Resources | Tokmakoff Group

Resources

Educational Resources

Concepts in Biophysical Chemistry
Lecture notes on physical concepts for molecular biophysics.

Time-Dependent Quantum Mechanics and Spectroscopy
Online textbook

Nonlinear and Two-Dimensional Spectroscopy
Notes, worksheets, and video lectures on nonlinear and two-dimensional spectroscopy.

Tokmakoff Group Theses

IR Spectroscopy of Proteins

Computational Amide I Spectroscopy of Proteins
Open-source programs to calculate amide I IR and 2D IR spectra from molecular dynamics simulations.

g_amide: Predicts amide I vibrational frequencies, couplings for peptide amide groups along an MD trajectory.
g_spec: Converts frequency and dipole trajectories into simulated linear and nonlinear optical spectra.
Reference: “Computational Amide I 2D IR Spectroscopy as a Probe of Protein Structure and Dynamics,” Mike Reppert and Andrei Tokmakoff, Annu. Rev. Phys. Chem. 67, 359-386 (2016).

Introduction to 2D IR Spectroscopy of Proteins
Carlos Baiz, Mike Reppert and Andrei Tokmakoff, in Ultrafast Infrared Vibrational Spectroscopy, ed. by Michael D. Fayer (Taylor & Francis, New York, 2013), pp. 361-404.

Amide I FTIR and 2D IR Spectra for 16 Proteins
Reference: “Coherent two-dimensional infrared spectroscopy: Quantitative analysis of protein secondary structure in solution,” Carlos Baiz, Sam Peng, Mike Reppert, Kevin Jones, and Andrei Tokmakoff, Analyst 137, 1793-1799 (2012).

Protein Side Chain Absorption in the Infrared Finger Print Region
Notes, worksheets, and video lectures on nonlinear and two-dimensional spectroscopy.

Infrared Optics

Dispersion of Infrared Optical Materials
Data for describing the propagation of ultrafast mid-IR pulses through dispersive media.

Absorption Coefficient of Infrared Optical Materials