PECD study of a single-conformer molecule: a critical comparison of experiment and theory.

In this work we address a specific experimental and theoretical question regarding the influence of a conformational population in the modeling of photoelectron circular dichroism (PECD) spectroscopy. In the past two decades, PECD has revealed a rich and complex phenomenology in molecular processes with unprecedented insight, especially in molecular geometry sensitivity. Since the early development of this spectroscopy, theory has pointed out the importance of conformer influence on PECD; in particular, the rotation of methyl groups was surprisingly found to be responsible for strong modulation of the PECD signal. Here, to advance understanding of the effect of rotations, we have chosen to study norcamphor, a single-conformer molecule, as a benchmark for a PECD comparison between experiment and theory at the density functional theory (DFT) and time-dependent density functional theory (TDDFT) levels. The excellent agreement between experimental data and theory for norcamphor sheds light on the influence of rotations and gives a solid explanation for the reasonable qualitative agreement in the PECD of camphor, where three methyl groups are added to the same molecular structure.

Resonant circular dichroism of chiral metal-organic complex.

A sizable enhancement of the circular dichroism in photoelectron spectroscopy has been measured and computed for the metal complex Δ-cobalt(III) tris-acetylacetonate highest occupied molecular orbital state in the region of the Co 3p→3d Fano resonance. In the resonance the dichroism reaches the maximum value of 5% and even changes its sign as compared to the direct photoionization channel. We ascribe this enhancement to electron correlation processes, namely, with the coupling between discrete excitations and the continuum, which is correctly described in the time dependent density functional theory (TDDFT) framework. These findings open new physical aspects of photoelectron circular dichroism that now can be interpreted not only via the simple direct ionization, but also through more complex electron correlation processes.

The valence electronic structure and conformational flexibility of epichlorohydrin.

The electronic structure of epichlorohydrin is investigated in the whole valence region by a combined experimental and theoretical study. The issue of controversial assignments of the molecular electronic structure is here addressed. Photoelectron spectra (PES) and Threshold Photoelectron spectra (TPES) of room temperature molecules in the gas phase are recorded. Geometries and energies of the stable conformers due to internal rotation of the C-C-C-Cl dihedral angle, gauche-II (g-II), gauche-I (g-I), and cis, are calculated, and the effect of the conformational flexibility on the photoionization energetics is studied by DFT and 2h-1p Configuration Interaction (CI) methods. Strong breakdown of the Koopmans Theorem (KT) is obtained for the four outermost ionizations, which are further investigated by higher level ab initio calculations. The full assignment of the spectrum is put on a firm basis by the combination of experimental and theoretical results. The orbital composition from correlated calculations is found closer to the DFT orbitals, which are then used to analyze the electronic structure of the molecule. The Highest Occupied Molecular Orbital (HOMO) and HOMO--2 are n(O)/n(Cl) mixed orbitals. The nature of each valence MO is generally preserved in all the conformers, although the magnitude of the n(O)/n(Cl) mixing in HOMO and HOMO--2 varies to some extent with the C-C-C-Cl dihedral angle. The low energy part of the HOMO PE band is predicted to be substantially affected by the conformational flexibility, as experimentally observed in the spectra. The rest of the spectrum is described in terms of the dominant conformer g-II, and a good agreement between experiment and theory is found. The inner-valence PE spectrum is characterized by satellite structures, due to electron correlation effects, which are interpreted by means of 2h-1p CI calculations.

Chirality transfer from a single chiral molecule to 2D superstructures in alaninol on the Cu(100) surface.

The formation of 2D chiral monolayers obtained by self-assembly of chiral molecules on surfaces has been widely reported in the literature. Control of chirality transfer from a single molecule to surface superstructures is a challenging and important aspect for tailoring the properties of 2D nanostructures. However, despite the wealth of investigations performed in recent years, how chiral transfer takes place on a large scale still remains an open question. In this paper we report a coupling of scanning tunneling microscopy and low energy electron diffraction measurements with an original theoretical approach, combining molecular dynamics and essential dynamics with density functional theory, to investigate self-assembled chiral structures formed when alaninol adsorbs on Cu(100). The peculiarity of this system is related to the formation of tetrameric molecular structures which constitute the building blocks of the self-assembled chiral monolayer. Such characteristics make alaninol/Cu(100) a good candidate to reveal chiral expression changes. We find that the deposition of alaninol enantiomers results in the formation of isolated tetramers that are aligned along the directions of the substrate at low coverage or when geometrical confinement prevents long-range order. Conversely, a rotation of 14° with respect to the Cu(100) unit vectors is observed when small clusters of tetramers are formed. An insight to the process leading to a 2D globally chiral surface has been obtained by monitoring molecular assemblies as they grow from the early stages of adsorption, suggesting that the distinctive orientation of the self-assembled monolayer originates from a balance of cooperating forces which start acting only when tetramers pack together to form small clusters.

2-amino-1-propanol versus 1-amino-2-propanol: valence band and C 1s core-level photoelectron spectra.

Valence band and C 1s core-level photoelectron spectra of S-(+)-2-amino-1-propanol (alaninol) and S-(+)-1-amino-2-propanol (isopropanolamine) have been studied by means of synchrotron radiation photoelectron spectroscopy in gas phase. The alaninol, the reduced derivative of the alanine, is a good test system of amino acid-like structures. The isopropanolamine, presenting the inversion of the two functional groups of the alaninol at the chiral carbon, offers the opportunity to study the effect of -OH and -NH(2) structural position on the photoelectron spectra. The influence of the conformational contribution on the electronic structure and the photoelectron spectra has been interpreted using density functional and ab initio theoretical calculations. Agreement has been achieved by taking into account the presence, in gas phase, of two conformers with different population ratios in both chiral systems. The C 1s core-level spectra of alaninol and isopropanolamine are reported and the peak positions of the three carbon atoms of the molecules are assigned.

Vibrational state dependence of beta and D asymmetry parameters: the case of the highest occupied molecular orbital photoelectron spectrum of methyl-oxirane.

The beta angular asymmetry and D dichroic asymmetry parameters of the methyl-oxirane highest occupied molecular orbital (HOMO) band have been experimentally investigated with vibrational resolution using synchrotron radiation. A theoretical calculation of the Franck-Condon factors between vibrational ground state and different ionic vibrational states, in the Born-Oppenheimer harmonic approximation, has been performed in order to gain information on the vibrational states mainly involved in the HOMO photoelectron band. The general good agreement between theoretical and experimental results allows a reliable assignment of the major features. The experimental determination of beta and D shows their dependence on the different final vibrational states. This paper reports, for the first time, experimental evidence of the dependence of the dichroic D parameter on the vibrational excitation of the ion.

An AFM investigation of oligonucleotides anchored on unoxidized crystalline silicon surfaces.

Carboxylic terminated monolayers have been covalently attached on phosphorous doped crystalline (100) silicon surfaces using a cathodic electro grafting technique. The functionalization concentration and efficiency have been evaluated with different techniques. In particular, topographic images, performed with an atomic force microscope, were used to optimize the protocol in order to obtain a surface whose characteristics of uniformity and reproducibility are ideal for a bio-electronic device. Phase lag images of the functionalized surfaces were also performed, and show non-topographic structures that have been interpreted as areas of different molecule self-orientation. Poly-thymine oligonucleotides have been anchored on such a surface to form a nano-biosensing device capable to react selectively with a specific target molecule, a poly-adenine oligonucleotide. AFM images of high density (approximately 3x10(12) mol/cm2) single strand and double strand covered samples show toroidal shaped structures formed by the self-assembly of the oligonucleotides on the silicon surface.

Valence photoionization dynamics in circular dichroism of chiral free molecules: the methyl-oxirane.

The dynamical behavior of circular dichroism for valence photoionization processes in pure enantiomers of randomly oriented methyl-oxirane molecules has been studied by circularly polarized synchrotron radiation. Experimental results of the dichroism coefficient obtained for valence photoionization processes as a function of photon energy have been compared with theoretical values predicted by state-of-the-art ab initio density-functional theory. The circular dichroism measured at low electron kinetic energies was as large as 11%. Trends in the experimental dynamical behavior of the dichroism coefficients D(i)(omega) have been observed. Agreement between experimental and theoretical results permits unambiguous identification of the enantiomer and of the individual orbitals.

AFM characterization of solid-supported lipid multilayers prepared by spin-coating.

Lipids are the principal components of biologically relevant structures as cellular membranes. They have been the subject of many studies due to their biological relevance and their potential applications. Different techniques, such as Langmuir-Blodgett and vesicle-fusion deposition, are available to deposit ordered lipid films on etched surfaces. Recently, a new technique of lipid film deposition has been proposed in which stacks of a small and well-controlled number of bilayers are prepared on a suitable substrate using a spin-coater. We studied the morphological properties of multi-layers made of cationic and neutral lipids (DOTAP and DOPC) and mixtures of them using dynamic mode atomic force microscopy (AFM). After adapting and optimizing, the spin-coating technique to deposit lipids on a chemically etched Silicon (1,0,0) substrate, a morphological nanometer-scale characterization of the aforementioned samples has been provided. The AFM study showed that an initial layer of ordered vesicles is formed and, afterward, depending on details of the spin-coating preparation protocol and to the dimension of the silicon substrate, vesicle fusion and structural rearrangements of the lipid layers may occur. The present data disclose the possibility to control the lipid's structures by acting on spin-coating parameters with promising perspectives for novel applications of lipid films.

Diffraction anomalous fine structure of forbidden reflection of super-ordered GaInP.

We used DAFS to probe super-ordered domains in InGaP/GaAs epitaxial growth. The sample was lattice matched InGaP epitaxially grown on GaAs with a substrate miscut angle of 6 degrees with respect to the (001) direction. InGaP epi-layer exhibited (111)-type alloy ordering, of alternating InP and GaP like planes and giving rise to a (-5/2,5/2,-5/2) Bragg peak reflection which becomes allowed. Structural data can be extracted, at the same time, for the surroundings of Gallium in the bulk and in the epi-layer from allowed reflections, while the forbidden reflection gives structural details around Gallium in the ordered domains. Difference with the bulk InGaP Fourier transform confirms the symmetry selectivity of chosen reflections for the super-ordered domains.

X-ray Absorption Spectroscopy Studies of Ruthenoxane Phthalocyanine Derivative HO-[(Pc)RuO](n)()-H.

Comprehensive EXAFS investigation carried out on ruthenoxane phthalocyanine and on its chemical precursors ruthenium phthalocyanine dimer and ruthenium bis-pyridine phthalocyanine are reported. The distances around the ruthenium atom were obtained by data analysis and confirm the structural models already proposed for the first two compounds and indicate two pyridines axially coordinated to the central metal for the adduct.

An EXAFS, and preliminary X-ray crystallographic, investigation of an iron-containing product from the lichen Cladonia deformis.

An iron-containing product in the acetone extract from the lichen Cladonia deformis has been investigated using chemical, spectroscopic and X-ray crystallographic methods. Visible-near UV, EPR and IR spectra indicate that the iron is present as high-spin Fe(III) and coordinates in an oxygen-containing environment arising from graciliformin (or graciliformin-like) ligands. This has been confirmed by an XAS (X-ray absorption) study using synchrotron radiation. Comparison of the EXAFS and XANES results with those obtained from a model, tris(pent-2,4-dionato)Fe(III), and detailed fitting using the single-scattering, curved-wave formalism for the EXAFS strongly supports the presence of a Fe(III) coordinated to five oxygen atoms from the graciliformin.