Molecular Dynamics of Biomolecules

1. Introduction

Over the course of billions of years of evolution, nature has selected specific molecules for use as the “building blocks” of life. One fundamental example of this may be found in DNA. If the DNA molecule is damaged this could cause harmful mutations of the information it carries. Another is the biological pigmentation molecules known as melanin, one class of this is Eumelanin, found in hair, skin and eyes; whose primary function is to be the first line of defence in protecting the organism from the potentially damaging effects of ultra-violet (UV) radiation. It is made up of three main building blocks that are strikingly similar to the DNA bases adenine and guanine (fig 1). 

An important question to ask is what is inherently special about this configuration that it is used in such vital roles across a diverse range of living organisms. One key idea centres on the idea of photostability. In the early years on earth there was no ozone layer to protect organisms from potentially damaging UV radiation. Any excess energy absorbed must be dispersed. This can be done in one of three ways: a bond in the molecule can be broken, which has serious implications; the molecule can fluoresce, emitting a photon of light; or the electronic energy could be coupled into vibrational degrees of freedom that can easily dissipate through the molecule into the surrounding environment. Fluorescence quantum yields have been shown to be very low in these molecules. It has been postulated that the vibrational process is particularly rapid and efficient for these molecules, causing higher than normal photostability. If it is found that both DNA bases and Eumelanins are photostable then self protection can be seen at work, with melanins being the first line of defence, and the DNA itself being the last line of defence.
Diagrams of various molecules

Figure 1.Top: The 4 DNA basis. Bottom: The indole molecule and the 3 constituent building blocks of the eumelanin polymer.

The advance of femtosecond pulsed lasers has made it possible to probe the dynamics of molecules in real time in a way that was not possible before. The processes we are interested in take place in a few hundred femtoseconds (1 femtosecond = 10-15s) and to observe them a pulse of a similar length is required. An initial “pump” pulse excites the molecule and sets the chain of events in motion. A precisely controlled time later a secondary “probe” pulse ionises the molecule. Examining the free electron kinetic energies and angular directions can reveal how the molecule relaxes over time. Large molecules like DNA and melanin have many vibrational states and processes and it is a challenge to model the results. Small parts of these molecules can be understood more easily and give us insight into the molecule as a whole. Our group has chosen a stepwise approach in order to build up a picture of the larger molecule while understanding the contributions of constituent parts.



2. Experimental Set up

The equipment (fig 2) required for these experiments include a femtosecond pulsed laser system, a vacuum chamber, and a detection system. Because the time frame of the process is extremely short, ultrafast pulses of UV light are required. A Ti:Sapphire laser in conjunction with chirped pulse amplification (CPA), emits at around 800 nm (red light) with pulses around 50 - 100fs long. Nonlinear processes can be utilised to reduce the wavelength to 200 - 300nm (UV radiation). The same system can be used to generate both the probe and the tuneable pump pulse, with a delay stage accurately controlling the time difference between them. In order to excite only the molecules of interest and not background molecules a vacuum (~10-8 Torr) is required. The laser pulses enters the vacuum chamber via a window. The molecules are inserted using an Even Lavie pulsed nozzle, where they intersect with the laser pulses and are ionised. A specially designed electric field accelerates all the resultant electrons towards a position sensitive detector. This consists of a micro channel plate (MCP) amplifier, a phosphor screen, and a CCD camera. Using this apparatus we can image the angular and kinetic energy information for each pump – probe delay. This gives us the full energy, angle, time information that is required to explore the relaxation pathways within the molecules.


Figure 2. Schematic overview of velocity-map imaging spectrometer setup. For photographs, please see Research


3. Further Reading

R. A. Livingstone, J. O. F. Thompson, M. Iljina, R. J. Donaldson, B. J. Sussman, M. J. Paterson & D. Townsend, Time-resolved photoelectron imaging of excited state relaxation dynamics in phenol, catechol, resorcinol and hydroquinoneJ. Chem. Phys., 137, 184304, (2012).