Publications

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A molecular-scale interpretation of interfacial processes is often downplayed in the analysis of traditional water treatment methods. However, such an approach is critical for the development of enhanced performance in traditional desalination and water treatments. Water confined between surfaces, within channels, or in pores is ubiquitous in technology and nature. Its physical and chemical properties in such environments are unpredictably different from bulk water. As a result, advances in water desalination and purification methods may be accomplished through an improved analysis of water behavior in these challenging environments using state-of-the-art microscopy, spectroscopy, experimental, and computational methods.

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Single-wall carbon nanotubes (SWNTs) have shown great promise in novel applications in molecular electronics, biohazard detection, and composite materials. Commercially synthesized nanotubes exhibit a wide dispersion of geometries and conductivities, and tend to aggregate. Hence the key to using these materials is the ability to solubilize and sort carbon nanotubes according to their geometric/electronic properties. One of the most effective dispersants is single-stranded DNA (ssDNA), but there are many outstanding questions regarding the interaction between nucleic acids and SWNTs. In this work we focus on the interactions of SWNTs with single monomers of nucleic acids, as a first step to answering these outstanding questions. We use atomistic molecular dynamics simulations to calculate the binding energy of six different nucleotide monophosphates (NMPs) to a (6,0) single-wall carbon nanotube in aqueous solution. We find that the binding energies are generally favorable, of the order of a few kcal/mol. The binding energies of the different NMPs were very similar in salt solution, whereas we found a range of binding energies for NMPs in pure water. The binding energies are sensitive to the details of the association of the sodium ions with the phosphate groups and also to the average conformations of the nucleotides. We use electronic structure (Density Functional Theory (DFT) and Moller-Plesset second order perturbation to uncorrelated Hartree Fock theory (MP2)) methods to complement the classical force field study. With judicious choices of DFT exchange correlation functionals, we find that DFT, MP2, and classical force field predictions are in qualitative and even quantitative agreement; all three methods should give reliable and valid predictions. However, in one important case, the interactions between ions and metallic carbon nanotubes--the SWNT polarization-induced affinity for ions, neglected in most classical force field studies, is found to be extremely large (on the order of electron volts) and may have important consequences for various SWNT applications. Finally, the adsorption of NMPs onto single-walled carbon nanotubes were studied experimentally. The nanotubes were sonicated in the presence of the nucleotides at various weight fractions and centrifuged before examining the ultraviolet absorbance of the resulting supernatant. A distinct Langmuir adsorption isotherm was obtained for each nucleotide. All of the nucleotides differ in their saturation value as well as their initial slope, which we attribute to differences both in nucleotide structure and in the binding ability of different types or clusters of tubes. Results from this simple system provide insights toward development of dispersion and separation methods for nanotubes: strongly binding nucleotides are likely to help disperse, whereas weaker ones may provide selectivity that may be beneficial to a separation process.

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We report on our studies of the structural properties of a hydrogen molecule dissolved in liquid water. The radial distribution function, coordination number and coordination number distribution are calculated using different representations of the interatomic forces within molecular dynamics (MD), Monte Carlo (MC) and ab initio molecular dynamics (AIMD) simulation frameworks. Although structural details differ in the radial distribution functions generated from the different force fields, all approaches agree that the average and most probable number of water molecules occupying the inner hydration sphere around hydrogen is 16. Furthermore, all results exclude the possibility of clathrate-like organization of water molecules around the hydrophobic molecular hydrogen solute.

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Carbon nanotubes (CNT) are unique nanoscale building blocks for a variety of materials and applications, from nanocomposites, sensors and molecular electronics to drug and vaccine delivery. An important step towards realizing these applications is the ability to controllably self-assemble the nanotubes into larger structures. Recently, amphiphilic peptide helices have been shown to bind to carbon nanotubes and thus solubilize them in water. Furthermore, the peptides then facilitate the assembly of the peptide-wrapped nanotubes into supramolecular, well-aligned fibers. We investigate the role that molecular modeling can play in elucidating the interactions between the peptides and the carbon nanotubes in aqueous solution. Using ab initio methods, we have studied the interactions between water and CNTs. Classical simulations can be used on larger length scales. However, it is difficult to sample in atomistic detail large biomolecules such as the amphiphilic peptide of interest here. Thus, we have explored both new sampling methods using configurational-bias Monte Carlo simulations, and also coarse-grained models for peptides described in the literature. An improved capability to model these inorganichiopolymer interfaces could be used to generate improved understanding of peptide-nanotube self-assembly, eventually leading to the engineering of new peptides for specific self-assembly goals.

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We apply density functional theory (DFT) and the DFT+U technique to study the adsorption of transition metal porphine molecules on atomistically flat Au(111) surfaces. DFT calculations using the Perdew?Burke?Ernzerhof exchange correlation functional correctly predict the palladium porphine (PdP) low-spin ground state. PdP is found to adsorb preferentially on gold in a flat geometry, not in an edgewise geometry, in qualitative agreement with experiments on substituted porphyrins. It exhibits no covalent bonding to Au(111), and the binding energy is a small fraction of an electronvolt. The DFT+U technique, parametrized to B3LYP-predicted spin state ordering of the Mn d-electrons, is found to be crucial for reproducing the correct magnetic moment and geometry of the isolated manganese porphine (MnP) molecule. Adsorption of Mn(II)P on Au(111) substantially alters the Mn ion spin state. Its interaction with the gold substrate is stronger and more site-specific than that of PdP. The binding can be partially reversed by applying an electric potential, which leads to significant changes in the electronic and magnetic properties of adsorbed MnP and 0.1 {angstrom} changes in the Mn-nitrogen distances within the porphine macrocycle. We conjecture that this DFT+U approach may be a useful general method for modeling first-row transition metal ion complexes in a condensed-matter setting.

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We investigate the liquid structure, ion hydration, and some thermodynamic properties associated with the rigid geometry approximation to water by applying ab initio molecular dynamics simulations (AIMD) with the Perdew-Burke-Ernzerhof (PBE) exchange-correlation functional at T = 320 K. We vary the rigid water geometry in order to locate a class of practical water models that yield reasonable liquid structure and dynamics, and to examine the progression of AIMD-predicted water behavior as the OH bond length varies. Water constrained at the optimal PBE gas phase geometry yields reasonable pair correlation functions. The predicted liquid phase pressure, however, is large ({approx}8.0 kbar). Although the O-H bond in water should elongate when transferred from gas to the condensed phase, when it is constrained to 0.02, or even just 0.01 {angstrom} longer than the optimal gas phase value, liquid water is predicted to be substantially overstructured compared to experiments. Zero temperature calculations of the thermodynamic properties of cubic ice underscore the sensitivity toward small variations in the O-H bond length. We examine the hydration structures of potassium, chloride, and formate ions in one rigid PBE water model. The results are in reasonable agreement with unconstrained AIMD simulations.

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