Molecules-in-molecules fragment-based method for the evaluation of Raman spectra of large molecules

Abstract

We present the first implementation of the evaluation Raman spectra of large molecules using the molecules-in-molecules (MIM) fragment-based method (MIM-Raman). Molecular fragments and associated overlapping subsystems are constructed by cutting the C–C bonds in the large molecule based on the connectivity information and a number-based fragmentation scheme. After saturating the dangling bonds with hydrogen link-atoms, independent energy and Raman frequency calculations are performed on each subsystem. Subsequently, link-atom-related forces, Hessian and polarisability derivative matrix elements are projected back onto the corresponding host and supporting atoms through the Jacobian projection method. In the two-layer model (MIM2), the long-range interactions, absent in the single layer model (MIM1), are taken into account through a second layer at a lower level of theory. The MIM-Raman method is benchmarked on a set of large linear and cage molecules. The MIM extrapolated energy and Raman spectra are compared with the full calculations at B3LYP/6-311G(d,p) or B3LYP/6-311+G(d,p) levels of theory. The benchmark analysis of 21 molecules at MIM2 show an accuracy improvement of 85% in energies, 74% in Raman frequencies and 66% in intensities over MIM1. The implementation and benchmark analysis validates the MIM-Raman model for exploring Raman spectra of large molecules in the future.

Keywords:

• linear scaling hybrid methods
• Raman spectrum
• Jacobi link-atom projection
• density functional theory
• α-cyclodextrin
• biomolecules

Acknowledgements

This work was supported by funding from NSF Grant No. CHE-1266154 at Indiana University. The authors thank the Indiana University Big Red II, Supercomputing facility for computing time.

Disclosure statement

No potential conflict of interest was reported by the authors.

Additional information

Funding

This work was supported by funding from NSF Grant [number CHE-1266154] at Indiana University.