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James J De Yoreo

Publications and source records attributed to James J De Yoreo.

9 recordsLinked to original sources
PubMed2006

Effect of ring substitution position on the structural conformation of mercaptobenzoic acid self-assembled monolayers on Au(111).

Near-edge X-ray absorption fine structure (NEXAFS) spectroscopy, photoemission spectroscopy (PES), and contact angle measurements have been used to examine the structure and bonding of self-assembled monolayers (SAMs) prepared on Au(111) from the positional isomers of mercaptobenzoic acid (MBA). The isomer of MBA and solvent chosen in SAM preparation has considerable bearing upon film morphology. Carbon K-edge NEXAFS measurements indicate that the monomers of 2-, 3-, and 4-MBA have well-defined orientations within their respective SAMs. Monomers of 3- and 4-MBA assume an upright orientation on the Au substrates in monolayers prepared using an acetic acid in ethanol solvent. The aryl ring and carboxyl group of these molecules are tilted from the surface normal by a colatitudal angle of approximately 30 degrees . Preparation of 4-MBA SAMs using pure ethanol solvent, a more traditional means of synthesis, had no appreciable effect upon the monomer orientation. Nonetheless, S(2p) PES measurements illustrate that it results in extensive bilayer formation via carboxyl group hydrogen-bonding between 4-MBA monomers. In 2-MBA monolayers prepared using acetic acid/ethanol solvent, the monomers adopt a more prostrate orientation on the Au substrates, in which the aryl ring and carboxyl group of the molecules are tilted approximately 50 degrees from the surface normal. This configuration is consistent with an interaction between both the mercaptan sulfur and carboxyl group of 2-MBA with the underlying substrate. S(2p) and C(1s) PES experiments provide supporting evidence for a bidentate interaction between 2-MBA and Au(111).

Journal Article↗
PubMed2006

Physical controls on directed virus assembly at nanoscale chemical templates.

Viruses are attractive building blocks for nanoscale heterostructures, but little is understood about the physical principles governing their directed assembly. In situ force microscopy was used to investigate organization of Cowpea Mosaic Virus engineered to bind specifically and reversibly at nanoscale chemical templates with sub-30 nm features. Morphological evolution and assembly kinetics were measured as virus flux and inter-viral potential were varied. The resulting morphologies were similar to those of atomic-scale epitaxial systems, but the underlying thermodynamics was analogous to that of colloidal systems in confined geometries. The 1D templates biased the location of initial cluster formation, introduced asymmetric sticking probabilities, and drove 1D and 2D condensation at sub-critical volume fractions. The growth kinetics followed a t(1/2) law controlled by the slow diffusion of viruses. The ability of poly(ethylene glycol) (PEG) to induce the lateral expansion of virus clusters away from the 1D templates suggests a significant role for weak interactions.

Comovirus↗
PubMed2006

Molecular modulation of calcium oxalate crystallization.

Calcium oxalate monohydrate (COM) is the primary constituent of the majority of renal stones. Osteopontin (OPN), an aspartic acid-rich urinary protein, and citrate, a much smaller molecule, are potent inhibitors of COM crystallization at levels present in normal urine. Current concepts of the role of site-specific interactions in crystallization derived from studies of biomineralization are reviewed to provide a context for understanding modulation of COM growth at a molecular level. Results from in situ atomic force microscopy (AFM) analyses of the effects of citrate and OPN on growth verified the critical role of site-specific interactions between these growth modulators and individual steps on COM crystal surfaces. Molecular modeling investigations of interactions of citrate with steps and faces on COM crystal surfaces provided links between the stereochemistry of interaction and the binding energy levels that underlie mechanisms of growth modification and changes in overall crystal morphology. The combination of in situ AFM and molecular modeling provides new knowledge that will aid rationale design of therapeutic agents for inhibition of stone formation.

Animals↗
PubMed2005

Mechanisms of classical crystal growth theory explain quartz and silicate dissolution behavior.

The central control of mineral weathering rates on biogeochemical systems has motivated studies of dissolution for more than 50 years. A complete physical picture that explains widely observed variations in dissolution behavior is lacking, and some data show apparent serious inconsistencies that cannot be explained by the largely empirical kinetic "laws." Here, we show that mineral dissolution can, in fact, be understood through the same mechanistic theory of nucleation developed for mineral growth. In principle, this theory should describe dissolution but has never been tested. By generalizing nucleation rate equations to include dissolution, we arrive at a model that predicts how quartz dissolution processes change with undersaturation from step retreat, to defect-driven and homogeneous etch pit formation. This finding reveals that the "salt effect," recognized almost 100 years ago, arises from a crossover in dominant nucleation mechanism to greatly increase step density. The theory also explains the dissolution kinetics of major weathering aluminosilicates, kaolinite and K-feldspar. In doing so, it provides a sensible origin of discrepancies reported for the dependence of kaolinite dissolution and growth rates on saturation state by invoking a temperature-activated transition in the nucleation process. Although dissolution by nucleation processes was previously unknown for oxides or silicates, our mechanism-based findings are consistent with recent observations of dissolution (i.e., demineralization) in biological minerals. Nucleation theory may be the missing link to unifying mineral growth and dissolution into a mechanistic and quantitative framework across the continuum of driving force.

Journal Article↗
PubMed2005

Modulation of calcium oxalate monohydrate crystallization by citrate through selective binding to atomic steps.

The majority of human kidney stones are composed primarily of calcium oxalate monohydrate (COM) crystals. Thus, determining the molecular modulation of COM crystallization by urinary constituents is crucial for understanding and controlling renal stone disease. A comprehensive molecular-scale view of COM shape modification by citrate, obtained through a combination of in situ atomic force microscopy and molecular modeling, is presented here. We find that while the most important factors determining binding strength are coordination between COO- groups on citrate and Ca ions in the lattice, as well as H-bonds formed between the OH group of citrate and an oxalate group, the nonplanar geometry of the steps provides the most favorable environment due to the ability of the step-edge to accommodate all Ca-COO- coordinations with minimal strain. However, binding to all steps and terraces on the (010) face is much less favorable than on the (101) face due to electrostatic repulsion between oxalate and COO- groups. For example, the maximum binding energy, -166.5 kJ mol(-1), occurs for the [101] step on the (101) face, while the value for the [021] step on the (010) face is only -56.9 kJ mol(-1). This high selectivity leads to preferential binding to steps on the (101) face that pins step motion. Yet anisotropy in interaction strength on this face drives anisotropic changes in step kinetics that are responsible for shape modification of macroscopic COM crystals. Thus, the molecular scale growth kinetics and the bulk crystal habit are fully consistent with the simulations.

Binding Sites↗
PubMed2003

Entropic barriers in nanoscale adhesion studied by variable temperature chemical force microscopy.

Intermolecular interactions drive the vast majority of condensed phase phenomena from molecular recognition to protein folding to particle adhesion. Complex energy barriers encountered in these interactions include contributions from van der Waals forces, hydrogen bonding, and solvent medium. With the spectacular exception of hydrophobic interactions, contributions from the medium are usually considered secondary. We report a variable temperature force microscopy study of the interactions between several hydrogen bonds in different solvents that challenges this point of view. Surprisingly, we observed an increase in the strength of the interaction between carboxylic acid groups in ethanol as the temperature increased. Moreover, when we switched to a nonpolar solvent we observed the opposite behavior: The binding force decreased as the temperature increased. Kinetic model of bond dissociation provided quantitative interpretation of our measurements. We attributed the observed phenomena to a large entropic contribution from the ordered solvent layers that are forming on the probe and sample surfaces upon detachment. The observed reversal in the force vs temperature trend is a manifestation of a transition between thermodynamic and kinetic regimes of unbinding predicted by the model. Our results indicate that entropic barriers dominated by the interactions of solvent molecules with the surface exist in a much wider variety of systems than previously thought.

Carboxylic Acids↗