Sydney R. Hall

The chemistry of Eremophila SPP—VI* : Stereochemistry and crystal structure of dihydroxyserrulatic acid

Abstract The structure of the title compound has been shown to be ( 6 ), a diterpenoid analogue of the cadinene group. Standard degradation has given the naphthalene ( 14 ). The relative stereochemistry is established by crystal structure of dihydroxyserrulatic acid which has been determined by X-ray diffraction at 295 K, and refined by least squares to a residual of 0.059 for 1480 observed reflections. Crystals are orthorhombic, P 2 1 2 1 2 1 , a = 15.514 (3), b =14.029 (3), c =8.681 (2)A, Z =4.

Pentakis(methoxycarbonyl)cyclopentadiene chemistry. Part 1. Preparation and properties of the diene, and of derivatives containing the alkali metals or thallium(I): crystal and molecular structures of HC5(CO2Me)5, Li[C5(CO2Me)5]·H2O, K[C5(CO2Me)5]·MeOH, and Tl[C5CO2Me)5]

The alkali metal (Li, Na, K, Rb, and Cs) and thallium(I) derivatives of HC5(CO2Me)5 have been prepared and characterised; their i.r., u.v., 1H, and l3C n.m.r. spectra are reported and discussed. Single-crystal X-ray structure determinations have been carried out on the diene and its Li, K, and Tl salts at 295 K. In the solid, as in non-polar solvents, the diene has the fulvenoid configuration, with the acidic proton bridging two adjacent carbonyl groups. This configuration is preserved in univalent metal cation salts. Lithium is four-co-ordinate (from two carbonyl oxygens, the water molecule, and a carbonyl oxygen from a second anion). In the potassium salt, the metal is co-ordinated by methanol, and five carbonyl oxygens from three different anions; all carbonyl oxygens of each anion are likewise involved in co-ordination to three different metal atoms. In the thallium salt the metal has irregular five-co-ordination, with two chelating carbonyl groups from one anion and three from separate anions; all carbonyl oxygens of each anion co-ordinate to four different metal atoms.

The Molecular Information File (MIF): Core Specifications of a New Standard Format for Chemical Data

The initial core data definitions of a universal data exchange format for chemical information is proposed. The Molecular Information File (MIF) represents a coalescence of two major format developments: the Standard Molecular Data Format (SMD) and the Crystallographic Information File that conforms to the STAR (Self-Defining Text Archive and Retrieval) syntax. Essentially, the MIF is a re-expression of the major SMD concepts using STAR syntax. The core data items, defined here, cover chemical connectivity representations, stereochemistry, and associated data for complete 2D and 3D molecules and for 2D substructural queries.

Extensions to the STAR File Syntax

The STAR File [Hall J. Chem. Inf. Comput. Sci. 1991, 31, 326-333; Hall and Spadaccini J. Chem. Inf. Comput. Sci. 1994, 34, 505-508] format represents a universal language adopted for electronic data and metadata exchange in the molecular-structure sciences [Hall et al. Acta Crystallogr. Sect. A 1991, 47, 655-685; International Tables for International Tables for Crystallography. Vol. G: Definition and exchange of crystallographic data; Springer: Dordrecht, The Netherlands, 2005; Allen et al. J. Chem. Inf. Comput. Sci. 1995, 35, 412-427] and used by the International Union for Crystallography for publication submissions and database depositions. This paper describes an extended STAR syntax that facilitates richer and more specific data definition and typing and a commensurate improvement in precise data description.

DDLm: A New Dictionary Definition Language

A previous paper [Spadaccini and Hall J. Chem. Inf. Model. doi:10.1021/ci300074v] details extensions to the STAR File [Hall J. Chem. Inf. Comput. Sci. 1991, 31, 326-333] syntax that will improve the exchange and archiving of electronic data. This paper describes a dictionary definition language (DDLm) for defining STAR File data items in a domain dictionary. A dictionary that defines the ontology and vocabulary of a discipline is built with DDLm, which is itself implemented in STAR, and is extensible and machine parsable. The DDLm is semantically rich and highly specific; provides strong data typing, data enumerations, and ranges; enables relationship keys between data items; and uses imbedded methods written in dREL [Spadaccini et al. J. Chem. Inf. Model. doi:10.1021/ci300076w] for data validation and evaluation and for refining data definitions. It promotes the modular definition of the discipline ontology and reuse through the ability to import definitions from other local and remote dictionaries, thus encouraging the sharing of data dictionaries within and across domains.

Relational expressions in STAR file dictionaries.

The STAR File (J. Chem. Inf Comput. Sci. 1994, 34, 505-508) is used widely in structural chemistry for exchanging numerical and text information with scientific journals and databases. These exchanges are increasingly dependent on data dictionaries to facilitate automatic data validation and checking. Definitions in data dictionaries are constructed using attribute descriptors, and this paper describes a method attribute for specifying the relationships between data items as an executable script written in a new relational expression language called dREL. The addition of this attribute improves the precision and the semantic content of dictionaries by providing relational representations of data, as well as facilitating the direct evaluation of derivable data items. The capacity to evaluate derivative data directly from the combination of primitive data and dictionary expressions is expected to change future archival approaches. The design concepts of the relational expression language dREL parser, which are applicable to any discipline, are described.

dREL: a relational expression language for dictionary methods.

The provision of precise metadata is an important but a largely underrated challenge for modern science [Nature 2009, 461, 145]. We describe here a dictionary methods language dREL that has been designed to enable complex data relationships to be expressed as formulaic scripts in data dictionaries written in DDLm [Spadaccini and Hall J. Chem. Inf. Model.2012 doi:10.1021/ci300075z]. dREL describes data relationships in a simple but powerful canonical form that is easy to read and understand and can be executed computationally to evaluate or validate data. The execution of dREL expressions is not a substitute for traditional scientific computation; it is to provide precise data dependency information to domain-specific definitions and a means for cross-validating data. Some scientific fields apply conventional programming languages to methods scripts but these tend to inhibit both dictionary development and accessibility. dREL removes the programming barrier and encourages the production of the metadata needed for seamless data archiving and exchange in science.

Specification of a relational dictionary definition language (DDL2)

The dictionary definition language version 2 (DDL2) extends the version 1 DDL used by the IUCr for the description of data items common to all crystallographic studies (i.e. core items). The DDL2 extensions were introduced primarily to address two issues arising during the development of a CIF dictionary for the terminology of macromolecular crystallography: the need to accurately describe the hierarchical nature of macromolecular structure and associated structural features, and the desire to encode dictionary definitions in a manner that would permit more detailed software-driven validation. This chapter presents the attribute sets described by the DDL2 language and illustrates their relational character. DDL2 attributes are classified in categories with unique key items; these categories play the roles of tables in a relational database structure. The relationships between categories are illustrated graphically and are described in detail in the chapter. The organization of DDL2 reflects the organization of the data model the attributes of which it describes (i.e. in the mmCIF and related data dictionaries). Consequently, the dictionary of DDL2 attributes is itself constructed in the DDL2 formalism. The use of a self-referential data description scheme allows the consistency and relational integrity of the data model to be independently verified.

Synthesis and structure of, and bonding in some derivatives of 2,6,9,10-tetraoxatricyclo[3.3.1.13,8]decane

Five derivatives of 2,6,9,10-tetraoxatricyclo[3.3.1.13,8]decane were synthesized and their molecular structures in the solid state were determined by means of X-ray diffraction analysis. In addition, the structures of all the molecules were optimized at different levels of computational quantum chemistry (HF/6-31G*, B3LYP/6-31G*). Experimentally determined bond lengths were compared with their calculated counterparts, and striking differences between the Hartree–Fock (HF) results and the experimental data could be traced back to the lack of correlation energy in the geometry optimizations. Two of the compounds under consideration are diastereomers and their relative stability was not only calculated with a conventional ab initio method (ZPE+MP2/6-31G*//HF/6-31G*), but also within the framework of density functional theory (B3LYP/6-31G*). In some of the calculations the influence of the solvent was included in single point calculations by means of an electrostatic model. Moreover, combining experimental as well as computational results, the exclusive axial orientation of a Cl atom in one of the compounds could be explained by an interplay of kinetic and energetic effects.

Structural studies of some serrulatane diterpenes

The crystal structures of methyl (15S)-7,8,16-trihydroxyserrulatan-19-oate (1) and 2,7,8,20-tetrahydroxyserrulat-14-ene (2) have been established by single crystal X-ray diffraction techniques at 295 K, being refined by least squares to residuals of 0.046 and 0.053 for 1 153 and 1 513 ‘observed’ reflections respectively. Crystals of (1) are orthorhombic, P212121, a= 21.78(2), b= 18.42(2), c= 5.101(3)A, Z= 4 while those of (2) are monoclinic, C2, a= 14.96(1), b= 12.315(6), c= 21.75(1)A, β= 107.21(5)°, Z= 8. As well as establishing total relative stereochemistry in (1), an interesting intramolecular hydrogen-bonding system is observed, together with an alicyclic ring conformation differing from that found in the previously studied dihydroxyserrulatic acid (3). In (2), the two independent molecules of the asymmetric unit have different conformations, corresponding broadly to those of (1) and (3).