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Amber is a molecular dynamics (MD) software package first conceived by Peter Kollman, his lab and collaborators to simulate biomolecular systems. The pmemd module is available as a serial version for central processing units (CPUs), NVIDIA and Advanced Micro Devices (AMD) graphics processing unit (GPU) versions as well as Message Passing Interface (MPI) parallel versions. Advanced capabilities include thermodynamic integration, replica exchange MD and accelerated MD methods. A brief update to the software and recently added capabilities is described in this Application Note. 

Herein reported is a strategy for constructing vicinal 4°/3° carbons via reductive Cope rearrangement. Substrates have been designed which exhibit Cope rearrangement kinetic barriers of ∼23 kcal mol −1 with isoenergetic favorability (Δ G ∼ 0). These fluxional/shape-shifting molecules can be driven forward by chemoselective reduction to useful polyfunctionalized building blocks. 

Light-harvesting and intramolecular energy funneling are fundamental processes in natural photosynthesis. A comprehensive knowledge of the main structural, dynamic, and optical properties that regulate the efficiency of such processes can be deciphered through the study of artificial light-harvesting antennas, capable of mimicking natural systems. Dendrimers are some of the most explored artificial light-harvesting molecules. However, they have to be well-defined and highly branched conjugated structures, creating intramolecular energy gradients that guarantee efficient and unidirectional energy transfer. Herein, we explore the contributions of the different mechanisms responsible for the highly efficient energy funneling in a large, complex poly(phenylene–ethynylene) dendrimer, whose architecture was particularly designed to conduct the initially absorbed photons toward a spatially localized energy sink away from its surface, avoiding its quenching by the environment. For this purpose, the nonradiative photoinduced energy relaxation and redistribution are simulated by using nonadiabatic excited state molecular dynamics. In this way, the two possible direct and indirect pathways for exciton migrations, previously reported by time-resolved spectroscopy, are defined. Our results stimulate future developments of new synthetic dendrimers for applications in molecular-based photonic devices in which an enhancement in the photoemission efficiency can be predicted by changes in the detailed balance between the different intramolecular energy transfer pathways. 

In the Big Data era, a change of paradigm in the use of molecular dynamics is required. Trajectories should be stored under FAIR (findable, accessible, interoperable and reusable) requirements to favor its reuse by the community under an open science paradigm. 

Explored was the competitive ring-closing metathesis vs. ring-rearrangement metathesis of bicyclo[3.2.1]octenes prepared by a simple and convergent synthesis from bicyclic alkylidenemalono-nitriles and allylic electrophiles. It was uncovered that ring-closing metathesis occurs exclusively on the tetraene-variant, yielding unique, stereochemically and functionally rich polycyclic bridged frameworks, whereas the reduced version (a triene) undergoes ring-rearrangement metathesis to 5 – 6 – 5 fused ring systems resembling the isoryanodane core.