Stay calm and focus on the learning outcomes: Tools for taking biophysical chemistry online.

Course specific learning outcomes are an important tool to define the scope of a course and can be very helpful when designing experiments and assessments. With slight modification, these learning outcomes can serve as a guide when transitioning to the distance learning format especially in courses with a traditional lab. Here we present such an example for the biophysical chemistry course.

Teaching vibrational spectra to assign themselves.

A new paradigm for assigning vibrational spectra is described. Instead of proceeding from potential to Hamiltonian to eigenvalues/eigenvectors/intensities to spectrum, the new method goes "backwards" directly from spectrum to eigenvectors. The eigenvectors then "assign" the spectrum, in that they identify the basis states that contribute to each eigenvalue.

Assessing Gaussian Process Regression and Permutationally Invariant Polynomial Approaches To Represent High-Dimensional Potential Energy Surfaces.

The mathematical representation of large data sets of electronic energies has seen substantial progress in the past 10 years. The so-called Permutationally Invariant Polynomial (PIP) representation is one established approach. This approach dates from 2003, when a global potential energy surface (PES) for CH was reported using a basis of polynomials that are invariant with respect to the 120 permutations of the five equivalent H atoms.

Vibrational tug-of-war: The pK dependence of the broad vibrational features of strongly hydrogen-bonded carboxylic acids.

Medium and strong hydrogen bonds give rise to broad vibrational features frequently spanning several hundred wavenumbers and oftentimes exhibiting unusual substructures. These broad vibrational features can be modeled from first principles, in a reduced dimensional calculation, that adiabatically separates low-frequency modes, which modulate the hydrogen bond length, from high-frequency OH stretch and bend modes that contribute to the vibrational structure. Previously this method was used to investigate the origin of an unusual vibrational feature frequently found in the spectra of dimers between carboxylic acids and nitrogen-containing aromatic bases that spans over 900 cm and contains two broad peaks.

A combined electronic structure and molecular dynamics approach to computing the OH vibrational feature of strongly hydrogen-bonded carboxylic acids.

Medium and strong hydrogen bonds give rise to vibrational features that can span several hundreds of wavenumbers and have unusual line shapes. For example, dimers consisting of carboxylic acids hydrogen-bonded to nitrogen-containing aromatic bases exhibit a vibrational feature that spans over 900 cm and contains two very broad peaks. In this report, we demonstrate how this feature can be reproduced using a combined molecular dynamics (MD) and electronic structure "spectral map" approach, which has been very successful in modeling the vibrational spectrum of water in different environments.

Origin of the Hadži ABC structure: An ab initio study.

Medium and strong hydrogen bonds are well known to give rise to broad features in the vibrational spectrum often spanning several hundred wavenumbers. In some cases, these features can span over 1000 cm(-1) and even contain multiple broad peaks. One class of strongly hydrogen-bonded dimers that includes many different phosphinic, phosphoric, sulfinic, and selenic acid homodimers exhibits a three-peaked structure over 1500 cm(-1) broad.

Origin of the 900 cm(-1) broad double-hump OH vibrational feature of strongly hydrogen-bonded carboxylic acids.

Medium and strong hydrogen bonds are common in biological systems. Here, they provide structural support and can act as proton transfer relays to drive electron and/or energy transfer. Infrared spectroscopy is a sensitive probe of molecular structure and hydrogen bond strength but strongly hydrogen-bonded structures often exhibit very broad and complex vibrational bands.

Flexural rigidity measurements of biopolymers using gliding assays.

Microtubules are cytoskeletal polymers which play a role in cell division, cell mechanics, and intracellular transport. Each of these functions requires microtubules that are stiff and straight enough to span a significant fraction of the cell diameter. As a result, the microtubule persistence length, a measure of stiffness, has been actively studied for the past two decades(1).