Dr Niek Buurma

Publication

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Research

The two main areas of research in the group (development of conjugated DNA-binders & study of organic reactions in aqueous solutions) encompass several linked projects.

Targeting DNA

DNA is an important target for potential drugs and genosensors. Molecules allowing control over selectivity and affinity for DNA are therefore of particular interest as genosensors (and/or therapeutic agents). We develop new DNA-binding motifs consisting of fully conjugated systems which display changes in optoelectronic properties upon interaction with DNA in collaboration with Prof. Simon Pope. These molecules are used as sensitisers in biosensors that detect the presence of bacterial pathogens through detecting their unique DNA sequences, often in collaboration with Pedro Estrela (University of Bath). In these sensors, formation of a double helix between a capture strand and a target strand is highlighted because the sensitisers bind to the formed duplex DNA.

Similarly, molecules targeting DNA can be used in applications in forensics. We develop dyes for facile and safe detection of biological trace evidence in crime scenes, without degrading the evidence in the process. We have identified several compounds of interest which we are testing using physical chemistry methods in models of crime scenes to assess sensitivity and selectivity.

Apart from being an interesting target for biomedical and forensic applications, DNA in itself forms a versatile building block for a range of 3D structures. Combining these 3D structures with DNA-binding molecules having interesting electronic properties opens up the world of nanobioelectronics. In this area, we are developing new approaches and analytical techniques to identify the building blocks for self-assembled functional nanostructures.

For an overview of these applications, see our book chapter in “DNA in Supramolecular Chemistry and Nanotechnology”.

Organic Reactivity in Aqueous Solutions

Our interest in organic reactivity focuses on aqueous solutions.

Kinetic and mechanistic studies of racemisation reactions in aqueous solutions are one of our key areas of interest. Despite tremendous interest in enantioselective synthesis, the area of chiral stability had been ignored for decades. As a result, significant resources are spent on enantioselective synthesis of pointless stereogenic centres, i.e. stereogenic centres that will quickly racemise when used in biologically relevant solutions. We have developed the first quantitative prediction of racemisation risk with general applicability. This predictive method allows researchers in industry and academia to avoid unstable stereogenic centres and was published as a “Hot Paper” in Angewandte Chemie . This research has obvious applications in medicinal chemistry and beyond.

We also apply our understanding of reaction medium effects in aqueous solutions in the development of transition metal-catalysed reactions using both molecular complexes and nanoparticles as catalysts. We are interested in mechanistic studies of photochemical fading processes and we carry out such studies in collaboration with the group of Dr Joe Beames (University of Birmingham).

Finally, we apply our kinetic approaches to the study of degradation of pharmaceuticals in systems mimicking the environment, with translation to actual environmental systems in collaboration with Dr Ben Ward

Model and Biophysical Method Development

Our research frequently requires the development of new mathematical models or the development of new experimental techniques.

One of the techniques used for the study of interactions with DNA and other (bio)macromolecules is isothermal titration calorimetry (ITC). We develop data-analysis software for complex (coupled) equilibria. Our software combines modular combination of interaction processes, optimisation algorithms from artificial intelligence, and powerful post-fitting parameter-validity analysis. This combination ensures maximum flexibility in data analysis while keeping parameters statistically significant. Our software is used worldwide and often forms the basis of collaborations with academia and industry.

Our studies of reactions and interactions also require development of mathematical models for the analysis of experimental data. For example, in addition to our software for the analysis of complex ITC data, we have developed models for the global analysis of pH- and temperature-dependent enzyme kinetics, for the analysis of kinetic data for catalysis by gold nanoparticles encapsulated within a thermosensitive shell, and for cooperative binding of metals to bivalent host systems.

Because of the need for quantitative data, much of our research is also supported by analytical chemistry. The use of existing analytical techniques and development of new techniques is therefore also important.

A significant part of this work is in collaboration with the Medicines Discovery Institute

Machine Learning and Automating Chemistry

The group has developed data-analysis software for well over a decade. The machine learning (sometimes called artificial intelligence) algorithms used in data analysis also offer potential in reaction optimisation. We are using such algorithms, running on Raspberry Pi computers, to develop low-cost automated reaction-optimisation systems in collaboration with the group of Joe Beames (University of Birmingham). One of the reasons for developing these systems is that we believe that reaction-optimisation platforms should be affordable to all research groups so that research in chemistry remains accessible to everyone who wants to explore a good synthetic idea.

For more information on specific projects available with Dr Niek Buurma please review the Molecular Synthesis section of our research project themes.

Teaching

CH5203 Organic Chemistry of Multiply bonded Systems

CH5206 Keys skills

CH5210 Practical

CH5230 Medcinal Chemistry Practical

CH3315 Structure and mechanism in organic chemistry

CH4405 Advanced Techniques in Biophysical Chemistry

CHT206 Structure and mechanism in organic chemistry

CHT216 Colloquium

CHT229 Advanced Techniques in Biophysical Chemistry

CHT232 Key skills for postgraduate chemists

Details of modules can be found in course finder.

Biography

Niek obtained his MSc (1997, cum laude) and PhD (2003, cum laude) under the supervision of Prof. Dr. Jan B. F. N. Engberts at the University of Groningen, the Netherlands. Niek was then a Postdoctoral Research Fellow at the University of Sheffield (2002-2006) with Prof C. A. Hunter and Dr. I. Haq. Niek was appointed Lecturer in Physical Organic Chemistry at Cardiff University in 2006.

Niek won the Unilever Research Prize 1998.

As a volunteer director of the Dutch Network for Academics in the UK (DNA-UK), Niek is a member of the ACB of CONNECTS-UK, the first pan-EU platform in the UK aimed at fostering scientific collaborations between the EU and the UK.

Professional memberships

• Director of the Dutch Network for Academics in the UK (DNA-UK),
• ACB member of the EU-funded CONNECTS-UK project,
• Member of the Royal Society of Chemistry, 
• Secretary of the RSC Physical Organic Chemistry Group,
• Fellow of the Higher Education Academy, 
• Member of the Core Team of the EPSRC Directed Assembly Network.

Academic positions

• Maître de Conférences invité at l’Université de Toulouse 3 - Paul Sabatier 2016

Supervisions

Current supervision

Ibrahim Alkhaibari Alkhaibari

Oliver McHugh

Hessa Althani

Nada Al Joaied

Razan Khalid R Alharbi

Alice Jeffers

Yueqiang Wang