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https://www.readbyqxmd.com/read/28820594/on-the-restrained-proton-indicator-in-combined-quantum-mechanics-molecular-mechanics-dynamics-simulations-of-proton-transfer-through-a-carbon-nanotube
#1
Adam W Duster, Hai Lin
Recently, a collective variable "proton indicator" was purposed for tracking an excess proton solvated in bulk water in molecular dynamics simulations. In this work, we demonstrate the feasibility of utilizing the position of this proton indicator as a reaction coordinate to model an excess proton migrating through a hydrophobic carbon nanotube in combined quantum-mechanics/molecular-mechanics simulations. Our results indicate that applying a harmonic restraint to the proton indicator in the bulk solvent near the nanotube pore entrance leads to the recruitment of water molecules into the pore...
August 18, 2017: Journal of Physical Chemistry. B
https://www.readbyqxmd.com/read/28820195/photoelectron-spectroscopy-of-isolated-luciferin-and-infraluciferin-anions-in-vacuo-competing-photodetachment-photofragmentation-and-internal-conversion
#2
Joanne L Woodhouse, Mariana Assmann, Michael A Parkes, Helen Grounds, Steven J Pacman, James C Anderson, Graham A Worth, Helen H Fielding
The electronic structure and excited-state dynamics of the ubiquitous bioluminescent probe luciferin and its furthest red-shifted analogue infraluciferin have been investigated using photoelectron spectroscopy and quantum chemistry calculations. In our electrospray ionization source, the deprotonated anions are formed predominantly in their phenolate forms and are directly relevant to studies of luciferin and infraluciferin as models for their unstable oxyluciferin and oxyinfraluciferin emitters. Following photoexcitation in the range 357-230 nm, we find that internal conversion from high-lying excited states to the S1(1ππ*) state competes efficiently with electron detachment...
August 18, 2017: Physical Chemistry Chemical Physics: PCCP
https://www.readbyqxmd.com/read/28818636/east-west-paths-to-unconventional-computing
#3
REVIEW
Andrew Adamatzky, Selim Akl, Mark Burgin, Cristian S Calude, José Félix Costa, Mohammad Mahdi Dehshibi, Yukio-Pegio Gunji, Zoran Konkoli, Bruce MacLennan, Bruno Marchal, Maurice Margenstern, Genaro J Martínez, Richard Mayne, Kenichi Morita, Andrew Schumann, Yaroslav D Sergeyev, Georgios Ch Sirakoulis, Susan Stepney, Karl Svozil, Hector Zenil
Unconventional computing is about breaking boundaries in thinking, acting and computing. Typical topics of this non-typical field include, but are not limited to physics of computation, non-classical logics, new complexity measures, novel hardware, mechanical, chemical and quantum computing. Unconventional computing encourages a new style of thinking while practical applications are obtained from uncovering and exploiting principles and mechanisms of information processing in and functional properties of, physical, chemical and living systems; in particular, efficient algorithms are developed, (almost) optimal architectures are designed and working prototypes of future computing devices are manufactured...
August 14, 2017: Progress in Biophysics and Molecular Biology
https://www.readbyqxmd.com/read/28817382/quantum-mechanical-force-fields-for-condensed-phase-molecular-simulations
#4
Timothy J Giese, Darrin M York
Molecular simulations are powerful tools for providing atomic-level details into complex chemical and physical processes that occur in the condensed phase. For strongly interacting systems where quantum many-body effects are known to play an important role, density-functional methods are often used to provide the model with the potential energy used to drive dynamics. These methods, however, suffer from two major drawbacks. First, they are often too computationally intensive to practically apply to large systems over long time scales, limiting their scope of application...
August 17, 2017: Journal of Physics. Condensed Matter: An Institute of Physics Journal
https://www.readbyqxmd.com/read/28817145/coherent-electronic-and-nuclear-dynamics-in-a-rhodamine-heterodimer-dna-supramolecular-complex
#5
M Cipolloni, B Fresch, I Occhiuto, P Rukin, K G Komarova, A Cecconello, I Willner, R D Levine, F Remacle, E Collini
Elucidating the role of quantum coherences in energy migration within biological and artificial multichromophoric antenna systems is the subject of an intense debate. It is also a practical matter because of the decisive implications for understanding the biological processes and engineering artificial materials for solar energy harvesting. A supramolecular rhodamine heterodimer on a DNA scaffold was suitably engineered to mimic the basic donor-acceptor unit of light-harvesting antennas. Ultrafast 2D electronic spectroscopic measurements allowed identifying clear features attributable to a coherent superposition of dimer electronic and vibrational states contributing to the coherent electronic charge beating between the donor and the acceptor...
August 17, 2017: Physical Chemistry Chemical Physics: PCCP
https://www.readbyqxmd.com/read/28814630/inverted-region-electron-transfer-as-a-mechanism-for-enhancing-photosynthetic-solar-energy-conversion-efficiency
#6
Hiroki Makita, Gary Hastings
In all photosynthetic organisms, light energy is used to drive electrons from a donor chlorophyll species via a series of acceptors across a biological membrane. These light-induced electron-transfer processes display a remarkably high quantum efficiency, indicating a near-complete inhibition of unproductive charge recombination reactions. It has been suggested that unproductive charge recombination could be inhibited if the reaction occurs in the so-called inverted region. However, inverted-region electron transfer has never been demonstrated in any native photosynthetic system...
August 16, 2017: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/28813152/coherent-exciton-delocalization-in-a-two-state-dna-templated-dye-aggregate-system
#7
Brittany L Cannon, Donald L Kellis, Lance Kenneth Patten, Paul H Davis, Jeunghoon Lee, Elton Graugnard, Bernard Yurke, William B Knowlton
Coherent exciton delocalization in dye aggregate systems gives rise to a variety of intriguing optical phenomena, including J- and H-aggregate behavior and Davydov splitting. Systems that exhibit coherent exciton delocalization at room temperature are of interest for the development of artificial light-harvesting devices, colorimetric detection schemes, and quantum computers. Here, we report on a simple dye system templated by DNA that exhibits tunable optical properties. At low salt and DNA concentrations, a DNA duplex with two internally functionalized Cy5 dyes (i...
August 16, 2017: Journal of Physical Chemistry. A
https://www.readbyqxmd.com/read/28812080/computational-design-of-ph-switchable-control-agents-for-nitroxide-mediated-polymerization
#8
Ganna Gryn'ova, Leesa M Smith, Michelle L Coote
In the present work we use accurate quantum chemistry to evaluate several known and novel nitroxides bearing acid-base groups as pH-switchable control agents for room temperature NMP. Based on G3(MP2,CC)(+)//M06-2X/6-31+G(d) calculations with UAKS-CPCM/M06-2X/6-31+G(d) solvation corrections, a number of novel nitroxides are predicted to be suitable for controlled polymerization of bulk styrene at room temperature when deprotonated (i.e. negatively charged), while remaining inert when neutral. These include an α-ethyl analogue of 3-carboxy-PROXYL and novel derivatives of 2,2,5-trimethyl-4-phenyl-3-azahexane-3-nitroxide (TIPNO) that have been modified to include acidic groups...
August 16, 2017: Physical Chemistry Chemical Physics: PCCP
https://www.readbyqxmd.com/read/28812068/mechanistic-investigations-of-the-2-coumaranone-chemiluminescence
#9
Stefan Schramm, Isabelle Navizet, Durga Prasad Karothu, Pascal Oesau, Veronika Bensmann, Dieter Weiss, Rainer Beckert, Panče Naumov
2-Coumaranones are evolving as a new, efficient, versatile, and synthetically accessible platform for the next generation chemiluminescent probes. Despite the favorable quantum yields, the exact mechanism of their chemiluminescence remains elusive. Here, we analyze the details of the mechanism of the 2-coumaranone chemiluminescence using a combination of experimental and computational methods. By using EPR spectroscopy we show that superoxide radical anions are involved in the reactions, in support of the hypothesis that the mechanism includes a single electron transfer step...
August 16, 2017: Physical Chemistry Chemical Physics: PCCP
https://www.readbyqxmd.com/read/28811554/a-new-method-to-investigate-the-catalytic-mechanism-of-yhde-pyrophosphatase-by-using-a-pyrophosphate-fluorescence-probe
#10
Qingya Shen, Hongwei Tan, Guo-Wen Xing, Jimin Zheng, Zongchao Jia
YhdE is a Maf (multicopy associated filamentation) proteins from Escherichia coli which exhibits pyrophosphatase activity towards selected nucleotides, although its catalytic mechanism remains unclear. Herein we used a novel fluorescence probe (4-isoACBA-Zn(II) complex) to characterize the enzymatic properties of YhdE and its mutant, establishing a new method for assaying pyrophosphatase catalytic function. Our results reveal for the first time that the new fluorescence sensor confers high sensitivity and specificity and pyrophosphate (PPi) is the direct catalytic product of YhdE...
August 15, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28810788/direct-measurement-of-site-specific-rates-of-reactions-of-h-with-c3h8-i-c4h10-and-n-c4h10
#11
Chia-Chieh Lin, Wei-Yu Chen, Hiroyuki Matsui, Niann-Shiah Wang
We measured the rates of abstraction of a hydrogen atom from specific sites in propane C3H8, 2-methyl propane (i-C4H10), and butane (n-C4H10); the sites are a primary hydrogen of C3H8 and i-C4H10 and a secondary hydrogen of n-C4H10. The excellent reproducibility of conditions of a diaphragm-less shock tube enabled us to conduct comparative measurements of the evolution of H atoms in three mixtures-(i) 0.5 ppm C2H5I + Ar, (ii) 0.5 ppm C2H5I + 50-100 ppm alkane as C3H8 or i-C4H10 or n-C4H10 + Ar, and (iii) the same concentrations of alkane + Ar without C2H5I-in the temperature range 1000-1200 K and at a pressure of 2...
August 14, 2017: Journal of Chemical Physics
https://www.readbyqxmd.com/read/28810761/closures-of-the-functional-expansion-hierarchy-in-the-non-markovian-quantum-state-diffusion-approach
#12
Gerhard Ritschel, Walter T Strunz, Alexander Eisfeld
To find a practical scheme to numerically solve the non-Markovian Quantum State Diffusion equation (NMQSD), one often uses a functional expansion of the functional derivative that appears in the general NMQSD equation. This expansion leads to a hierarchy of coupled operators. It turned out that if one takes only the zeroth order term into account, one has a very efficient method that agrees remarkably well with the exact results for many cases of interest. We denote this approach as zeroth order functional expansion (ZOFE)...
August 14, 2017: Journal of Chemical Physics
https://www.readbyqxmd.com/read/28810759/lanthanum-mediated-dehydrogenation-of-1-and-2-butynes-spectroscopy-and-formation-of-la-c4h4-isomers
#13
Wenjin Cao, Dilrukshi Hewage, Dong-Sheng Yang
La atom reactions with 1-butyne and 2-butyne are carried out in a laser-vaporization molecular beam source. Both reactions yield the same La-hydrocarbon products from the dehydrogenation and carbon-carbon bond cleavage and coupling of the butynes. The dehydrogenated species La(C4H4) is characterized with mass-analyzed threshold ionization (MATI) spectroscopy and quantum chemical computations. The MATI spectra of La(C4H4) produced from the two reactions exhibit two identical transitions, each consisting of a strong origin band and several vibrational intervals...
August 14, 2017: Journal of Chemical Physics
https://www.readbyqxmd.com/read/28809816/modeling-the-non-equilibrium-process-of-the-chemical-adsorption-of-ammonia-on-gan-0001-reconstructed-surfaces-based-on-steepest-entropy-ascent-quantum-thermodynamics
#14
Akira Kusaba, Guanchen Li, Michael R von Spakovsky, Yoshihiro Kangawa, Koichi Kakimoto
Clearly understanding elementary growth processes that depend on surface reconstruction is essential to controlling vapor-phase epitaxy more precisely. In this study, ammonia chemical adsorption on GaN(0001) reconstructed surfaces under metalorganic vapor phase epitaxy (MOVPE) conditions (3Ga-H and Nad-H + Ga-H on a 2 × 2 unit cell) is investigated using steepest-entropy-ascent quantum thermodynamics (SEAQT). SEAQT is a thermodynamic-ensemble based, first-principles framework that can predict the behavior of non-equilibrium processes, even those far from equilibrium where the state evolution is a combination of reversible and irreversible dynamics...
August 15, 2017: Materials
https://www.readbyqxmd.com/read/28808316/habituation-based-synaptic-plasticity-and-organismic-learning-in-a-quantum-perovskite
#15
Fan Zuo, Priyadarshini Panda, Michele Kotiuga, Jiarui Li, Mingu Kang, Claudio Mazzoli, Hua Zhou, Andi Barbour, Stuart Wilkins, Badri Narayanan, Mathew Cherukara, Zhen Zhang, Subramanian K R S Sankaranarayanan, Riccardo Comin, Karin M Rabe, Kaushik Roy, Shriram Ramanathan
A central characteristic of living beings is the ability to learn from and respond to their environment leading to habit formation and decision making. This behavior, known as habituation, is universal among all forms of life with a central nervous system, and is also observed in single-cell organisms that do not possess a brain. Here, we report the discovery of habituation-based plasticity utilizing a perovskite quantum system by dynamical modulation of electron localization. Microscopic mechanisms and pathways that enable this organismic collective charge-lattice interaction are elucidated by first-principles theory, synchrotron investigations, ab initio molecular dynamics simulations, and in situ environmental breathing studies...
August 14, 2017: Nature Communications
https://www.readbyqxmd.com/read/28805818/all-electric-control-of-donor-nuclear-spin-qubits-in-silicon
#16
Anthony J Sigillito, Alexei M Tyryshkin, Thomas Schenkel, Andrew A Houck, Stephen A Lyon
The electronic and nuclear spin degrees of freedom of donor impurities in silicon form ultra-coherent two-level systems that are potentially useful for applications in quantum information and are intrinsically compatible with industrial semiconductor processing. However, because of their smaller gyromagnetic ratios, nuclear spins are more difficult to manipulate than electron spins and are often considered too slow for quantum information processing. Moreover, although alternating current magnetic fields are the most natural choice to drive spin transitions and implement quantum gates, they are difficult to confine spatially to the level of a single donor, thus requiring alternative approaches...
August 14, 2017: Nature Nanotechnology
https://www.readbyqxmd.com/read/28805229/a-ground-state-potential-energy-surface-for-hono-based-on-a-neural-network-with-exponential-fitting-functions
#17
Ekadashi Pradhan, Alex Brown
The minimum energy structures, i.e., trans-HONO, cis-HONO, HNO2, and OH + NO, as well as the corresponding transition states, i.e., TStrans↔cis, TS1,2H-shift, and TS1,3H-shift, on the ground state potential energy surface (PES) of HONO have been characterized at the CCSD(T)-F12/cc-pVTZ-F12 level of theory. Using the same level of theory, a six-dimensional (6D) PES, encompassing the trans- and cis-isomers as well as the associated transition state, is fit in a sum-of-products form using neural network exponential fitting functions...
August 14, 2017: Physical Chemistry Chemical Physics: PCCP
https://www.readbyqxmd.com/read/28800535/computational-investigation-of-the-nitrosation-mechanism-of-piperazine-in-co2-capture
#18
Qi Yu, Pan Wang, Fangfang Ma, Hong-Bin Xie, Ning He, Jingwen Chen
Quantum chemistry calculations and kinetic modeling were performed to investigate the nitrosation mechanism and kinetics of diamine piperazine (PZ), an alternative solvent for widely used monoethanolamine in postcombustion CO2 capture (PCCC), by two typical nitrosating agents, NO2(-) and N2O3, in the presence of CO2. Various PZ species and nitrosating agents formed by the reactions of PZ, NO2(-), and N2O3 with CO2 were considered. The results indicated that the reactions of PZ species having NH group with N2O3 contribute the most to the formation of nitrosamines in the absorber unit of PCCC and follow a novel three-step nitrosation mechanism, which is initiated by the formation of a charge-transfer complex...
August 4, 2017: Chemosphere
https://www.readbyqxmd.com/read/28800392/coarse-grained-directed-simulation
#19
Glen M Hocky, Thomas Dannenhoffer-Lafage, Gregory A Voth
Many free-energy sampling and quantum mechanics/molecular mechanics (QM/MM) computations on protein complexes have been performed where, by necessity, a single component is studied isolated in solution while its overall configuration is kept in the complex-like state by either rigid restraints or harmonic constraints. A drawback in these studies is that the system's native fluctuations are lost, both due to the change of environment and the imposition of the extra potential. Yet, we know that having both accurate structure and fluctuations is likely crucial to achieving correct simulation estimates for the subsystem within its native larger protein complex context...
August 11, 2017: Journal of Chemical Theory and Computation
https://www.readbyqxmd.com/read/28799760/biomolecular-structure-information-from-high-speed-quantum-mechanical-electronic-spectra-calculation
#20
Jakob Seibert, Christoph Bannwarth, Stefan Grimme
A fully quantum mechanical (QM) treatment to calculate electronic absorption (UV-Vis) and circular dichroism (CD) spectra of typical biomolecules with thousands of atoms is presented. With our highly efficient sTDA-xTB method, spectra averaged along structures from molecular dynamics (MD) simulations can be computed in a reasonable time frame on standard desktop computers. This way, non-equilibrium structure and conformational as well as purely quantum mechanical effects like charge-transfer or exciton-coupling are included...
August 11, 2017: Journal of the American Chemical Society
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