Nanoscale reduced volumes with novel properties can be produced from 2D materials like graphene. Mild thermal annealing imposes vast and varied amounts of water intercalation into the graphene-mica interface, resulting in the formation of nanoblisters and impacting the local environment for applications such as reactions confined at the solid-solid interface. Atomic force microscopy imaging (AFM) and micro-Fourier transform infrared (micro-FTIR) spectroscopy characterization after 60-120 °C anneals revealed large volumes of water readily intercalate into graphene-mica nanoblisters, elucidating water transport behavior under mild reaction conditions. The inflation and deflation of graphene nanoblisters throughout the annealing process is attributed to the contraction of the graphene capping layer upon cooling from the annealing temperature, due to the independence of nanoblister aspect ratios from nanoblister volume or surface area. The intercalated water volume was estimated by the distended volumes of each nanoblister and exhibit an equilibrium trend established after 2 h of annealing. This water equilibrium occurs at a variety of temperatures, but higher temperatures favor graphene contraction and distention to accommodate larger volumes of water. Nanoblister volumes are set during the cooling process, indicating a kinetic trapping effect that can influence physical properties and reactivity for all systems confined at the graphene-mica interface.

The polymerization of 1,4-benzenediboronic acid (BDBA) on mica to form a covalent organic framework (COF-1) reveals a dramatic increase in crystallinity when physically confined by exfoliated graphene. COF-1 domains formed under graphene confinement are highly geometric in shape and on the order of square micrometers in size, while outside of the exfoliated flakes, the COF-1 does not exhibit long-range mesoscale structural order, according to atomic force microscopy imaging. Micro-Fourier transform infrared spectroscopy confirms the presence of COF-1 both outside and underneath the exfoliated graphene flakes, and density functional theory calculations predict that higher mobility and self-assembly are not causes of this higher degree of crystallinity for the confined COF-1 domains. The most likely origin of the confined COF-1's substantial increase in crystallinity is from enhanced dynamic covalent crystallization due to the water confined beneath the graphene flake.

Scanning tunneling microscopy was used to study the self-assembly of three molecules on the Au(111) surface: 2-naphthoic acid, quinaldic acid, and 3-quinoline carboxylic acid. All three compounds consist of two fused six-membered rings functionalized at the same position with a carboxylic acid group. Despite their chemical similarity, widely different structures were observed to result from self-assembly after pulse deposition. 2-Naphthoic acid forms cyclically hydrogen-bonded pentamers, a metastable structure that transitions to rows of dimers upon gentle annealing. Quinaldic acid and 3-quinoline carboxylic acid form dimers, tetramers, and hexamers, but no pentamers. Differences in self-assembly between these three compounds are attributed to the ability of quinaldic acid and 3-quinoline carboxylic acid to form zwitterionic species.

Traditionally, the goal of self-assembly and supramolecular chemistry is to engineer an equilibrium structure with a desired geometry and functionality; this is achieved through careful choice of molecular monomers, growth conditions, and substrate. Supramolecular assemblies produced under nonequilibrium conditions, in contrast, can form metastable structures with conformations quite different from those accessible in equilibrium self-assembly. The study of nonequilibrium growth of clusters potentially impacts the study of nucleation in atmospheric aerosols, nucleation in organic crystallization, and mesoscale organization for systems ranging from biological molecules to molecular electronics. In our experiments, we prepare surface monolayers of small organic and organometallic molecules through direct injection of a solution onto a substrate in high vacuum. During this process, the rapid evaporation of small solution droplets in high vacuum can lead to nonequilibrium growth conditions. The resulting structures are then characterized by scanning tunneling microscopy. Among the features observed in these experiments are cyclic, hydrogen-bonded pentamers. For carboxylic acids, the two-molecule ring dimer is the common binding motif. Large, cyclic hydrogen-bonded systems are uncommon, especially so for rings with five members. Despite this, pentagonal clusters appear to be a general phenomenon for systems containing adjacent strong and weak hydrogen-bonding elements on five-member aromatic rings. Regular pentamers have been observed as metastable structures for ferrocenecarboxylic acid, indole-2-carboxylic acid, and isatin (1-H-indole-2,3-dione). Electronic structure calculations confirm the relative stability of these structures with respect to the dimer or catemer conformations which are observed in the solid-state crystal structures. For ferrocenecarboxylic acid, cyclic pentamers undergo further self-assembly, resulting in long-range order in conjunction with local 5-fold rotational symmetry. This system is the first reported self-assembled molecular quasicrystal, and it remains the only example of a hydrogen-bonded quasicrystal. This supramolecular structure forms as a result of the cocrystallization of hydrogen-bonded cyclic pentamers with intercalated molecular dimers. The shared bonding to a single dimer is responsible for locking the adjacent pentamers in specific distances and orientations, which produces the quasicrystal. Careful analysis of experimental data provides evidence that, in some cases, metastable clusters are formed in solution and then subsequently adsorb on the surface. This is a unusual mechanism for supramolecular assembly, and it has important implications for understanding questions in crystal growth, namely: what the initial stages of crystal growth are as molecules are first precipitating from solution; what role the solvent plays in determining crystal structure; and whether solvent-mediated clustering is important in the broader phenomenon of solid-state polymorphism.

Monolayers of two pairs of structural isomers were deposited on Au(111) and observed via scanning tunneling microscopy in ultrahigh vacuum. We observe exclusively cyclic pentamers of isatin (1H-indole-2,3-dione), whereas its structural isomer, phthalimide (isoindole-1,3-dione), self-assembles primarily into close-packed arrays, with alternate structures that include kinetically locked disordered clusters and tetramer networks. Removal of the phthalimide NH group and its replacement with a CH2 group produces 1,3-indandione, which, despite the loss of the hydrogen-bond donor site, self-assembles into similar structures: close-packed areas and tetramer networks. The equivalent analog for isatin, 1,2-indandione, does not form pentamers and instead forms only close-packed areas and disordered regions. By iteratively altering the chemical structure, we demonstrate the influence that the chemical structure has on the resulting two-dimensional self-assembly.

The direct injection of a 9,10-phenanthrenequinone in tetrahydrofuran solution on a Au(111) substrate in high vacuum results in the formation of metastable clusters with a non-intuitive structure. Metastable, rectangular tetramers of this molecule form in which the net molecular dipoles all orient toward the center of the cluster. This structure does not allow for additional hydrogen bonding and thus the origin of its metastability is not clear. We compare this feature to other structures observed on this surface, as well as those formed during the deposition of 9-fluorenone, which does not exhibit this anomalous clustering behavior.

A series of experiments and electronic structure calculations were performed to identify metastable 1,1'-ferrocenedicarboxylic acid supramolecular structures formed during solution deposition in a vacuum on a Au(111) substrate, as well as to observe their evolution into more stable species under mild annealing conditions. Electrospray ionization mass spectrometry measurments were performed to determine which species are likely to be present in the rapidly evaporating droplet, and these experiments found that a hexamer can exist in solution during deposition, albeit as a metastable species. The molecular clusters present after solution deposition were observed and analyzed using ultrahigh-vacuum scanning tunneling microscopy, and the initial monolayer contains four basic classes of structures: ordered dimer domains, tilted dimer rows, square tetramers, and rectangular chiral hexamers. Electronic structure calculations indicate that the chiral hexamers consist of a central dimer surrounded by four molecules oriented to form birfurcated hydrogen bonds with other carboxylic acid groups and weaker hydrogen bonds with hydrogens from the aromatic rings. The calculations also indicated that the tetramers are clusters held together by carboxylic acid dimer bonds on each ring oriented perpendicular to each other, and that this conformation is slightly more stable than two dimers for a cluster of four molecules. Annealing this surface at. 50 degrees C for 1 h results in the formation of both isolated tetramers and ordered tetramer rows at the expense of the end-to-end dimer domains, with few chiral hexamers remaining. Further annealing at 50 degrees C, as well as annealing at 65 degrees C drives the system to form chiral dimer domains, as well as several other minor structures. Annealing at 75 degrees C resulted in a dramatic decrease in apparent surface coverage, and most ordered structures existed as large tilted dimer rows, whether isolated or in ordered domains. This drop in surface coverage is likely due to some combination of decomposition of the molecule, desorption, or the growth of three-dimensional crystal structures. The observed coexistence of many forms of ordered dimer structures after annealing, indicates that the equilbrium conformation of 1,1'-ferrocenedicarboxylic acid is some array of ordered dimers, and the variety of supramolecular structures present after annealing is an indicator that this system evolves under kinetically controlled growth conditions.

Self -assembled monolayers of 1H-indole-2,3-dione (isatin), 3 -methyl 2-oxindole, and 7-fluoroisatin are observed on the Au(111) surface via scanning tunneling microscopy (STM). We observed that isatin forms pentamers with density functional theory providing support for a cyclic structure stabilized by both N-H...O and C-H...O hydrogen bonds between neighboring molecules. The C-H...O bond is made between the 7-position C H acting as the hydrogen bond donor and the 3 -position carbonyl as the hydrogen bond acceptor, and calculations show that the isatin pentamer structure is 12 kJ/mol more stable than the dimer. When the 3-position carbonyl is removed and replaced with a methyl group (3-methyl 2-oxindole), we observe a monolayer with a mixture of catemer chains and pentameric clusters that are qinlitatively different from those of isatin. Pentamer formation is completely broken when the 7 position hydrogen is removed and replaced with fluorine; the monolayer of 7-fluoroisatin is composed of a mixture of close packed ordered domains and hexamer clusters. The role of C-H...O bonding in forming isatin pentamers is supported by electrospray ionization mass spectrometry measurements, which show a propensity for isatin cluster formation, including magic -number isatin pentamers, while 3 -methyl 2-oxindole and 7-fluoroisatin show relatively little clustering under the same conditions.

The preparation of 7-Fc(+) -8-Fc-7,8-nido-[C2 B9 H10 ](-) (Fc(+) FcC2 B9 (-) ) demonstrates the successful incorporation of a carborane cage as an internal counteranion bridging between ferrocene and ferrocenium units. This neutral mixed-valence Fe(II) /Fe(III) complex overcomes the proximal electronic bias imposed by external counterions, a practical limitation in the use of molecular switches. A combination of UV/Vis-NIR spectroscopic and TD-DFT computational studies indicate that electron transfer within Fc(+) FcC2 B9 (-) is achieved through a bridge-mediated mechanism. This electronic framework therefore provides the possibility of an all-neutral null state, a key requirement for the implementation of quantum-dot cellular automata (QCA) molecular computing. The adhesion, ordering, and characterization of Fc(+) FcC2 B9 (-) on Au(111) has been observed by scanning tunneling microscopy.

Monolayers of indole-2-carboxylic acid and indole-3-carboxylic acid on gold are studied using ultrahigh-vacuum scanning tunneling microscopy. Both molecules form symmetric, cyclic, hydrogen-bonded pentamers, a structure that is stabilized by the presence of a weak hydrogen-bond donor (NH or CH) adjacent to the carboxylic acid on the five-membered ring. In addition to pentamers, indole-2-carboxylic acid forms hexamers and catemer chains, while indole-3-carboxylic acid monolayers are generally disordered. Density functional theory calculations show that pentamers and hexamers have stability comparable to dimers or short catemers. The coexistence of all of these structures likely arises from the nonequilibrium conditions present in solution during pulse deposition of the monolayer.

Low-temperature scanning tunneling microscopy is used to observe self-assembled structures of ferrocenedicarboxylic acid (Fc(COOH)2) on the Au(111) surface. The surface is prepared by pulse-deposition of Fc(COOH)2 dissolved in methanol, and the solvent is evaporated before imaging. While the rows of hydrogen-bonded dimers that are common for carboxylic acid species are observed, the majority of adsorbed Fc(COOH)2 is instead found in six-molecule clusters with a well-defined and chiral geometry. The coverage and distribution of these clusters are consistent with a random sequential adsorption model, showing that solution-phase species are determinative of adsorbate distribution for this system under these reaction conditions.

A combined helium atom scattering and density functional perturbation theory study has been performed to elucidate the surface phonon dispersion relations for both the CH3-Si(111)-(1 × 1) and CD3-Si(111)-(1 × 1) surfaces. The combination of experimental and theoretical methods has allowed characterization of the interactions between the low energy vibrations of the adsorbate and the lattice waves of the underlying substrate, as well as characterization of the interactions between neighboring methyl groups, across the entire wavevector resolved vibrational energy spectrum of each system. The Rayleigh wave was found to hybridize with the surface rocking libration near the surface Brillouin zone edge at both the M̄-point and K̄-point. The calculations indicated that the range of possible energies for the potential barrier to the methyl rotation about the Si-C axis is sufficient to prevent the free rotation of the methyl groups at a room temperature interface. The density functional perturbation theory calculations revealed several other surface phonons that experienced mode-splitting arising from the mutual interaction of adjacent methyl groups. The theory identified a Lucas pair that exists just below the silicon optical bands. For both the CH3- and CD3-terminated Si(111) surfaces, the deformations of the methyl groups were examined and compared to previous experimental and theoretical work on the nature of the surface vibrations. The calculations indicated a splitting of the asymmetric deformation of the methyl group near the zone edges due to steric interactions of adjacent methyl groups. The observed shifts in vibrational energies of the -CD3 groups were consistent with the expected effect of isotopic substitution in this system.

The interplay of the librations of a covalently bound organic adlayer with the lattice waves of an underlying semiconductor surface was characterized using helium atom scattering in conjunction with analysis by density functional perturbation theory. The Rayleigh wave dispersion relation of CH3- and CD3-terminated Si(111) surfaces was probed across the entire surface Brillouin zone by the use of inelastic helium atom time-of-flight experiments. The experimentally determined Rayleigh wave dispersion relations were in agreement with those predicted by density functional perturbation theory. The Rayleigh wave for the CH3- and CD3-terminated Si(111) surfaces exhibited a nonsinusoidal line shape, which can be attributed to the hybridization of overlayer librations with the vibrations of the underlying substrate. This combined synthetic, experimental, and theoretical effort clearly demonstrates the impact of hybridization between librations of the overlayer and the substrate lattice waves in determining the overall vibrational band structure of this complex interface.

The scattering of atomic and molecular beams from well-characterized surfaces is a useful method for studying the dynamics of gas-surface interactions, providing precise information on the energy and momentum exchange which occur in such encounters. We apply this technique to new systems including disordered films of macromolecules, complex interfaces of macromolecular systems, and hybrid organic-semiconductor interfaces. Time-lapse atomic force microscopy studies of diblock copolymer structural evolution and fluctuations complement the scattering data to give a more complete understanding of dynamical processes in these complex disordered films. Our new scattering findings quantitatively characterize changes in interfacial dynamics including confinement in thin films of poly(methyl methacrylate) and changes in the physical properties of poly(ethylene terephthalate) films as they transform from the glassy to their semicrystalline phase. Further measurements on a hybrid organic-semiconductor interface, methyl-terminated silicon (111), reveal that the surface thermal motion and gas-surface energy accommodation are dominated by local molecular vibrations while the interfacial lattice dynamics remain accessible through helium scattering. High temperature atomic force microscopy allows direct, real-time visualization of structural reorganization and defect migration in poly(styrene)block-poly(methyl methacrylate) films, revealing details of film reorganization and thermal annealing. Moreover, we employed lithographically created channels to guide the alignment of polymer microdomains. This, in turn, allows direct observation of the mechanisms for diffusion and annihilation of dislocation and disclination defects. In summary, this paper elaborates on the power of combining atom scattering and scanning probe microscopy to interrogate the vibrational dynamics, energy accommodation, energy flow, and structural reorganization in complex interfaces.

The surface dynamics of amorphous and semicrystalline polymer films have been measured using helium atom scattering. Time-of-flight data were collected to resolve the elastic and inelastic scattering components in the diffuse scattering of neutral helium atoms from the surface of a thin poly(ethylene terephthalate) film. Debye–Waller attenuation was observed for both the amorphous and semicrystalline phases of the polymer by recording the decay of elastically scattered helium atoms with increasing surface temperature. Thermal attenuation measurements in the specular scattering geometry yielded perpendicular mean-square displacements of 2.7•10 -4 Å 2 K -1 and 3.1•10 -4 Å 2 K -1 for the amorphous and semicrystalline surfaces, respectively. The semicrystalline surface was consistently ∼15% softer than the amorphous across a variety of perpendicular momentum transfers. The Debye–Waller factors were also measured at off-specular angles to characterize the parallel mean-square displacements, which were found to increase by an order of magnitude over the perpendicular mean-square displacements for both surfaces. In contrast to the perpendicular motion, the semicrystalline state was ∼25% stiffer than the amorphous phase in the surface plane. These results were uniquely accessed through low-energy neutral helium atom scattering due to the highly surface-sensitive and nonperturbative nature of these interactions. The goal of tailoring the chemical and physical properties of complex advanced materials requires an improved understanding of interfacial dynamics, information that is obtainable through atomic beam scattering methods.

The surface structure and vibrational dynamics of CH(3)-Si(111) and CD(3)-Si(111) surfaces were measured using helium atom scattering. The elastic diffraction patterns exhibited a lattice constant of 3.82 Å, in accordance with the spacing of the silicon underlayer. The excellent quality of the observed diffraction patterns, along with minimal diffuse background, indicated a high degree of long-range ordering and a low defect density for this interface. The vibrational dynamics were investigated by measurement of the Debye-Waller attenuation of the elastic diffraction peaks as the surface temperature was increased. The angular dependence of the specular (θ(i)=θ(f)) decay revealed perpendicular mean-square displacements of 1.0×10(-5) Å(2) K(-1) for the CH(3)-Si(111) surface and 1.2×10(-5) Å(2) K(-1) for the CD(3)-Si(111) surface, and a He-surface attractive well depth of ∼7 meV. The effective surface Debye temperatures were calculated to be 983 K for the CH(3)-Si(111) surface and 824 K for the CD(3)-Si(111) surface. These relatively large Debye temperatures suggest that collisional energy accommodation at the surface occurs primarily through the Si-C local molecular modes. The parallel mean-square displacements were 7.1×10(-4) and 7.2×10(-4) Å(2) K(-1) for the CH(3)-Si(111) and CD(3)-Si(111) surfaces, respectively. The observed increase in thermal motion is consistent with the interaction between the helium atoms and Si-CH(3) bending modes. These experiments have thus yielded detailed information on the dynamical properties of these robust and technologically interesting semiconductor interfaces.

Integrase is an enzyme found in human immunodeficiency virus, which is required for the viral life cycle, yet has no human cellular homologue. For this reason, HIV integrase (IN) has become an important target for the development of new AIDS therapeutics. Irreversible affinity ligands have proven to be valuable tools for studying a number of enzyme and protein systems, yet to date there have been no reports of such affinity ligands for the study of IN. As an initial approach toward irreversible ligand design directed against IN, we appended isothiocyanate functionality onto caffeic acid phenethyl ester (CAPE), a known HIV integrase inhibitor. The choice of isothiocyanate as the reactive functionality, was based on its demonstrated utility in the preparation of affinity ligands directed against a number of other protein targets. Several isomeric CAPE isothiocyanates were prepared to explore the enzyme topography for reactive nitrogen and sulfur nucleophiles vicinal to the enzyme-bound CAPE. The preparation of these CAPE isothiocyanates, required development of new synthetic methodology which employed phenyl thiocarbamates as latent isothiocyanates which could be unmasked near the end of the synthetic sequence. When it was observed that beta-mercaptoethanol (beta-ME), which is required to maintain the catalytic activity of soluble IN (a F185KC280S mutant), reacted with CAPE isothiocyanate functionality to form the corresponding hydroxyethylthiocarbamate, a variety of mutant IN were examined which did not require the presence of beta-ME for catalytic activity. Although in these latter enzymes, CAPE isothiocyanate functionality was presumed to be present and available for acylation by IN nucleophiles, they were equally effective against Cys to Ser mutants. One conclusion of these studies, is that upon binding of CAPE to the integrase, nitrogen or sulfur nucleophiles may not be properly situated in the vicinity of the phenethyl aryl ring to allow reaction with and covalent modification of reactive functionality, such as isothiocyanate groups. The fact that introduction of the isothiocyanate group onto various positions of the phenethyl ring or replacement of the phenyl ring with naphthyl rings, failed to significantly affect inhibitory potency, indicates a degree of insensitivity of this region of the molecule toward structural modification. These findings may be useful in future studies concerned with the development and use of HIV-1 integrase affinity ligands.