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44874-GB6
Ultrafast Infrared Spectroscopy as a Probe of Molecular Dynamics: A Molecular Modeling Study
Throughout the past 16 months, this grant has supported three students working on two projects. One of these students has graduated and the other two are continuing their research this academic year. One project combined classical simulations and electronic structure methods to examine the vibrational spectroscopy of carbonmonoxymyoglobin. Experiments performed on this system concluded that the vibrational frequency of the CO moiety (and thus the protein environment) fluctuates on two timescales: on the order of 100 fs and on the picosecond scale. The question then becomes: what motion within the protein occurs on these timescales?
This can be addressed readily through molecular dynamics simulations. In order to perform such a simulation, one must relate the coordinates of the atoms to the frequency of the CO stretch. Previous simulations on this system assumed that this frequency is proportional to the external electric field.[1] To test this assumption, we performed 100 calculations of the CO frequency from electronic structure methods using atomic coordinates from the classical simulation. We found no relationship between these frequencies and the electric field.
We first sought to confirm that our frequency calculations were accurate. To calculate the frequency, we stretch the CO bond in the presence of the protein and calculate the energy. As these calculations are quite time consuming, we must limit the number of data points in this stretch as much as possible. Computational limitations also require that we use a very limited number of the total atoms in the system. This is acceptable as it is generally true that only the nearest neighbors to the chromophore significantly influence its frequency. By systematically examining the manner in which we stretch the CO bond and the way in which we select the portions of the protein that are included in these calculations, we have uncovered some errors. There are two fragments that we are currently testing and should those results be favorable, we believe that we would be correctly calculating the frequency.
Thus far, the elimination of these errors has not altered our conclusion that there is little correlation between the electric field and the frequency. However, we were able to find an excellent correlation between the frequency and a linear combination of the Fe-C distance and two coordinates describing motion within the porphyrin ring. Using this correlation, we find a distribution of frequencies that is twice the width of the infrared spectrum. However, motional narrowing leads to a calculated spectrum that is much narrower than the experiment. Since establishing this correlation, we have identified two additional protein fragments that need to be included in the frequency calculations, which may dampen the motional narrowing. We are also exploring the effects of quantum mechanics on the time evolution of the frequency which has thus far been neglected.
The second project examines water evaporation through organic monolayers. Well-formed monolayers of long-chain surfactants can reduce the rate of water evaporation by as much as a factor of 10,000. With the discovery of the ubiquity of uncharacterized organic material in tropospheric aerosols, it stands to reason that these will affect the growth rates of the aerosols. However, a single layer of butanol molecules coating a solution of concentrated sulfuric acid has almost no effect on the rate of water evaporation. Our goal is to understand this surprising result using computer modeling.
Our system consists of pure water coated with an alcohol surfactant. Rather than calculate the rate of evaporation directly, we can obtain data much more rapidly measuring the converse process of condensation (since at equilibrium, the rate of both processes must be equal). With a butanol surfactant, the rate of condensation falls significantly as surfactant is added in contrast to the experiment which shows almost no effect. This discrepancy could be due to inadequacies of the model or that the bulk is room temperature water as opposed to supercooled concentrated sulfuric acid.
Mechanistically, we have concluded that without exception, if a molecule forms a hydrogen bond with an interfacial molecule, it will condense. Should it fail to form that hydrogen bond, it will be deflected from the surface. At low coverage, it is not surprising to find most of the molecules condense by evading the surfactant molecules. As coverage increases, fewer waters manage to find such gaps and more of the molecules will hydrogen bond to the alcohol and then gradually drift into the bulk. At a monolayer of coverage, these two mechanisms occur with nearly equal rates.
We are currently working toward a more direct comparison to the experiments. To this end, we have performed calculations evaluating the temperature dependence of our results and we intend to use salt solutions to determine the dependence on ionic strength. We have also varied the chain length of the surfactant molecules to compare to the experimental trends for longer chain surfactants.
