Biomedical subjects

Santiago D Solares

Publications and source records attributed to Santiago D Solares.

9 recordsLinked to original sources

PubMed2006

Scanning tunneling microscopy of ethylated Si(111) surfaces prepared by a chlorination/alkylation process.

Scanning tunneling microscopy (STM) and computational modeling have been used to study the structure of ethyl-terminated Si(111) surfaces. The ethyl-terminated surface was prepared by treating the H-terminated Si(111) surface with PCl5 to form a Cl-terminated Si(111) surface with subsequent exposure to C(2)H(5)MgCl in tetrahydrofuran to produce an alkylated Si(111) surface. The STM data at 77 K revealed local, close-packed, and relatively ordered regions with a nearest-neighbor spacing of 0.38 nm as well as disordered regions. The average spot density corresponded to approximately 85% of the density of Si atop sites on an unreconstructed Si(111) surface. Molecular dynamics simulations of a Si(111) surface randomly populated with ethyl groups to a total coverage of approximately 80% confirmed that the ethyl-terminated Si(111) surface, in theory, can assume reasonable packing arrangements to accommodate such a high surface coverage, which could be produced by an exoergic surface functionalization route such as the two-step chlorination/alkylation process. Hence, it is possible to consistently interpret the STM data within a model suggested by recent X-ray photoelectron spectroscopic data and infrared absorption data, which indicate that the two-step halogenation/alkylation method can provide a relatively high coverage of ethyl groups on Si(111) surfaces.

Journal Article↗

PubMed2006

Quantum mechanics calculations of the thermodynamically controlled coverage and structure of alkyl monolayers on Si(111) surfaces.

The heat of formation, Delta E, for silicon (111) surfaces terminated with increasing densities of the alkyl groups CH3- (methyl), C2H5- (ethyl), (CH3)2CH- (isopropyl), (CH3)3C- (tert-butyl), CH3(CH2)5- (hexyl), CH3(CH2)7- (octyl), and C6H5- (phenyl) was calculated using quantum mechanics (QM) methods, with unalkylated sites being H-terminated. The free energy, Delta G, for the formation of both Si-C and Si-H bonds from Si-Cl model compounds was also calculated using QM, with four separate Si-H formation mechanisms proposed, to give overall Delta G(S) values for the formation of alkylated Si(111) surfaces through a two step chlorination/alkylation method. The data are in good agreement with measurements of the packing densities for alkylated surfaces formed through this technique, for Si-H free energies of formation, Delta G(H), corresponding to a reaction mechanism including the elimination of two H atoms and the formation of a C=C double bond in either unreacted alkyl Grignard groups or tetrahydrofuran solvent.

Journal Article↗

PubMed2006

Theoretical investigation of the structure and coverage of the Si(111)-OCH3 surface.

The surface structure, strain energy, and charge profile of the methoxylated Si(111) surface, Si(111)-OCH3, has been studied using quantum mechanics, and the results are compared to those obtained previously for Si(111)-CH3 and Si(111)-C2H5. The calculations indicate that 100% coverage is feasible for Si(111)-OCH3 (similar to the methylated surface), as compared to only approximately 80% coverage for the ethylated surface. These differences can be understood in terms of nearest-neighbor steric and electrostatic interactions. Enthalpy and free energy calculations indicate that the formation of the Si(111)-OCH3 surface from Si(111)-H and methanol is favorable at 300 K. The calculations have also indicated the conditions under which stacking faults can emerge on Si(111)-OCH3, and such conditions are contrasted with the behavior of Si(111)-CH3 and Si(111)-CH2CH3 surfaces, for which stacking faults are calculated to be energetically feasible when etch pits with sufficiently long edges are present on the surface.

Journal Article↗

PubMed2006

Chlorination-methylation of the hydrogen-terminated silicon(111) surface can induce a stacking fault in the presence of etch pits.

Recently, we reported STM images of the methylated Si(111) surface [prepared through chlorination-alkylation of the Si(111)-H surface] taken at 4.7 K, indicating that the torsion angle of the methyl group with respect to the subsurface silicon layer is phi = 23 +/- 3 degrees . Repulsions between H atoms in adjacent methyl groups are minimized at 30 degrees , while repulsions between H atoms and second layer Si atoms are minimized at 60 degrees . The experimental result of 23 degrees is surprising because it suggests a tendency of the methyl group toward the eclipsed configuration (0 degrees ) rather than staggered (60 degrees ). In contrast, extensive fully periodic quantum mechanical Density Functional Theory studies of this surface give an equilibrium torsion angle of 37.5 degrees , indicating a tendency toward the staggered configuration. This discrepancy can be resolved by showing that the CH3 on the step edges and etch pits interacts repulsively with the CH3 on the surface terraces unless a stacking fault is introduced between the first and second silicon layers of the Si(111)-CH3 surface terraces. We propose that this could occur during the chlorination-alkylation of the Si(111)-H surface. This stacking fault model predicted phi = 22.5 degrees measured with respect to the bulk (corresponding to phi = 37.5 degrees with respect to the second layer Si atoms). This model can be tested by measuring the orientation of the CH3 within the etch pits, which should have phi = 37.5 degrees , or by making a surface without etch pits, which should have phi = 37.5 degrees .

Journal Article↗

PubMed2005

Density functional theory study of the geometry, energetics, and reconstruction process of Si111 surfaces.

We report the structures and energies from first principles density functional calculations of 12 different reconstructed (111) surfaces of silicon, including the 3x3 to 9x9 dimer-adatom-stacking fault (DAS) structures. These calculations used the Perdew-Burke-Ernzerhof generalized gradient approximation of density functional theory and Gaussian basis functions. We considered fully periodic slabs of various thicknesses. We find that the most stable surface is the DAS 7x7 structure, with a surface energy of 1.044 eV/1x1 cell (1310 dyn/cm). To analyze the origins of the stability of these systems and to predict energetics for more complex, less-ordered systems, we develop a model in which the surface energy is partitioned into contributions from seven different types of atom environments. This analysis is used to predict the surface energy of larger DAS structures (including their asymptotic behavior for very large unit cells) and to study the energetics of the sequential size change (SSC) model proposed by Shimada and Tochihara for the observed dynamical reconstruction of the Si(111) 1x1 structure. We obtain an energy barrier at the 2x2 cell size and confirm that the 7x7 regular stage of the SSC model (corresponding to the DAS 7x7 reconstruction) provides the highest energy reduction per unit cell with respect to the unreconstructed Si111 1x1 surface.

Journal Article↗

PubMed2005

Influence of the carbon nanotube probe tilt angle on the effective probe stiffness and image quality in tapping-mode atomic force microscopy.

Previous studies have shown that when using carbon nanotubes (CNTs) as tapping-mode AFM probes, their tilt angle with respect to vertical (denoted phi) must be close to 0 degrees to obtain high-quality images and that very poor images are obtained for phi > 30 degrees . Here we present a quantitative theoretical investigation of the effect of phi on tapping-mode AFM imaging for single-wall and multiwall nanotube (SWNT and MWNT, respectively) probes of diameters 3.4-5.5 nm and aspect ratio 7.5, which have been found ideal for imaging via TEM. Using molecular and classical dynamics, we investigate the effect of phi on CNT probe stiffness (quantified through the maximum gradient of the tip-sample interaction force) and show that it decreases linearly with increasing phi, becoming negligible at around phi approximately 40 degrees , thus confirming the conclusions of previous studies. We find that MWNT probe stiffness is proportional to the number of walls, but that the difference in stiffness between SWNTs and MWNTs also decreases linearly with increasing phi and becomes negligible at around phi approximately 40 degrees . The simulated cross-sectional scans of a sample SWNT using two different values of phi show that the image can be distorted and shifted laterally when phi is large, in some cases giving measured heights appreciably greater than the sample dimensions. We show analytically that the tip-sample forces that occur during imaging can be significantly lower when CNT probes are used instead of conventional probes, even in the absence of buckling, and that they can be further reduced by increasing phi. On the basis of this result, we propose the design of free-standing kinked probes for the characterization of sensitive samples, whereby the probe approaches the sample at a vertical orientation and possesses a tilted section that regulates the tip-sample interaction forces.

Journal Article↗

PubMed2005

Linear artificial molecular muscles.

Two switchable, palindromically constituted bistable [3]rotaxanes have been designed and synthesized with a pair of mechanically mobile rings encircling a single dumbbell. These designs are reminiscent of a "molecular muscle" for the purposes of amplifying and harnessing molecular mechanical motions. The location of the two cyclobis(paraquat-p-phenylene) (CBPQT(4+)) rings can be controlled to be on either tetrathiafulvalene (TTF) or naphthalene (NP) stations, either chemically ((1)H NMR spectroscopy) or electrochemically (cyclic voltammetry), such that switching of inter-ring distances from 4.2 to 1.4 nm mimics the contraction and extension of skeletal muscle, albeit on a shorter length scale. Fast scan-rate cyclic voltammetry at low temperatures reveals stepwise oxidations and movements of one-half of the [3]rotaxane and then of the other, a process that appears to be concerted at room temperature. The active form of the bistable [3]rotaxane bears disulfide tethers attached covalently to both of the CBPQT(4+) ring components for the purpose of its self-assembly onto a gold surface. An array of flexible microcantilever beams, each coated on one side with a monolayer of 6 billion of the active bistable [3]rotaxane molecules, undergoes controllable and reversible bending up and down when it is exposed to the synchronous addition of aqueous chemical oxidants and reductants. The beam bending is correlated with flexing of the surface-bound molecular muscles, whereas a monolayer of the dumbbell alone is inactive under the same conditions. This observation supports the hypothesis that the cumulative nanoscale movements within surface-bound "molecular muscles" can be harnessed to perform larger-scale mechanical work.

Biomimetic Materials↗

PubMed2005

Mechanisms of single-walled carbon nanotube probe-sample multistability in tapping mode AFM imaging.

When using single-walled carbon nanotube (SWNT) probes to create AFM images of SWNT samples in tapping mode, elastic deformations of the probe and sample result in a decrease in the apparent width of the sample. Here we show that there are two major mechanisms for this effect, smooth gliding and snapping, and compare their dynamics to the case when a conventional silicon tip is used to image a bare silicon surface. Using atomistic and continuum simulations, we analyze in detail the shape of the tip-sample interaction potential for three model cases and show that in the absence of adhesion and friction forces, more than two discrete, physically meaningful solutions of the oscillation amplitude are possible when snapping occurs (in contrast to the existence of one attractive and one repulsive solution for conventional silicon AFM tips). We present experimental results indicating that a continuum of amplitude solutions is possible when using SWNT tips and explain this phenomenon with dynamic simulations that explicitly include tip-sample adhesion and friction forces. We also provide simulation results of SWNT tips imaging Si(111)-CH3 surface step edges and Au nanocrystals, which indicate that SWNT probe multistability may be a general phenomenon, not limited to SWNT samples.

Gold↗

PubMed2005

Low-temperature STM images of methyl-terminated Si(111) surfaces.

Low-temperature scanning tunneling microscopy (STM) has been used to image CH(3)-terminated Si(111) surfaces that were prepared through a chlorination/alkylation procedure. The STM data revealed a well-ordered structure commensurate with the atop sites of an unreconstructed 1 x 1 overlayer on the silicon (111) surface. Images collected at 4.7 K revealed bright spots, separated by 0.18 +/- 0.01 nm, which are assigned to adjacent H atoms on the same methyl group. The C-H bonds in each methyl group were observed to be rotated by 7 +/- 3 degrees away from the center of an adjacent methyl group and toward an underlying Si atom. Hence, the predominant interaction that determines the surface structure arises from repulsions between hydrogen atoms on neighboring methyl groups, and secondary interactions unique to the surface are also evident.

Hydrocarbons↗