Biomarkers are critical tools employed in cancer research, as diagnostic implements in the early detection of cancer. Successful bioconjugation is vital for improving the sensitivity and specificity in which it requires for the early detection of ovarian cancer. This study aims to understand the bioconjugation process by studying molecular interactions with Raman and FT-IR spectroscopies. In each bioconjugation stage, we explore the molecular structure change by analyzing the vibrational signature of molecular bond to improve the coupling efficiency. Specifically, this study is looking at the differences after successful coupling of amine coated iron particles with glutaraldehyde and avidin and glutaraldehyde.

With the development of designed foldamers that display biological activity and aid in drug delivery processes, there is an increasing interest in exploring the inherent conformational properties of model foldamers to understand better the subtle counter-balance of forces at play β-amino acids have one additional backbone carbon atom that extends the spacing between amide groups, thereby providing flexibility in construction of β- and α/β- peptides, leading to secondary structures that either mimic or are complementary to those found in nature. Here we explore the conformational preferences of a series of β- and α/β- dipeptides under jet-cooled conditions in the gas phase. The molecules are brought into the gas phase using laser desorption. Our studies include two capped α/β - dipeptides, Ac-L-Ala-β³-(R)-hAla-NHBn and Ac-β³-(R)-hAla-L-Ala-NHBn as structural isomers, and one capped pure β³-dipeptide, Ac-(R)-hAla-β³-(S)-hAla-NHBn . By incorporating an NHBn cap, a UV chromophore is present that can be used to record resonant two-photon ionization (R2PI) spectra. Conformation-specific infrared and ultraviolet spectra are then recorded using resonant ion-dip infrared (RIDIR) and IR-UV hole burning spectroscopies, respectively. With this set of peptides, we are able to probe the effect of a chirality switch at a single chiral center on inherent local conformational preferences. Following an exhaustive computational search of the conformational potential energy surface, low-lying minima are optimized and IR spectra calculated for comparison with the experimental RIDIR spectra provide conformational assignments. Lowest-energy conformers are observed for the α/β-peptides and assigned to C7/C8 (C8/C7) hydrogen-bonded architectures, while for the pure β³-peptide analog, only one conformer is observed experimentally and assigned to a C12 hydrogen-bonded architecture.

The cis-3-hexenal (c3-HA) is known as an odor molecule of grass and that the c3-HA easily isomerizes to trans-2-hexenal (t2-HA). The ground-state rotational spectrum of the c3-HA was observed and analyzed by molecular beam Fourier transform microwave spectroscopy combined with quantum chemical calculations. The sample of the c3-HA is a little unstable in the metal nozzle because the observed spectrum of the c3-HA was getting weaker and then the rotational spectra of the t2-HA appeared. We identified one conformer: the cis-S'GS', where S', G, and S' denote the skew' around the OC(1)-C(2)H2 axis, gauche around the C(1)C(2)-C(3)C(4) axis, and skew' around the C(3)C(4)-C(5)C(6) axis, respectively, for which a-type, b-type, and c-type transitions were observed.

γ-Hexanolactone (5-ethyldihydro-2-furanone) (γ-HL) is an odor molecule that is included in a natural food such as pineapple. The rotational spectra of γ-HL were observed by a Fourier transform microwave spectrometer combined with a heated nozzle of 303 K. The three conformers in expected to six were observed.For the first conformer, 65 a-type, 48 b-type, and 22 c-type transitions were assigned. Similarly, 41 a-type, 40 b-type, and 12 c-type transitions for the second one were assigned and 50 a-type and 34 b-type transitions for the third one. A comparison of the observed rotational constants with those calculated by ab initio MO method led us to conclude that the second conformer is the eq-T in which an ethyl group attached to C(5) is in an equatorial position (eq), where T and G denote the conformations about the C(6)-C(5) bond, with T and G designating trans and gauche, respectively. We identified that the first and third conformers are eq-G' and eq-G, respectively, because of absence of the c-type transitions and large pseudo-inertial defect for third one. The eq-G' of the γ-HL was calculated to be the most stable. The splittings due to internal rotation of the methyl group were observed for all the three conformers and were analyzed by the XIAM program. The rotational constants thus derived agree with the predictions made by quantum chemical calculations, MP2/6-311++G(d,p) within 0.9%.

Rotational spectra of the 1-pentanethiol (1-C₅SH) were observed using a Fourier transform microwave spectrometer. Eight sets of the 1-C₅SH were assigned by combined with the quantum chemical calculations. The four Sets 1-4 of a-type R-branch transitions of 1-C₅SH were observed in diluted Ar. Another four Sets 5-8 of a-type transition were observed near the four Sets 1-4 in diluted Ne instead of Ar. The Set 1 has the most intense spectrum and small splittings due to the torsional motion of the SH group and the internal rotation of the CH₃ group of the TTTg conformer of the 1-C₅SH. In the case of 1-C₅SH there are four operations; the first generating operation is the relative orientation of CH₃ groups around the C(5)H₃C(4)H₂-C(3)H₂C(2)H₂C(1)H₂SH axis, leading to gauche and trans conformers, G or T, the second is around C(3)-C(2) axis and the third is around C(2)-C(1) axis, leading to gauche and trans conformers, G, G’ or T, and the fourth is around C(1)-SH also leading to gauche and trans orientations, g, g’ or t. For Set 2, a-, b-, and c-type transitions were observed and assigned as to TTGg’ conformer. Only a-type transitions of the Sets 3 and 4 were observed. The obtained rotational constants of the Sets 3 and 4 agreed with the calculated values of the TGTg/TGTg’ and GTTg/GTTg’, respectively. Comparing the obtained rotational constants with the quantum chemical calculations, the Sets 5 and 6 were assigned as to be TTTt and TTGg, respectively. Similarly Sets 3, 7, 4 and 8 were assigned as TGTg’, TGTg, GTTg and GTTg’, respectively.

Titan, a moon of Saturn, has an atmosphere that is similar to prebiotic earth, which is nitrogen rich. Pentenenitriles are of importance as they are potential precursors to hetro-aromatic compounds like pyridine. This talk will describe our broadband microwave studies of trans 3-pentenenitrile (t-3PN) under jet-cooled conditions. Strong-field coherence breaking (SFCB) was used to selectively modulate the intensities of microwave transitions in a conformer-specific manner, aiding analysis. Two conformers of t-3PN were identified and the rotational transitions were assigned. The talk will compare the conformational preferences of 3-pentenenitrile with its isomer, 4-pentenenitrile, previously studied in our laboratory. The studies of t-3PN serve as a necessary foundation for subsequent studies of its pyrolysis over the 300K-850K temperature range, using a modified Chen nozzle followed by supersonic expansion. We combined CP-FTMW instrument with vacuum ultraviolet (VUV) time-of-flight mass spectrometry (TOF-MS) to obtain mass-correlated broadband microwave spectra. The temperature dependence of the mass spectra aid in identifying the carriers of new transitions appearing in the microwave spectrum. The thermal decomposition of t-3PN produces a range of products, including those that are both radical and molecular in nature.

The rotational spectrum of 2-bromopyridine was measured with a cavity FTMW spectrometer, and the complete nuclear quadrupole coupling tensors of ⁷⁹Br, ⁸¹Br, and ¹⁴N were determined. These tensors are interpreted using the Extended Townes-Dailey (ETD) analysisS. E. Novick J. Mol. Spectrosc. 267 13-18, 2011. which allows us to predict orbital electron populations. These results are compared to ab initio Intrinsic Atomic Orbital (IAO) populations. The ETD analysis for the ¹⁴N nucleus requires expressing the orbitals as sp² hybrids and performing rotations on the measured quadrupole tensors and the calculated IAO populations.

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Footnotes:

S. E. Novick J. Mol. Spectrosc. 267 13-18, 2011..

r0pt Figure Dipole forbidden, nuclear electric quadrupole allowed transitions in microwave spectroscopy are manifested through a linkage in off-diagonal components of the quadrupole coupling tensor. It is hypothesized that these transitions, due to their transition pathways, could possibly be used to differentiate chirality in a microwave three-wave mixing (3WM)-type experiment. In order to test this hypothesis, 2-bromo-1,1,1,3-tetrafluoroethane was chosen, as it is chiral, possesses a large quadrupolar nucleus and is heavy enough to generate the needed mixing to bring about these forbidden transitions. Because this the first known rotational study of the molecule, traditional rotational spectroscopy utilizing CP-FTMW techniques was performed first. This presentation will describe the collection of spectra, structural analysis, and observed dipole forbidden transitions of the title molecule.

One powerful feature of molecular rotational spectroscopy is the ability to obtain quantitative information for the positions of individual atoms in the structure through the analysis of singly-substituted isotopologue spectra. However, because the structural information comes from changes in the moments-of-inertia, the signs of the atom coordinates in the principal axis system are not available. This project explores the ability to obtain the carbon framework geometry of a molecule from isotopologue spectra. The first step of the analysis examines the distributions of carbon-carbon atom distances, C-C-C bond angles, and correlations between the bond angles and bond distances found in molecules. The “rules” for acceptable structures are obtained through the analysis of about 100 optimized structures from quantum chemistry that were available in lab. These rules are then used to find acceptable carbon framework geometries from the 8^N−1 possible carbon frameworks that come from the sign ambiguity of the substitution coordinates. In the test case of a molecule with 6 carbon atoms, cyclohexene oxide, these rules produced a single (and correct) carbon atom framework from the 32,768 possibilities. For molecules with 12 carbon atoms, a relatively large number of possible carbon atom frameworks are found to be consistent with the structure constraints: about 100,000 out of the 8.6 billion possible geometries. The results of the analysis as a function of molecular mass (number of carbon atoms) and structural characteristics (compact structures compared to structures with long alkyl tails, for example) will be presented. Approaches to assigning quality scores to candidate carbon atom frameworks that meet the structure conditions with the goal of ranking the most likely molecular structures will also be discussed.