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https://www.readbyqxmd.com/read/28214530/automaton-model-of-protein-dynamics-of-conformational-and-functional-states
#1
REVIEW
Andrei Khrennikov, Ekaterina Yurova
In this conceptual paper we propose to explore the analogy between ontic/epistemic description of quantum phenomena and interrelation between dynamics of conformational and functional states of proteins. Another new idea is to apply theory of automata to model the latter dynamics. In our model protein's behavior is modeled with the aid of two dynamical systems, ontic and epistemic, which describe evolution of conformational and functional states of proteins, respectively. The epistemic automaton is constructed from the ontic automaton on the basis of functional (observational) equivalence relation on the space of ontic states...
February 15, 2017: Progress in Biophysics and Molecular Biology
https://www.readbyqxmd.com/read/28213139/antimycobacterial-antimicrobial-activity-experimental-ft-ir-ft-raman-nmr-uv-vis-dsc-and-dft-transition-state-chemical-reactivity-nbo-nlo
#2
Poonam Rawat, R N Singh, Alok Ranjan, Sartaj Ahmad, Rajat Saxena
As part of a study of pyrrole hydrazone, we have investigated quantum chemical calculations, molecular geometry, relative energy, vibrational properties and antimycobacterial/antimicrobial activity of pyrrole-2-carboxaldehyde isonicotinyl hydrazone (PCINH), by applying the density functional theory (DFT) and Hartree Fock (HF). Good reproduction of experimental values is obtained and with small percentage error in majority of the cases in comparison to theoretical result (DFT). The experimental FT-IR and Raman wavenumbers were compared with the respective theoretical values obtained from DFT calculations and found to agree well...
February 11, 2017: Spectrochimica Acta. Part A, Molecular and Biomolecular Spectroscopy
https://www.readbyqxmd.com/read/28211902/simultaneous-observation-of-particle-and-wave-behaviors-of-entangled-photons
#3
Zhong-Xiao Man, Yun-Jie Xia, Nguyen Ba An
We theoretically study wave-particle duality of two entangled photons in the spirit of quantum version of delayed-choice experiments using Hadamard gate controlled by the quantum state of an ancilla and show that the two photons may globally exhibit particle-like, wave-like or simultaneously both particle-like and wave-like behavior. We prove that the obtained results cannot be satisfactorily explained by any hidden-variable theory. We also propose an efficient and experimentally feasible scheme without using any ancilla and controlled-gates to directly (i...
February 13, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28211720/dynamical-response-near-quantum-critical-points
#4
Andrew Lucas, Snir Gazit, Daniel Podolsky, William Witczak-Krempa
We study high-frequency response functions, notably the optical conductivity, in the vicinity of quantum critical points (QCPs) by allowing for both detuning from the critical coupling and finite temperature. We consider general dimensions and dynamical exponents. This leads to a unified understanding of sum rules. In systems with emergent Lorentz invariance, powerful methods from quantum field theory allow us to fix the high-frequency response in terms of universal coefficients. We test our predictions analytically in the large-N O(N) model and using the gauge-gravity duality and numerically via quantum Monte Carlo simulations on a lattice model hosting the interacting superfluid-insulator QCP...
February 3, 2017: Physical Review Letters
https://www.readbyqxmd.com/read/28211709/pt-symmetric-real-dirac-fermions-and-semimetals
#5
Y X Zhao, Y Lu
Recently, Weyl fermions have attracted increasing interest in condensed matter physics due to their rich phenomenology originated from their nontrivial monopole charges. Here, we present a theory of real Dirac points that can be understood as real monopoles in momentum space, serving as a real generalization of Weyl fermions with the reality being endowed by the PT symmetry. The real counterparts of topological features of Weyl semimetals, such as Nielsen-Ninomiya no-go theorem, 2D subtopological insulators, and Fermi arcs, are studied in the PT symmetric Dirac semimetals and the underlying reality-dependent topological structures are discussed...
February 3, 2017: Physical Review Letters
https://www.readbyqxmd.com/read/28211059/a-multipolar-approach-to-the-interatomic-covalent-interaction-energy
#6
Evelio Francisco, Daniel Menéndez Crespo, Aurora Costales, Ángel Martín Pendás
Interatomic exchange-correlation energies correspond to the covalent energetic contributions to an interatomic interaction in real space theories of the chemical bond, but their widespread use is severely limited due to their computationally intensive character. In the same way as the multipolar (mp) expansion is customary used in biomolecular modeling to approximate the classical Coulomb interaction between two charge densities ρA(r) and ρB(r), we examine in this work the mp approach to approximate the interatomic exchange-correlation (xc) energies of the Interacting Quantum Atoms method...
February 16, 2017: Journal of Computational Chemistry
https://www.readbyqxmd.com/read/28210878/the-role-of-weak-interactions-in-lignin-polymerization
#7
Ángel Sánchez-González, Francisco J Martín-Martínez, J A Dobado
Lignin is the most abundant natural polymer composed by aromatic moieties. Its chemical composition and its abundance have focused efforts to unlock its potential as a source of aromatic compounds for many years. The lack of a proper way for lignin de-polymerization has hampered its success as a natural solution for commodity aromatic chemicals, which is also due to the lack of understanding of the underlying mechanisms of lignin polymerization. A fuller fundamental understanding of polymerization mechanisms could lead to improvements in de-polymerization strategies, and therefore a proper methodology and a predictive theoretical framework are required for such purpose...
March 2017: Journal of Molecular Modeling
https://www.readbyqxmd.com/read/28208472/non-markovian-linear-response-theory-for-quantum-open-systems-and-its-applications
#8
H Z Shen, D X Li, X X Yi
The Kubo formula is an equation that expresses the linear response of an observable due to a time-dependent perturbation. It has been extended from closed systems to open systems in recent years under the Markovian approximation, but is barely explored for open systems in non-Markovian regimes. In this paper, we derive a formula for the linear response of an open system to a time-independent external field. This response formula is available for both Markovian and non-Markovian dynamics depending on parameters in the spectral density of the environment...
January 2017: Physical Review. E
https://www.readbyqxmd.com/read/28208355/signatures-of-bifurcation-on-quantum-correlations-case-of-the-quantum-kicked-top
#9
Udaysinh T Bhosale, M S Santhanam
Quantum correlations reflect the quantumness of a system and are useful resources for quantum information and computational processes. Measures of quantum correlations do not have a classical analog and yet are influenced by classical dynamics. In this work, by modeling the quantum kicked top as a multiqubit system, the effect of classical bifurcations on measures of quantum correlations such as the quantum discord, geometric discord, and Meyer and Wallach Q measure is studied. The quantum correlation measures change rapidly in the vicinity of a classical bifurcation point...
January 2017: Physical Review. E
https://www.readbyqxmd.com/read/28208317/quantum-kramers-model-corrections-to-the-linear-response-theory-for-continuous-bath-spectrum
#10
Ilya Rips
Decay of the metastable state is analyzed within the quantum Kramers model in the weak-to-intermediate dissipation regime. The decay kinetics in this regime is determined by energy exchange between the unstable mode and the stable modes of thermal bath. In our previous paper [Phys. Rev. A 42, 4427 (1990)PLRAAN1050-294710.1103/PhysRevA.42.4427], Grabert's perturbative approach to well dynamics in the case of the discrete bath [Phys. Rev. Lett. 61, 1683 (1988)PRLTAO0031-900710.1103/PhysRevLett.61.1683] has been extended to account for the second order terms in the classical equations of motion (EOM) for the stable modes...
January 2017: Physical Review. E
https://www.readbyqxmd.com/read/28207277/proton-dynamics-in-protein-mass-spectrometry
#11
Jinyu Li, Wenping Lyu, Giulia Rossetti, Albert Konijnenberg, Antonino Natalello, Emiliano Ippoliti, Modesto Orozco, Frank Sobott, Rita Grandori, Paolo Carloni
Native electrospray ionization/ion mobility-mass spectrometry (ESI/IM-MS) allows an accurate determination of low-resolution structural features of proteins. Yet, the presence of proton dynamics, observed already by us for DNA in the gas phase, and its impact on protein structural determinants, have not been investigated so far. Here, we address this issue by a multi-step simulation strategy on a pharmacologically relevant peptide, the N-terminal residues of amyloid-β peptide (Aβ(1-16)). Our calculations reproduce the experimental maximum charge state from ESI-MS and are also in fair agreement with collision cross section (CCS) data measured here by ESI/IM-MS...
February 16, 2017: Journal of Physical Chemistry Letters
https://www.readbyqxmd.com/read/28205402/quantum-chemistry-descriptors-for-photosensitizers-based-on-macrocycles
#12
Fernanda Bettanin, Felipe C T Antonio, Kathia M Honorio, Paula Homem-de-Mello
Phthalocyanines, porphyrins, and chlorins have been widely studied as photosensitizers. Both experimental and computational strategies are employed in order to propose new and more active molecules derived from those macrocycles. In this context, there are two main strategies used: (i) the addition of different substituents and (ii) the complexation of the macrocycle with different metallic ions. In this work, we present selected descriptors based on quantum chemistry calculations for forty macrocycles, including some approved drugs...
February 2017: Chemical Biology & Drug Design
https://www.readbyqxmd.com/read/28204941/microscopic-progression-in-the-free-radical-addition-reaction-modeling-geometry-energy-and-kinetics
#13
Yun Zhang, Hong Huang, Zhiling Liang, Houhe Liu, Ling Yi, Jinhong Zhang, Zhiqiang Zhang, Cheng Zhong, Yugang Huang, Guodong Ye
The free radical addition reaction is very important in UV curing. The benzoyl radical is the most commonly observed radical. In the addition process, the benzoyl radical adds to an acrylate monomer, forming a primary radical that has great value for subsequent research. In this article, a quantum chemical method was used to study the microscopic progression from the reactive complex to the saddle point. The reactions of three monomers (amylene, allyl methyl ether and methyl acrylate) with a benzoyl radical were evaluated in terms of geometry and energy...
March 2017: Journal of Molecular Modeling
https://www.readbyqxmd.com/read/28201900/discriminating-single-molecule-sensing-by-crown-ether-based-molecular-junctions
#14
Ali K Ismael, Alaa Al-Jobory, Iain Grace, Colin J Lambert
Crown-ether molecules are well known to selectively bind alkali atoms, so by incorporating these within wires, any change in electrical conductance of the wire upon binding leads to discriminating sensing. Using a density functional theory-based approach to quantum transport, we investigate the potential sensing capabilities of single-molecule junctions formed from crown ethers attached to anthraquinone units, which are in turn attached to gold electrodes via alkyl chains. We calculate the change in electrical conductance for binding of three different alkali ions (lithium, sodium, and potassium)...
February 14, 2017: Journal of Chemical Physics
https://www.readbyqxmd.com/read/28201896/plasmon-coupled-resonance-energy-transfer-a-real-time-electrodynamics-approach
#15
Wendu Ding, Liang-Yan Hsu, George C Schatz
This paper presents a new real-time electrodynamics approach for determining the rate of resonance energy transfer (RET) between two molecules in the presence of plasmonic or other nanostructures (inhomogeneous absorbing and dispersive media). In this approach to plasmon-coupled resonance energy transfer (PC-RET), we develop a classical electrodynamics expression for the energy transfer matrix element which is evaluated using the finite-difference time-domain (FDTD) method to solve Maxwell's equations for the electric field generated by the molecular donor and evaluated at the position of the molecular acceptor...
February 14, 2017: Journal of Chemical Physics
https://www.readbyqxmd.com/read/28199945/contribution-of-methane-sulfonic-acid-to-new-particle-formation-in-the-atmosphere
#16
Hailiang Zhao, Xiaotong Jiang, Lin Du
Methane sulfonic acid (MSA) is present in substantial concentrations in the gas phase over oceans and coastal regions. We present an investigation into the contribution of MSA to new particle formation with the common atmospheric aerosol nucleation precursors including MSA, methanol, formic acid, acetone, dimethylether, formaldehyde, methyl formate, by making use a quantum chemical approach. Density functional theory calculations indicate that these bimolecular complexes are characterized by the presence of strong inter-molecular hydrogen bonds (SOH⋯O) with large binding energies and thermodynamic equilibrium constants...
February 7, 2017: Chemosphere
https://www.readbyqxmd.com/read/28199110/kinetics-of-hydrogen-abstraction-and-addition-reactions-of-3-hexene-by-%C3%A8-h-radicals
#17
Feiyu Yang, Fuquan Deng, Youshun Pan, Yingjia Zhang, Chenglong Tang, Zuohua Huang
Rate coefficients of H-atom abstraction and H-atom addition reactions of 3-hexene by the hydroxyl radicals were determined using both conventional transition-state theory and canonical variational transition-state theory, with potential energy surface (PES) evaluated at the CCSD(T)/CBS//BHandHLYP/6-311G (d, p) level and quantum mechanical effect corrected by the compounded methods including one-dimensional Wigner method, multi-dimensional zero-curvature tunneling method and small-curvature tunneling method...
February 15, 2017: Journal of Physical Chemistry. A
https://www.readbyqxmd.com/read/28195668/towards-monodisperse-star-shaped-ladder-type-conjugated-systems-design-synthesis-stabilized-blue-electroluminescence-and-amplified-spontaneous-emission
#18
Wen-Yong Lai, Yi Jiang, Mei Fang, Si-Ju Chang, Jin-Jin Huang, Shuang-Quan Chu, Shan-Ming Hu, Cheng-Fang Liu, Wei Huang
A novel series of monodisperse star-shaped ladder-type oligo(p-phenylene)s, named as TrL-n (n = 1-3), have been explored. Their thermal and electrochemical properties, fluorescence transients, photoluminescence quantum yields, density functional theory calculations, electroluminescence (EL) and amplified spontaneous emission (ASE) properties have been systematically investigated to unravel the molecular design on optoelectronic properties. The resulting materials showed excellent structural perfection free of chemical defects, exhibiting great thermal stability (Td: 404-418°C and Tg:147-184°C) and amorphous glassy morphologies...
February 14, 2017: Chemistry: a European Journal
https://www.readbyqxmd.com/read/28195284/temperature-dependence-of-x-ray-absorption-and-nuclear-magnetic-resonance-spectra-probing-quantum-vibrations-of-light-elements-in-oxides
#19
Ruidy Nemausat, Christel Gervais, Christian Brouder, Nicolas Trcera, Amélie Bordage, Cristina Coelho-Diogo, Pierre Florian, Aydar Rakhmatullin, Ion Errea, Lorenzo Paulatto, Michele Lazzeri, Delphine Cabaret
A combined experimental-theoretical study on the temperature dependence of the X-ray absorption near-edge structure (XANES) and nuclear magnetic resonance (NMR) spectra of periclase (MgO), spinel (MgAl2O4), corundum (α-Al2O3), berlinite (α-AlPO4), stishovite and α-quartz (SiO2) is reported. Predictive calculations are presented when experimental data are not available. For these light-element oxides, both experimental techniques detect systematic effects related to quantum thermal vibrations which are well reproduced by density-functional theory simulations...
February 14, 2017: Physical Chemistry Chemical Physics: PCCP
https://www.readbyqxmd.com/read/28194972/fragment-based-approach-for-the-evaluation-of-nmr-chemical-shifts-for-large-biomolecules-incorporating-the-effects-of-the-solvent-environment
#20
K V Jovan Jose, Krishnan Raghavachari
We present an efficient implementation of the molecules-in-molecules (MIM) fragment-based quantum chemical method for the evaluation of NMR chemical shifts of large biomolecules. Density functional techniques have been employed in conjunction with large basis sets and including the effects of the solvent environment in these calculations. The MIM-NMR method is initially benchmarked on a set of (alanine)10 conformers containing strong intramolecular interactions. The incorporation of a second low level of theory to recover the missing long-range interactions in the primary fragmentation scheme is critical to yield reliable chemical shifts, with a mean absolute deviation (MAD) from direct unfragmented calculations of 0...
February 14, 2017: Journal of Chemical Theory and Computation
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