Surface-enhanced Raman scattering (SERS) spectra of hemoglobin of mouse and rabbit with self-assembled nano-silver film

The nano-silver film was prepared by electrolysis method. Transmission electron microscopy (TEM) and scanning electron microscopy (SEM) were employed to detect the morphology of the nano-silver particles. The SERS spectra of the hemoglobin (rabbit and mouse) on nano-silver film were gained. It could be known from the SERS spectra that the nano-silver films could enhance the Raman signal of the hemoglobin efficiently, and the sodium citrate and PBS create no influence to the SERS spectra of the hemoglobin. Using this electrolysis technique to fabricate highly bio-active, stable, reusable, and low-cost SERS substrate will be useful in the development of hemoglobin detection. (C) 2013 Elsevier B.V. All rights reserved

Parallel Implementation of Density Functional Theory Methods in the Quantum Interaction Computational Kernel Program

We present the details of a GPU capable exchange correlation (XC) scheme integrated into the open source QUantum Interaction Computational Kernel (QUICK) program. Our implementation features an octree based numerical grid point partitioning scheme, GPU enabled grid pruning and basis/primitive function prescreening and fully GPU capable XC energy and gradient algorithms. Benchmarking against the CPU version demonstrated that the GPU implementation is capable of delivering an impres- sive performance while retaining excellent accuracy. For small to medium size protein/organic molecular systems, the realized speedups in double precision XC energy and gradient computation on a NVIDIA V100 GPU were 60 to 80-fold and 140 to 780- fold respectively as compared to the serial CPU implementation. The acceleration gained in density functional theory calculations from a single V100 GPU significantly exceeds that of a modern CPU with 40 cores running in parallel. </div

Effect of lithium ion doping on cubic Gd1.88Eu0.12O3: Enhancement of photoluminescence and thermal stability

Li+-doped cubic Gd1.88Eu0.12O3 powders were synthesized at 1200 degrees C by the solid state reaction method. Under excitation of the charge transfer band of Eu3+ at 245 nm, the Gd1.88Eu0.12O3 exhibited a dominant photoluminescence (PL) red emission peak at 611 nm, which is attributed to the electric dipole transition D-5(0) -> F-7(2) of Eu3+. The dominant PL red emission peak intensity increased with Li+ doping and reached a maximum in the range from 12 to 16 mol%. This intensity was approximately 3 times higher than that of undoped Gd1.88Eu0.12O3. Chemical composition analysis revealed that the Li+ species was completely evaporated from the samples by the heat treatment up to 1200 degrees C. However, during the heat treatment at 600-1000 degrees C, the doped Li+ could promote formation of a liquid phase, which enhanced the crystallite growth of cubic Gd1.28Eu0.12O3 by Ostwald ripening. The thermal stability of the cubic Gd1.88Eu0.12O3 was also improved with respect to the amount of Li+ doping. Even after annealing at 1300 degrees C (higher than the cubic/monoclinic phase transformation temperature of 1250 degrees C) for 72 h, X-ray diffraction pattern analysis indicated that the relative fraction of the cubic phase in the 12 mol% Li+-doped sample was as high as 90%. The relationship between the amount of Li+ doping and the asymmetric ratio evaluated for the PL emission spectrum and PL quantum efficiency of the cubic Gd1.88Eu0.12O3 samples suggested that, in addition to enhanced crystallite growth, the formation of additional oxygen vacancies promoted by Li+ doping contributed to simultaneous enhancement in the PL red emission intensity and the thermal stability of cubic Gd1.88Eu0.12O3 investigated in this study. (C) 2015 Elsevier B.V. All rights reserved

Conformational Analysis and Parallel QM/MM X‑ray Refinement of Protein Bound Anti-Alzheimer Drug Donepezil

The recognition and association of donepezil with acetylcholinesterase (AChE) has been extensively studied in the past several decades because of the former’s use as a palliative treatment for mild Alzheimer disease. Herein, we examine the conformational properties of donepezil and we re-examine the donepezil-AChE crystal structure using combined quantum mechanical/molecular mechanical (QM/MM) X-ray refinement tools. Donepezil’s conformational energy surface was explored using the M06 suite of density functionals and with the MP2/complete basis set (CBS) method using the aug-cc-pVXZ (<i>X</i> = D and T) basis sets. The donepezil-AChE complex (PDB 1EVE) was also rerefined through a parallel QM/MM X-ray refinement approach based on an in-house ab initio code QUICK, which uses the message passing interface (MPI) in a distributed SCF algorithm to accelerate the calculation via parallelization. In the QM/MM rerefined donepezil structure, coordinate errors that previously existed in the PDB deposited geometry were improved leading to an improvement of the modeling of the interaction between donepezil and the aromatic side chains located in the AChE active site gorge. As a result of the rerefinement there was a 93% reduction in the donepezil conformational strain energy versus the original PDB structure. The results of the present effort offer further detailed structural and biochemical inhibitor-AChE information for the continued development of more effective and palliative treatments of Alzheimer disease

Photoluminescence and cathodoluminescence properties of Li+ doped Gd1.88Eu0.12O3

Li+-doped cubic Gd1.88Eu0.12O3 phosphors were synthesized at 1200 degrees C in air by co-precipitation (CP) and solid state reaction (SS) methods. X-ray diffraction analysis revealed that, regardless of synthetic method, the average crystallite size for Li+-free Gd1.88Eu0.12O3 was approximately 400 nm, then increased with the amount of Li+ and at 20 mol%, reached about 2.3 mu m. Under excitation of the charge transfer band of Eu3+ at 245 nm, Gd1.88Eu0.12O3 exhibited a dominant photoluminescence (PL) red emission peak at 611 nm assigned to the electric dipole transition D-5(0) -> F-7(2) of Eu3+. The red emission peak intensity increased consistently with the amount of Li+-doping, while CP method was found to be effective in improving the red emission intensity at lower amounts of L-i+-doping from 0 to 8 mol%. Cathodoluminescence (CL) property was studied by mounting the synthesized phosphor on a vacuum fluorescent display (VFD) operated at an anode voltage of 50V. The Gd1.88Eu0.12O3 exhibited a similar spectrum with an intense red emission peak at 611 nm, and the highest luminance intensity for the CL red emission was achieved for 8 mol% Li+-doped Gd1.88Eu0.12O3 synthesized by SS method. The evaluation results of PL and CL properties suggested that, besides the crystallite size of Gd1.88Eu0.12O3, dispersion property of Eu3+ ions in the host Gd2O3 was an important factor for improving luminescent properties of Gd1.88Eu0.12O3. Moreover, under the present VFD operating condition at the low excitation voltage, it was thought to be essential for improving CL emission intensity to maintain a sufficient surface area of Gd1.88Eu0.12O3. (C)2015 The Ceramic Society of Japan. All rights reserved

Relationship between Eu3+ substitution sites and photoluminescence properties of SrIn2O4:Eu3+ spinel phosphors

Eu3+-doped SrIn2O4 phosphors were synthesized by the solid solution method at 1400 degrees C in air. The chemical composition of the phosphors was systematically changed to study the relation between the Eu3+ substitution site and photoluminescence (PL) properties. Under excitation of the F-7(0)-> L-5(6) transition of Eu3+ at 393 nm, the SrIn2O4:Eu3+ exhibited dominant red emission peaks at 611, 616 and 623 nm, which are attributed to the electric dipole transition D-5(0)-> F-7(2) of Eu3+. The results of X-ray diffraction analysis combined with PL spectroscopic analysis revealed that Eu3+ ions occupied two different crystallographic In3+ sites in the host SrIn2O4, while it was found to be impossible to substitute Sr2+ with Eu3+ prior to the Eu3+ substitution at the In3+ sites in the SrIn2O4. The intensity of the red emission peaks increased with the total amount of dopant Eu3+ ion at the two In3+ sites, and reached a maximum at 25 mol% Eu3+-doping (SrIn2-xO4:xEu(3+), x=0.25). Moreover, a small amount (< 10 mol%) of Eu3+ at the Sr2+ site in the SrIn2-xO4:xEu(3+) was found to contribute to enhance the red emission peak intensity at 616 nm. As a result, the highest red emission intensity evaluated as the total emission peak intensities at the 611, 616 and 623 nm was achieved for Sr0.92In1.75O4:0.33Eu(3+) in which Eu3+ ion concentrations at the In3+ and Sr2+ sites were simultaneously optimized as 25 and 8 mol%, respectively (Sr1-yIn2-xO4:(x+y)Eu3+, x=0.25, y=0.08). This red emission intensity was 2.2 times higher than that of the phosphor without contribution of the Eu3+ at the Sr2+ site (SrIn2-xO4:xEu(3+), x=0.25). The critical energy transfer distance of Eu3+ ion in the Sr0.92In1.75O4:0.33Eu(3+) phosphor was determined to be 0.817 nm, and the electric multipolar interaction was suggested as the dominant mechanism for concentration quenching of PL emission due to Eu3+ ions in the Eu3+-doped SrIn2O4 phosphors investigated in this study. (C) 2015 Elsevier B.V. All rights reserved

Catalytic Mechanism of Aromatic Prenylation by NphB

NphB is an aromatic prenyltransferase that catalyzes the attachment of a 10-carbon geranyl group to aromatic substrates. Importantly, NphB exhibits a rich substrate selectivity and product regioselectivity. A systematic computational study has been conducted in order to address several question associated with NphB-catalyzed geranylation. The reaction mechanism of the prenylation step has been characterized as a S_N1 type dissociative mechanism with a weakly stable carbocation intermediate. A novel π-chamber composed of Tyr121, Tyr216, and 1,6-DHN is found to be important in stabilizing the carbocation. The observed difference in the rates of product formation from 5- and 2-prenylation arises from the differing orientations of the aromatic substrate in the resting state. 4-Prenylation shares the same resting state with 5-prenylation, but the lower free energy barrier for carbocation formation makes the latter reaction more facile. The high free energy barrier associated with 7-prenylation is caused by the unfavorable orientation of 1,6-DHN in active site pocket, along with the difficulty of proton elimination after the prenylation step. A water-mediated proton transfer facilitates the loss of hydrogen at the prenylation site to form the final prenylated product. Interestingly, the same crystallographically observed water molecule has been found to be responsible for proton loss in all three experimentally identified products. After proton transfer, the relaxation of the final product from a sp³ carbon center to a sp² center triggers a “spring-loaded” product release mechanism which pushes the final product out of the binding pocket toward the edge of the active site. The hydrogen bond interactions between the two hydroxyl groups of the aromatic product and the side chains of Ser214 and Tyr288 help to “steer” the movement of the product. In addition, mutagenesis studies identify these same two side chains as being responsible for the observed regioselectivity, particularly 2-prenylation. These observations provide valuable insights into NphB chemistry, offering an opportunity to better engineer the active site and to control the reactivity in order to obtain high yields of the desired product(s). Furthermore, the S_N1 reaction mechanism observed for NphB differs from the prenylation reaction found in, for example, the farnesyltransferase, which proceeds via an S_N2-like reaction pathway. The spring-loaded release mechanism highlighted herein also offers novel insights into how enzymes facilitate product release

Mechanism of Formation of the Nonstandard Product in the Prenyltransferase Reaction of the G115T Mutant of FtmPT1: A Case of Reaction Dynamics Calling the Shots?

FtmPT1 is a fungal indole prenyltransferase that affords Tryprostatin B from Brevianamide F and dimethylallyl pyrophosphate; however, when a single residue in the active site is mutated (Gly115Thr), a novel five-membered ring compound is obtained as the major product with Tryprostatin B as the minor product. Herein, we describe detailed studies of the catalysis of the Gly115Thr mutant of FtmPT1 with a focus on the observed regioselectivity of the reaction. We employ one- and two-dimensional potential of mean force simulations to explore the catalytic mechanism, along with molecular dynamics simulations exploring the reaction dynamics of the prenyl transfer reaction. Single-point electronic structure calculations were also used to explore the performance of the self-consistent charge density functional tight-binding method to model specific reaction steps. Importantly, we observe that the two reaction pathways have comparable activation parameters and propose that the origin of the novel product is predicated, at least in part, on the topology of the potential energy surface as revealed by reaction dynamics studies

Solution-Processed VO2-SiO2 Composite Films with Simultaneously Enhanced Luminous Transmittance, Solar Modulation Ability and Anti-Oxidation property

Recently, researchers spare no efforts to fabricate desirable vanadium dioxide (VO2) film which provides simultaneously high luminous transmittance and outstanding solar modulation ability, yet progress towards the optimization of one aspect always comes at the expense of the other. Our research devotes to finding a reproducible economic solution-processed strategy for fabricating VO2-SiO2 composite films, with the aim of boosting the performance of both aspects. Compare to VO2 film, an improvement of 18.9% (from 29.6% to 48.5%) in the luminous transmittance as well as an increase of 6.0% (from 9.7% to 15.7%) in solar modulation efficiency is achieved when the molar ratio of Si/V attains 0.8. Based on the effective medium theory, we simulate the optical spectra of the composite films and the best thermochromic property is obtained when the filling factor attains 0.5, which is consistent with the experimental results. Meanwhile, the improvement of chemical stability for the composite film against oxidation has been confirmed. Tungsten is introduced to reduce the phase transition temperature to the ambient temperature, while maintain the thermochromism required for application as smart window. Our research set forth a new avenue in promoting practical applications of VO2-based thermochromic fenestration

Harnessing the Power of Multi-GPU Acceleration into the Quantum Interaction Computational Kernel Program

We report a new multi-GPU capable ab initio Hartree-Fock/density functional theory implementation integrated into the open source QUantum Interaction Computational Kernel (QUICK) program. Details on the load balancing algorithms for electron repulsion integrals and exchange correlation quadrature across multiple GPUs are described. Benchmarking studies carried out on up to 4 GPU nodes, each containing 4 NVIDIA V100-SMX2 type GPUs demonstrate that our implementation is capable of achiev- ing excellent load balancing and high parallel efficiency. For representative medium to large size protein/organic molecular sys- tems, the observed efficiencies remained above 86%. The accelerations on NVIDIA A100, P100 and K80 platforms also have real- ized parallel efficiencies higher than 74%, paving the way for large-scale ab initio electronic structure calculations.</div