Measuring the mechanical properties of molecular conformers.

Scanning probe-actuated single molecule manipulation has proven to be an exceptionally powerful tool for the systematic atomic-scale interrogation of molecular adsorbates. To date, however, the extent to which molecular conformation affects the force required to push or pull a single molecule has not been explored. Here we probe the mechanochemical response of two tetra(4-bromophenyl)porphyrin conformers using non-contact atomic force microscopy where we find a large difference between the lateral forces required for manipulation. Remarkably, despite sharing very similar adsorption characteristics, variations in the potential energy surface are capable of prohibiting probe-induced positioning of one conformer, while simultaneously permitting manipulation of the alternative conformational form. Our results are interpreted in the context of dispersion-corrected density functional theory calculations which reveal significant differences in the diffusion barriers for each conformer. These results demonstrate that conformational variation significantly modifies the mechanical response of even simple porpyhrins, potentially affecting many other flexible molecules.

Interdigitating organic bilayers direct the short interlayer spacing in hybrid organic-inorganic layered vanadium oxide nanostructures.

Layered metal oxides provide a single-step route to sheathed superlattices of atomic layers of a variety of inorganic materials, where the interlayer spacing and overall layered structure forms the most critical feature in the nanomaterials' growth and application in electronics, health, and energy storage. We use a combination of computer simulations and experiments to describe the atomic-scale structure, dynamics and energetics of alkanethiol-intercalated layered vanadium oxide-based nanostructures. Molecular dynamics (MD) simulations identify the unusual substrate-constrained packing of the alkanethiol surfactant chains along each V(2)O(5) (010) face that combines with extensive interdigitation between chains on opposing faces to maximize three-dimensional packing in the interlayer regions. The findings are supported by high resolution electron microscopy analyses of synthesized alkanethiol-intercalated vanadium oxide nanostructures, and the preference for this new interdigitated model is clarified using a large set of MD simulations. This dependency stresses the importance of organic-inorganic interactions in layered material systems, the control of which is central to technological applications of flexible hybrid nanomaterials.

The role of ellipticity on the preferential binding site of Ce and La in C78-D3h--a density functional theory study.

Endohedral metallofullerenes that encapsulate one or several atoms, or a cluster of atoms have molecular properties making them useful both in technology and in bio-medical applications. Some fullerenes are found to have two metal atoms incarcerated and it has been recently found that two Ce atoms are incorporated into the C(78)-D(3h) (78 : 5) cage. In this study, we report calculations on the structural and electronic properties of Ce(2)@C(78) using density functional theory (DFT). While Ce(2)@C(80)-I(h) (D(3d)) and La(2)@C(80)-I(h) (D(2h)) have different ground state structures, we have found that Ce(2)@C(78) has a D(3h) ground state structure just as La(2)@C(78). The encapsulated Ce atoms bind strongly to the C(78)-D(3h) cage with a binding energy (BE) of 5.925 eV but not as strong as in Ce@C(82)-C(2v) nor in Ce(2)@C(80)-I(h). The elliptical nature of the cage plays a crucial role and accommodates the two Ce atoms at opposite ends of the C(3) axis with a maximized inter atomic distance (4.078 A). This means that the effect of the additional f-electron repulsion in M(2)@C(78) with M = Ce compared to M = La, is less pronounced than in Ce(2)@C(80) compared to La(2)@C(80). We compare the results to the elliptical M(2)@C(72) (#10611) (M = La, Ce), and with a range of additional Ce and La endohedral fullerenes and explain the role ellipticity has in the preferential binding site of Ce and shed light on the formation mechanism of these nanostructures.

Molecular dynamics study of naturally occurring defects in self-assembled monolayer formation.

One of the major challenges for nanofabrication, in particular microcontact printing (mu-CP), is the control of molecular diffusion, or "ink spreading", for the creation of nanopatterns with minimized "smudging" at pattern boundaries. In this study, fully atomistic computer simulations were used to measure the impact of naturally occurring domain boundaries on the diffusion of excess alkanethiol ink molecules on printed alkanethiol self-assembled monolayers (SAM). A periodic unit cell containing approximately one million atoms and with a surface area of 56 nm x 55 nm was used to model a hexadecanethiol SAM on Au(111), featuring SAM domain boundaries and a range of concentrations of excess hexadecanethiol ink molecules diffusing on top. This model was simulated for a total of approximately 80 ns of molecular dynamics. The simulations reveal that domain boundaries impede the diffusion of excess ink molecules and can, in some cases, permanently trap excess inks. There is competition between ink spreading and ink trapping, with the ink/SAM interaction strongly dependent on both the ink concentration and the SAM orientation at domain boundaries. SAM defects thus provide potential diffusion barriers for the control of excess ink spreading, and simulations also illustrate atom-scale mechanisms for the repair of damaged areas of the SAM via self-healing. The ability of domain boundaries to trap excess ink molecules is accounted for using an accessible volume argument, and trapping is discussed in relation to experimental efforts to reduce molecular spreading on SAMs for the creation of ultrahigh resolution nanopatterns.

Quantification of ink diffusion in microcontact printing with self-assembled monolayers.

Spreading of ink outside the desired printed area is one of the major limitations of microcontact printing (micro-CP) with alkanethiol self-assembled monolayers (SAMs) on gold. We use molecular dynamics (MD) computer simulations to quantify the temperature and concentration dependence of hexadecanethiol (HDT) ink spreading on HDT SAMs, modeling 18 distinct printing conditions using periodic simulation cells of approximately 7 nm edge length and printing conditions ranging from 7 ink molecules per cell at 270 K to 42 ink molecules per cell at 371K. The computed alkanethiol ink diffusion rates on the SAM are of the same order of magnitude as bulk liquid alkanethiol diffusion rates at all but the lowest ink concentrations and highest temperatures, with up to 20-30 times increases in diffusion rates at the lowest concentration-highest temperature conditions. We show that although alkanethiol surfaces are autophobic, autophobicity is not enough to pin the ink solutions on the SAM, and so any overinking of the SAM will lead to spreading of the printed pattern. Comparison of experimental and calculated diffusion data supports an interpretation of pattern broadening as a mixture of spreading on fully and partially formed SAMs, and the calculated spreading rates establish some of the fundamental limitations of mu-CP in terms of stamp contact time and desired pattern width.

Guanidinium chloride molecular diffusion in aqueous and mixed water-ethanol solutions.

Solutions containing guanidinium chloride (GdmCl), or equivalently guanidine hydrochloride (GdnHCl), are commonly used to denature macromolecules such as proteins and DNA in, for example, microfluidics studies of protein unfolding. To design and study such applications, it is necessary to know the diffusion coefficients for GdmCl in the solution. To this end, we use molecular dynamics simulations to calculate the diffusion coefficients of GdmCl in water and in water-ethanol solutions, for which no direct experimental measurements exist. The fully atomistic simulations show that the guandinium cation Gdm (+) diffusion decreases as the concentration of both Gdm (+) and ethanol in the solution increases. The simulations are validated against available literature data, both transformed measured viscosity values and computed diffusion coefficients, and we show that a prudent choice of water model, namely TIP4P-Ew, gives calculated diffusion coefficients in good agreement with the transformed measured viscosity values. The calculated Gdm (+) diffusion behavior is explained as a dynamic mixture of free cation, stacked cation, and ion-paired species in solution, with weighted contributions to Gdm (+) diffusion from the stacked and paired states helping explain measured viscosity data in terms of atom-scale dynamics.

A density functional study of Ce@C82: explanation of the Ce preferential bonding site.

Ce has been found experimentally to be preferentially incorporated into the C82 isomer of C2v symmetry as have other lanthanoids in M@C82 (M = La, Pr, Nd, etc.). We have investigated the underlying reason for this preference by calculating structural and electronic properties of Ce@C82 using density functional theory. The ground-state structure of Ce@C82 is found to have the cerium atom attached to the six-membered ring on the C2 axis of the C82-C2v cage, and the encapsulated atom is found to perturb the carbon cage due to chemical bonding. We have found Ce to favor this C2v chemisorption site in C82 by 0.62 eV compared to other positions on the inside wall of the cage. The specific preference of the metal atom to this six-membered ring is explained through electronic structure analysis, which reveals strong hybridization between the d orbitals of cerium and the pi orbitals of the cage that is particularly favorable for this chemisorption site. We propose that this symmetry dictated interaction between the cage and the lanthanide d orbital plays a crucial role when C82 forms in the presence of Ce to produce Ce@C82 and is also more generally applicable for the formation of other lanthanoid M@C82 molecules. Our theoretical computations are the first to explain this well-established fact. Last, the vibrational spectrum of Ce@C82 has been simulated and analyzed to gain insight into the metal-cage vibrations.

Modeling competitive guest binding to beta-cyclodextrin molecular printboards.

Anchoring of functionalized guest molecules to self-assembled monolayers (SAMs) is key to the development of molecular printboards for nanopatterning. One very promising system involves guest binding to immobilized beta-cyclodextrin (beta-CD) hosts, with guest:host recognition facilitated by a hydrophobic interaction between uncharged anchor groups on the guest molecule and beta-CD hosts self-assembled at gold surfaces. We use molecular dynamics free energy (MDFE) simulations to describe the specificity of guest:beta-CD association. We find good agreement with experimental thermodynamic measurements for binding enthalpy differences between three commonly used phenyl guests: benzene, toluene, and t-butylbenzene. van der Waals interaction with the inside of the host cavity accounts for almost all of the net stabilization of the larger phenyl guests in beta-CD. Partial and full methylation of the secondary rim of beta-CD decreases host rigidity and significantly impairs binding of both phenyl and larger adamantane guest molecules. The beta-CD cavity is also very intolerant of guest charging, penalizing the oxidized state of ferrocene by at least 7 kcal/mol. beta-CD hence expresses moderate specificity toward uncharged organic guest molecules by van der Waals recognition, with a much higher specificity calculated for electrostatic recognition of organometallic guests.

The Rotational-Torsional Spectrum of the g'Gg Conformer of Ethylene Glycol: Elucidation of an Unusual Tunneling Path.

The microwave spectrum of the energetically unfavored g'Gg conformer of ethylene glycol (CH(2)OH&bond;CH(2)OH) is reported. This spectrum is dominated by an interconversion geared-type large-amplitude motion during which each OH group in turn forms the intramolecular hydrogen bond. The microwave spectrum has been analyzed with the help of a Watson-type Hamiltonian plus a 1.4-GHz tunneling splitting. The rotational dependence of this tunneling splitting has been examined using an IAM approach and this yielded qualitative information on the tunneling path the molecule uses to interconvert between its two most stable conformers. Unexpectedly, but in agreement with ab initio calculations, when tunneling occurs between the energetically equivalent g'Gg and gGg' conformers, the OH groups are rotated stepwise through 240 degrees in the sense of a flip-flop rather than a concerted rotation and the molecule goes through the more stable g'Ga and aGg' forms. The electronic reasons for preferring a long rather than a short rotational path via a gGg form are discussed using calculated adiabatic vibrational modes. Copyright 2001 Academic Press.

Comparison of algorithms for error-compensated kinetic determinations without prior knowledge of reaction orders or rate constants.

This paper describes the evaluation of algorithms written for error-compensated kinetic determinations, that do not need prior knowledge of reaction orders or rate constants. Results are reported for the quantification of acetoacetate in aqueous solution and urine. In addition to examination by nonlinear and linearized versions of the proposed new algorithms, the kinetic data were processed by a first-order model for comparison purposes. All the models yielded linear relationships between computed absorbance change and concentration; the new algorithms yield virtually identical results that represent better fits to the kinetic data than those obtained with the first-order model. The ability of the new algorithms to detect errors in the models is briefly discussed.

Linearized model for error-compensated kinetic determinations without prior knowledge of reaction order or rate constant.

This paper describes a new algorithm for calculation of reaction orders, rate constants, and initial and final values of detector signal from several signal vs time data points. The algorithm utilizes a linearized version of the rate equation and is intended primarily to provide initial estimates of these kinetic parameters for other curve-fitting methods. However, under some circumstances, the linearized model can provide sufficiently reliable results that subsequent processing by other methods is not needed. Simulated data with different levels of superimposed noise, data densities, reaction orders, rate constants, and signal change are used to evaluate the algorithm both for its primary purpose of providing initial estimates for other curve-fitting methods and as an independent method. Results are compared with those obtained with a nonlinear least-squares method and two initial-rate methods. The new algorithm provides less reliable results than those obtained by the nonlinear curve-fitting method for some situations (e.g. reaction orders greater than two, low data densities) but has the advantage that it is applicable to reaction orders at and near unity where the nonlinear method to which it is compared fails.