Browsing by Subject "Models, Chemical"

Now showing 1 - 11 of 11

Open Access
Analyzing site selectivity in Rh2(esp)2-catalyzed intermolecular C-H amination reactions.
(J Am Chem Soc, 2014-04-16) Bess, Elizabeth N; DeLuca, Ryan J; Tindall, Daniel J; Oderinde, Martins S; Roizen, Jennifer L; Du Bois, J; Sigman, Matthew S
Predicting site selectivity in C-H bond oxidation reactions involving heteroatom transfer is challenged by the small energetic differences between disparate bond types and the subtle interplay of steric and electronic effects that influence reactivity. Herein, the factors governing selective Rh2(esp)2-catalyzed C-H amination of isoamylbenzene derivatives are investigated, where modification to both the nitrogen source, a sulfamate ester, and substrate are shown to impact isomeric product ratios. Linear regression mathematical modeling is used to define a relationship that equates both IR stretching parameters and Hammett σ(+) values to the differential free energy of benzylic versus tertiary C-H amination. This model has informed the development of a novel sulfamate ester, which affords the highest benzylic-to-tertiary site selectivity (9.5:1) observed for this system.
Open Access
Dimensional study of the caging order parameter at the glass transition.
(Proc Natl Acad Sci U S A, 2012-08-28) Charbonneau, Patrick; Ikeda, Atsushi; Parisi, Giorgio; Zamponi, Francesco
The glass problem is notoriously hard and controversial. Even at the mean-field level, little is agreed upon regarding why a fluid becomes sluggish while exhibiting but unremarkable structural changes. It is clear, however, that the process involves self-caging, which provides an order parameter for the transition. It is also broadly assumed that this cage should have a gaussian shape in the mean-field limit. Here we show that this ansatz does not hold. By performing simulations as a function of spatial dimension d, we find the cage to keep a nontrivial form. Quantitative mean-field descriptions of the glass transition, such as mode-coupling theory, density functional theory, and replica theory, all miss this crucial element. Although the mean-field random first-order transition scenario of the glass transition is qualitatively supported here and non-mean-field corrections are found to remain small on decreasing d, reconsideration of its implementation is needed for it to result in a coherent description of experimental observations.
Restricted
Hard-sphere crystallization gets rarer with increasing dimension.
(Phys Rev E Stat Nonlin Soft Matter Phys, 2009-12) van Meel, JA; Charbonneau, B; Fortini, A; Charbonneau, P
We recently found that crystallization of monodisperse hard spheres from the bulk fluid faces a much higher free-energy barrier in four than in three dimensions at equivalent supersaturation, due to the increased geometrical frustration between the simplex-based fluid order and the crystal [J. A. van Meel, D. Frenkel, and P. Charbonneau, Phys. Rev. E 79, 030201(R) (2009)]. Here, we analyze the microscopic contributions to the fluid-crystal interfacial free energy to understand how the barrier to crystallization changes with dimension. We find the barrier to grow with dimension and we identify the role of polydispersity in preventing crystal formation. The increased fluid stability allows us to study the jamming behavior in four, five, and six dimensions and to compare our observations with two recent theories [C. Song, P. Wang, and H. A. Makse, Nature (London) 453, 629 (2008); G. Parisi and F. Zamponi, Rev. Mod. Phys. (to be published)].
Open Access
Highly parallel acoustic assembly of microparticles into well-ordered colloidal crystallites.
(Soft Matter, 2016-01-21) Owens, Crystal E; Shields, C Wyatt; Cruz, Daniela F; Charbonneau, Patrick; López, Gabriel P
The precise arrangement of microscopic objects is critical to the development of functional materials and ornately patterned surfaces. Here, we present an acoustics-based method for the rapid arrangement of microscopic particles into organized and programmable architectures, which are periodically spaced within a square assembly chamber. This macroscale device employs two-dimensional bulk acoustic standing waves to propel particles along the base of the chamber toward pressure nodes or antinodes, depending on the acoustic contrast factor of the particle, and is capable of simultaneously creating thousands of size-limited, isotropic and anisotropic assemblies within minutes. We pair experiments with Brownian dynamics simulations to model the migration kinetics and assembly patterns of spherical microparticles. We use these insights to predict and subsequently validate the onset of buckling of the assemblies into three-dimensional clusters by experiments upon increasing the acoustic pressure amplitude and the particle concentration. The simulations are also used to inform our experiments for the assembly of non-spherical particles, which are then recovered via fluid evaporation and directly inspected by electron microscopy. This method for assembly of particles offers several notable advantages over other approaches (e.g., magnetics, electrokinetics and optical tweezing) including simplicity, speed and scalability and can also be used in concert with other such approaches for enhancing the types of assemblies achievable.
Open Access
Inside-out Z rings--constriction with and without GTP hydrolysis.
(Molecular microbiology, 2011-07) Osawa, Masaki; Erickson, Harold P
The bacterial tubulin homologue FtsZ forms a ring-like structure called the Z ring that drives cytokinesis. We showed previously that FtsZ-YFP-mts, which has a short amphipathic helix (mts) on its C terminus that inserts into the membrane, can assemble contractile Z rings in tubular liposomes without any other protein. Here we study mts-FtsZ-YFP, where the membrane tether is switched to the opposite side of the protofilament. This assembled 'inside-out' Z rings that wrapped around the outside surface of tubular liposomes. The inside-out Z rings were highly dynamic, and generated a constriction force that squeezed the tubular liposomes from outside. This is consistent with models where the constriction force is generated by curved protofilaments bending the membrane. We used this system to test how GTP hydrolysis by FtsZ is involved in Z-ring constriction. Without GTP hydrolysis, Z rings could still assemble and generate an initial constriction. However, the constriction quickly stopped, suggesting that Z rings became rigidly stabilized in the absence of GTP hydrolysis. We propose that remodelling of the Z ring, mediated by GTP hydrolysis and exchange of subunits, is necessary for the continuous constriction.
Open Access
Modulating unimolecular charge transfer by exciting bridge vibrations.
(J Am Chem Soc, 2009-12-23) Lin, Zhiwei; Lawrence, Candace M; Xiao, Dequan; Kireev, Victor V; Skourtis, Spiros S; Sessler, Jonathan L; Beratan, David N; Rubtsov, Igor V
Ultrafast UV-vibrational spectroscopy was used to investigate how vibrational excitation of the bridge changes photoinduced electron transfer between donor (dimethylaniline) and acceptor (anthracene) moieties bridged by a guanosine-cytidine base pair (GC). The charge-separated (CS) state yield is found to be lowered by high-frequency bridge mode excitation. The effect is linked to a dynamic modulation of the donor-acceptor coupling interaction by weakening of H-bonding and/or by disruption of the bridging base-pair planarity.
Open Access
Physical and economic potential of geological CO2 storage in saline aquifers.
(Environ Sci Technol, 2009-03-15) Eccles, Jordan K; Pratson, Lincoln; Newell, Richard G; Jackson, Robert B
Carbon sequestration in sandstone saline reservoirs holds great potential for mitigating climate change, but its storage potential and cost per ton of avoided CO2 emissions are uncertain. We develop a general model to determine the maximum theoretical constraints on both storage potential and injection rate and use it to characterize the economic viability of geosequestration in sandstone saline aquifers. When applied to a representative set of aquifer characteristics, the model yields results that compare favorably with pilot projects currently underway. Over a range of reservoir properties, maximum effective storage peaks at an optimal depth of 1600 m, at which point 0.18-0.31 metric tons can be stored per cubic meter of bulk volume of reservoir. Maximum modeled injection rates predict minima for storage costs in a typical basin in the range of $2-7/ ton CO2 (2005 U.S.$) depending on depth and basin characteristics in our base-case scenario. Because the properties of natural reservoirs in the United States vary substantially, storage costs could in some cases be lower or higher by orders of magnitude. We conclude that available geosequestration capacity exhibits a wide range of technological and economic attractiveness. Like traditional projects in the extractive industries, geosequestration capacity should be exploited starting with the low-cost storage options first then moving gradually up the supply curve.
Open Access
Physical and economic potential of geological CO2 storage in saline aquifers.
(Environ Sci Technol, 2009-03-15) Eccles, JK; Jackson, Robert; Newell, Richard G; Pratson, L
Carbon sequestration in sandstone saline reservoirs holds great potential for mitigating climate change, but its storage potential and cost per ton of avoided CO2 emissions are uncertain. We develop a general model to determine the maximum theoretical constraints on both storage potential and injection rate and use it to characterize the economic viability of geosequestration in sandstone saline aquifers. When applied to a representative set of aquifer characteristics, the model yields results that compare favorably with pilot projects currently underway. Over a range of reservoir properties, maximum effective storage peaks at an optimal depth of 1600 m, at which point 0.18-0.31 metric tons can be stored per cubic meter of bulk volume of reservoir. Maximum modeled injection rates predict minima for storage costs in a typical basin in the range of $2-7/ ton CO2 (2005 U.S.$) depending on depth and basin characteristics in our base-case scenario. Because the properties of natural reservoirs in the United States vary substantially, storage costs could in some cases be lower or higher by orders of magnitude. We conclude that available geosequestration capacity exhibits a wide range of technological and economic attractiveness. Like traditional projects in the extractive industries, geosequestration capacity should be exploited starting with the low-cost storage options first then moving gradually up the supply curve.
Open Access
Statistical analysis of crystallization database links protein physico-chemical features with crystallization mechanisms.
(PLoS One, 2014) Fusco, Diana; Barnum, Timothy J; Bruno, Andrew E; Luft, Joseph R; Snell, Edward H; Mukherjee, Sayan; Charbonneau, Patrick
X-ray crystallography is the predominant method for obtaining atomic-scale information about biological macromolecules. Despite the success of the technique, obtaining well diffracting crystals still critically limits going from protein to structure. In practice, the crystallization process proceeds through knowledge-informed empiricism. Better physico-chemical understanding remains elusive because of the large number of variables involved, hence little guidance is available to systematically identify solution conditions that promote crystallization. To help determine relationships between macromolecular properties and their crystallization propensity, we have trained statistical models on samples for 182 proteins supplied by the Northeast Structural Genomics consortium. Gaussian processes, which capture trends beyond the reach of linear statistical models, distinguish between two main physico-chemical mechanisms driving crystallization. One is characterized by low levels of side chain entropy and has been extensively reported in the literature. The other identifies specific electrostatic interactions not previously described in the crystallization context. Because evidence for two distinct mechanisms can be gleaned both from crystal contacts and from solution conditions leading to successful crystallization, the model offers future avenues for optimizing crystallization screens based on partial structural information. The availability of crystallization data coupled with structural outcomes analyzed through state-of-the-art statistical models may thus guide macromolecular crystallization toward a more rational basis.
Open Access
The kinase Grk2 regulates Nedd4/Nedd4-2-dependent control of epithelial Na+ channels.
(Proc Natl Acad Sci U S A, 2004-08-10) Dinudom, Anuwat; Fotia, Andrew B; Lefkowitz, Robert J; Young, John A; Kumar, Sharad; Cook, David I
Epithelial Na(+) channels mediate the transport of Na across epithelia in the kidney, gut, and lungs and are required for blood pressure regulation. They are inhibited by ubiquitin protein ligases, such as Nedd4 and Nedd4-2, with loss of this inhibition leading to hypertension. Here, we report that these channels are maintained in the active state by the G protein-coupled receptor kinase, Grk2, which has been previously implicated in the development of essential hypertension. We also show that Grk2 phosphorylates the C terminus of the channel beta subunit and renders the channels insensitive to inhibition by Nedd4-2. This mechanism has not been previously reported to regulate epithelial Na(+) channels and provides a potential explanation for the observed association of Grk2 overactivity with hypertension. Here, we report a G protein-coupled receptor kinase regulating a membrane protein other than a receptor and provide a paradigm for understanding how the interaction between membrane proteins and ubiquitin protein ligases is controlled.
Open Access
Transition dynamics and magic-number-like behavior of frictional granular clusters.
(Phys Rev E Stat Nonlin Soft Matter Phys, 2012-07) Tordesillas, Antoinette; Walker, David M; Froyland, Gary; Zhang, Jie; Behringer, Robert P
Force chains, the primary load-bearing structures in dense granular materials, rearrange in response to applied stresses and strains. These self-organized grain columns rely on contacts from weakly stressed grains for lateral support to maintain and find new stable states. However, the dynamics associated with the regulation of the topology of contacts and strong versus weak forces through such contacts remains unclear. This study of local self-organization of frictional particles in a deforming dense granular material exploits a transition matrix to quantify preferred conformations and the most likely conformational transitions. It reveals that favored cluster conformations reside in distinct stability states, reminiscent of "magic numbers" for molecular clusters. To support axial loads, force chains typically reside in more stable states of the stability landscape, preferring stabilizing trusslike, three-cycle contact triangular topologies with neighboring grains. The most likely conformational transitions during force chain failure by buckling correspond to rearrangements among, or loss of, contacts which break the three-cycle topology.