Bioactive Molecules is one of the four research themes of the Institute of Biology Leiden.

Microbial Sciences' contribution to the Bioactive Molecules research theme is to discover new bioactive molecules and enzymes and unravel their mechanisms of action, regulatory networks, and the (bio)synthetic pathways required for their production.

Even a small quantum computer should be able to simulate exactly the properties and behaviour of new molecules. This would take chemistry to an entirely new level. Better solar panels, more powerful batteries, saving lots of energy in the chemical industry: the applications have the potential to transform…

Plant Sciences' contribution to the Bioactive Molecules research theme is to identify new plant bioactive molecules, and unravel their mechanisms of action in plant development or health, and the regulatory networks and (bio)synthetic pathways required for their production.

Animal Sciences’ contribution to the Bioactive Molecules research theme includes research on molecules from natural sources, such as plants, insects, and snake venom, with the aim to identify novel anti-cancer, anti-inflammatory, anti-microbial, and anti-diabetic agents.

Our DNA molecules are packaged by proteins in compact structures. The aim of this project is to understand how modern gene editing techniques nevertheless get access to their target in the DNA.

Schneider

Since the early 1990s, one can isolate the optical signal of a single molecule and single-molecule spectroscopy has quickly grown into an important research field.

This thesis revolves around the electronic spectroscopy of molecules in the laboratory and the search for the carriers of the diffuse interstellar bands (DIBs).

While bioinformatics methods deal with the analysis of sequence information (be it proteins or DNA), the field of cheminformatics is concerned with the analysis of small-molecule datasets.

Promotor: Prof.dr. E. F. van Dishoeck, Co-promotor: A. N. Heays

Intrigued by the way cells autonomously regulate their fate, we strive to understand and visualize cellular processes as the basis of Cell Signaling.

The main focus of the thesis is the discovery and development of novel inhibitors of bacterial metallo-β-lactamases (MBLs).

Deficiency of glucocerebrosidase (GBA) underlies Gaucher disease, a common lysosomal storage disorder. Carriership for Gaucher disease has recently been identified as major risk for parkinsonism. Presently, no method exists to visualize active GBA molecules in situ. We here report the design, synthesis…

MHC class I and MHC class II molecules present peptides to the immune system to drive proper T cell responses. Pharmacological modulation of T-cell responses can offer treatment options for a range of immune-related diseases.

This perspective addresses four challenges facing theorists whose aim is to make quantitatively accurate predictions for reactions of molecules on metal surfaces, and suggests ways of meeting these challenges, focusing on dissociative chemisorption reactions of H2, N2, and CH4.

Promotor: M. Ubbink, Co-promotor: G. Siegal

Promotor: Prof.dr. T. Hankemeier, Co-Promotor: R.J. Vreeken

This thesis is a collection of experimental attempts to enhance photoluminescence of fluorescent molecules and quantum dots with single gold nanorods (GNRs) and relevant applications.

Promotor: M. Ubbink, Co-promotor: G. Siegal

Large areas of space are filled by molecular clouds that consist of gas and dust grains that are the remnants of dead stars. When these clouds start collapsing, the decreasing temperature and increasing density cause gas particles to start accreting onto dust grain surfaces.

I will give a general introduction to the field of molecular electronics, its history, methods and challenges. I will also introduce the subject of my investigation and provide a brief outlook to the remainder of our thesis.

Promotores: Prof.dr. G.W. Canters, Prof.dr. T.J. Aartsma

Promotor: Prof.dr. M.A.G.J. Orrit

Several techniques are explored for going beyond the born-oppenheimer static surface model for molecule-surface reactions.

In this thesis we investigated the ability of two-photon multifocal microscopy for single-molecule microscopy in live cells and organisms.

In human cells, a meter-long DNA is condensed inside a micrometer-sized cell nucleus. Simultaneously, the genetic code must remain accessible for its replication and transcription to functional proteins.

This thesis examines the link between simple molecules and the underlying structure and chemistry within protoplanetary disks - the birthplaces of planets.

Promotor: J.M. van Ruitenbeek, Co-Promotor: S.J. van der Molen

Promotor: M.A.G.J. Orrit

Can we find new chemical and biological sensing routes on the edge and surface of graphene to improve the potential of graphene to act as a sensor?

It is possible to treat the dynamics of the dissociation of hydrogen on metal surfaces quantum mechanically, while taking into account the motion in all six molecular degrees of freedom without making approximations. Because the approximations of neglecting surface phonons and electron-hole pair excitation…

Walsh

Promotor: M. Ubbink, Co-promotor: G. Siegal

Promotor: Prof.dr. G.J. Kroes

Catalysis is of extreme relevance in the production of everyday materials and plays a central role in many aspects of our life.

Science, Leiden Institute of Chemistry (LIC)

PhD Defence

Planets are formed in disks of gas and dust around young stars.

Freshwater is an important resource, but at a great risk of species decline due to habitat loss, pollution and over-exploitation, and invasive alien species.

Detecting molecules with temperature instead of chemical reactions: that’s what scientists from the Leiden Institute of Physics want to do. They are developing a sensor that utilizes special nanoparticles to keep track of certain molecules. In this way, they can for example see how well new drugs do…

Although Sander Wezenberg just started working in Leiden in March this year, he already managed to win a Vidi grant from NWO. Inspired by nature, Wezenberg wants to bring synthetic molecules to life and teach them to communicate. But who exactly is Wezenberg and what drives him?

Biophysicist Rolf Harkes has developed a microscope to optically localize individual molecules in living cells. It improves monitoring of diseases like cancer and Parkinson’s at the cellular level. Defende PhD thesis on t13 January 2016.

Can new variants of daptomycin and the polymyxins be found?

We aim to develop A. niger strains that produce more starch degrading enzymes even in the absence of starch.

The E2CB programme has been launched to bring CO2 emissions to zero by 2050. The goal: to produce all raw materials for the chemical industry from sustainable sources. Professor of Electrochemistry Marc Koper is involved in the project.

Can we make a better vancomycin?

Is it possible to diagnose diseases using molecular switches? The new international consortium LogicLab will address this question. Leiden chemist Sylvestre Bonnet and Leiden pharmacologist Thomas Hankemeier are involved in the project. LogicLab will run for four years and will receive over 3.5 million…

Can the venom of snakes, scorpions and other animals be sources of new antibiotics?

Natural product inspired antibiotics to address resistance