Atomistic QM/MM simulations have been carried out on the complete photocycle of Photoactive Yellow Protein, a bacterial photoreceptor, in which blue light triggers isomerization of a covalently bound chromophore. The "chemical role" of the protein cavity in the control of the photoisomerization step has been elucidated. Isomerization is facilitated due to preferential electrostatic stabilizatio...

We propose a new scheme of the photoactivation and the photobleaching for Dronpa with molecular dynamics method and density functional theory. These processes can be explained by considering cis-trans isomerization in neutral state of chromophore. The proton transfer from anionic to neutral chromophore makes cis-trans isomerization possible via hula-twist rotation process, since the space for c...

We have simulated the isomerization of 38-atom Lennard-Jones clusters (LJ38) – a well-known prototype system for global-optimization and energy landscape analyses – over a wide range of temperatures using a combination of molecular dynamics (MD) and temperature accelerated dynamics (TAD). At high temperatures, we find that (surprisingly) MD with steepest descent quenches (MDSDQ) is effective fo...

Partially deuterated protonated water dimers, H2O·H(+)·D2O, H2O·D(+)·HDO, and HDO·H(+)·HDO, as important intermediates of isotopic labeled reaction of H3O(+) + D2O, undergo direct dissociation and indirect dissociation, i.e., isomerization before the dissociation. With Rice-Ramsperger-Kassel-Marcus theory and ab initio calculations, we have computed their dissociation and isomerization rate con...

The rearrangements for 2-phospha-4-silabicyclo[1.1.0]butane, analogous to the valence isomerization of the hydrocarbons bicyclobutane, 1,3-butadiene, and cyclobutene, were studied at the (U)QCISD(T)/6-311+G**//(U)QCISD/6-31G* level of theory. The monocyclic 1,2-dihydro-1,2-phosphasiletes are shown to be the thermodynamically preferred product, in contrast to the isomerization of the hydrocarbon...

Isomerization of glucose to fructose is a key reaction step in the efficient production valuable renewable chemical intermediates from biomass. Zeolites have been widely used promote isomerization, but only limited structure-activity relationship has established and applied optimize reaction. In this work, commercial Y zeolites were modified by alkaline-treatment their physicochemical propertie...

Classical simulations of the reactions between HCO+/COH+ and hydrogen atoms, as well as their deuterated variants, have been carried out on an ab initio interpolated potential energy surface. The surface is constructed at the quadratic configuration interaction with single and double excitation level of ab initio calculation. At low energies we observe reaction channels associated with the isom...

*Correspondence to: Alessandro A Sartori; Email: [email protected] Submitted: 06/18/13; Accepted: 06/20/13 http://dx.doi.org/10.4161/cc.26077 Comment on: Steger M, et al. Mol Cell 2013; 50:333-43; PMID:23623683; http://dx.doi.org/10.1016/j.molcel.2013.03.023 The repair of DNA double-strand breaks (DSBs) is highly complex. To maintain genome integrity and avoid tumorigenesis, cells choreograph...