On Ultrafast Time-Domain TeraHertz Spectroscopy in the Condensed Phase: Linear Spectroscopic Measurements of Hydrogen-Bond Dynamics of Astrochemical Ice Analogs and Nonlinear TeraHertz Kerr Effect Measurements of Vibrational Quantum Beats

Much of the chemistry that affects life on planet Earth occurs in the condensed phase. The TeraHertz (THz) or far-infrared (far-IR) region of the electromagnetic spectrum (from 0.1 THz to 10 THz, 3 cm^-1 to 300 cm^-1, or 3000 μm to 30 μm) has been shown to provide unique possibilities in the study of condensed-phase processes. The goal of this work is to expand the possibilities available in the THz region and undertake new investigations of fundamental interest to chemistry. Since we are fundamentally interested in condensed-phase processes, this thesis focuses on two areas where THz spectroscopy can provide new understanding: astrochemistry and solvation science. To advance these fields, we had to develop new instrumentation that would enable the experiments necessary to answer new questions in either astrochemistry or solvation science. We first developed a new experimental setup capable of studying astrochemical ice analogs in both the TeraHertz (THz), or far-Infrared (far-IR), region (0.3 - 7.5 THz; 10 - 250 cm^-1) and the mid-IR (400 - 4000 cm^-1). The importance of astrochemical ices lies in their key role in the formation of complex organic molecules, such as amino acids and sugars in space. Thus, the instruments are capable of performing variety of spectroscopic studies that can provide especially relevant laboratory data to support astronomical observations from telescopes such as the Herschel Space Telescope, the Stratospheric Observatory for Infrared Astronomy (SOFIA), and the Atacama Large Millimeter Array (ALMA). The experimental apparatus uses a THz time-domain spectrometer, with a 1750/875 nm plasma source and a GaP detector crystal, to cover the bandwidth mentioned above with ~10 GHz (~0.3 cm^-1) resolution.

Using the above instrumentation, experimental spectra of astrochemical ice analogs of water and carbon dioxide in pure, mixed, and layered ices were collected at different temperatures under high vacuum conditions with the goal of investigating the structure of the ice. We tentatively observe a new feature in both amorphous solid water and crystalline water at 33 cm^-1 (1 THz). In addition, our studies of mixed and layered ices show how it is possible to identify the location of carbon dioxide as it segregates within the ice by observing its effect on the THz spectrum of water ice. The THz spectra of mixed and layered ices are further analyzed by fitting their spectra features to those of pure amorphous solid water and crystalline water ice to quantify the effects of temperature changes on structure. From the results of this work, it appears that THz spectroscopy is potentially well suited to study thermal transformations within the ice.

To advance the study of liquids with THz spectroscopy, we developed a new ultrafast nonlinear THz spectroscopic technique: heterodyne-detected, ultrafast THz Kerr effect (TKE) spectroscopy. We implemented a heterodyne-detection scheme into a TKE spectrometer that uses a stilbazoiumbased THz emitter, 4-N,N-dimethylamino-4-N-methyl-stilbazolium 2,4,6-trimethylbenzenesulfonate (DSTMS), and high numerical aperture optics which generates THz electric field in excess of 300 kV/cm, in the sample. This allows us to report the first measurement of quantum beats at terahertz (THz) frequencies that result from vibrational coherences initiated by the nonlinear, dipolar interaction of a broadband, high-energy, (sub)picosecond THz pulse with the sample. Our instrument improves on both the frequency coverage, and sensitivity previously reported; it also ensures a backgroundless measurement of the THz Kerr effect in pure liquids. For liquid diiodomethane, we observe a quantum beat at 3.66 THz (122 cm^-1), in exact agreement with the fundamental transition frequency of the υ4 vibration of the molecule. This result provides new insight into dipolar vs. Raman selection rules at terahertz frequencies.

To conclude we discuss future directions for the nonlinear THz spectroscopy in the Blake lab. We report the first results from an experiment using a plasma-based THz source for nonlinear spectroscopy that has the potential to enable nonlinear THz spectra with a sub-100 fs temporal resolution, and how the optics involved in the plasma mechanism can enable THz pulse shaping. Finally, we discuss how a single-shot THz detection scheme could improve the acquisition of THz data and how such a scheme could be implemented in the Blake lab. The instruments developed herein will hopefully remain a part of the groups core competencies and serve as building blocks for the next generation of THz instrumentation that pushes the frontiers of both chemistry and the scientific enterprise as a whole.

Prediction of Multi-Target Networks of Neuroprotective Compounds with Entropy Indices and Synthesis, Assay, and Theoretical Study of New Asymmetric 1,2-Rasagiline Carbamates

In a multi-target complex network, the links (L-ij) represent the interactions between the drug (d(i)) and the target (t(j)), characterized by different experimental measures (K-i, K-m, IC50, etc.) obtained in pharmacological assays under diverse boundary conditions (c(j)). In this work, we handle Shannon entropy measures for developing a model encompassing a multi-target network of neuroprotective/neurotoxic compounds reported in the CHEMBL database. The model predicts correctly >8300 experimental outcomes with Accuracy, Specificity, and Sensitivity above 80%-90% on training and external validation series. Indeed, the model can calculate different outcomes for >30 experimental measures in >400 different experimental protocolsin relation with >150 molecular and cellular targets on 11 different organisms (including human). Hereafter, we reported by the first time the synthesis, characterization, and experimental assays of a new series of chiral 1,2-rasagiline carbamate derivatives not reported in previous works. The experimental tests included: (1) assay in absence of neurotoxic agents; (2) in the presence of glutamate; and (3) in the presence of H2O2. Lastly, we used the new Assessing Links with Moving Averages (ALMA)-entropy model to predict possible outcomes for the new compounds in a high number of pharmacological tests not carried out experimentally.

A chemically inert Rashba split interface electronic structure of C-60, FeOEP and PTCDA on BiAg2/Ag(111) substrates

The fields of organic electronics and spintronics have the potential to revolutionize the electronics industry. Finding the right materials that can retain their electrical and spin properties when combined is a technological and fundamental challenge. We carry out the study of three archetypal organic molecules in intimate contact with the BiAg2 surface alloy. We show that the BiAg2 alloy is an especially suited substrate due to its inertness as support for molecular films, exhibiting an almost complete absence of substrate-molecular interactions. This is inferred from the persistence of a completely unaltered giant spin-orbit split surface state of the BiAg2 substrate, and from the absence of significant metallic screening of charged molecular levels in the organic layer. Spin-orbit split states in BiAg2 turn out to be far more robust to organic overlayers than previously thought.

Photolysis of iron–siderophore chelates promotes bacterial–algal mutualism

Marine microalgae support world fisheries production and influence climate through various mechanisms. They are also responsible for harmful blooms that adversely impact coastal ecosystems and economies. Optimal growth and survival of many bloom-forming microalgae, including climatically important dinoflagellates and coccolithophores, requires the close association of specific bacterial species, but the reasons for these associations are unknown. Here, we report that several clades of Marinobacter ubiquitously found in close association with dinoflagellates and coccolithophores produce an unusual lower-affinity dicitrate siderophore, vibrioferrin (VF). Fe-VF chelates undergo photolysis at rates that are 10–20 times higher than siderophores produced by free-living marine bacteria, and unlike the latter, the VF photoproduct has no measurable affinity for iron. While both an algal-associated bacterium and a representative dinoflagellate partner, Scrippsiella trochoidea, used iron from Fe-VF chelates in the dark, in situ photolysis of the chelates in the presence of attenuated sunlight increased bacterial iron uptake by 70% and algal uptake by >20-fold. These results suggest that the bacteria promote algal assimilation of iron by facilitating photochemical redox cycling of this critical nutrient. Also, binary culture experiments and genomic evidence suggest that the algal cells release organic molecules that are used by the bacteria for growth. Such mutualistic sharing of iron and fixed carbon has important implications toward our understanding of the close beneficial interactions between marine bacteria and phytoplankton, and the effect of these interactions on algal blooms and climate.

From Tunneling to Hopping: A Comprehensive Investigation of Charge Transport Mechanism in Molecular Junctions Based on Oligo(p-phenylene ethynylene)s

The charge transport mechanism of oligo(p-phenylene ethynylene)s with lengths ranging from 0.98 to 5.11 nm was investigated using modified scanning tunneling microscopy break junction and conducting probe atomic force microscopy methods. The methods were based on observing the length dependence of molecular resistance at single molecule level and the current-voltage characteristics in a wide length distribution. An intrinsic transition from tunneling to hopping charge transport mechanism was observed near 2.75 nm. A new transitional zone was observed in the long length molecular wires compared to short ones. This was not a simple transition between direct tunneling and field emission, which may provide new insights into transport mechanism investigations. Theoretical calculations provided an essential explanation for these phenomena in terms of molecular electronic structures.

The enhancement effect of Eu3+ on electro-oxidation of ethanol at Pt electrode

It is reported for the first time that the slow electrochemical kinetics process for the electro-oxidation of ethanol can be promoted by changing the electrochemical environment. The electro-oxidation of ethanol at a Pt electrode in the presence of Eu3+ cations was studied and an enhancement effect was exhibited. Cyclic voltammetry experiment results showed that the peak current density for the electro-oxidation of ethanol was increased in the presence of EU3+ in the ethanol solution. A preliminary discussion of the mechanism of the enhancement effect is given. This is based on a CO stripping experiment, which shows that either the onset potential or the peak potential of CO oxidation is shifted negatively after adding Eu3+ to the solution.

Measuring the electronic decay constant of alkanedithiols by electrochemical impedance spectroscopy

Several methods have been used for the measurement of the electronic decay constant (beta) of organic molecules. However, each of them has some disadvantages. For the first time, electrochemical impedance spectroscopy (EIS) was used to obtain the 18 value by measuring the tunneling resistance through alkanedithiols. The tunneling resistance through alkanedithiols increases exponentially with the molecular length in terms of the mechanism of coherent nonresonant tunneling. beta was 0.51 +/- 0.01 per carbon.

Characterization of the rutin-metal complex by electrospray ionization tandem mass spectrometry

According to the strong application background of bioflavonoid and metal-flavonoid complexes, novel electrospray ionization tandem mass spectrometry (ESI-MSn) was applied to investigate the structure and fragmentation mechanism of transition metal-rutin complexes. In the full-scan mass spectra, different stoichiometric ratios of rutin-metal complexes were found. In the reaction between rutin and Cu, four kinds of complexes with four different stoichiometric ratios were produced. In the reaction between rutin and Zn, Mn(II), and Fe(II), only two kind of complexes with stoichiometric ratios of 1:1 and 1:2 occured. In further tandem mass spectrometric experiments of different rutin-metal complexes, product fragments, came from the neutral loss of the external rhamnose and the internal glucose unit, oligosaccharide chain, aglycone, and small organic molecules. According to the MSn data, we proposed a mechanism for all fragments of the rutin-Cu complex A and the structure of two rutin-Cu complexes, C and D.

Functionalization of single-walled carbon nanotubes with Prussian blue

Chemical functionalization of single-walled carbon nanotubes (SWNTs) has constructed plenty of new structures with ample new properties into them. But the modification was often confined to organic molecules, either by covalence or non-covalence. In this report, SWNTs were successfully functionalized with one kind of electroactive inorganic compounds: Prussian blue (PB). And the molecular interactions between them were firstly investigated. Interestedly, pi-pi stacking interaction coupled with ionic interaction was found between SWNTs and PB. The electrochemical properties of SWNTs-PB were also investigated. It would pave a new pathway to manipulate molecular entities of SWNTs by cooperation with functional inorganic electroactive compounds.

Formation of a supported hybrid bilayer membrane on gold: A sterically enhanced hydrophobic effect

Adsorption of a monolayer of didecanoyl-L-alpha-phosphatidylcholine (DDPC) from dispersions of small unilamellar vesicles onto hydrophobic surfaces was investigated by mean of cyclic voltammetry and impedance spectroscopy. The hydrophobic surfaces were self-assembled monolayers of 2-mereapto-3-n-octylthiophene (MOT) on gold. One characteristic of the MOT monolayer is its permeability to organic molecules in aqueous solution, thus providing a more energetically favorable hydrophobic surface for the addition of phospholipid vesicles. The kinetics of the lipid monolayer formation were followed by measuring the time-dependent interfacial capacitance. Unusual values of thickness and capacitance of the MOT/ DDPC bilayers were observed. An interdigitating conformation of the bilayer structure was proposed to interpret the experimental results, The horseradish peroxidase reconstituted into the bilayer demonstrated the expected protein activity, showing practical use in research and in biosensor application.

Effect of configuration and conformation on the spin multiplicity in xylylene type biradicals

The singlet-triplet splitting energy gap DeltaE(S.T) = E-S - E-T is calculated for the ortho-, meta-, and para-xylylenes and their heteroatomic analogous by means of AM1-CI approach. It is shown that when the radical centers R-.(R-.=H2C.-,H2N.+- or HN.-) are twisted sufficiently Tar out of conjugation with the benzene ring, DeltaE(S.T) tends to zero or is negative, i.e, ortho-, meta-, and para-phenylenes turn into weak ferromagnetic or antiferromagnetic coupling unit, while they are strong ferromagnetic (meta-isomers) or antiferromagnetic (ortho-, para-isomers) coupling units under planar conformation. It is suggested that serious twisted conformation is not recommended candidate for the design of novel high-spin molecules with stable high-spin ground states by ortho- or para-phenylene coupling unit.

Studies of the ortho effect in fragmentations of acetyl ion adducts of disubstituted benzenes

The ion-molecule reactions of disubstituted benzenes under chemical ionization conditions with acetyl chloride as reagent gas were examined, and the fragmentation reactions of the adduct ions (mostly proton and acetyl ion adducts) were studied by collision-induced dissociation. Electron-releasing substituents favored the adduct reactions, and electron-withdrawing groups did not. The position and properties of substituting groups had an effect on the relative abundances of the adduct ions. Several examples of the ortho effect were observed. The fragmentation reaction of the adduct ions formed by ortho-benzenediamine with the acetyl ion was similar to the reductive alkylation reaction of amines in the condensed phase. Copyright (C) 2001 John Wiley & Sons, Ltd.

Positive- and negative-ion matrix-assisted laser desorption/ionization mass spectrometry of saccharides

Matrix-assisted laser desorption/ionization (MALDI) mass spectrometry (MS) of oligosaccharides and polysaccharides has been investigated in detail, It is demonstrated that cationized species of oligosaccharides, [M+Na](+) and [M+K](+), are dominant products under the MALDI condition, and negative ions of oligosaccharides are not formed to any significant extent in this process, The molecular masses of polysaccharides are similarly determined by positive- and negative-ion MALDI-MS with the help of column chromatography. The distinction between positive- and negative-ion MALDI mass spectra of oligo-and polysaccharides indicates that the MALDI processes for saccharides vary with molecular mass. The matrix plays a more important role in the ionization process for oligosaccharides, while in the desorption process for polysaccharides. (C) 1998 John Wiley & Sons, Ltd.

Chemical bond analysis of nonlinearity of urea crystal

A novel and quantitative study on structure-property relationships has been carried out in urea crystal, based on the dielectric theory of complex crystals and the modified Levine bond charge model, mainly from the chemical bond viewpoint. For the first time, it was treated like this, and the bond parameters and linear and nonlinear characteristics of constituent chemical bonds were presented quantitatively. The theoretical result agrees satisfactorily with the experimental datum and can reasonably explain the nonlinear origin of urea crystal, that is, the C-N bond in the conjugated system of bonds O double left arrow C<--N-H. At the same time, the novel method should be a useful tool toward the future development of the search for new nonlinear optical (NLO) materials in the organic crystal field.

In situ scanning tunneling microscopy studies of nanometer size palladium particles on highly oriented pyrolytic graphite

A special electrodeposition process of palladium was studied by cyclic voltammetry, X-ray photoelectron spectroscopy (XPS) and in situ scanning tunneling microscopy (STM). A kind of palladium(IV) complex was attached to the highly oriented pyrolytic graphite (HOPG) electrode surface by electro-oxidation of palladium(II) complex first, and was then reduced to palladium particles. The surface complexes and particles of palladium were both characterized by in situ STM and XPS. The Pd particles are in the nanometer range of size and exhibit electrocatalytic activity towards the oxidation of hydrazine and hydroxylamine.