<br/>Alkynes serve as effective probes in biochemical vibrational frequency studies because of their unique and strong Raman signals at frequencies where biological molecules are Raman inactive. Molecular dynamics (MD) models of these signals can provide deep molecular and mechanistic insight. In order to model such alkyne-probed biochemistry experiments, an efficient method for calculating alkyne vibrational frequencies must be developed; here we seek a spectroscopic map. Investigations of alkynes in different solvent environments can aid in developing a universally applicable spectroscopic map for predicting accurate vibrational frequencies and deepening our understanding of alkyne vibrational modes. Seven terminal alkyne probes were solvated in water using Packmol and parameterized with the CHARMM36 forcefield. These systems underwent MD simulations to capture snapshots of the probe interacting with the surrounding solvent molecules. Once extracted, the snapshots can be treated quantum mechanically to determine the alkyne vibrational frequencies in each system. In this work, we ran these MD simulations, developed snapshot extraction code, and have begun to run quantum calculations on the 1000 MD snapshots of each probe in water. Our next focus is classifying a quantum mechanics region utilizing the extraction code and DVR frequency computations. This will translate into applying the extraction code for the remaining 6 probes in various solvents and further training of a spectroscopic map.

Developing a spectroscopic map for modeling the vibrational frequencies of terminal alkyne probes

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