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Phillip S Thomas, Tucker Carrington, Jay Agarwal, Henry F Schaefer
We use a direct product basis, basis vectors computed by evaluating matrix-vector products, and rank reduction to calculate vibrational energy levels of uracil and naphthalene, with 12 and 18 atoms, respectively. A matrix representing the Hamiltonian in the direct product basis and vectors with as many components as there are direct product basis functions are neither calculated nor stored. We also introduce an improvement of the Hierarchical Intertwined Reduced-Rank Block Power Method (HI-RRBPM), proposed previously in Thomas and Carrington, Jr...
August 14, 2018: Journal of Chemical Physics
Zhehong Gan, Ivan Hung, Yusuke Nishiyama, Jean-Paul Amoureux, Olivier Lafon, Hiroki Nagashima, Julien Trébosc, Bingwen Hu
By irradiating and observing at twice the 14 N Larmor frequency, overtone (OT) nuclear magnetic resonance (NMR) is capable of obtaining 14 NOT spectra without first-order quadrupolar broadening. Direct excitation and detection of the usually "forbidden" double-quantum transition is mediated by the perturbation from the large quadrupole interaction to the spin states quantized by the Zeeman interaction. A recent study [L. A. O'Dell and C. I. Ratcliffe, Chem. Phys. Lett. 514 , 168 (2011)] has shown that 14 NOT NMR under magic-angle spinning (MAS) can yield high-resolution spectra with typical second-order quadrupolar line shapes allowing the measurement of 14 N chemical shift and quadrupolar coupling parameters...
August 14, 2018: Journal of Chemical Physics
Kunaal Joshi, Ishant Tiwari, Amitabha Nandi, P Parmananda
In the present paper, the possibility of invoking stochastic resonance (SR, periodic and aperiodic) by regulating the operating value of an appropriate parameter is explored. The operating values of these parameters are defined as the set point of the system throughout the present paper. Brusselator, a mathematical model [I. Prigogine and R. Lefever, J. Chem. Phys. 48, 1695 (1968)JCPSA60021-960610.1063/1.1668896] of nonlinear chemical reactions, is used for this purpose. We consider the effect of intrinsic noise in the Brusselator due to the Markovian nature of the chemical reactions...
July 2018: Physical Review. E
Adelina Voukadinova, Mónika Valiskó, Dirk Gillespie
Classical density functional theory (DFT) is a useful tool to compute the structure of the electrical double layer because it includes ion-ion correlations due to excluded-volume effects (i.e., steric correlations) and ion screening effects (i.e., electrostatic correlations beyond the electrostatic mean-field potential). This paper systematically analyzes the accuracies of three different electrostatic excess free-energy functionals, as compared to Monte Carlo (MC) simulations of the planar electrical double layer, over a large parameter space...
July 2018: Physical Review. E
Shampa Chakraborty, Shyamaprosad Goswami, Ching Kheng Quah, Bholanath Pakhira
Single-crystal X-ray structures of dimeric quinoxaline aldehyde (QA), quinoxaline dihydrazone (DHQ) and HQNM (Goswami S et al. 2013 Tetrahedron Lett. 54 , 5075-5077. (doi:10.1016/j.tetlet.2013.07.051); Goswami S et al. 2014 RSC Adv. 4 , 20 922-20 926. (doi:10.1039/C4RA00594E); Goswami S et al. 2014 New J. Chem. 38 , 6230-6235. (doi:10.1039/C4NJ01498G)) are reported along with the theoretical study. Among them, QA is not acting as an active probe, but DHQ and HQNM are serving as selective and sensitive probe for the Fe3+ cation and the Ni2+ cation, respectively...
June 2018: Royal Society Open Science
Vivekanand Shukla, Rafael B Araujo, Naresh K Jena, Rajeev Ahuja
Graphene's emergence can be viewed as a positive upheaval in 2D materials research. Along the same line, the realization of a related elemental 2D material, borophene, is another breakthrough. To circumvent the stability issues of borophene, which is reported to have been synthesized on metallic substrates under extreme conditions, hydrogenation of borophene (otherwise called as borophane or hydrogen boride or boron hydride) has been a plausible solution, but only proposed computationally. A recent report (H...
August 15, 2018: Physical Chemistry Chemical Physics: PCCP
Ralph Welsch
Thermal rate constants for the prototypical water-forming H2 +OH→H+H2 O reaction are calculated for temperatures between 150K and 600K using rigorous quantum dynamics calculations including all degrees of freedom. Results are reported for a recent, highly accurate neural network potential (NN1) [J. Chem. Phys. 138, 154301 (2013)] and compared to results obtained on a previous, semi-empirical potential (SE) [Chem. Phys. Lett. 21, 73 (1980)]. Rate constants computed on both potentials significantly differ in their temperature dependence and differences of over an order of magnitude in the rates are found...
August 15, 2018: Angewandte Chemie
Nadja A Henke, Jonas Frohwitter, Petra Peters-Wendisch, Volker F Wendisch
Corynebacterium glutamicum is a workhorse of industrial amino acid production employed for more than five decades for the million-ton-scale production of L-glutamate and L-lysine. This bacterium is pigmented due to the biosynthesis of the carotenoid decaprenoxanthin. Decaprenoxanthin is a carotenoid with 50 carbon atoms, and, thus, C. glutamicum belongs to the rare group of bacteria that produce long-chain C50 carotenoids. C50 carotenoids have been mainly isolated from extremely halophilic archaea (Kelly and Jensen, Acta Chem Scand 21:2578, 1967; Pfander, Pure Appl Chem 66:2369-2374, 1994) and from Gram-positive bacteria of the order Actinomycetales (Netzer et al...
2018: Methods in Molecular Biology
Jenieve Cumberland, Tetiana Lopatkina, Matthew Murachver, Piotr Popov, Viktor Kenderesi, Ágnes Buka, Elizabeth K Mann, Antal Jákli
The interactions of phospholipids with liquid crystals have formed the basis for attractive biosensor technologies, but many questions remain concerning the basic physics and chemistry of these interactions. Phospholipids such as 1,2-dilauroyl-sn-glycero-3-phosphocholine (DLPC), at sufficiently high (∼1 μM) concentrations and/or sufficiently long times, turn the liquid crystal director perpendicular to the LC/water interface. If the other side of the LC film is in contact with a surface that prefers perpendicular alignment, the LC film appears completely dark between crossed polarizers...
August 15, 2018: Soft Matter
Mohammad Ahmadi, Hassan Hassanzadeh, Jalal Abedi
Significant advances have been achieved in understanding the main molecular mechanisms leading to asphaltene aggregation. However, the existing computational deficiency of molecular dynamic simulations did not allow full reproduction of the complex aggregation behavior of asphaltene in the past. In this work, we use the Brownian dynamics simulation to investigate asphaltene aggregation behavior at larger length and time scales that have not been previously accessed by molecular simulations. This enabled us to completely render the formation of the clusters of asphaltene nanoaggregates and the resulting fractal or network of aggregates during the aggregation process...
August 14, 2018: Journal of Physical Chemistry. B
Giuseppe Sansone, Antti J Karttunen, Denis Usvyat, Martin Schütz, Jan Gerit Brandenburg, Lorenzo Maschio
Black phosphorus is a bulk solid allotrope of elemental phosphorus and can be seen as an infinite stack of phosphorene sheets. It is interesting from a technological point of view as well as from an electronic structure perspective due to the importance of electron correlation effects. In a recent paper [M. Schütz, L. Maschio, A. J. Karttunen and D. Usvyat, J. Phys. Chem. Lett., 2017, 8, 1290-1294] a highly accurate exfoliation energy has been computed. Building upon these results we carefully benchmark various dispersion-corrected density functional approximations...
August 14, 2018: Chemical Communications: Chem Comm
L A Ferreira, V N Uversky, B Y Zaslavsky
The binodal model pioneered by Guan et al. [Y. Guan, T. H. Lilley, T. E. Treffry, J. Chem. Soc. Faraday Trans., 89 (1993) 4283-4298] remains the most successful in regard to the quantitative description of phase diagrams among various theoretical models proposed to describe phase separation in aqueous mixtures of polymers. This is a semi-empirical model based on the assumption that any point on the binodal line may be viewed as a saturated solution of the phase-forming compound-1 in the solution of the phase-forming compound-2...
September 14, 2018: Journal of Chromatography. A
Tianqi Ma, Tianwu Zang, Qinghua Wang, Jianpeng Ma
This paper reports a method for high-accuracy protein structural refinement, which is a direct extension of the method in our recent publication (J. Chem. Phys. 149, 072319 (2018))). It combines a parallel continuous simulated tempering (PCST) method with a temperature-dependent restraint and a blind model selection scheme. In this work, a single-reference-based restraint in previous work was changed to an ensemble-based model (EBM), in which the non-bonded Lennard-Jones term for each contacting atomic pair in previous restraining potential was replaced by a multi-Gaussian function whose parameters are derived from an ensemble of structures such as the ones from various CASP participating groups...
August 10, 2018: Protein Science: a Publication of the Protein Society
Stanislav Bellaousov, Mohammad Kayedkhordeh, Raymond J Peterson, David H Mathews
Nanoscale nucleic acids can be designed to be nano-machines, pharmaceuticals, or probes for detecting pathogens and other molecules. RNA secondary structures can form the basis of self-assembling nanostructures. There are only four natural RNA bases, therefore it can be difficult to design sequences that fold to a single, specified structure because many other structures are often possible for a given sequence. One approach taken by state-of-the-art sequence design methods is to select sequences that fold to the specified input structure using stochastic, iterative refinement...
August 10, 2018: RNA
Jingwei Zhang, Junling An, Yu Qu, Xingang Liu, Yong Chen
We first coupled indoor emissions and biomass burning emissions into the WRF-Chem model besides the other four potential HONO sources (i.e., traffic emissions, soil emissions, and heterogeneous reactions on aerosol and ground surfaces). Eight simulations were performed in the Beijing-Tianjin-Hebei region (BTH) of China in August of 2006. The results indicated that traffic emissions and heterogeneous reactions on ground and aerosol surfaces were the key sources of HONO at night, accounting for ~41%, ~27% and ~20% of the nighttime simulated HONO concentrations, respectively...
August 5, 2018: Science of the Total Environment
Samuel D Griggs, Nathan Thompson, Daniel T Tape, Marie Fabre, Paul A Clarke
Correction for 'Synthesis of highly substituted 2-spiropiperidines' by Samuel D. Griggs et al., Org. Biomol. Chem., 2018, DOI: 10.1039/c8ob01272e.
August 10, 2018: Organic & Biomolecular Chemistry
A Martín Pendás, E Francisco
An electron counting technique that easily provides Lewis structures from real space analyses of general wavefunctions is proposed. We base our approach on reformulating the adaptive natural density partitioning (AdNDP) algorithm proposed by Zubarev and Boldyrev (Phys. Chem. Chem. Phys., 2008, 10, 5207) in position space through the use of domain-averaged cumulant densities, which take into account many-electron correlations. Averages are performed over the basins provided by the quantum theory of atoms in molecules...
August 10, 2018: Physical Chemistry Chemical Physics: PCCP
Lishu Guo, Michela Carraro, Geppo Sartori, Giovanni Minervini, Ove Eriksson, Valeria Petronilli, Paolo Bernardi
Modification with arginine-specific glyoxals modulates the permeability transition (PT) of rat liver mitochondria, with inhibitory or inducing effects that depend on the net charge of the adduct(s) (Johans et al., (2005) J. Biol. Chem. 280, 12130-12136). Here we show that phenylglyoxal (PGO) affects the PT in a species-specific manner (inhibition in mouse and yeast, induction in human and Drosophila mitochondria). Following the hypotheses (i) that the effects are mediated by conserved arginine(s) and (ii) that the PT is mediated by the F-ATP synthase, we have narrowed the search to 60 arginines...
August 9, 2018: Journal of Biological Chemistry
Michael L Poltash, Jacob W McCabe, Mehdi Shirzadeh, Arthur Laganowsky, Brian H Clowers, David H Russell
A new instrument configuration for native ion mobility-mass spectrometry (IM-MS) is described. Macromolecule ions are generated by using a static ESI source coupled to an RF ion funnel and these ions are then mobility and mass analyzed using a periodic focusing drift tube IM analyzer, and an Orbitrap mass spectrometer. The instrument design retains the capabilities for first-principles determination of rotationally-averaged ion-neutral collision cross sections and high-resolution measurements in both mobility and mass analysis modes for intact protein complexes...
August 9, 2018: Analytical Chemistry
Zhibin Du, Akbar Ali
The Wiener polarity index (usually denoted by Wp ) of an alkane is the number of unordered pairs of carbon atoms which are separated by three carbon-carbon bonds. This topological index Wp is useful for predicting the boiling points of alkanes. Deng [MATCH Commun. Math. Comput. Chem. 66 (2011) 305] proved that the maximum Wp value among all alkanes, with n carbon atoms, is 3n-15 . The main purpose of present paper is to find all those alkanes with n carbon atoms, which attain the maximum value of Wp .
August 9, 2018: Molecular Informatics
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