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https://www.readbyqxmd.com/read/28651057/how-to-identify-plasmons-from-the-optical-response-of-nanostructures
#1
Runmin Zhang, Luca Bursi, Joel D Cox, Yao Cui, Caroline M Krauter, Alessandro Alabastri, Alejandro Manjavacas, Arrigo Calzolari, Stefano Corni, Elisa Molinari, Emily A Carter, F Javier Garcia de Abajo, Hui Zhang, Peter Nordlander
A promising trend in plasmonics involves shrinking the size of plasmon-supporting structures down to a few nanometers, thus enabling control over light-matter interaction at extreme-subwavelength scales. In this limit, quantum-mechanical effects, such as nonlocal screening and size quantization, strongly affect the plasmonic response, rendering it substantially different from classical predictions. For very small clusters and molecules, collective plasmonic modes are hard to distinguish from other excitations such as single-electron transitions...
June 26, 2017: ACS Nano
https://www.readbyqxmd.com/read/28648259/semisynthesis-and-spectral-characterization-of-5-methylpyranopelargonidin-and-4-methylfuropelargonidin-and-their-separation-and-detection-in-strawberry-fruit-wine
#2
Ondřej Kurka, Lukáš Kučera, Helena Pelantová, Marek Kuzma, Vladimír Havlíček, Petr Bednář
Condensation of anthocyanins and their aglycons with small organic molecules yields more stable natural dyes, e.g. pyranoanthocyanins arising spontaneously in various food products. Reaction of pelargonidin with acetone produces two isomeric anthocyanidin dyes - 5-methylpyranopelargonidin and 4-methylfuropelargonidin. A robust semipreparative liquid chromatographic method was developed to isolate both derivatives from a simple aged solution of pelargonidin in methanol: acetone: 37% aqueous hydrochloric acid (1:1:0...
June 17, 2017: Journal of Chromatography. A
https://www.readbyqxmd.com/read/28648071/elucidation-of-the-catalytic-mechanism-of-a-miniature-zinc-finger-hydrolase
#3
Abir Ganguly, Trung Quan Luong, Oliver Brylski, Michael Dirkmann, David Möller, Simon Ebbinghaus, Frank Schulz, Roland Winter, Elsa Sanchez-Garcia, Walter Thiel
To improve our mechanistic understanding of zinc metalloenzymes, we report a joint computational and experimental study of a minimal carbonic anhydrase (CA) mimic, a 22-residue Zn-finger hydrolase. We combine classical molecular dynamics (MD) simulations, quantum mechanics/molecular mechanics (QM/MM) geometry optimizations, and QM/MM free energy simulations with ambient and high-pressure kinetic measurements to investigate the mechanism of the hydrolysis of the substrate p-nitrophenylacetate (pNPA). The zinc center of the hydrolase prefers a pentacoordinated geometry, as found in most naturally occurring CAs and CA-like enzymes...
June 24, 2017: Journal of Physical Chemistry. B
https://www.readbyqxmd.com/read/28644616/importance-of-a-fully-anharmonic-treatment-of-equilibrium-isotope-fractionation-properties-of-dissolved-ionic-species-as-evidenced-by-li-aq
#4
Romain Dupuis, Magali Benoit, Mark E Tuckerman, Merlin Méheut
Equilibrium fractionation of stable isotopes is critically important in fields ranging from chemistry, including medicinal chemistry, electrochemistry, geochemistry, and nuclear chemistry, to environmental science. The dearth of reliable estimates of equilibrium fractionation factors, from experiment or from natural observations, has created a need for accurate computational approaches. Because isotope fractionation is a purely quantum mechanical phenomenon, exact calculation of fractionation factors is nontrivial...
June 23, 2017: Accounts of Chemical Research
https://www.readbyqxmd.com/read/28643778/a-decoherence-free-subspace-in-a-charge-quadrupole-qubit
#5
Mark Friesen, Joydip Ghosh, M A Eriksson, S N Coppersmith
Quantum computing promises significant speed-up for certain types of computational problems. However, robust implementations of semiconducting qubits must overcome the effects of charge noise that currently limit coherence during gate operations. Here we describe a scheme for protecting solid-state qubits from uniform electric field fluctuations by generalizing the concept of a decoherence-free subspace for spins, and we propose a specific physical implementation: a quadrupole charge qubit formed in a triple quantum dot...
June 23, 2017: Nature Communications
https://www.readbyqxmd.com/read/28641435/validating-and-implementing-modified-filinov-phase-filtration-in-semiclassical-dynamics
#6
Matthew S Church, Sergey V Antipov, Nandini Ananth
The Mixed Quantum-Classical Initial Value Representation (MQC-IVR) is a recently introduced approximate semiclassical (SC) method for the calculation of real-time quantum correlation functions. MQC-IVR employs a modified Filinov filtration (MFF) scheme to control the overall phase of the SC integrand, extending the applicability of SC methods to complex systems while retaining their ability to accurately describe quantum coherence effects. Here, we address questions regarding the effectiveness of the MFF scheme in combination with SC dynamics...
June 21, 2017: Journal of Chemical Physics
https://www.readbyqxmd.com/read/28640604/parametrizaton-of-a-reactive-force-field-reaxff-for-molecular-dynamics-simulations-of-si-nanoparticles
#7
Giovanni Barcaro, Susanna Monti, Luca Sementa, Vincenzo Carravetta
A novel computational approach, based on classical reactive molecular dynamics simulations (RMD) and quantum chemistry (QC) global energy optimizations, is proposed for modelling large Si nanoparticles. The force field parameters, which can describe bond breaking and formation, are derived by reproducing energetic and structural properties of a set of Si clusters increasing in size. These reference models are obtained through a new protocol based on a joint high temperature RMD/low temperature Basin Hopping QC search...
June 22, 2017: Journal of Chemical Theory and Computation
https://www.readbyqxmd.com/read/28640186/analysis-of-serotonin-molecules-on-silver-nanocolloids-a-raman-computational-and-experimental-study
#8
Felicia S Manciu, John D Ciubuc, Emma M Sundin, Chao Qiu, Kevin E Bennet
Combined theoretical and experimental analysis of serotonin by quantum chemical density functional calculations and surface-enhanced Raman spectroscopy, respectively, is presented in this work to better understand phenomena related to this neurotransmitter's detection and monitoring at very low concentrations specific to physiological levels. In addition to the successful ultrasensitive analyte detection on silver nanoparticles for concentrations as low as 10(-11) molar, the relatively good agreement between the simulated and experimentally determined results indicates the presence of all serotonin molecular forms, such as neutral, ionic, and those oxidized through redox reactions...
June 22, 2017: Sensors
https://www.readbyqxmd.com/read/28639614/a-coherent-quantum-annealer-with-rydberg-atoms
#9
A W Glaetzle, R M W van Bijnen, P Zoller, W Lechner
There is a significant ongoing effort in realizing quantum annealing with different physical platforms. The challenge is to achieve a fully programmable quantum device featuring coherent adiabatic quantum dynamics. Here we show that combining the well-developed quantum simulation toolbox for Rydberg atoms with the recently proposed Lechner-Hauke-Zoller (LHZ) architecture allows one to build a prototype for a coherent adiabatic quantum computer with all-to-all Ising interactions and, therefore, a platform for quantum annealing...
June 22, 2017: Nature Communications
https://www.readbyqxmd.com/read/28636392/hybrid-cpu-gpu-integral-engine-for-strong-scaling-ab-initio-methods
#10
Jörg Kussmann, Christian Ochsenfeld
We present a parallel integral algorithm for two-electron contributions occurring in Hartree-Fock and hybrid density functional theory that allows for a strong scaling parallelization on inhomogeneous compute clusters. With a particular focus on graphic processing units, we show that our approach allows an efficient use of CPUs and graphics processing units (GPUs) simultaneously, although the different architectures demand conflictive strategies in order to ensure efficient program execution. Furthermore, we present a general strategy to use large basis sets like quadruple-ζ split valence on GPUs and investigate the balance between CPUs and GPUs depending on l-quantum numbers of the corresponding basis functions...
June 21, 2017: Journal of Chemical Theory and Computation
https://www.readbyqxmd.com/read/28635268/isotope-controlled-selectivity-by-quantum-tunneling-hydrogen-migration-versus-ring-expansion-in-cyclopropylmethylcarbenes
#11
Ashim Nandi, Dennis Gerbig, Peter R Schreiner, Weston Thatcher Borden, Sebastian Kozuch
Using the tunneling-controlled reactivity of cyclopropylmethylcar-bene, we demonstrate the viability of isotope-controlled selectivity (ICS), a novel non-classical control element of chemical reactivity where a molecular system with two conceivable products of tunneling exclusively produces one or the other, depending only on isotopic composition. Our multidimensional small-curvature tunneling (SCT) computations indicate that under cryogenic conditions, 1-methoxycyclopropylmethylcarbene shows rapid H-migration to 1-methoxy-1-vinylcyclopropane, whereas deuterium-substituted 1-methoxycyclopropyl-d3-methylcarbene undergoes ring expansion to 1-d3-methylcyclobutene...
June 21, 2017: Journal of the American Chemical Society
https://www.readbyqxmd.com/read/28632395/design-synthesis-and-multitarget-biological-profiling-of-second-generation-anti-alzheimer-rhein-huprine-hybrids
#12
Francisco Javier Pérez-Areales, Nibal Betari, Antonio Viayna, Caterina Pont, Alba Espargaró, Manuela Bartolini, Angela De Simone, José Fernando Rinaldi Alvarenga, Belén Pérez, Raimon Sabate, Rosa Maria Lamuela-Raventós, Vincenza Andrisano, Francisco Javier Luque, Diego Muñoz-Torrero
AIM: Simultaneous modulation of several key targets of the pathological network of Alzheimer's disease (AD) is being increasingly pursued as a promising option to fill the critical gap of efficacious drugs against this condition. MATERIALS & METHODS: A short series of compounds purported to hit multiple targets of relevance in AD has been designed, on the basis of their distinct basicities estimated from high-level quantum mechanical computations, synthesized, and subjected to assays of inhibition of cholinesterases, BACE-1, and Aβ42 and tau aggregation, of antioxidant activity, and of brain permeation...
June 20, 2017: Future Medicinal Chemistry
https://www.readbyqxmd.com/read/28632392/lewis-acid-promoted-hydrogenation-of-co2-and-hcoo-by-amine-boranes-mechanistic-insight-from-computational-approach
#13
Lisa Roy, Boyli Ghosh, Ankan Paul
We employ quantum chemical calculations to study the hydrogenation of carbon dioxide by amine-boranes, NMe3BH3 ((Me3)AB) and NH3BH3 (AB) weakly bonded to a bulkier Lewis acid, Al(C6F5)3 (LA). Additionally, computations has also been conducted to elucidate the mechanism of hydrogenation of carbon dioxide by (Me3)AB while captured between one Lewis Base (P(o-tol3), (LB)) and two Lewis acids, Al(C6F5)3. In agreement to the experiments, our computational study predicts that hydride transfer to conjugated HCO2(‒), generated in the reaction of (Me3)AB-LA with CO2, is not feasible...
June 20, 2017: Journal of Physical Chemistry. A
https://www.readbyqxmd.com/read/28632384/finite-field-method-for-nonlinear-optical-property-prediction-using-rational-function-approximants
#14
Anand H G Patel, Ahmed A K Mohammed, Peter A Limacher, Paul Woodson Ayers
The finite-field (FF) method is a quick, easy-to-implement tool for the prediction of nonlinear optical properties. Here, we present and explore a novel variant of the FF method, which uses a rational function to fit a molecule's energy with respect to an electric field. Similarly to previous FF methods, factors crucial for the method's accuracy were tuned. These factors include: the number of terms in the function, the distribution of fields used to construct the approximation, and the initial field in the approximation...
June 20, 2017: Journal of Physical Chemistry. A
https://www.readbyqxmd.com/read/28632381/molecular-modeling-of-the-interactions-between-carborane-containing-analogs-of-indomethacin-and-cyclooxygenase-2
#15
Menyhárt-Botond Sárosi, Wilma Neumann, Terry P Lybrand, Evamarie Hey-Hawkins
Molecular modeling studies were performed in order to gain insight into the binding mode and interaction of carborane-containing derivatives of indomethacin methyl ester with the cyclooxygenase 2 (COX 2) isoform, and to assess the predictive capability of the computational tools available for studying carboranes, a unique class of pharmacophores. Docking simulations were able to identify the correct binding mode and reproduced the experimental binding affinity trends with encouraging quality. Nevertheless, the docking results needed to be verified through extensive and resource intensive quantum chemical calculations, and the interpretation of the theoretical results would not have been straightforward without the supporting experimental data...
June 20, 2017: Journal of Chemical Information and Modeling
https://www.readbyqxmd.com/read/28630971/2-thiouracil-intersystem-crossing-photodynamics-studied-by-wavelength-dependent-photoelectron-and-transient-absorption-spectroscopies
#16
José A Sánchez-Rodríguez, Abed Mohamadzade, Sebastian Mai, Brennan Ashwood, Marvin Pollum, Philipp Marquetand, Leticia González, Carlos E Crespo-Hernández, Susanne Ullrich
Single-atom substitution within a natural nucleobase-such as replacing oxygen by sulfur in uracil-can result in drastic changes in the relaxation dynamics after UV excitation. While the photodynamics of natural nucleobases like uracil are dominated by pathways along singlet excited states, the photodynamics of thiobases like 2-thiouracil populate the triplet manifold with near unity quantum yield. In the present study, a synergistic approach based on time-resolved photoelectron spectroscopy (TRPES), time-resolved absorption spectroscopy (TRAS), and ab initio computations has been particularly successful at unraveling the underlying photophysical principles and describing the dissimilarities between the natural and substituted nucleobases...
June 20, 2017: Physical Chemistry Chemical Physics: PCCP
https://www.readbyqxmd.com/read/28628316/soft-sphere-continuum-solvation-in-electronic-structure-calculations
#17
Giuseppe Fisicaro, Luigi Genovese, Oliviero Andreussi, Sagarmoy Mandal, Nisanth N Nair, Nicola Marzari, Stefan Goedecker
We present an implicit solvation approach where the interface between the quantum-mechanical solute and the surrounding environment is described by a fully continuous permittivity built up with atomic-centered ``soft'' spheres. This approach combines many of the advantages of the self-consistent continuum solvation model in handling solutes and surfaces in contact with complex dielectric environments or electrolytes in electronic-structure calculations. In addition it is able to describe accurately both neutral and charged systems...
June 19, 2017: Journal of Chemical Theory and Computation
https://www.readbyqxmd.com/read/28627890/improved-description-of-sulfur-charge-anisotropy-in-opls-force-fields-model-development-and-parameterization
#18
Xin Cindy Yan, Michael J Robertson, Julian Tirado-Rives, William L Jorgensen
The atomic point-charge model used in most molecular mechanics force fields does not represent well the electronic anisotropy that is featured in many directional non-covalent interactions. Sulfur participates in several types of such interactions with its lone pairs and σ-holes. The current study develops new models, via the addition of off-atom charged sites, for a variety of sulfur compounds in the OPLS-AA and OPLS/CM5 force fields to address the lack of charge anisotropy. Parameter optimization is carried out to reproduce liquid-state properties, torsional and non-covalent energetics from reliable quantum mechanical calculations, and electrostatic potentials...
June 19, 2017: Journal of Physical Chemistry. B
https://www.readbyqxmd.com/read/28626246/the-complexity-of-divisibility
#19
Johannes Bausch, Toby Cubitt
We address two sets of long-standing open questions in linear algebra and probability theory, from a computational complexity perspective: stochastic matrix divisibility, and divisibility and decomposability of probability distributions. We prove that finite divisibility of stochastic matrices is an NP-complete problem, and extend this result to nonnegative matrices, and completely-positive trace-preserving maps, i.e. the quantum analogue of stochastic matrices. We further prove a complexity hierarchy for the divisibility and decomposability of probability distributions, showing that finite distribution divisibility is in P, but decomposability is NP-hard...
September 1, 2016: Linear Algebra and its Applications
https://www.readbyqxmd.com/read/28625051/excited-state-deactivation-pathways-and-the-photocyclization-of-bn-doped-polyaromatics
#20
Joshua A Snyder, Peter Grüninger, Holger F Bettinger, Arthur E Bragg
Boron-nitrogen doping of polyaromatic hydrocarbons (PAH), such as borazine-core hexabenzocoronene, presents possibilities for tuning the properties of organic electronics and nanographene materials while preserving structural characteristics of pure hydrocarbons. Previous photochemical studies have demonstrated extension of a borazine-core PAH network (1,2:3,4:5,6 tris(o,o'-biphenylylene) borazine, 1) by photoinduced cyclodehydrogenation. We present steady-state and fs-to-μs resolved spectroscopic studies of the photophysics of 1 and a related borazine-core PAH in order to characterize competing excited-state relaxation pathways that determine the efficacy of bond formation by photocyclization...
June 18, 2017: Journal of Physical Chemistry. A
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