formed by the bases in nucleosides have been suggested. The dimensions of one of these new pairs, adenine-guanine, are such that this pair would apparently fit in the Watson-Crick DNA helix. The evidence cited by Spencer against the possible existence in DNA of a pairing adenine-thymine guanine-eytosine which, differs from that formulated by Watson & Crick has been examined and is considered to be inconclusive. Particular attention has been given to the conformational relationship between the base and the sugar, and a torsional angle, (φCN, has been defined. This is the angle between the trace of the plane of the base and the projection of the C-O bond of the furanose ring when viewed along the glycosidic C-N bond. Values of this angle in known structures and proposed models have been tabulated, and the implications concerning possible conformations are considered.

A test for rigid‐body vibrations based on a generalization of Hirshfeld's `rigid‐bond' postulate

A simple test for the validity of the rigid-body model for molecular vibrations in crystals is proposed.

Correlation of Internal Torsional Motion with Overall Molecular Motion in Crystals

The simple one-parameter Dunitz–White model for internal torsional motion accompanying overall molecular motion in crystals ignores the correlations between this torsion and the overall translation and libration. These correlations are explicitly considered here, in quadratic approximation (based on the linear approximation for displacements). For each attached rigid group (ARG) undergoing a torsional libration, there are, in addition to the mean-square libration amplitude, six correlations to be considered, three with the overall molecular libration and three with the overall translation. Because it is impossible from the observed quadratic mean displacements to distinguish the torsional motion from the overall molecular libration parallel to the torsional axis, the present analysis emphasizes the overall libration parallel to the torsional axis, which we term \Lambda. In the general case there are only six determinable parameters for each ARG. If the torsional axis of the ARG lies on a molecular symmetry element, the number of parameters is reduced to three or fewer. Examples of analyses with these correlations included, and without them, are compared.

The Structure of Vitamin BFormula I. An Outline of the Crystallographic Investigation of Vitamin BFormula

The structure of vitamin B12 has been examined by the X-ray analysis of four different crystal structures, air-dried and wet vitamin B 12, the selenocyanate derivative of B12, and a hexacarboxylic acid prepared by the degradation of the vitamin by Cannon, Johnson and Todd. The analysis turned on the possibility of identifying some of the atomic positions in the molecule in very confused appproximate electron density distributions calculated using only evidence of cobalt or cobalt and selenium contributions to phase the terms employed in the calculation. The recognition of atomic sites depended on a general knowledge of atomic sizes and geometry, on chemical evidence of the existence of a nucleotide-like group in the B12 crystals, and on the presence, immediately surrounding each cobalt atom, of a nucleus which was identical in very different crystals. Once the positions of the atoms in the nucleus and nucleotide were identified, the refinement of the electron density distributions in the different crystals proceeded in a fairly direct manner to establish the arrangement of all the remaining atoms in the molecules. The atomic arrangements found lead to the deduction of the chemical structure of a large part of the vitamin B12 molecule and of the stereochemical organization of the whole. Of particular interest is the evident relation of the molecular nucleus found to porphyrins of type I I I and to porphobilinogen.

Concept, structure, and binding in complexation

Structural molecular complexation is central to biological phenomena. Enzymic catalysis and inhibition, immunological response, storage and retrieval of genetic information, replication, biological regulatory function, drug action, and ion transfer all involve structural recognition in complexation. At least one of the partners in most of the complexes of evolutionary chemistry is large and complicated enough to inhibit studies of its detailed structure and an analysis of the forces that control its shape.

The Structure of Vitamin BFormula. II. The Crystal Structure of a Hexacarboxylic Acid Obtained by the Degradation of Vitamin BFormula

A hexacarboxylic acid, obtained by the degradation of vitamin B12 by Cannon, Johnson & Todd in 1953 has been examined by X-ray analytical methods. These lead to a solution of both the crystal and chemical structure of the acid. The crystals are orthorhombic, a = 24·58, b = 15·52, c = 13·32 Å, space group, P212121, n = 4. The asymmetric unit is found to consist essentially of one molecule of hexacarboxylic acid, C46H58O13N6. CoCl, two molecules of water and one of acetone. The hexacarboxylic acid molecule has a central cobalt atom in approximately octahedral co-ordination attached to one cyanide group, one chlorine atom and four nitrogen atoms of the corrin nucleus. The nucleus itself is substituted by acetic and propionic acid groups, a lactam ring and a number of methyl groups. The position of the cobalt atom in the crystal structure was first found from Patterson projections and the remaining atomic positions then derived from a series of calculated approximations to the three-dimensional electron density distribution. For these calculations, phases were derived from structure factors calculated on gradually increasing numbers of selected atomic positions from the stage of ρ1, where only the cobalt atom sites were known, to ρ10 where 73 atoms, not counting hydrogen, had been placed. The process was not quite straightforward; particular difficulty was experienced in finding the positions of the atoms of one side-chain which may be affected by disorder. The parameters of the atoms have been refined by two cycles of least-squares calculations. A number of observations were made in the course of the analysis which bear on the further use of non-centrosymmetric Fourier syntheses in the study of complex structures. An appendix by A. Vos deals with intensity anomalies observed on the X-ray photographs of the hexacarboxylic acid which provide evidence of its absolute configuration. An appendix by K. N. Trueblood summarizes various aspects of the analysis of the hexacarboxylic acid, seen as a whole.

A host–guest complex: tert-butylammonium perchlorate complex of 3,6,9,12,15-pentaoxa-21-azabicyclo[15.3.1]heneicosa-1(20),17,19-triene (monopyrido-18-crown-6) at 113 K

C 15H2aNOs. C4H12 N+ . C10 2, orthorhombic, Pna2t, a -- 12.309 (2), b = 20.821 (3), c = 9.237 (1) /~, U = 2367.2 (6)/k a, Z = 4, D x = 1.321 Mg m -3. Least-squares refinement for 2568 reflections (measured at 113 K) gave a final discrepancy index R(F) = 0.038. The crown-ether tert-butylammonium cation complex has approximate m symmetry; the tert- BuNH + forms hydrogen bonds to two O atoms and the pyridine N atom in the macrocyclic ring.

The structure of vitamin B12 - IV. The X-ray analysis of air-dried crystals of B12

Measurements were made during 1948-9 of all the intensities of hkl reflexions observable with chromium Koc X-radiation from air-dried crystals of vitamin B12. Calculations parallel with those of J. G. White were carried out on these data. The positions of the cobalt atoms in the crystal structure were found from three-dimensional Patterson series and the positions of 90 atoms of the B12 molecule and 7 water molecules were derived through three successive approximations to the three-dimensional electron density distribution. The choice of atomic positions was checked against superposition maps derived from the original Patterson series, and assisted by comparisons with other B12 derivatives. Minor differences appear between the positions derived here and in III; some of these may be real differences due to the state of dryness of the crystals.

The tert-butylammonium perchlorate complex of 2,3-naphtho-18-crown-6 at 115 K.

In the title complex, tert-butylammonium perchlorate-2,5,8,11,14,17-hexaoxatricyclo[16.8.0.0(20,25]hexac osa- 1(26),18,20(25),21,23-pentaene-ethyl acetate-dichloromethane (4/4/1/1), C4H12N+.C20H26O6.ClO4-.0.25C4-H8O2.0.25CH2Cl2 , the tert-butylammonium cation binds to the macrocyclic host (Chemical Abstracts name: 2,3,5,6,8,9,11,12,14,15-decahydro-1,4,7,10,13,16-hexaoxanaphtho [2,3- b]cyclooctadecin) in the expected tripod arrangement, while the perchlorate anion links naphthyl groups in the crystal through C-H...O-Cl-O...H-C interactions. Thermal motion analysis indicates that the tert-butylammonium group and the perchlorate anion each librate with respect to the host, with amplitudes of 6.2 (4) and 11.4 (2) degrees, respectively.

Thermal motion of tert‐butyl groups III. tert‐Butyl substituents in aromatic hydrocarbons, the view from the bottom of the well

The rigidity of the tert-butyl group (TBG) as a substituent in aromatic hydrocarbons is investigated, with a modified Hirshfeld test of anisotropic displacement parameters (ADPs) as a primary criterion. Four new structures are analyzed, along with low-temperature studies of a previously published crowded supermesityl dimer; three of the five structures meet the primary test. Most of the TBGs meet the Hirshfeld test at 100 K, and the ADPs are improved by omitting low-order data in the final refinement. The three most precise structures yield a wide variation in libration amplitudes (and in estimated rotation barriers) for 13 unique TBGs. A similar range of values is found in analyses of structures in the Cambridge Crystallographic Database. The libration amplitudes are calculated with the program THMA14C, with each TBG as an attached rigid group (ARG). Packing analysis suggests that large ADPs, especially for some individual TBG methyl groups, correspond to voids in the crystal. Published barriers to TBG reorientation, determined by solid-state NMR spin-lattice relaxation methods, for six related crystalline compounds are compared with barriers calculated from their crystal structure data.