9 research outputs found
Effect on Ring Current of the KekuleĢ Vibration in Aromatic and Antiaromatic Rings
Derivative currentādensity maps are used to follow the changes in ring-current (and hence, on the magnetic criterion, the changes in aromaticity) with the KekuleĢ vibrations of the prototypical aromatic, antiaromatic, and nonaromatic systems of benzene, cyclooctatetraene (COT), and borazine. Maps are computed at the ipsocentric CHF/6-31G**//RHF/6-31G** level. The first-derivative map for benzene shows a growing-in of localized bond currents, and the second-derivative map shows a pure, paratropic āantiring-currentā, leading to the conclusion that vibrational motion along the KekuleĢ mode will reduce the net aromaticity of benzene, on average. For planar-constrained <i>D</i><sub>4<i>h</i></sub> COT, the KekuleĢ mode (positive for reduction of bond-length alternation) increases paratropicity at both first and second order, indicating an average increase in antiaromaticity with zero-point motion along this mode. On the ring-current criterion, breathing expansions of benzene and <i>D</i><sub>4<i>h</i></sub> COT reduce aromaticity and increase antiaromaticity, respectively
Simulating the Pyrolysis of Polyazides: a Mechanistic Case Study of the [P(N<sub>3</sub>)<sub>6</sub>]<sup>ā</sup> Anion
Pyrolysis of the homoleptic azido complex [PĀ(N<sub>3</sub>)<sub>6</sub>]<sup>ā</sup> was simulated using density functional
theory based molecular dynamics and analyzed further using electronic-structure
calculations in atom-centered basis sets to calculate the geometries
and electronic structures. Simulations at 600 and 1200 K predict a
thermally induced and, on the simulation time scale, irreversible
dissociation of an azido anion. The ligand loss is accompanied by
a barrierless (free-energy) transition of the geometry of the complex
coordination sphere from octahedral to trigonal bipyramidal. [PĀ(N<sub>3</sub>)<sub>5</sub>] is fluxional and engages in pseudorotation
via a Berry mechanism
Effect of Ring Size and Migratory Groups on [1,<i>n</i>] Suprafacial Shift Reactions. Confirmation of Aromatic and Antiaromatic Transition-State Character by Ring-Current Analysis
Suprafacial sigmatropic
shift reactions of 5-substituted cyclopentadienes,
3-substituted cyclopropenes, and 7-substituted cycloheptatrienes have
been studied computationally at the MP2/6-31+G* level for structures
and energetics and with the ipsocentric method at the CHF/6-31G**
level to calculate currentādensity maps. The hydrogen shifts
in cyclopentadienes have a diatropic ring current indicating aromatic,
cyclopentadienide anion character. This result stands in contrast
to the fluorine shift in 5-fluorocyclopentadiene which requires much
more energy and has a paratropic ring current in the TS pointing to
antiaromatic, cyclopentadienyl cation character. [1,3] hydrogen shifts
in cyclopropenes are very difficult, passing through transition states
that have an extended CāC bond. For 3-fluorocyclopropene, the
[1,3] fluorine shift is much easier than the hydrogen shift. For 7-fluorocycloheptatriene,
the [1,7] hydrogen shift is predicted but requires very high energy
and has a paratropic ring current and antiaromatic character. The
[1,7] suprafacial fluorine shift is relatively easy, having a TS with
cycloheptatrienyl cation character. Patterns of currents, and the
reversal for H and F migration, are rationalized by orbital analysis
based on the ipsocentric method. Calculated charges and structural
features for reactants and transition states support these conclusions
Concurrence between Current Density, Nucleus-Independent Chemical Shifts, and Aromatic Stabilization Energy: The Case of Isomeric [4]- and [5]Phenylenes
The 17 isomers of the [4]- and [5]Āphenylenes
have been studied
with three different computational levels of current-density analysis
(CDA) and by calculation of the out-of-plane contribution to nucleus-independent
chemical shifts (NICS<sub>Ļzz</sub>). Current-density maps for
these isomeric phenylenes are typically dominated by strong paratropic
ring currents in four-membered rings. The relative energies of the
isomers, which differ only through the effects of differential strain
and aromaticity, were computed at the B3LYP/6-311G* computational
level. It was found that the three levels of CDA correlate well among
themselves and with NICS<sub>Ļzz</sub>. The latter correlation
is improved when the ring sum āNICS<sub>Ļzz</sub> for
each isomer is correlated to the ring-current sum ā<i>J</i> extracted from CDA. The strain-corrected relative energies
of the isomers correlate linearly with āNICS<sub>Ļzz</sub>. In particular, the compatibility of different summed quantities
with easily computed HuĢckelāLondon ring currents suggests
a simply calculated measure for dealing with global aromaticity of
polycyclic systems
Unidentified specimen sp.
Accurately measuring carbon flows is a challenge for
understanding
processes such as diverse intracellular metabolic pathways and predator-prey
interactions. Combined with stable isotope probing (SIP), single-cell
Raman spectroscopy was demonstrated for the first time to link the
food chain from carbon substrate to bacterial prey up to predators
at the single-cell level in a quantitative and nondestructive manner. <i>Escherichia coli</i> OP50 with different <sup>13</sup>C content,
which were grown in a mixture of <sup>12</sup>C- and fully carbon-labeled <sup>13</sup>C-glucose (99%) as a sole carbon source, were fed to the
nematode. The <sup>13</sup>C signal in <i>Caenorhabditis elegans</i> was proportional to the <sup>13</sup>C content in <i>E. coli</i>. Two Raman spectral biomarkers (Raman bands for phenylalanine at
1001 cm<sup>ā1</sup> and thymine at 747 cm<sup>ā1</sup> Raman bands), were used to quantify the <sup>13</sup>C content in <i>E. coli</i> and <i>C. elegans</i> over a range of
1.1ā99%. The phenylalanine Raman band was a suitable biomarker
for prokaryotic cells and thymine Raman band for eukaryotic cells.
A biochemical mechanism accounting for the Raman red shifts of phenylalanine
and thymine in response to <sup>13</sup>C-labeling is proposed in
this study and is supported by quantum chemical calculation. This
study offers new insights of carbon flow via the food chain and provides
a research tool for microbial ecology and investigation of biochemical
pathways
Stable Isotope Probing and Raman Spectroscopy for Monitoring Carbon Flow in a Food Chain and Revealing Metabolic Pathway
Accurately measuring carbon flows is a challenge for
understanding
processes such as diverse intracellular metabolic pathways and predator-prey
interactions. Combined with stable isotope probing (SIP), single-cell
Raman spectroscopy was demonstrated for the first time to link the
food chain from carbon substrate to bacterial prey up to predators
at the single-cell level in a quantitative and nondestructive manner. <i>Escherichia coli</i> OP50 with different <sup>13</sup>C content,
which were grown in a mixture of <sup>12</sup>C- and fully carbon-labeled <sup>13</sup>C-glucose (99%) as a sole carbon source, were fed to the
nematode. The <sup>13</sup>C signal in <i>Caenorhabditis elegans</i> was proportional to the <sup>13</sup>C content in <i>E. coli</i>. Two Raman spectral biomarkers (Raman bands for phenylalanine at
1001 cm<sup>ā1</sup> and thymine at 747 cm<sup>ā1</sup> Raman bands), were used to quantify the <sup>13</sup>C content in <i>E. coli</i> and <i>C. elegans</i> over a range of
1.1ā99%. The phenylalanine Raman band was a suitable biomarker
for prokaryotic cells and thymine Raman band for eukaryotic cells.
A biochemical mechanism accounting for the Raman red shifts of phenylalanine
and thymine in response to <sup>13</sup>C-labeling is proposed in
this study and is supported by quantum chemical calculation. This
study offers new insights of carbon flow via the food chain and provides
a research tool for microbial ecology and investigation of biochemical
pathways
Visible Mie Scattering from Hollow Silica Particles with Particulate Shells
A series of colloidal nanocomposite
dispersions are synthesized
by alcoholic dispersion polymerization of styrene in the presence
of an ultrafine silica sol. The original core/shell polystyrene/silica
nanocomposite particles have mean diameters ranging from 321 to 471
nm, as determined by dynamic light scattering. Upon calcination of
the polystyrene cores, some shrinkage occurs but intact hollow silica
shells are observed by transmission electron microscopy. On visual
inspection, these silica residues display remarkable colors that vary
depending on the particle diameter. When examined in transmittance
mode (i.e., with an illuminated background) the silica powders appear
yellow to red in color, but when viewed in reflectance (i.e., with
a dark background) relatively intense blue/green colors are observed.
The latter phenomenon has been analyzed by visible reflectance spectroscopy
and the reflectance maximum depends on the dimensions of the silica
shell, which are in turn dictated by the initial nanocomposite particle
diameter. Small-angle X-ray scattering is used to determine the packing
density of the silica nanoparticles, both in the original polystyrene/silica
nanocomposite particles and in the calcined silica shells. Combined
with geometrical considerations, this allows the equivalent <i>uniform</i> silica shell thickness to be calculated for a <i>particulate</i> silica shell and this parameter is then related
to the theoretical predictions made by Retsch et al. for hollow particles
comprising uniform silica shells (see Retsch, M.; Schmelzeisen, M.;
Butt, H. J.; Thomas, E. L. <i>Nano Lett.</i>, <b>2011</b>, <i>11</i>, 1389)
Correcting for a Density Distribution: Particle Size Analysis of CoreāShell Nanocomposite Particles Using Disk Centrifuge Photosedimentometry
Many types of colloidal particles possess a coreāshell
morphology.
In this Article, we show that, if the core and shell densities differ,
this morphology leads to an inherent density distribution for particles
of finite polydispersity. If the shell is denser than the core, this
density distribution implies an artificial narrowing of the particle
size distribution as determined by disk centrifuge photosedimentometry
(DCP). In the specific case of polystyrene/silica nanocomposite particles,
which consist of a polystyrene core coated with a monolayer shell
of silica nanoparticles, we demonstrate that the particle density
distribution can be determined by analytical ultracentrifugation and
introduce a mathematical method to account for this density distribution
by reanalyzing the raw DCP data. Using the mean silica packing density
calculated from small-angle X-ray scattering, the real particle density
can be calculated for each data point. The corrected DCP particle
size distribution is both broader and more consistent with particle
size distributions reported for the same polystyrene/silica nanocomposite
sample using other sizing techniques, such as electron microscopy,
laser light diffraction, and dynamic light scattering. Artifactual
narrowing of the size distribution is also likely to occur for many
other polymer/inorganic nanocomposite particles comprising a low-density
core of variable dimensions coated with a high-density shell of constant
thickness, or for coreāshell latexes where the shell is continuous
rather than particulate in nature
Base-Catalyzed Dehydration of 3āSubstituted Benzene <i>cis</i>-1,2-Dihydrodiols: Stabilization of a Cyclohexadienide Anion Intermediate by Negative Aromatic Hyperconjugation
Evidence that a 1,2-dihydroxycyclohexadienide anion is
stabilized
by aromatic ānegative hyperconjugationā is described.
It complements an earlier inference of āpositiveā hyperconjugative
aromaticity for the cyclohexadienyl cation. The anion is a reactive
intermediate in the dehydration of benzene <i>cis</i>-1,2-dihydrodiol
to phenol. Rate constants for 3-substituted benzene <i>cis</i>-dihydrodiols are correlated by Ļ<sup>ā</sup> values
with Ļ = 3.2. Solvent isotope effects for the reactions are <i>k</i><sub>H<sub>2</sub>O</sub>/<i>k</i><sub>D<sub>2</sub>O</sub> = 1.2ā1.8. These measurements are consistent
with reaction via a carbanion intermediate or a concerted reaction
with a ācarbanion-likeā transition state. These and
other experimental results confirm that the reaction proceeds by a
stepwise mechanism, with a change in rate-determining step from proton
transfer to the loss of hydroxide ion from the intermediate. Hydrogen
isotope exchange accompanying dehydration of the parent benzene <i>cis</i>-1,2-dihydrodiol was not found, and thus, the proton
transfer step is subject to internal return. A rate constant of ā¼10<sup>11</sup> s<sup>ā1</sup>, corresponding to rotational relaxation
of the aqueous solvent, is assigned to loss of hydroxide ion from
the intermediate. The rate constant for internal return therefore
falls in the range 10<sup>11</sup>ā10<sup>12</sup> s<sup>ā1</sup>. From these limiting values and the measured rate constant for hydroxide-catalyzed
dehydration, a p<i>K</i><sub>a</sub> of 30.8 Ā± 0.5
was determined for formation of the anion. Although loss of hydroxide
ion is hugely exothermic, a concerted reaction is not enforced by
the instability of the intermediate. Stabilization by negative hyperconjugation
is proposed for 1,2-dihydroxycyclohexadienide and similar anions,
and this proposal is supported by additional experimental evidence
and by computational results, including evidence for a diatropic (āaromaticā)
ring current in 3,3-difluorocyclohexadienyl anion