A theoretical study of the 1B2u and 1B1u vibronic bands in benzene

The two lowest bands, 1B2u and 1B1u, of the electronic spectrum of the benzene molecule have been studied theoretically using a new method to compute vibronic excitation energies and intensities. The complete active space (CAS) self-contained field (SCF) method (with six active π-orbitals) was used to compute harmonic force field for the ground state and the 1B2u and 1B1u electronic states. A linear approximation has been used for the transition dipole as a function of the nuclear displacement coordinates. Derivatives of the transition dipole were computed using a variant of the CASSCF state interaction method. Multiconfigurational second-order perturbation theory (CASPT2) was used to obtain absolute excitation energies (12 active π-orbitals). The results show that the approach works well. Vibrational progressions are well described in both bands and intensities, and energies are in agreement with experiment, in particular when CASPT2 derived geometries are used. One interesting result is that computed vertical energies fall about 0.1 eV on the high energy side of the band [email protected]

A robust normalized local filter to estimate compositional heterogeneity directly from cryo-EM maps

Abstract Cryo electron microscopy (cryo-EM) is used by biological research to visualize biomolecular complexes in 3D, but the heterogeneity of cryo-EM reconstructions is not easily estimated. Current processing paradigms nevertheless exert great effort to reduce flexibility and heterogeneity to improve the quality of the reconstruction. Clustering algorithms are typically employed to identify populations of data with reduced variability, but lack assessment of remaining heterogeneity. Here we develope a fast and simple algorithm based on spatial filtering to estimate the heterogeneity of a reconstruction. In the absence of flexibility, this estimate approximates macromolecular component occupancy. We show that our implementation can derive reasonable input parameters, that composition heterogeneity can be estimated based on contrast loss, and that the reconstruction can be modified accordingly to emulate altered constituent occupancy. This stands to benefit conventionally employed maximum-likelihood classification methods, whereas we here limit considerations to cryo-EM map interpretation, quantification, and particle-image signal subtraction

Cryo-EM reconstruction of the chlororibosome to 3.2 Å resolution within 24 h

The introduction of direct detectors and the automation of data collection in cryo-EM have led to a surge in data, creating new opportunities for advancing computational processing. In particular, on-the-fly workflows that connect data collection with three-dimensional reconstruction would be valuable for more efficient use of cryo-EM and its application as a sample-screening tool. Here, accelerated on-the-fly analysis is reported with optimized organization of the data-processing tools, image acquisition and particle alignment that make it possible to reconstruct the three-dimensional density of the 70S chlororibosome to 3.2 Å resolution within 24 h of tissue harvesting. It is also shown that it is possible to achieve even faster processing at comparable quality by imposing some limits to data use, as illustrated by a 3.7 Å resolution map that was obtained in only 80 min on a desktop computer. These on-the-fly methods can be employed as an assessment of data quality from small samples and extended to high-throughput approaches