From e-Science to Publication@Source

Self Archiving is not yet a popular route in Chemistry. However the Comb-e-Chem e-Science programme is showing the importance of collecting and maintaining a full digitally available record of the research from laboratory through analysis to published document using the Grid. This highlights the importance of self archiving not only published documents but the data that lies behind these documents

National Crystallography Service (NCS) Grid Service

Conference poster about the NCS Grid Service.The EPSRC funded National Crystallography Service (NCS) is a facility available to the entire UK academic Chemistry community. The EPSRC funds a team of experts and 'state of the art' instrumentation, based in Southampton University School of Chemistry, to provide this service. This is an exceptionally important service as crystal structure determination is easily the most information rich method of characterisation of a compound and many research papers cannot be published without confirmation of identity by crystal structure analysis

Coordination polymers and polygons using di-pyridyl-thiadiazole spacers and substituted phosphorodithioato NiII complexes: potential and limitations for inorganic crystal engineering

Coordinatively unsaturated P-substituted dithiophosphonato, dithiophosphato, and dithiophosphito complexes {[Ni?(MeO)2PS2)2] (1), [Ni((EtO)2PS2)2] (2), [Ni(MeOdtp)2] (3), and [Ni((Ph)2PS2)2] (4)} were reacted with the bis-functional ligands 3,5-di-(4-pyridyl)-1,2,4-thiadiazole (L1) and 3,5-di-(3-pyridyl)-1,2,4-thiadiazole (L2) to give the coordination polymers (1–4·L1)?, (3·L2)?, and (4·L2·2C7H8)? and the discrete dimers (1–2·L2)2, all characterised by single crystal X-ray diffraction. A comparison of the structures shows that L1 can be exploited for the predictable assembly of undulating chains independent of the nature of the NiII complex, while L2 allows for the existence of different supramolecular constructs ensuing from different ligand conformations deriving from the rotation of the pyridyl rings

ECSES - examining crystal structures using 'e-science': a demonstrator employing web and grid services to enhance user participation in crystallographic experiments

An application of e-science methodology and grid networking technology is presented that opens up new possibilities to enhance the operation of large high-throughput service-crystallography facilities, exemplified by the UK National Crystallography Service (NCS). A seamless distributed computing approach is used to provide remote secure visualization, monitoring and interaction with the laboratory and the diffraction experiment, supervision and input to the data workup and analysis processes, and to enable dissemination and further use of the resulting structural data. The architecture of the system is based on web and grid services (in particular the use of Globus, v1.1.4), which provide a secure environment for two-way information flow and communication between the service users and operators. This capability will enhance operations of instrument and software automation by providing more efficient use of the resources, increasing the throughput of samples and enabling interactions with distributed chemistry information databases, computational services and networks. The viability of these interactions is assessed and directions for future crystallography services suggested. The setup would be equally applicable to protein or powder crystallography services

eBank UK linking research data, scholarly communication and learning

This paper presents an overview of the changing landscape of scholarly communication and describes outcomes from the innovative eBank UK project, which seeks to build links from e-research through to e-learning. As introduction, the scholarly knowledge cycle is described and the role of digital repositories and aggregator services in linking datasets from Grid-enabled projects to e-prints through to peer-reviewed articles as resources in portals and Learning Management Systems, are assessed. The development outcomes from the eBank UK project are presented including the distributed information architecture, requirements for common ontologies, data models, metadata schema, open linking technologies, provenance and workflows. Some emerging challenges for the future are presented in conclusion

Systematic Study into the Salt Formation of Functionalised Organic Substrates- ECM 2004 Poster

There is currently a great amount of interest in the use of salts in the pharmaceutical industry because the physiochemical properties of the solid forms can be modified without altering the biochemical properties of the drug. Much effort has been expended in screening to select the best salt form and a number of empirical rules have been proposed such as the ‘rule of three’, which states that a successful salt formation generally requires a difference of three pKa units between the conjugate acid and the conjugate base. However, this rule does not always hold and the reasons are often unclear. The idea of this project is to perform a detailed systematic study of organic salt formation through a series of designed experiments, in order to obtain a broader and better understanding of the chemical descriptors, or factors that might be involved. A set of descriptors that describe molecular properties relevant to salt formation have been identified. For the initial experiments, a collection of salt forming acids has been assembled from the Cambridge Structural Database [1], and other sources, and their descriptor values calculated. These acids define a chemical space from which the compounds for the experiments can be chosen. The experiments aim to explore this chemical space whilst building statistical models that will allow an understanding of how the descriptors affect salt formation. Findings from the chemical space investigation coupled with experimental results from this study will be presented. This work is part of the Combechem E-science project at the University of Southampton.[1] F. H. Allen and O. Kennard (1993). Chem. Des. Autom. News, 8, 31-37

Combinatorial chemistry and the Grid

Chemistry has always made extensive use of the developing computing technology and available computing power though activities such as modelling, simulation and chemical structure interpretational - activities conveniently summarised as computational chemistry. Developing procedures in chemical synthesis and characterisation, particularly in the arena of parallel and combinatorial methodology, have generated ever increasing demands on both Computational Chemistry and Computer Technology. Significantly, the way in which networked services are being conceived to assist collaborative research pushes the use of data acquisition, remote interaction & control, computation, and visualisation, well beyond the traditional computational chemistry programmes, towards the basic issue of handling chemical information and knowledge. The rate at which new chemical data can now be generated in Combinatorial and Parallel synthesis and screening processes, means that the data can only realistically be handled efficiently by increased automation of the data analysis as well as the experimentation and collection. Without this automation we run the risk of generating information without the ability to understand it

The 'end to end' crystallographic experiment in an e-Science environment: From conception to publication.

Recent developments at the UK National Crystallography Service (NCS), in collaboration with the CombeChem eScience testbed and the eBank-UK projects, have been aimed at developing an eScience infrastructure to facilitate the crystallographic experiment from end to end. A seamless distributed computing approach is shown to be able to transform a conventional but high throughput service, to enable access and secure remote operation with the visualisation of the diffraction experiment, through the data workup and analysis to the dissemination and further use of the resulting structural data. Access to use the NCS facilities and expertise and a mechanism to submit samples is granted through a secure Grid infrastructure. The user may then monitor and steer the data collection aspects of their experiments and results data staged to a securely accessible location. Publication of ALL the results data generated during the course of the experiment is then enabled by means of an Open Access Data Repository. This repository publicises its content through Open Archive Initiative (OAI) protocols, which enable harvester and aggregator services to make the data searchable and accessible via data portals

Grid-enabling an existing instrument-based national service

Recent work by the ‘CombeChem’ project together with the UK National Crystallography Service (NCS) has integrated the NCS into a Grid environment. The existing high-throughput crystallography facility is enhanced by on-line feedback with the ability to monitor and steer diffraction experiments remotely. Grid-based security mechanisms are used to determine authorisation attributes and hence to allow user interaction at appropriate stages, together with access of a database recording the status of the submitted samples. The user can monitor the position of their samples, be alerted to all stages from submission to experiment and then analysis, visualise raw data as it is generated, be involved in the key decision-making during the parameterisation and initialization of the experiment and then track the data collection to ensure its successful completion. Results data are staged to a secure area and made available for download (either the raw diffraction data or a refined structure generated by NCS staff)

Systematic Study into the Salt Formation of Functionalised Organic Substrates: Nottingham 2003 E-Science Poster

There is currently a great amount of interest in the use of salts in the pharmaceutical industry because the physiochemical properties of the solid forms can be modified without altering the biochemical properties of the drug. Much effort has been expended in screening to select the best salt form and a number of empirical rules have been proposed such as the ‘rule of three’, which states that a successful salt formation generally requires a difference of three pKa units between the conjugate acid and the conjugate base. However, this rule does not always hold and the reasons are often unclear. The idea of this project is to perform a detailed systematic study of organic salt formation through a series of designed experiments, in order to obtain a broader and better understanding of the chemical descriptors, or factors, that might be involved. A set of descriptors that describe molecular properties relevant to salt formation have been identified. For the initial experiments, a collection of salt forming acids has been assembled from the Cambridge Structural Database [1], and other sources, and their descriptor values calculated. These acids define a chemistry space from which the compounds for the first experiments can be chosen. The experiments aim to explore this chemical space whilst building statisical models that will allow understanding of how the descriptors affect salt formation. Preliminary results from this study will be presented. This work is part of the Combechem E-science project at the University of Southampton. 1. F. H. Allen and O. Kennard (1993). Chem. Des. Autom. News, 8, 1, 31-37