Resonance Raman spectroscopy and density functional theory calculation study of photodecay dynamics of tetra(4-carboxyphenyl) porphyrin

The 397.9 nm, 416.0 nm and 435.7 nm resonance Raman spectra were acquired for meso-tetrakis(4-carboxyphenyl)porphyrin (TCPP) in tetrahydrofuran solution, and the Raman effect of relaxation dynamics was analyzed according to Herzberg-Teller (vibronic coupling) contributions. Density functional calculations were done to help the elucidation of the Soret (B(x) and B(y)-band) electronic transitions and the corresponding photo relaxation dynamics of TCPP. The spectra indicate that the Franck-Condon region photo relaxation dynamics upon S(0) → S(4) electronic transition are predominantly along the totally symmetric C(m)-ph stretch and Porphin ring breath stretch, and simultaneously along the asymmetric ν(C(m)-Phenyl) + δ(N-H) and ν(C(α)-C(m)-C(α))(as) + def (pyr) vibrational relaxation processes. The excited state structural dynamics of TCPP determined from the resonance Raman spectra show that the internal conversion between the B(y) and B(x) electronic states occurs in tens of femtoseconds, and the electronic relaxation dynamics were firstly interpreted taking into account the time-dependent wave packet theory and Herzberg-Teller (vibronic coupling) contributions.     

High-performance scalable molecular dynamics simulations of a polarizable force field based on classical Drude oscillators in NAMD

Incorporating the influence of induced polarization in large-scale atomistic molecular dynamics (MD) simulations is a critical challenge in the progress toward computations of increased accuracy. One computationally efficient treatment is based on the classical Drude oscillator in which an auxiliary charged particle is attached by a spring to each nucleus. Here, we report the first implementation of this model in the program NAMD. An extended Lagrangian dynamics with a dual-Langevin thermostat scheme applied to the Drude-nucleus pairs is employed to efficiently generate classical dynamic propagation near the self-consistent field limit. Large-scale MD simulations based on the Drude polarizable force field scale very well on massively distributed supercomputing platforms, the computational demand being only about 50-100% higher than for nonpolarizable models. As an illustration, a large-scale 150 mM NaCl aqueous salt solution is simulated, and the calculated ionic conductivity is shown to be in excellent agreement with experiment.     

Crystallographic snapshots of tyrosine phenol-lyase show that substrate strain plays a role in C-C bond cleavage

The key step in the enzymatic reaction catalyzed by tyrosine phenol-lyase (TPL) is reversible cleavage of the Cβ-Cγ bond of L-tyrosine. Here, we present X-ray structures for two enzymatic states that form just before and after the cleavage of the carbon-carbon bond. As for most other pyridoxal 5'-phosphate-dependent enzymes, the first state, a quinonoid intermediate, is central for the catalysis. We captured this relatively unstable intermediate in the crystalline state by introducing substitutions Y71F or F448H in Citrobacter freundii TPL and briefly soaking crystals of the mutant enzymes with a substrate 3-fluoro-L-tyrosine followed by flash-cooling. The X-ray structures, determined at ~2.0 ? resolution, reveal two quinonoid geometries: "relaxed" in the open and "tense" in the closed state of the active site. The "tense" state is characterized by changes in enzyme contacts made with the substrate's phenolic moiety, which result in significantly strained conformation at Cβ and Cγ positions. We also captured, at 2.25 ? resolution, the X-ray structure for the state just after the substrate's Cβ-Cγ bond cleavage by preparing the ternary complex between TPL, alanine quinonoid and pyridine N-oxide, which mimics the α-aminoacrylate intermediate with bound phenol. In this state, the enzyme-ligand contacts remain almost exactly the same as in the "tense" quinonoid, indicating that the strain induced by the closure of the active site facilitates elimination of phenol. Taken together, structural observations demonstrate that the enzyme serves not only to stabilize the transition state but also to destabilize the ground state.     

Structural basis of the antiproliferative activity of largazole, a depsipeptide inhibitor of the histone deacetylases

Largazole is a macrocyclic depsipeptide originally isolated from the marine cyanobacterium Symploca sp., which is indigenous to the warm, blue-green waters of Key Largo, Florida (whence largazole derives its name). Largazole contains an unusual thiazoline-thiazole ring system that rigidifies its macrocyclic skeleton, and it also contains a lipophilic thioester side chain. Hydrolysis of the thioester in vivo yields largazole thiol, which exhibits remarkable antiproliferative effects and is believed to be the most potent inhibitor of the metal-dependent histone deacetylases (HDACs). Here, the 2.14 ?-resolution crystal structure of the HDAC8-largazole thiol complex is the first of an HDAC complexed with a macrocyclic inhibitor and reveals that ideal thiolate-zinc coordination geometry is the key chemical feature responsible for its exceptional affinity and biological activity. Notably, the core structure of largazole is conserved in romidepsin, a depsipeptide natural product formulated as the drug Istodax recently approved for cancer chemotherapy. Accordingly, the structure of the HDAC8-largazole thiol complex is the first to illustrate the mode of action of a new class of therapeutically important HDAC inhibitors.     

Phosphate uptake by TiO2: batch studies and NMR spectroscopic evidence for multisite adsorption

Systematic studies, combining batch experiments with NMR spectroscopic methods, are carried out for phosphate sorption on titanium dioxide (TiO(2)). It is found that phosphate sorption on TiO(2) decreases with increasing pH, whereas the phosphate uptake by TiO(2) increases with increasing ionic strength of the solution. In I ≤ 0.1 M, the sorption sharply increases and reaches a near maximum and then followed by little changes showing Langmuir-type behavior, whereas in I = 0.7 M, non-Langmuirian uptake becomes evident as equilibrium phosphate concentrations increase in solution. The sorption of phosphate on TiO(2) is rapid and mostly irreversible at pH 4.5 and 7.0. At pH 9.0, however, the phosphate sorption is initially reversible and followed by resorption of phosphate on TiO(2) at the system re-equilibration. (31)P{(1)H} cross-polarization and magic angle spinning (CP/MAS) NMR spectra contain at least four main peaks which appear similar in position and width under all adsorption conditions, but vary in intensity with surface loading. The spectral characteristics of these peaks, including cross-polarization dynamics and chemical shift anisotropy obtained from spinning sideband analysis, suggest that they arise from distinct inner-sphere adsorption complexes, most of which are protonated. These results indicate that uptake of phosphate by TiO(2) occurs by formation of several types of surface complexes.     

Pseudo-random number generation for Brownian Dynamics and Dissipative Particle Dynamics simulations on GPU devices

Brownian Dynamics (BD), also known as Langevin Dynamics, and Dissipative Particle Dynamics (DPD) are implicit solvent methods commonly used in models of soft matter and biomolecular systems. The interaction of the numerous solvent particles with larger particles is coarse-grained as a Langevin thermostat is applied to individual particles or to particle pairs. The Langevin thermostat requires a pseudo-random number generator (PRNG) to generate the stochastic force applied to each particle or pair of neighboring particles during each time step in the integration of Newton’s equations of motion. In a Single-Instruction-Multiple-Thread (SIMT) GPU parallel computing environment, small batches of random numbers must be generated over thousands of threads and millions of kernel calls. In this communication we introduce a one-PRNG-per-kernel-call-per-thread scheme, in which a micro-stream of pseudorandom numbers is generated in each thread and kernel call. These high quality, statistically robust micro-streams require no global memory for state storage, are more computationally efficient than other PRNG schemes in memory-bound kernels, and uniquely enable the DPD simulation method without requiring communication between threads.     

Optical Characterization of Optofluidic Waveguides Using Scattered Light Imaging

The use of scattered light images is shown to be an attractive method for the characterization of optofluidic waveguides. The method is shown to be capable of measuring waveguide propagation losses and transmissions between solid and liquid-core structures. Measurement uncertainties are considered and characterized and were typically less than 15%.     

Transverse beam spin asymmetries at backward angles in elastic electron-proton and quasielastic electron-deuteron scattering

We have measured the beam-normal single-spin asymmetries in elastic scattering of transversely polarized electrons from the proton, and performed the first measurement in quasielastic scattering on the deuteron, at backward angles (lab scattering angle of 108°) for Q2 = 0.22 GeV2/c2 and 0.63 GeV2/c2 at beam energies of 362 and 687 MeV, respectively. The asymmetry arises due to the imaginary part of the interference of the two-photon exchange amplitude with that of single-photon exchange. Results for the proton are consistent with a model calculation which includes inelastic intermediate hadronic (πN) states. An estimate of the beam-normal single-spin asymmetry for the scattering from the neutron is made using a quasistatic deuterium approximation, and is also in agreement with theory.     

Efficiency pedestal in quasi-phase-matching devices with random duty-cycle errors

It is shown that random duty-cycle errors in quasi-phase-matching (QPM) nonlinear optical devices enhance the efficiency of processes far from the QPM peak. An analytical theory is shown to agree well with numerical solutions of second-harmonic generation (SHG) in disordered QPM gratings. The measured efficiency of 1550?nm band SHG in a periodically poled lithium niobate (PPLN) waveguide away from the QPM peak agrees with observations of domain disorder in a PPLN wafer by Zygo interferometry. If suppression of parasitic nonlinear interactions is important in a specific application of QPM devices, control of random duty-cycle errors is critical.     

CARIBU: a new facility for the study of neutron-rich isotopes

The Californium Rare Ion Breeder Upgrade (CARIBU) to the ATLAS superconducting linac facility is currently being commissioned. It provides low-energy and re-accelerated beams of neutron-rich isotopes obtained from ²⁵²Cf fission. The fission products from a ²⁵²Cf source are stopped in a large high-intensity gas catcher, thermalized and extracted through an RFQ cooler, accelerated to 50 kV and mass separated in a high-resolution separator before being sent to either an ECR charge breeder for post-acceleration through the ATLAS linac or to a low-energy experimental area. This approach gives access to beams of very neutron-rich isotopes, many of which have not been available at low or Coulomb barrier energies previously. These beams provide unique opportunities for measurements along the r-process path. To take advantage of these unique possibility, the reaccelerated beams from CARIBU will be made available at the experimental stations of ATLAS to serve equipment such as Gammasphere, HELIOS and the reaction spectrometers. In addition, the Canadian Penning Trap (CPT) mass spectrometer has been moved to the CARIBU low-energy experimental area and a new injection line has been built. The new injection line consists of a RFQ buncher sitting on a 50 kV high-voltage platform that will accumulate the mass separated 50 kV radioactive beams, cool and extract them as a pulsed beam of 3 keV. This beam can be sent either to a tape station for diagnostics and tuning, or a cryogenic linear trap for preparation before transfer to the high-precision Penning trap where the mass measurements will take place. Initial CARIBU commissioning is proceeding with a 2 mCi source that will be replaced by a 100 mCi source as the commissioning proceeds. Final operation will use a 1 Ci source and attain yield in excess of 10⁷ ions/sec for the most intense beams at low energy, an order of magnitude less for reaccelerated beams.