Molecular self-assembly is the spontaneous association of molecules under equilibrium conditions into stable, structurally well-defined aggregates joined by noncovalent bonds. Molecular self-assembly is ubiquitous in biological systems and underlies the formation of a wide variety of complex biological structures. Understanding self-assembly and the associated noncovalent interactions that connect complementary interacting molecular surfaces in biological aggregates is a central concern in structural biochemistry. Self-assembly is also emerging as a new strategy in chemical synthesis, with the potential of generating nonbiological structures with dimensions of 1 to 10(2) nanometers (with molecular weights of 10(4) to 10(10) daltons). Structures in the upper part of this range of sizes are presently inaccessible through chemical synthesis, and the ability to prepare them would open a route to structures comparable in size (and perhaps complementary in function) to those that can be prepared by microlithography and other techniques of microfabrication.

Molecular self-assembly and nanochemistry: A chemical strategy for the synthesis of nanostructures

The electronic structure of benzene on graphite (0001) is computed using the $GW$ approximation for the electron self-energy. The benzene quasiparticle energy gap is predicted to be 7.2 eV on graphite, substantially reduced from its calculated gas-phase value of 10.5 eV. This decrease is caused by a change in electronic correlation energy, an effect completely absent from the corresponding Kohn-Sham gap. For weakly coupled molecules, this correlation energy change can be described as a surface polarization effect. A classical image potential model illustrates the impact for other conjugated molecules on graphite.

https://escholarship.org/content/qt1bz3c818/qt1bz3c818.pdf

Renormalization of Molecular Electronic Levels at Metal-Molecule Interfaces

A new theory of solvent effects on the optical rotations of chiral molecules is presented. The frequency-dependent electric dipole−magnetic dipole polarizability, βαβ(ν), is calculated using density functional theory (DFT). Solvent effects are included using the polarizable continuum model (PCM). DFT/PCM calculations of sodium D line specific rotations, [α]D, have been carried out for seven conformationally rigid chiral organic molecules (fenchone, camphor, α-pinene, β-pinene, camphorquinone, verbenone, and methyloxirane) for a diverse set of seven solvents (cyclohexane, carbon tetrachloride, benzene, chloroform, acetone, methanol, and acetonitrile). The predicted variation in [α]D for the solvents cyclohexane, acetone, methanol, and acetonitrile are in excellent agreement with experiment for all seven molecules. For the solvents carbon tetrachloride, benzene, and chloroform, agreement is much poorer. Since only electrostatic solute−solvent interactions are included in the PCM, our results lead to the con...

Polarizable Continuum Model (PCM) Calculations of Solvent Effects on Optical Rotations of Chiral Molecules

The interacting boson model.

Cavity ring-down polarimetry (CRDP), a new, ultrasensitive method for probing circular birefringence and circular dichroism, has been developed by extending the well-established technique of pulsed cavity ring-down spectroscopy (CRDS). The concurrent incorporation of polarization elements into the stable resonator, injection optics, and detection train of a conventional CRDS apparatus is found to permit the quantitative measurement of optical rotation and differential absorption induced by the presence of chiral compounds. The sensitivity of this novel scheme is sufficient to allow (low-pressure) gas-phase species to be interrogated under ambient conditions, a fact highlighted by the direct determination of specific rotation at 355 nm for gaseous samples of α-pinene, β-pinene, cis-pinane, limonene, fenchone, and propylene oxide. Although usually precluded by the signal discrimination limits imposed upon traditional polarimeters, such gas-phase studies of nonresonant optical activity in the visible and nea...

Cavity Ring-Down Polarimetry (CRDP): A New Scheme for Probing Circular Birefringence and Circular Dichroism in the Gas Phase

Detailed theoretical analyses are presented for cavity ring-down polarimetry, a recently developed scheme for probing circular birefringence (nonresonant rotatory dispersion) and circular dichroism (resonant differential absorption) with unprecedented sensitivity. Aside from elucidating the nature of time-resolved signals generated by various modes of operation, the influence of instrumental imperfections on polarimetric response is examined. The unique ability of cavity ring-down polarimetry to interrogate nonresonant optical activity in low-pressure chiral vapors is demonstrated by extracting specific rotation parameters at two complementary excitation wavelengths (355 nm and 633 nm) for gaseous samples of α-pinene, β-pinene, and cis-pinane. The resulting isolated-molecule properties are contrasted with those derived from conventional solution-phase experiments and state-of-the-art ab initio calculations.

Cavity ring-down polarimetry (CRDP): theoretical and experimental characterization

Emission spectra obtained from jet-cooled disulfur monoxide (S2O) molecules have been interpreted by means of a novel Lie algebraic formalism that makes possible the facile evaluation of multidimensional Franck–Condon factors. Fluorescence accompanying selective excitation of isolated vibronic bands in the S2O C 1A′←X 1A′(π*←π) absorption system has been dispersed under moderate spectral resolution, allowing assignment of ground state levels possessing up to 20 quanta of vibration in the ν2 S–S stretching mode [Evib(X)⩽13 900 cm−1]. Aside from providing a rigorous and economical description for the inherently anharmonic nature of highly-excited polyatomic species, our algebraic approach enables quantitative information on molecular wavefunctions to be extracted directly from spectroscopic data. The emerging picture of S2O vibrational dynamics suggests that the X 1A′ potential surface is substantially more “local” in character than the C 1A′ manifold. While the observed pattern of X 1A′ vibrational e...

/pdf/the-vibronically-resolved-emission-spectrum-of-disulfur-28yuy5az04.pdf

The vibronically-resolved emission spectrum of disulfur monoxide (S2O): An algebraic calculation and quantitative interpretation of Franck–Condon transition intensities

The structural distortion of high-generation poly(amidoamine) (PAMAM) dendrimers at the liquid/solid interface was investigated in situ using tapping mode atomic force microscopy (AFM). With a substantial compression along the surface normal but minor lateral expansion, isolated PAMAM dendrimers at the water/mica interface exhibit dimensions similar to those reported for the same species in dense, dried arrays, rather than those of isolated, dried units. On graphite substrates, adsorbed dendrimers exhibit weaker adhesion forces than on mica. AFM images of lower generation dendrimers at the water/graphite interface reveal additional features interpreted as large three-dimensional aggregates.

AFM Studies of High-Generation PAMAM Dendrimers at the Liquid/Solid Interface

Self-assembled monolayers of free-base naphthalocyanine are examined in the context of analogous phthalocyanine films, revealing the influence of the more extended π-electron system on monolayer properties. Naphthalocyanine was vapor-deposited on a graphite substrate in ultrahigh vacuum and investigated in situ at low temperature (50 K) using scanning tunneling microscopy (STM). The crystallographic monolayer parameters of the deposited films were determined by means of submolecularly resolved STM images. In addition, vacancies in the monolayer have allowed for an accurate measurement of single molecule azimuthal angles. In STM topographs with submolecular resolution, a clear difference is evident between tunneling images corresponding to occupied and unoccupied sample states. The intramolecular structure exhibited by the STM images can be understood qualitatively by considering frontier orbitals calculated for isolated molecules. Moreover, single point tunneling spectra show a distinct signature of the o...

Tunneling Voltage Polarity Dependent Submolecular Contrast of Naphthalocyanine on Graphite. A STM Study of Close-Packed Monolayers under Ultrahigh-Vacuum Conditions

Thomas Müller

Papers

Cavity Ring-Down Polarimetry (CRDP): A New Scheme for Probing Circular Birefringence and Circular Dichroism in the Gas Phase

Cavity ring-down polarimetry (CRDP): theoretical and experimental characterization

The vibronically-resolved emission spectrum of disulfur monoxide (S2O): An algebraic calculation and quantitative interpretation of Franck–Condon transition intensities

AFM Studies of High-Generation PAMAM Dendrimers at the Liquid/Solid Interface

Tunneling Voltage Polarity Dependent Submolecular Contrast of Naphthalocyanine on Graphite. A STM Study of Close-Packed Monolayers under Ultrahigh-Vacuum Conditions