English (United Kingdom)

https://curated-unify.zendy.io/wp-json/zendy-region/v1/featured_content/oa?rat=en

https://curated-unify.zendy.io/wp-json/zendy-region/v1/highlighted_journal/

Global: Zendy Plus annual

Presents the access of premium content as premium feature

Premium Content

Presents the keyphrase highlighting as premium feature

Keyphrase Highlighting

Presents the summarisation as premium feature

Summarisation

Insights

Presents the pdf analysis as premium feature

PDF Analysis

Presents the zaia usage as premium feature

ZAIA

Global: Zendy Tools annual

Global: Zendy Free Plan

Global: Zendy Tools monthly

Global: Zendy Plus monthly

Analytic second derivatives of electrostatic embedding (EE) quantummechanics/molecular mechanics (QM/MM) energy are important for performingvibrational analysis and simulating vibrational spectra of quantum systemsinteracting with an environment represented as a classical electrostaticpotential. The main bottleneck of EE-QM/MM second derivatives is the solutionof coupled perturbed equations for each MM atom perturbation. Here, we exploitthe Q-vector method {[J. Chem. Phys., 151, 041102 (2019)]} to workaround thisbottleneck. We derive the full analytic second derivative of the EE-QM/MMenergy, which allows to compute QM, MM and QM-MM Hessian blocks in an efficientand easy to implement manner. To show the capabilities of our method, wecompute the normal modes for the full \textit{arabidopsis thaliana} plantcryptochrome. We show that the flavin adenine dinucleotide vibrations (QMsubsystem) strongly mix with protein modes. We compute approximate vibroniccouplings for the lowest bright transition, from which we extract spectraldensities and the homogeneous broadening of FAD absorption spectrum in proteinusing vibrationally resolved electronic spectrum simulations.

Efficient analytic second derivative of electrostatic embedding QM/MM energy: normal mode analysis of plant cryptochrome