Molecular Level Interactions Notes PDF

Module structure  Fundamentals of light  Propagation of light in waveguides  Light interaction with matter  Lasers  Photobiology basics  Biophotonics applications  Bioimaging  Tissue engineering  Topics to be covered  Atoms and Molecules  Molecular level...

Module structure  Fundamentals of light  Propagation of light in waveguides  Light interaction with matter  Lasers  Photobiology basics  Biophotonics applications  Bioimaging  Tissue engineering  Topics to be covered  Atoms and Molecules  Molecular level interactions  Absorption, spontaneous emission, stimulated emission  Fate of excited molecules  Fluorescence  Light scattering  Rayleigh, Mie, Raman, spectroscopy  Introduction  Light interaction with bulk matter was previously introduced – reflection, refraction, diffraction  At a molecular level, the time varying electric fields of light interact with matter because matter contains electric charges  The forces exerted on charges and dipoles in atoms and molecules cause them to accelerate  Rotational - microwaves or far infrared light,  Vibrational - infrared light,  Electronic - visible and ultra-violet light  However, as the energy increases from microwave to UV, all movements become possible making the spectra much more complicated  Absorption and emission to be presented next involve quantized electronic and vibrational states of molecules  Absorption  Absorption is the process whereby a transition from a quantized lower energy state (m) to a higher energy state (n) occurs with the difference in energy being supplied by a photon (hf) n  The difference in energy between states m and n (En-Em) must match the energy of the photon (hf) m  The photon is annihilated in the process  If the photon energy does not match the difference in energy states, absorption may still occur but the photon is re- radiated immediately (in about 10 femtoseconds). This results in From Fundamentals of Photonics phenomena such as Rayleigh scattering  Spontaneous emission  Spontaneous emission is a random process where by an excited energy state (n) returns to a stable lower energy state n (m) by giving up the energy difference as a photon  Spontaneous emission is m independent of the number of photons that may already be present  The phase and direction of the emitted photon will be From Fundamentals of Photonics completely random  Stimulated emission  A photon with energy equal to the energy gap stimulates an excited state to return to a lower energy state, thus giving off a second photon n  The original photon is retained in this process m  The second photon has identical frequency, phase, direction and polarization to the original photon – it is a clone of the original photon  This is the process behind the operation of lasers From Fundamentals of Photonics  Potential energy curves  Diagram shows the ground state and an excited electronic energy state of a molecule  Both states have a number of vibrational states (labelled by the v´ and v´´ numbers)  Photon absorption generally occurs from a v ´´=0 ground state  Photon emission generally occurs from an excited electronic state with v´=0 A. Gilbert and J. Baggott, Essentials of Molecular Photochemistry, CRC Press, 1991  Excited states of molecules  Molecules (or a group of molecules – an aggregate) will enter excited states when they absorb photons  Excited states are unstable and so the molecules will look to return to the ground state as soon as possible  Once excited, there are number of ways in which this absorbed energy can be released  Some routes may return the molecules to their ground states directly whilst other routes may have intermediate excited states  Whether direct or indirect, the process whereby energy is released will either be radiative or non-radiative  Several process can compete with each other for the deactivation of an excited state  A molecule in an excited state is given by A* whilst its ground state is given by A  Excited states of molecules - 2 Electronic excitation in a molecule/molecular aggregate Photoinduced Photochemistry Photophysical Processes e.g.photosynthesis Electron transfer (i) Photoionization A* → A+ + e- (ii) Electron transfer D* + A → D+ + A- Radiative Nonradiative Energy Excited state Process Process transfer complex A* + B → A + B* formation (i) Excimer A* + A → (A-A)* Fluorescence (i) State-to-state crossing (ii) Exciplex Phosphorescence (ii) Vibrational relaxation A* + B → (A-B)*  Photochemistry  Photochemistry describes the absorption of light by molecules and resulting chemical reactions and a stable compound.  There are a number of photochemical routes by which an excited molecule can loose its energy, for example  Photoassociation:- A* + B → A-B  Photodecomposition:- A* → B + C  These and other photochemical process have considerable significance in biology (for example, photosynthesis and vision) and will be covered in the “Photobiology Basics” section  Photophysical process  A Jablonski Diagram shows the energy transitions involved in a photophysical process  Singlet states are named S0, S1, S2. With increasing state number, the minimum energy also increases  S0 generally represents the ground state  The short lines within a state (like a ladder) are quantized vibrational VR = vibrational relaxation states IC = internal conversion  Straight arrowed lines are transitions linked to photon absorption or emission J.A. Barltrop and J.D. Coyle, Principles of Photochemistry, John Wiley & Sons, 1978  Vibrational relaxation  Vertical ‘squiggly’ lines on the Jablonski diagram indicate energy lost through vibrational relaxation  Unless the transition is between two zero-point vibrational states, the excited species will have an excess of vibrational (and rotational) energy in addition to its electronic energy  By colliding with other molecules, this energy is converted into translational energy which raises the temperature of the material through heating  If collisions are infrequent (in gaseous states), energy can be lost through photon emission in the infra red range where the photon energy corresponds to the energy between two consecutive vibrational energy levels  State-to-state crossing  The horizontal squiggly line on the Jablonski diagram shows changes in quantum states without changes in energy. This is a non-radiative processes and are called internal conversion (IC)  Internal conversion occurs between singlet states (e.g. S1→S0, S2→S1)  Internal conversion is a rapid process  Through a combination of vibrational relaxations, a Sn state will rapidly (in a few picoseconds or less) relax to the lowest vibrational level of S1  Tonic water  Quinine  Absorb 250 and 350nm  Emit 450nm  Fluorescence  Fluorescence is the process by which an excited singlet state (Sn) returns to the singlet ground state (S0) by the spontaneous emission of a photon. P. Atkins and J. de Paula, Physical Chemistry 8th ed., Oxford University Press, 2006  Fluorescence - 2  The initial photon absorption normally takes the molecule from the zero vibrational state (v´´= 0) of the ground state (S0) to an excited electronic state (S1, S2, etc) with some vibrational energy (v´≠ 0)  This energy is lost through collisions as the excited molecule steps down the vibrational ladder to the lowest vibrational energy state in the excited electronic state (e.g. v´= 3 → 2 →1 → 0)  The excited molecule then returns to the ground state by emitting a photon  Absorption spectrum arises from 1-0, 2-0, 3-0, etc vibrational transitions. (note: numbers imply v´- v´´ transitions. E.g. the absorption transition shown in the diagram is a 6-0)  The spectrum suggests transitions from the ground state to certain vibrational states in the excited electronic state are more favourable than others  The fluorescence spectrum also has a similar shape suggesting certain vibrational states in the ground state are more favourable destinations. The emission transition shown in the diagram is a 0-1, but 0-0, 0-2, 0-3 transitions are also possible  Fluorescence - 3  0-0 absorption and fluorescence transitions can be coincident (both involve the same wavelength of light) as shown on the spectrum diagram  As energy is lost to vibrations, the emitted photon has a lower energy than the transmitted photon. This is why the fluorescent spectrum is at a higher wavelength than the absorption spectrum  The vivid oranges and greens of fluorescent dyes are due to the absorption of UV and the emission in visible  Fluorescence is generally a rapid process happening within a few nanoseconds of the initial excitation  Fluorescence is used widely in many applications such as, environmental monitoring, clinical chemistry, DNA sequencing and cell identification  Summary  The oscillating electric field of light interacts with matter to excite dipoles in atoms and molecules  Absorption, spontaneous emission and stimulated emission are some of the key processes that involve light and matter on a microscopic scale  Molecules excited by the absorption of light can return to the ground state by radiative or non-radiative routes  Non-radiative means include vibrational relaxation which causes heating and photochemical reactions  Radiative means include fluorescence where the emitted photon is of lower energy than the one absorbed