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 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...

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...

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 mono-metallic and bi-metallic catalysts have been prepared by impregnating with solutions containing a compound of h2ptcl6,wo3 and 1ml hcl (0.1 mol). it should be noted that the catalysts’ activity and selectivity have been determined under these conditions : 450-5000c ,and 15-25atm by h2. for converting n-heptane , the molar ratio h2/c7h16 is 5 , and lhsv is 1.5ml/h. it has been proved tha...

*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...

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...

RPE65 is essential for isomerization of vitamin A to the visual chromophore. Mutations in RPE65 cause early-onset blindness, and Rpe65-deficient mice lack 11-cis-retinal but overaccumulate alltrans-retinyl esters in the retinal pigment epithelium (RPE). RPE65 is proposed to be a substrate chaperone but may have an enzymatic role because it is closely related to carotenoid oxygenases. We hypothe...