=chemistry =methods =instruments =characterization =materials =optics
FTIR
FTIR is a common way to determine what chemicals are present in a
sample. For a molecule to absorb a photon, it must have some electric
charges that can vibrate at about the same frequency as that photon. Many
common bonds (such as C=O) have some charge separation and a vibrational
frequency in the infrared spectrum that's fairly consistent.
other modern techniques
If
we're considering possible improvements to FTIR, we should think about
other methods currently used to characterize molecules, and how they compare
to FTIR.
1H
NMR can determine what atoms are bonded to hydrogen or deuterium atoms,
and what kind of hydrogen bonding is happening. If you want to know where a
hydrogen atom came from in a reaction, using some deuterium is the only good
way to tell. University chemistry departments often have small NMR machines
now, but they're still much more expensive than FTIR.
X-ray
crystallography has historically been the main way to determine crystal
structures. The main problem is that a macroscopic crystal must be made, and
that's often impractical for complex molecules.
Cryo-EM is an alternative to X-ray crystallography that works on
microscopic crystals, which are easier to make. This technique has
determined many previously unknown protein structures. However, the machines
for it are currently rare and very expensive, and (small) crystals still
need to be made.
cryo-FTIR
The frequency
resolution for detecting what light was absorbed is theoretically limited
only by Doppler
broadening from thermal vibrations. At low temperatures, it's possible
to get very good resolution. So, cryogenic FTIR is used by some laboratories
now.
The vibrational frequency of bonds is changed slightly by
hydrogen bonding, nearby atoms in the molecule, and nearby charges. With
good frequency resolution, it's possible to tell not just what bond types
are present, but what's near them. But those small shifts in frequencies are
only useful if you know what they mean.
getting more data
Cryo-FTIR
has good resolution, and understanding what its data means is a bigger
problem than not having enough data. However, there are ways to get more
data.
IR spectra change somewhat with temperature, so FTIR can be
done at multiple temperatures for more data.
Magnetic fields also
affect IR spectra: they cause vibrating charges in molecules to take
slightly curved paths, which affects their frequency and the strength of
their interactions. This effect is anisotropic and averaged across every
orientation of light-interacting molecules, but, molecules can only absorb a
photon when their orientation matches the right vibrational mode to the
photon polarization. So, IR spectra in a strong magnetic field should depend
on the relative orientation of the field and the light source, as well as
the field strength.
magnetic cryo-FTIR
I think
most of the useful data from magnetic effects on IR spectra could be
collected by simply rotating the polarization of a light source that's
perpendicular to field lines from a strong magnet, perhaps using a liquid
crystal polarization rotator. For maximum field strength, the magnet should
be shaped like a ring with a section cut out for the sample to go in.
Suppose an instrument is made which can determine, with good precision,
the change in IR spectra that happens when light polarization is rotated
relative to an applied magnetic field. What can be determined from that
information?
For a given spectral line, the change in absorption with
polarization should increase with increasing coplanarity of the associated
atomic movements.
For a given spectral line, the shift in wavelength
with polarization should be an indication of how the average frequency of
the associated atomic movements varies with angle.
Differential
magnetic cryo-FTIR could be a way to get information about the relative
orientation of bonds in molecules that doesn't require forming crystals.
previous work
"Magnetic
circular dichroism" and "magnetic linear dichroism" are known effects,
which have occasionally been used in experiments for decades,
mostly using
x-rays.
If the above technique is useful, and the physical
principles have been understood for decades, then why isn't it being used
now? There are 2 basic reasons:
- infrared
magnetic dichroism of most organic molecules is a weak effect
- results
have been hard to interpret
When magnetic dichroism
spectroscopy has been used with organic molecules, it's
mostly been used
on metalloproteins, because spin effects (from a bound metal atom with
an unpaired electron) make magnetic dichroism relatively strong and easier
to interpret.
What I'm proposing here is to do magnetic dichroism
spectroscopy of uncrystallized organic molecules using cryo-FTIR, and use
molecular simulations to determine the meaning of small frequency shifts of
spectral lines with light linear polarization relative to an applied
magnetic field. (Cryo-FTIR should give sufficiently good frequency
resolution for that.) However, those magnetic shifts of spectral lines of
organic molecules involve magnetic fields affecting the energy transfer
between different vibrational modes, which is complex and hard to predict.
As this paper notes:
Circular dichroism (CD) is an important technique in the structural characterisation of proteins, and especially for secondary structure determination. The CD of proteins can be calculated from first principles using the so-called matrix method, with an accuracy which is almost quantitative for helical proteins. Thus, for proteins of unknown structure, CD calculations and experimental data can be used in conjunction to aid structure analysis. Linear dichroism (LD) can be calculated using analogous methodology and has been used to establish the relative orientations of subunits in proteins and protein orientation in an environment such as a membrane. However, simple analysis of LD data is not possible, due to overlapping transitions.
What has changed to make that approach (potentially) more worthwhile?
- computers
have gotten much faster
- molecular simulation algorithms have improved
- photodetectors have improved somewhat
- strong (neodymium) permanent
magnets are available, potentially allowing for lower-cost instruments
molecule simulation
Computers have gotten faster. Is it now possible to determine exactly what
frequencies a molecule would absorb with simulation? Yes, but only for very
small molecules of just a few atoms, even with supercomputers - and there
are few enough of those that their properties can be found experimentally
instead. For larger molecules, some simplifications are needed.
Here's a review of some recent developments, and I'll describe some
heuristics that can be used.
It's easy to add together the spectra of
each bond's vibrations. The spectra of molecules is more complex than that
because those vibrations can interact, which means transfer of energy
between them. For a demonstration of this principle, we can look at
energy transfer
between pendulums. The energy transfer between a pair of pendulums
depends on the relative phase. When frequency is slightly different, the
relative phase stays similar for long enough for full energy transfer, then
it changes and energy transfer happens in the opposite direction. You can
see with those pendulums that energy transfer is greater when frequencies
are similar. That's one way to simplify simulations: energy transfer between
modes with large frequency differences can be ignored.
Another way to
simplify simulations is by ignoring interactions that involve many vibration
modes. In practice, the importance of interactions seems to decrease with
their complexity, so most of the net impact comes from 2-mode and 3-mode
interactions.
Another way to simplify simulations is to only consider
sets of vibrational modes that are near each other. More-distant vibrations
tend to have weaker interactions.
Even with these heuristics,
accurate enough simulations to determine which large molecules are present
from IR spectra are difficult. Different molecules can have spectral lines
that are close to each other, so highly accurate predictions can be
necessary. However, with magnetic linear dichroism spectroscopy, we don't
need to predict the exact positions of spectral lines - we can just predict
the direction in which spectral lines shift as polarization is
changed, for several different lines. This could reduce the accuracy
required from simulations.