Publications by authors named "Alexander Morozov"

74 Publications

Gas-phase synthesis of benzene via the propargyl radical self-reaction.

Sci Adv 2021 May 21;7(21). Epub 2021 May 21.

Department of Chemistry, University of Hawaii at Manoa, Honolulu, HI 96822, USA.

Polycyclic aromatic hydrocarbons (PAHs) have been invoked in fundamental molecular mass growth processes in our galaxy. We provide compelling evidence of the formation of the very first ringed aromatic and building block of PAHs-benzene-via the self-recombination of two resonantly stabilized propargyl (CH) radicals in dilute environments using isomer-selective synchrotron-based mass spectrometry coupled to theoretical calculations. Along with benzene, three other structural isomers (1,5-hexadiyne, fulvene, and 2-ethynyl-1,3-butadiene) and -benzyne are detected, and their branching ratios are quantified experimentally and verified with the aid of computational fluid dynamics and kinetic simulations. These results uncover molecular growth pathways not only in interstellar, circumstellar, and solar systems environments but also in combustion systems, which help us gain a better understanding of the hydrocarbon chemistry of our universe.
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http://dx.doi.org/10.1126/sciadv.abf0360DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8139581PMC
May 2021

Theoretical Study of the Phenoxy Radical Recombination with the O(P) Atom, Phenyl plus Molecular Oxygen Revisited.

J Phys Chem A 2021 May 30;125(18):3965-3977. Epub 2021 Apr 30.

Department of Chemistry and Biochemistry, Florida International University, Miami, Florida 33199, United States.

Quantum chemical calculations of the CHO potential energy surface (PES) were carried out to study the mechanism of the phenoxy + O(P) and phenyl + O reactions. CASPT2(15e,13o)/CBS//CASSCF(15e,13o)/DZP multireference calculations were utilized to map out the minimum energy path for the entrance channels of the phenoxy + O(P) reaction. Stationary points on the CHO PES were explored at the CCSD(T)-F12/cc-pVTZ-f12//B3LYP/6-311++G** level for the species with a single-reference character of the wave function and at the CASPT2(15e,13o)/CBS//B3LYP/6-311++G** level of theory for the species with a multireference character of the wave function. Conventional, variational, and variable reaction coordinate transition-state theories were employed in Rice-Ramsperger-Kassel-Marcus master equation calculations to assess temperature- and pressure-dependent phenomenological rate constants and product branching ratios. The main bimolecular product channels of the phenoxy + O(P) reaction are concluded to be -benzoquinone + H, 2,4-cyclopentadienone + HCO and, at high temperatures, also phenyl + O. The main bimolecular product channels of the phenyl + O reaction include 2,4-cyclopentadienone + HCO at lower temperatures and phenoxy + O(P) at higher temperatures. For both the phenoxy + O(P) and phenyl + O reactions, the collisional stabilization of peroxybenzene at low temperatures and high pressures competes with the bimolecular product channels.
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http://dx.doi.org/10.1021/acs.jpca.1c01545DOI Listing
May 2021

Gas-phase synthesis of corannulene - a molecular building block of fullerenes.

Phys Chem Chem Phys 2021 Mar 17;23(10):5740-5749. Epub 2021 Feb 17.

Department of Chemistry, University of Hawaii at Manoa, Honolulu, Hawaii 96822, USA.

Fullerenes (C, C) detected in planetary nebulae and carbonaceous chondrites have been implicated to play a key role in the astrochemical evolution of the interstellar medium. However, the formation mechanism of even their simplest molecular building block-the corannulene molecule (CH)-has remained elusive. Here we demonstrate via a combined molecular beams and ab initio investigation that corannulene can be synthesized in the gas phase through the reactions of 7-fluoranthenyl (CH˙) and benzo[ghi]fluoranthen-5-yl (CH˙) radicals with acetylene (CH) mimicking conditions in carbon-rich circumstellar envelopes. This reaction sequence reveals a reaction class in which a polycyclic aromatic hydrocarbon (PAH) radical undergoes ring expansion while simultaneously forming an out-of-plane carbon backbone central to 3D nanostructures such as buckybowls and buckyballs. These fundamental reaction mechanisms are critical in facilitating an intimate understanding of the origin and evolution of the molecular universe and, in particular, of carbon in our galaxy.
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http://dx.doi.org/10.1039/d0cp06537dDOI Listing
March 2021

Low-temperature gas-phase formation of indene in the interstellar medium.

Sci Adv 2021 Jan 1;7(1). Epub 2021 Jan 1.

Department of Chemistry, University of Hawai'i at Mānoa, Honolulu, HI 96822, USA.

Polycyclic aromatic hydrocarbons (PAHs) are fundamental molecular building blocks of fullerenes and carbonaceous nanostructures in the interstellar medium and in combustion systems. However, an understanding of the formation of aromatic molecules carrying five-membered rings-the essential building block of nonplanar PAHs-is still in its infancy. Exploiting crossed molecular beam experiments augmented by electronic structure calculations and astrochemical modeling, we reveal an unusual pathway leading to the formation of indene (CH)-the prototype aromatic molecule with a five-membered ring-via a barrierless bimolecular reaction involving the simplest organic radical-methylidyne (CH)-and styrene (CHCH) through the hitherto elusive methylidyne addition-cyclization-aromatization (MACA) mechanism. Through extensive structural reorganization of the carbon backbone, the incorporation of a five-membered ring may eventually lead to three-dimensional PAHs such as corannulene (CH) along with fullerenes (C, C), thus offering a new concept on the low-temperature chemistry of carbon in our galaxy.
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http://dx.doi.org/10.1126/sciadv.abd4044DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7775774PMC
January 2021

Slim-panel holographic video display.

Nat Commun 2020 11 10;11(1):5568. Epub 2020 Nov 10.

Samsung Advanced Institute of Technology, Samsung Electronics, Suwon, Gyeonggi-do, South Korea.

Since its discovery almost 70 years ago, the hologram has been considered to reproduce the most realistic three dimensional images without visual side effects. Holographic video has been extensively researched for commercialization, since Benton et al. at MIT Media Lab developed the first holographic video systems in 1990. However, commercially available holographic video displays have not been introduced yet for several reasons: narrow viewing angle, bulky optics and heavy computing power. Here we present an interactive slim-panel holographic video display using a steering-backlight unit and a holographic video processor to solve the above issues. The steering-backlight unit enables to expand the viewing angle by 30 times and its diffractive waveguide architecture makes a slim display form-factor. The holographic video processor computes high quality holograms in real-time on a single-chip. We suggest that the slim-panel holographic display can provide realistic three-dimensional video in office and household environments.
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http://dx.doi.org/10.1038/s41467-020-19298-4DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7655945PMC
November 2020

Agro-Morphological, Microanatomical and Molecular Cytogenetic Characterization of the Medicinal Plant L.

Plants (Basel) 2020 Oct 20;9(10). Epub 2020 Oct 20.

Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, 32 Vavilov St, 119991 Moscow, Russia.

L. is a medicinal plant well-known as a valuable source of isoquinoline alkaloids, which has a variety of pharmacological properties including anti-viral and anti-bacterial effects. However, considerable intraspecific bio-morphological variability in complicates raw material identification and verification. For the first time, we have brought into cultivation five populations of subsp. originated from different regions, and performed their agro-morphological, microanatomical and molecular cytogenetic characterization. All examined populations produced high seed (18.6-19.9 kg/ha) and raw material (0.84-1.08 t/ha) yields; total alkaloid contents were within 0.30-0.38%. Nevertheless, significant differences in plant morphology and yield-contributing traits were observed. The performed microanatomical analysis of leaves and flowers in double- and normal-flowered plants revealed micro-diagnostic features (including tissue topography, types of stomata, laticifers, structure of leaf mesophyll, hairs, sepals and petals) important for identification of raw materials. The analysis of chromosome morphology, DAPI-banding patterns, FISH mapping of 45S and 5S rDNA and also chromosome behavior in meiosis allowed us to identify for the first time all chromosomes in karyotypes and confirm relative genotype stability of the studied plants. Our findings indicate that the examined populations can be used in further breeding programs.
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http://dx.doi.org/10.3390/plants9101396DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7589513PMC
October 2020

Electrostatic potential between charged particles at an oil-water interface.

Phys Rev E 2020 Aug;102(2-1):020801

SUPA, School of Physics and Astronomy, The University of Edinburgh, Edinburgh EH9 3FD, Scotland, United Kingdom.

Electrostatic interactions between point charges embedded into interfaces separating dielectric media are omnipresent in soft matter systems and often control their stability. Such interactions are typically complicated and do not resemble their bulk counterparts. For instance, the electrostatic potential of a point charge at an air-water interface falls off as r^{-3}, where r is the distance from the charge, exhibiting a dipolar behavior. This behavior is often assumed to be generic, and is widely referred to when interpreting experimental results. Here we explicitly calculate the in-plane potential of a point charge at an interface between two electrolyte solutions with different, finite dielectric permittivities and Debye screening lengths, such as oil and water. We show that the asymptotic behavior of this potential is neither a dipole, which characterizes the potential at air-water interfaces, nor a screened monopole, which describes the bulk behavior in a single electrolyte solution. By considering the same problem in arbitrary dimensions, we find that the physics behind this difference can be traced to the asymmetric propagation of the interaction in the two media. Our results should be relevant to understand the effective potential acting between interfacial proteins in biofilms, and the self-assembly of charged colloids at droplet surfaces in oil-water emulsions.
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http://dx.doi.org/10.1103/PhysRevE.102.020801DOI Listing
August 2020

Pattern formation in active model C with anchoring: bands, aster networks, and foams.

Soft Matter 2020 Oct;16(38):8775-8781

SUPA, School of Physics and Astronomy, The University of Edinburgh, James Clerk Maxwell Building, Peter Guthrie Tait Road, Edinburgh, EH9 3FD, UK.

We study the dynamics of pattern formation in a minimal model for active mixtures made of microtubules and molecular motors. We monitor the evolution of the (conserved) microtubule density and of the (non-conserved) nematic order parameter, focusing on the effects of an "anchoring" term that provides a direct coupling between the preferred microtubule direction and their density gradient. The key control parameter is the ratio between activity and elasticity. When elasticity dominates, the interplay between activity and anchoring leads to formation of banded structures that can undergo additional bending, rotational or splaying instabilities. When activity dominates, the nature of anchoring instead gives rise to a range of active cellular solids, including aster-like networks, disordered foams and spindle-like patterns. We speculate that the introduced "active model C" with anchoring is a minimal model to describe pattern formation in a biomimetic analogue of the microtubule cytoskeleton.
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http://dx.doi.org/10.1039/d0sm00927jDOI Listing
October 2020

Symmetric Mixtures of Pusher and Puller Microswimmers Behave as Noninteracting Suspensions.

Phys Rev Lett 2020 Jul;125(1):018003

Division of Physical Chemistry, Lund University, P.O. Box 124, S-221 00 Lund, Sweden.

Suspensions of rear- and front-actuated microswimmers immersed in a fluid, known respectively as "pushers" and "pullers," display qualitatively different collective behaviors: beyond a characteristic density, pusher suspensions exhibit a hydrodynamic instability leading to collective motion known as active turbulence, a phenomenon which is absent for pullers. In this Letter, we describe the collective dynamics of a binary pusher-puller mixture using kinetic theory and large-scale particle-resolved simulations. We derive and verify an instability criterion, showing that the critical density for active turbulence moves to higher values as the fraction χ of pullers is increased and disappears for χ≥0.5. We then show analytically and numerically that the two-point hydrodynamic correlations of the 1∶1 mixture are equal to those of a suspension of noninteracting swimmers. Strikingly, our numerical analysis furthermore shows that the full probability distribution of the fluid velocity fluctuations collapses onto the one of a noninteracting system at the same density, where swimmer-swimmer correlations are strictly absent. Our results thus indicate that the fluid velocity fluctuations in 1∶1 pusher-puller mixtures are exactly equal to those of the corresponding noninteracting suspension at any density, a surprising cancellation with no counterpart in equilibrium long-range interacting systems.
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http://dx.doi.org/10.1103/PhysRevLett.125.018003DOI Listing
July 2020

Darcy's Law without Friction in Active Nematic Rheology.

Phys Rev Lett 2020 May;124(18):187801

SUPA, School of Physics and Astronomy, University of Edinburgh, Peter Guthrie Tait Road, Edinburgh EH9 3FD, United Kingdom.

We study the dynamics of a contractile active nematic fluid subjected to a Poiseuille flow. In a quasi-1D geometry, we find that the linear rheology of this material is reminiscent of Darcy's law in complex fluids, with a pluglike flow decaying to zero over a well-defined "permeation" length. As a result, the viscosity increases with size, but never diverges, thereby evading the yield stress predicted by previous theories. We find strong shear thinning controlled by an active Ericksen number quantifying the ratio between external pressure difference and internal active stresses. In 2D, the increase of linear regime viscosity with size only persists up to a critical length beyond which we observe active turbulent patterns, with very low apparent viscosity. The ratio between the critical and permeation length determining the stability of the Darcy regime can be made indefinitely large by varying the flow aligning parameter or magnitude of nematic order.
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http://dx.doi.org/10.1103/PhysRevLett.124.187801DOI Listing
May 2020

Diffusion processes modeling in magnetic resonance imaging.

Insights Imaging 2020 Apr 28;11(1):60. Epub 2020 Apr 28.

Central Institute of Traumatology and Orthopaedics named after N. N. Priorov, 10, ul. Priorova, Moscow, 127299, Russia.

Background: The paper covers modern approaches to the evaluation of neoplastic processes with diffusion-weighted imaging (DWI) and proposes a physical model for monitoring the primary quantitative parameters of DWI and quality assurance. Models of hindered and restricted diffusion are studied.

Material And Method: To simulate hindered diffusion, we used aqueous solutions of polyvinylpyrrolidone with concentrations of 0 to 70%. We created siloxane-based water-in-oil emulsions that simulate restricted diffusion in the intracellular space. To obtain a high signal on DWI in the broadest range of b values, we used silicon oil with high T: cyclomethicone and caprylyl methicone. For quantitative assessment of our phantom, we performed DWI on 1.5T magnetic resonance scanner with various fat suppression techniques. We assessed water-in-oil emulsion as an extracorporeal source signal by simultaneously scanning a patient in whole-body DWI sequence.

Results: We developed phantom with control substances for apparent diffusion coefficient (ADC) measurements ranging from normal tissue to benign and malignant lesions: from 2.29 to 0.28 mm/s. The ADC values of polymer solutions are well relevant to the mono-exponential equation with the mean relative difference of 0.91%.

Conclusion: The phantom can be used to assess the accuracy of the ADC measurements, as well as the effectiveness of fat suppression. The control substances (emulsions) can be used as a body marker for quality assurance in whole-body DWI with a wide range of b values.
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http://dx.doi.org/10.1186/s13244-020-00863-wDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7188746PMC
April 2020

Spectroscopic and Theoretical Insights into Surprisingly Effective Sm(III) Extraction from Alkaline Aqueous Media by -Phenylenediamine-Derived Sulfonamides.

Inorg Chem 2020 May 27;59(10):6884-6894. Epub 2020 Apr 27.

Department of Chemistry and Biochemistry, Florida International University, Miami, Florida 33199, United States.

Alkaline high-level waste (HLW) generated as a result of years of nuclear weapons production has complicated composition and requires comprehensive treatment methods, which would allow concentrating its most radiotoxic components in a small volume for geological disposal. We have investigated six alkyl-substituted -phenylenediamine-derived sulfonamides for extraction and consecutive stripping of Sm(III) from alkaline aqueous media. Up to 81% of Sm(III) recovery at pH 13.0-13.5 was achieved by disulfonamide () or /EtN in CHCl, measured after contact with organic phases and subsequent stripping with 0.1 M HNO. The use of EtN dramatically enhances Sm(III) extraction at lower pH ranges (10.5-11.5) but decreases extraction at pH 13.0-13.5, while control experiments with EtN and no showed no extraction. Analysis of the extraction equilibria gave a 1:1 sulfonamide-Sm(III) complexation ratio, with the extracted species also presumed to contain coordinated HO or OH, as also shown by DFT calculations. Titration experiments of sulfonamides with Sm(III) in CHCN were consistent with a 1:1 complexation ratio of to Sm(III) with a = 6.6 × 10 M derived from nonlinear regression analysis of the 1:1 binding isotherm. Theoretical DFT calculations determined the structures of possible species formed during extraction and the thermodynamics of extraction processes based on several initial [Sm(OH)(NO)(HO)] species and 1:1 Sm(III)/ complexes formed in the organic phase, in which complexes to Sm(III) in its bis-deprotonated form (denoted below as ). Organization of close ion pairs of type {Na[Sm()(OH)]·2HO} was shown to be thermodynamically favorable for extraction from alkaline aqueous media with pH = 13.0-13.5. Theoretical calculations also demonstrated thermodynamically favorable coordination to Am(III).
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http://dx.doi.org/10.1021/acs.inorgchem.0c00309DOI Listing
May 2020

Theoretical study of the reaction mechanism and kinetics of the phenyl + propargyl association.

Phys Chem Chem Phys 2020 Apr;22(13):6868-6880

Department of Chemistry and Biochemistry, Florida International University, Miami, Florida 33199, USA.

Potential energy surface for the phenyl + propargyl radical recombination reaction has been studied at the CCSD(T)-F12/cc-pVTZ-f12//B3LYP/6-311G** level of theory for the closed-shell singlet species and at the triplet-singlet gap CASPT2/cc-pVTZ-CCSD(T)-F12/cc-pVTZ-f12//CASSCF/cc-pVTZ level of theory for the diradical species. High-pressure limit rate constants for the barrierless channels were evaluated with variable reaction coordinate transition state theory (VRC-TST). Rice-Ramsperger-Kassel-Marcus Master Equation (RRKM-ME) calculations have been performed to assess temperature- and pressure-dependent phenomenological rate constants and product branching ratios. The entrance channels of the radical association reaction produce 3-phenyl-1-propyne and phenylallene which can further dissociate/isomerize into a variety of unimolecular and bimolecular products. Theoretical evidence is presented that, at combustion relevant conditions, the phenyl + propargyl recombination provides a feasible mechanism for the addition of a second five-member ring to the first six-member aromatic ring producing the prototype two-ring species indene and indenyl. Rate expressions for all important reaction channels in a broad range of temperatures and pressures have been generated for kinetic modeling.
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http://dx.doi.org/10.1039/d0cp00306aDOI Listing
April 2020

A combined rheometry and imaging study of viscosity reduction in bacterial suspensions.

Proc Natl Acad Sci U S A 2020 02 21;117(5):2326-2331. Epub 2020 Jan 21.

SUPA and School of Physics & Astronomy, The University of Edinburgh, Edinburgh EH9 3FD, United Kingdom.

Suspending self-propelled "pushers" in a liquid lowers its viscosity. We study how this phenomenon depends on system size in bacterial suspensions using bulk rheometry and particle-tracking rheoimaging. Above the critical bacterial volume fraction needed to decrease the viscosity to zero, [Formula: see text], large-scale collective motion emerges in the quiescent state, and the flow becomes nonlinear. We confirm a theoretical prediction that such instability should be suppressed by confinement. Our results also show that a recent application of active liquid-crystal theory to such systems is untenable.
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http://dx.doi.org/10.1073/pnas.1912690117DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7007524PMC
February 2020

Gas-Phase Formation of Fulvenallene (CH) via the Jahn-Teller Distorted Tropyl (CH) Radical Intermediate under Single-Collision Conditions.

J Am Chem Soc 2020 Feb 30;142(6):3205-3213. Epub 2020 Jan 30.

Department of Chemistry , University of Hawai'i at Manoa , Honolulu , Hawaii 96822 , United States.

The fulvenallene molecule (CH) has been synthesized via the elementary gas-phase reaction of the methylidyne radical (CH) with the benzene molecule (CH) on the doublet CH surface under single collision conditions. The barrier-less route to the cyclic fulvenallene molecule involves the addition of the methylidyne radical to the π-electron density of benzene leading eventually to a Jahn-Teller distorted tropyl (CH) radical intermediate and exotic ring opening-ring contraction sequences terminated by atomic hydrogen elimination. The methylidyne-benzene system represents a benchmark to probe the outcome of the elementary reaction of the simplest hydrocarbon radical-methylidyne-with the prototype of a closed-shell aromatic molecule-benzene-yielding nonbenzenoid fulvenallene. Combined with electronic structure and statistical calculations, this bimolecular reaction sheds light on the unusual reaction dynamics of Hückel aromatic systems and remarkable (polycyclic) reaction intermediates, which cannot be studied via classical organic, synthetic methods, thus opening up a versatile path to access this previously largely obscure class of fulvenallenes.
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http://dx.doi.org/10.1021/jacs.9b13269DOI Listing
February 2020

Synthesis and ε-Caprolactone Polymerization Activity of Electron-Deficient Gallium and Aluminum Species Containing a Charged Redox-Active dpp-Bian Ligand.

Inorg Chem 2019 Dec 5;58(24):16559-16573. Epub 2019 Nov 5.

G. A. Razuvaev Institute of Organometallic Chemistry , Russian Academy of Sciences , Tropinina 49 , Nizhny Novgorod 603950 , Russian Federation.

The synthesis of electron-deficient gallium- and aluminum-centered species containing a redox-active dpp-Bian ligand (dpp-Bian = 1,2-bis[(2,6-diisopropylphenyl)imino]acenaphthene) is described. The reaction of digallane [(dpp-Bian)Ga-Ga(dpp-Bian)] with [PhC][PF] or AgPF resulted in polyoxidized species [(dpp-Bian)GaF] (), [(dpp-Bian)H][PF] (), and [(dpp-Bian)GaF(OPF)] (). The reaction of digallane with B(CF) led to electron-deficient gallylene [(dpp-Bian)GaB(CF)] of a dpp-Bian radical anion. The soft oxidation of digallane with tosyl cyanide gave the trinuclear cationic species [(dpp-Bian)Ga(Tos)Ga(Tos)Ga(dpp-Bian)][Ga(CN)] () containing dpp-Bian radical anions. The reaction of [(dpp-Bian)AlEt] with 1 equiv of [PhC][B(CF)] resulted in the cationic complex [(dpp-Bian)AlEt][B(CF)] () of neutral dpp-Bian, while the treatment of [(dpp-Bian)AlEt(EtO)] with 1 equiv of [PhC][B(CF)] resulted in the compound [(dpp-Bian)AlEt(EtO)][B(CF)] () of a dpp-Bian radical anion. The reaction of diethylaluminum derivative [(dpp-Bian)AlEt] with 1 equiv of B(CF) gave the cationic complex [{(dpp-Bian)AlEt}F][EtB(CF)] () containing radical-anion dpp-Bian ligands. The paramagnetic compounds , , , , , and were characterized by electron paramagnetic resonance spectroscopy, and the diamagnetic complex was characterized by NMR spectroscopy. The molecular structures of - and were established by single-crystal X-ray diffraction analysis. Compounds and - were found to be active initiators for immortal ring-opening polymerization of ε-caprolactone.
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http://dx.doi.org/10.1021/acs.inorgchem.9b02592DOI Listing
December 2019

A simulation study of aggregation mediated by production of cohesive molecules.

Soft Matter 2019 Nov 31;15(44):9120-9132. Epub 2019 Oct 31.

SUPA, School of Physics and Astronomy, University of Edinburgh, Edinburgh, EH9 3FD, UK.

Mechanical interactions between biological cells can be mediated by secreted products. Here, we investigate how such a scenario could affect the cells' collective behaviour. We show that if the concentration field of secreted products around a cell can be considered to be in steady state, this scenario can be mapped onto an effective attractive interaction that depends on the local cell density. Using a field-theory approach, this density-dependent attraction gives rise to a cubic term in the Landau-Ginzburg free energy density. In continuum field simulations this can lead to "nucleation-like" appearance of homogeneous clusters in the spinodal phase separation regime. Implementing the density-dependent cohesive attraction in Brownian dynamics simulations of a particle-based model gives rise to similar "spinodal nucleation" phase separation behaviour.
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http://dx.doi.org/10.1039/c9sm01462dDOI Listing
November 2019

Molecular mass growth through ring expansion in polycyclic aromatic hydrocarbons via radical-radical reactions.

Nat Commun 2019 08 15;10(1):3689. Epub 2019 Aug 15.

Department of Chemistry and Biochemistry, Florida International University, Miami, FL, 33199, USA.

Polycyclic aromatic hydrocarbons (PAHs) represent key molecular building blocks leading to carbonaceous nanoparticles identified in combustion systems and extraterrestrial environments. However, the understanding of their formation and growth in these high temperature environments has remained elusive. We present a mechanism through laboratory experiments and computations revealing how the prototype PAH-naphthalene-can be efficiently formed via a rapid 1-indenyl radical-methyl radical reaction. This versatile route converts five- to six-membered rings and provides a detailed view of high temperature mass growth processes that can eventually lead to graphene-type PAHs and two-dimensional nanostructures providing a radical new view about the transformations of carbon in our universe.
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http://dx.doi.org/10.1038/s41467-019-11652-5DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6695427PMC
August 2019

Particle-resolved lattice Boltzmann simulations of 3-dimensional active turbulence.

Soft Matter 2019 Oct;15(39):7747-7756

Division of Physical Chemistry, Lund University, Box 124, S-221 00 Lund, Sweden.

Collective behaviour in suspensions of microswimmers is often dominated by the impact of long-ranged hydrodynamic interactions. These phenomena include active turbulence, where suspensions of pusher bacteria at sufficient densities exhibit large-scale, chaotic flows. To study this collective phenomenon, we use large-scale (up to N = 3 × 106) particle-resolved lattice Boltzmann simulations of model microswimmers described by extended stresslets. Such system sizes enable us to obtain quantitative information about both the transition to active turbulence and characteristic features of the turbulent state itself. In the dilute limit, we test analytical predictions for a number of static and dynamic properties against our simulation results. For higher swimmer densities, where swimmer-swimmer interactions become significant, we numerically show that the length- and timescales of the turbulent flows increase steeply near the predicted finite-system transition density.
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http://dx.doi.org/10.1039/c9sm00774aDOI Listing
October 2019

Rheological Behavior and in Situ Confocal Imaging of Bijels Made by Mixing.

Langmuir 2019 Aug 12;35(33):10927-10936. Epub 2019 Aug 12.

School of Physics and Astronomy , University of Edinburgh , James Clerk Maxwell Building, Peter Guthrie Tait Road , Edinburgh EH9 3FD , U.K.

Bijels (bicontinuous interfacially jammed emulsion gels) have the potential to be useful in many different applications due to their internal connectivity and the possibility of efficient mass transport through the channels. Recently, new methods of making the bijel have been proposed, which simplify the fabrication process, making commercial application more realistic. Here, we study the flow properties of bijels prepared by mixing alone using oscillatory rheology combined with confocal microscopy and also squeezing flow experiments. We found that the bijel undergoes a two-step yielding process where the first step corresponds to the fluidizing of the interface, allowing the motion of the structure, and the second step corresponds to the breaking of the structure. In the squeeze flow experiments, the yield stress of the bijel is observed to show a power law dependence on squeezing speed. However, when stress in excess of yield stress is plotted against shear rate, all the different squeeze flow data show a superposition.
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http://dx.doi.org/10.1021/acs.langmuir.9b00636DOI Listing
August 2019

Dry active turbulence in a model for microtubule-motor mixtures.

Soft Matter 2019 Aug 12;15(30):6038-6043. Epub 2019 Jul 12.

SUPA, School of Physics and Astronomy, The University of Edinburgh, James Clerk Maxwell Building, Peter Guthrie Tait Road, Edinburgh, EH9 3FD, UK.

We study the dynamics and phase behaviour of a dry suspension of microtubules and molecular motors. We obtain a set of continuum equations by rigorously coarse graining a microscopic model where motor-induced interactions lead to parallel or antiparallel ordering. Through numerical simulations, we show that this model generically creates either stable stripes, or a never-settling pattern where stripes periodically form, rotate and then split up. We derive a minimal model which displays the same instability as the full model, and clarifies the underlying physical mechanism. The necessary ingredients are an extensile flux arising from microtubule sliding and an interfacial torque favouring ordering along density gradients. We argue that our minimal model unifies various previous observations of chaotic behaviour in dry active matter into a general universality class.
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http://dx.doi.org/10.1039/c9sm00558gDOI Listing
August 2019

Phenotypic and molecular cytogenetic variability in calendula (Calendula officinalis L.) cultivars and mutant lines obtained via chemical mutagenesis.

Sci Rep 2019 06 24;9(1):9155. Epub 2019 Jun 24.

Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, 32 Vavilov St, Moscow, 119991, Russian Federation.

The morphological, meiotic and chromosomal variability were studied in two cultivars of Calendula officinalis L. and their mutant lines obtained though chemical mutagenesis using diethyl sulphate (DES) (0.04%, 0.08%) and dimethyl sulphate (DMS) (0.025%, 0.05%). The studied cultivars displayed different sensitivity to DMS and DES mutagens. More M1 plants with morphological changes were observed in C. officinalis cv. 'Zolotoe more' than in cv. 'Rajskij sad'. DMS and DES at low concentrations had positive effects on main agro-metrical traits in both cultivars including plant height, inflorescence diameter and number of inflorescences per plant. Dose-dependent increase in number of various meiotic abnormalities was revealed in both mutant lines. Comparative karyotype analysis and FISH-based visualization of 45S and 5S rDNA indicated a high level of karyotype stability in M1 and M2 plants. Seed treatments with DMS and DES at certain concentrations resulted in higher yields of inflorescences in M1 plants compared to the control. In M2 generation, dose-dependent reduction in the yields of inflorescences was observed. Our findings demonstrate that DMS and DES at low concentrations have great potential in calendula mutation breeding.
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http://dx.doi.org/10.1038/s41598-019-45738-3DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6591508PMC
June 2019

Elucidating the Chemical Dynamics of the Elementary Reactions of the 1-Propynyl Radical (CHCC; XA) with Methylacetylene (HCCCH; XA) and Allene (HCCCH; XA).

J Phys Chem A 2019 Jul 25;123(26):5446-5462. Epub 2019 Jun 25.

Department of Chemistry , University of Hawai'i at Manoa , Honolulu , Hawaii 96822 , United States.

The reactions of the 1-propynyl radical (CHCC; XA) with two CH isomers, methylacetylene (HCCCH; XA) and allene (HCCCH; XA), along with their (partially) deuterated counterparts were explored at collision energies of 37 kJ mol, exploiting crossed molecular beams to unravel the chemical reaction dynamics to synthesize distinct CH isomers under single collision conditions. The forward convolution fitting of the laboratory data along with ab initio and statistical calculations revealed that both reactions have no entrance barrier, proceed via indirect (complex-forming) reaction dynamics involving CH intermediates with life times longer than their rotation period(s), and are initiated by the addition of the 1-propynyl radical with its radical center to the π-electron density of the unsaturated hydrocarbon at the terminal carbon atoms of methylacetylene (C1) and allene (C1/C3). In the methylacetylene system, the initial collision complexes undergo unimolecular decomposition via tight exit transition states by atomic hydrogen loss, forming dimethyldiacetylene (CHCCCCCH) and 1-propynylallene (HCCCHCCCH) in overall exoergic reactions (123 and 98 kJ mol) with a branching ratio of 9.4 ± 0.1; the methyl group of the 1-propynyl reactant acts solely as a spectator. On the other hand, in the allene system, our experimental data exhibit the formation of the fulvene (c-CHCH) isomer via a six-step reaction sequence with two higher energy isomers-hexa-1,2-dien-4-yne (HCCCHCCCH) and hexa-1,4-diyne (HCCCHCCCH)-also predicted to be formed based on our statistical calculations. The pathway to fulvene advocates that, in the allene-1-propynyl system, the methyl group of the 1-propynyl reactant is actively engaged in the reaction mechanism to form fulvene. Because both reactions are barrierless and exoergic and all transition states are located below the energy of the separated reactants, the hydrogen-deficient CH isomers identified in our investigation are predicted to be synthesized in low-temperature environments, such as in hydrocarbon-rich atmospheres of planets and their moons such as Titan along with cold molecular clouds such as Taurus Molecular Cloud-1.
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http://dx.doi.org/10.1021/acs.jpca.9b03746DOI Listing
July 2019

Gas phase synthesis of [4]-helicene.

Nat Commun 2019 04 3;10(1):1510. Epub 2019 Apr 3.

Department of Chemistry, University of California, Berkeley, CA, 94720, USA.

A synthetic route to racemic helicenes via a vinylacetylene mediated gas phase chemistry involving elementary reactions with aryl radicals is presented. In contrast to traditional synthetic routes involving solution chemistry and ionic reaction intermediates, the gas phase synthesis involves a targeted ring annulation involving free radical intermediates. Exploiting the simplest helicene as a benchmark, we show that the gas phase reaction of the 4-phenanthrenyl radical ([CH]) with vinylacetylene (CH) yields [4]-helicene (CH) along with atomic hydrogen via a low-barrier mechanism through a resonance-stabilized free radical intermediate (CH). This pathway may represent a versatile mechanism to build up even more complex polycyclic aromatic hydrocarbons such as [5]- and [6]-helicene via stepwise ring annulation through bimolecular gas phase reactions in circumstellar envelopes of carbon-rich stars, whereas secondary reactions involving hydrogen atom assisted isomerization of thermodynamically less stable isomers of [4]-helicene might be important in combustion flames as well.
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http://dx.doi.org/10.1038/s41467-019-09224-8DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6447558PMC
April 2019

Theoretical Study of the Reaction Mechanism and Kinetics of the Phenyl + Allyl and Related Benzyl + Vinyl Associations.

J Phys Chem A 2019 Mar 25;123(9):1720-1729. Epub 2019 Feb 25.

Department of Chemistry and Biochemistry , Florida International University , Miami , Florida 33199 , United States.

Potential energy surfaces for the allyl + phenyl and benzyl + vinyl barrierless radical association reactions have been studied at the CCSD(T)-F12/cc-pVTZ-f12//B3LYP/6-311G** level of theory. Variable reaction coordinate transition state theory (VRC-TST) has been employed to evaluate high-pressure limit rate constants for the barrierless channels. Then, Rice-Ramsperger-Kassel-Marcus master equation (RRKM-ME) calculations have been performed to assess phenomenological rate constants and product branching ratios of various reaction channels at different temperatures and pressures. The initial step of both radical association reactions produces 3-phenylpropene which can further dissociate into a variety of bimolecular products including the indene precursor 1-phenylallyl + H. The results showed that at typical combustion conditions the collisional stabilization of 3-phenylpropene dominates both the phenyl + allyl and benzyl + vinyl reactions at temperatures below 1000 K and remains important at high pressures up to 2500 K. The main bimolecular products of the two reactions at high temperatures are predicted to be benzyl + vinyl and phenyl + allyl, respectively. The well-skipping mechanism to form 1-phenylallyl directly in the allyl + phenyl and benzyl + vinyl reactions appeared to be not significant, however, the reactions can provide some contributions into the formation of the indene precursor via the 3-phenylpropene stabilization/dissociation sequence and most of all, via the formation of 3-phenylpropene itself, which then can undergo H-abstraction by available radicals to produce 1-phenylallyl. The allyl + phenyl reaction can also contribute to the formation of two-ring PAH by producing benzyl radical at high temperatures, either by the well-skipping or stabilization/dissociation mechanisms; in turn, benzyl can readily react with acetylene or propargyl radical to form indene or naphthalene precursors, respectively. Rate expressions for all important reaction channels in a broad range of temperatures and pressures have been generated for kinetic modeling.
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http://dx.doi.org/10.1021/acs.jpca.9b00345DOI Listing
March 2019

Low valent Al(ii)-Al(ii) catalysts as highly active ε-caprolactone polymerization catalysts: indication of metal cooperativity through DFT studies.

Dalton Trans 2018 Oct;47(39):13800-13808

Institut de Chimie (UMR CNRS 7177), Université de Strasbourg, 4, rue Blaise Pascal, 67000 Strasbourg, France.

The present study first describes the reactivity of low valent Al(ii) and Ga(ii) complexes of the type (dpp-bian)M-M(dpp-bian) (1, M = Al; 2, Ga; dpp-bian2- = 1,2-bis-(2,6-iPr2-C6H3)-acenaphthenequinonediamido) with cyclic esters/carbonates such as ε-caprolactone (CL) and trimethylene carbonate (TMC). CL and TMC both readily coordinate to the Al(ii) species 1 to form the corresponding bis-adducts (dpp-bian)Al(L)-(L)Al(dpp-bian) (3, L = CL; 4, L = TMC), which were structurally characterized confirming that the Al(ii)-Al(ii) dimetallic backbone retains its integrity in the presence of such cyclic polar substrates. In contrast, the less Lewis acidic Ga(ii) analogue 2 shows no reaction in the presence of stoichiometric amounts of CL and TMC at room temperature. In combination with BnOH, the dinuclear Al(ii) species 1 revealed to be an extremely active Al(ii) initiator for the controlled ROP of CL at room temperature, outperforming all its Al(iii) congeners reported thus far. Detailed DFT studies on the ROP mechanism are consistent with a process occurring thanks to the metallic cooperativity between the two Al(ii) proximal (since directly bonded) metal centers in 1, which undoubtedly favors the ROP process through bimetallic activation and thus rationalizes the unusually high CL ROP activity at room temperature.
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http://dx.doi.org/10.1039/c8dt02614aDOI Listing
October 2018

Proximal Pocket Controls Alkene Oxidation Selectivity of Cytochrome P450 and Chloroperoxidase toward Small, Nonpolar Substrates.

J Phys Chem B 2018 08 8;122(32):7828-7838. Epub 2018 Aug 8.

Department of Chemistry and Biochemistry , Florida International University , 11200 8th Street , Miami , Florida 33199 , United States.

This paper examines the influence of the proximal pockets of cytochrome P450 and chloroperoxidase (CPO) on the relative favorability of catalytic epoxidation and allylic hydroxylation of olefins, a type of alkene oxidation selectivity. The study employs quantum mechanical models of the active site to isolate the proximal pocket's influence on the barrier for the selectivity-determining step for each reaction, using cyclohexene and cis-β-methylstyrene as substrates. The proximal pocket is found to preference epoxidation by 2-5 kcal/mol, the largest value being for CPO, converting the active heme-thiolate moiety from being intrinsically hydroxylation-selective to being intrinsically epoxidation-selective. This theoretical study, the first to correctly predict these enzymes' preference for epoxidation of allylic substrates, strongly suggests that the proximal pocket is the key determinant of alkene oxidation selectivity. The selectivity for epoxidation can be rationalized in terms of the proximal pocket's modulation of the thiolate's electron "push" and consequent influence on the heme redox potential and the basicity of the trans ligand.
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http://dx.doi.org/10.1021/acs.jpcb.8b04279DOI Listing
August 2018

A Theoretical Study of Pyrolysis of exo-Tetrahydrodicyclopentadiene and Its Primary and Secondary Unimolecular Decomposition Products.

J Phys Chem A 2018 Jun 24;122(22):4920-4934. Epub 2018 May 24.

Department of Chemistry , University of Hawaii at Manoa , Honolulu , Hawaii 96822 , United States.

Theoretical calculations of the rate constants and product branching ratios in the pyrolysis of exo-tetrahydrodicyclopentadiene (JP-10) and its initial decomposition products at combustion-relevant pressures and temperatures were performed and compared to the experimental results from the recently reported molecular beam photoionization mass spectrometry study of the pyrolysis of JP-10 ( Zhao et al. Phys. Chem. Chem. Phys. 2017 , 19 , 15780 - 15807 ). The results allow us to quantitatively assess the decomposition mechanisms of JP-10 by a direct comparison with the nascent product distribution-including radicals and thermally labile closed-shell species-detected in the short-residence-time molecular beam photoionization mass spectrometry experiment. In accord with the experimental data, the major products predicted by the theoretical modeling include methyl radical (CH), acetylene (CH), vinyl radical (CH), ethyl radical (CH), ethylene (CH), allyl radical (CH), 1,3-butadiene (CH), cyclopentadienyl radical (CH), cyclopentadiene (CH), cyclopentenyl radical (CH), cyclopentene (CH), fulvene (CH), benzene (CH), toluene (CH), and 5-methylene-1,3-cyclohexadiene (CH). We found that ethylene, allyl radical, cyclopentadiene, and cyclopentenyl radical are significant products at all combustion-relevant conditions, whereas the relative yields of the other products depend on temperature. The most significant temperature trends predicted are increasing yields of the C2 and C4 species and decreasing yields of the C1, C6, and C7 groups with increasing temperature. The calculated pressure effect on the rate constant for the decomposition of JP-10 via initial C-H bond cleavages becomes significant at temperatures above 1500 K. The initially produced radicals will react away to form closed-shell molecules, such as ethylene, propene, cyclopentadiene, cyclopentene, fulvene, and benzene, which were observed as the predominant fragments in the long-residence-time experiment. The calculated rate constants and product branching ratios should prove useful to improve the existing kinetic models for the JP-10 pyrolysis.
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http://dx.doi.org/10.1021/acs.jpca.8b02934DOI Listing
June 2018

Nonfluoroscopic catheter ablation of paroxysmal atrial fibrillation.

Pacing Clin Electrophysiol 2018 06 30;41(6):611-619. Epub 2018 Apr 30.

Herz- und Gefäßzentrum, Bad Bevensen, Germany.

Aims: Radiofrequency catheter ablation of atrial fibrillation (AF) is one of the most complex ablation procedures. Both patients and operators are exposed to scattered radiation. This study evaluated the safety and efficacy of intracardiac echo (ICE)-guided pulmonary vein isolation (PVI) without fluoroscopy.

Methods: We retrospectively analyzed the data of 481 consecutive patients with paroxysmal AF undergoing radiofrequency PVI with the CARTO 3 system (Biosense Webster, Diamond Bar, CA, USA). ICE-guided PVI without fluoroscopy and without CT/MRI integration (Nonfluoro group) was performed for 245 patients, and conventional fluoroscopy-guided PVI (Fluoro group) was performed for 236 patients. The primary safety endpoint was the incidence of major adverse events. The primary efficacy endpoint was freedom from AF during follow-up. Secondary endpoints included procedure duration, fluoroscopy duration, and acute PVI rate.

Results: Mean procedure times between groups were similar (108.8 ± 18.2 minutes in the Non-fluoro group vs 113.6 ± 26.8 minutes in the Fluoro group; P  =  not significant [NS]). Acute PVI was achieved in all patients, with mean radiofrequency application times of 43.4 ± 7.5 and 44.4 ± 10.7 minutes for the Nonfluoro and Fluoro groups, respectively (P  =  NS). The incidence of cardiac tamponade was 1.2% (3/245 patients) in the Nonfluoro group and 0.8% (2/236 patients) in the Fluoro group (P  =  NS). During 15.2 ± 4.1 months of follow-up, after a single procedure, AF recurrence was documented in 65 of 245 (26.5%) patients and 61 of 236 (25.8%) patients in the Nonfluoro and Fluoro groups, respectively (P  =  NS).

Conclusions: Nonfluoroscopic ICE-guided catheter ablation of AF without prior cardiac image integration or angiography is feasible and safe. PVI without fluoroscopy did not affect procedure duration or long-term efficacy.
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http://dx.doi.org/10.1111/pace.13321DOI Listing
June 2018

Kinetic theory of pattern formation in mixtures of microtubules and molecular motors.

Phys Rev E 2018 Feb;97(2-1):022412

SUPA, School of Physics and Astronomy, University of Edinburgh, James Clerk Maxwell Building, Peter Guthrie Tait Road, Edinburgh EH9 3FD, United Kingdom.

In this study we formulate a theoretical approach, based on a Boltzmann-like kinetic equation, to describe pattern formation in two-dimensional mixtures of microtubular filaments and molecular motors. Following the previous work by Aranson and Tsimring [Phys. Rev. E 74, 031915 (2006)PLEEE81539-375510.1103/PhysRevE.74.031915] we model the motor-induced reorientation of microtubules as collision rules, and devise a semianalytical method to calculate the corresponding interaction integrals. This procedure yields an infinite hierarchy of kinetic equations that we terminate by employing a well-established closure strategy, developed in the pattern-formation community and based on a power-counting argument. We thus arrive at a closed set of coupled equations for slowly varying local density and orientation of the microtubules, and study its behavior by performing a linear stability analysis and direct numerical simulations. By comparing our method with the work of Aranson and Tsimring, we assess the validity of the assumptions required to derive their and our theories. We demonstrate that our approximation-free evaluation of the interaction integrals and our choice of a systematic closure strategy result in a rather different dynamical behavior than was previously reported. Based on our theory, we discuss the ensuing phase diagram and the patterns observed.
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http://dx.doi.org/10.1103/PhysRevE.97.022412DOI Listing
February 2018
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