Graduate Student Ali Baumann will Present “(HCl)_m(H₂O)_n Clusters: Investigation into the dissociation point of strong acids using ab initio methods” to the Department.

Abstract:
While it is known that strong acids dissociate completely in water, little is known about the mechanism through which this occurs. This is due to the fact that it is difficult to study the mechanism experimentally. Although IR spectra vibrational peaks of (HCl)_m(H₂O)_n clusters have been produced, definitive assignment of the peaks has yet to occur. Ab initio calculations provide necessary insight into assignment of vibrational peaks for experimental data, along with insight into minimum energy structures of small clusters that are difficult to study accurately in experiment. This study examines the ionic dissociation of small (HCl)_m(H₂O)_n clusters (m = 1-­‐4, n = 1-­‐ 4) using theoretical methods. Optimization and frequency calculations were performed using MP2 and CCSD(T) methods with haXZ basis sets (X = D, T, Q). All structures that were studied were minimum energy structures on the potential energy surface, with one structure from each cluster being identified as a lowest energy structure. Proton transfer was seen in four pentamer structures, where m = 1, n = 4 and m = 2, n = 3, and were also the lowest energy structures.

Graduate Student Samantha Davila will Present “Analysis of Protein Conformation and Dynamics by Hydrogen/Deuterium Exchange Mass Spectrometry” to the Department

Abstract:
The relationships between structure, function, and dynamics are essential to fully understand a protein. There is no single analytical method capable of providing the extent and range of information required for complete protein analysis. The hydrogen/deuterium (H/D) exchange monitored by mass spectrometry has become a powerful tool for probing conformational dynamics and protein interactions. Deuteriums exchange at the amide hydrogens along the protein’s backbone providing a probe site at each amino acid throughout. Mass spectrometry can effectively monitor the exchange events as mass shifts as a result of the incorporation of deuterium into the protein. The rates of exchange are capable of revealing valuable insight into structural mobility, hydrogen bonding strength, as well as solvent accessibility. Combining proteolysis with the deuterium labeling experiment, under conditions that preserve the exchanges, allows for localizing exchange incidents to specific regions of the protein backbone. H/D exchange mass spectrometry has become a valuable technique for studying conformational dynamics as well as interactions in proteins, protein–ligand and protein–protein complexes.

References:

(1)    Burke, J. E.; Perisic, O.; Masson, G. R.; Vadas, O.; Williams, R. L. PNAS. 2012, DOI: 10.1073/pnas.1205508109

(2)    Burke, J. E.;  Vadas, O.; Berndt, A.; Finegan, T.; Perisic, O.; Williams, R. L. Structure. 2011, DOI: 10.1016/j.str.2011.06.003

(3)    Engen, J.R. Anal. Chem. 2009, DOI: 0.1021/ac901154s

Graduate Student Keshia Dykes will Present a Seminar to the Department

Graduate Student Coleman Howard will Present a Seminar to the Department

Abstract:
Ab initio wave function methods offer the most reliable way to calculate molecular properties of small chemical systems. This presentation examines efforts to reproduce experimental vibrational frequencies of the hydrogen-bonded dimers of water and hydrogen fluoride. Utilizing a high level of electron correlation with the coupled-cluster singles and doubles method, along with a perturbative approximation to connected triple excitations, the “gold-standard” CCSD(T) method is employed in conjunction with large, flexible atomic orbital basis sets to compute harmonic vibrational frequencies and dissociation energies expected to lie near the complete basis set (CBS) limit.  Accounting for anharmonicity with 2nd order vibrational perturbation theory (VPT2), fundamental vibrational transitions predicted from CCSD(T) computations are in excellent agreement with experiment, within a few cm-1 of experimental values for intramonomer vibrational modes of (H2O)2 and (HF)2. In addition, the importance of sufficient electron correlation is demonstrated by examining inaccuracies of the lower-scaling MP2 method in comparison with CCSD(T). Lastly, ongoing work with VPT2 in conjunction with the CCSD(T) method is shown to demonstrate how these computations may aid experimentalists in the assignment of vibrational modes in spectra.

Dr. Drew Hamilton from Mississippi State University will present “Digital Forensics and Anti-Forensics:  Navigating the Digital Fishbowl” to the department.

Abstract:
Any hands-on demonstration of the current state of the art in digital forensics is likely to increase one’s sense of paranoia.  For this reason, anti-forensics is a rapidly growing field.  Combined with never-ending operating system upgrades and ever-increasing numbers of mobile devices – digital forensics is a perennially changing field.  This is an entry-level talk that will define the elements of digital evidence.  Current tools and techniques will be covered as well as the general lack of privacy on a computer.  Digital data is difficult to eradicate or to hide.  Material posted on the Internet may be impossible to eradicate.  This presentation will discuss the implications of the forensic impacts of the so-called digital divide.  Also discussed will be key differences between digital forensics and other forensic fields.

Topics will include:
Elements of digital evidence
The Metasploit Framework
The Onion Router and network misdirection
Current trends in digital forensics versus anti-forensics
Digital forensics for the intelligence community versus
law enforcement

Graduate student Nuwan Kothalawala will present his dissertation research “Method development for mass spectrometric characterization of ultra-small nanomolecules and mass spectrometry imaging of biomolecules” to the department.

Abstract:

High sensitivity, good selectivity and remarkable identification capability facilitates the application of mass spectrometry (MS) in diverse fields. This talk outlines how this cutting edge technology is used to determine the chemical composition of the ultra-small nanomolecules (NMs) to atomic precision and obtain spatial resolution of selected biomolecules using mass spectrometric imaging (MSI). High resolution electrospray ionization mass spectrometry (ESI-MS) methods were developed to analyze the polar water-soluble NMs. These new methodologies express how ESI-MS parameters can be optimized to analyze the NMs based on their polarity, chain-length of the ligands, size and stability. In addition, new methods are presented on how to overcome common issues such as impurities in analytes, adduct formation and solvent clusters arising during the analysis of polar NMs. These also include the special approaches to enhance the peak intensities and lower the fragmentations. Further, new protocols are discussed to synthesize, separate and purify NMs in an unprecedented range from 100’s to 1000’s of atoms. Matrix assisted laser desorption ionization mass spectrometry imaging (MALDI-MSI) methods were developed to study biologically important molecules and their spatial location in different samples such as microbial colonies, animal tissues, plant tissues and forensic samples. The microbial species produce important natural products and metabolites. This talk has two themes based on method development for MSI to detect the important secondary metabolites including rapamycin and manzamine in bacteria colonies. After the discovery of standard imaging methods, MSI projects were further extended to image the important analytes in forensic samples, animal and plant tissues.

(1)        Kothalawala, N.; Kumara, C.; Ferrando, R.; Dass, A. Chemical Communications 2013, 49, 10850.

(2)        Kothalawala, N.; Lee West Iv, J.; Dass, A. Nanoscale 2014, 6, 683.

(3)        Waters, A. L.; Peraud, O.; Kasanah, N.; Sims, J.; Kothalawala, N.; Anderson, M. A.; Abbas, S. H.; Rao, K. V.; Jupally, V. R.; Kelly, M.; Dass, A.; Hill, R. T.; Hamann, M. T. Frontiers in Marine Science 2014, 1.

(4)        Cornett, D. S.; Reyzer, M. L.; Chaurand, P.; Caprioli, R. M. Nat Meth 2007, 4, 828.

Graduate student Praneeth Nimmala will present his dissertation research “Gold nanomolecules: Developing synthetic protocols, Characterization and investigating the ligand effects on structure and properties” to the department.

Abstract:

Gold nanoparticles are chemical entities in the size range 1 to 100 nm. They have been known to exist since ancient times in the fields of jewelry as they produce vibrant, size dependent, colors upon interaction with light. Gold is a preferred choice of metal for the synthesis of nanoparticles mainly due to its inertness to atmospheric conditions and most chemicals. Gold thiolate nanomolecules, which is the primary focus of this dissertation research, are chemical molecules with a fixed number of gold atoms and organo-thiolate ligands. They are of the form Au_x(SR)_y and possess molecule-like properties as a result of distinctive quantum confinement effects occurring at the nanoscale size. The optical and electronic properties of these molecules change as a function of “x” and “y”. The stability of these nanomolecules can be attributed due in part to their symmetrical geometry as evidenced by the X-ray crystallography and theoretical calculations.     Recent research in the field has focused on exploiting the size-dependent properties of gold nanomolecules in applications like nano-electronics, biological sensing and catalysis. But much of the hindrance to these advances come from the lack of established protocols to synthesize monodisperse nanomolecules in high yields. In my talk, the following topics related to the synthesis of gold nanomolecules are covered 1) One-phase synthesis protocol for synthesis of gold-thiolate nanomolecules wherein the gold salt and the capping ligands are essentially dissolved in a single solvent system. This protocols is peculiar in that it yields sizes like Au₆₇ and Au_~103-105 which are otherwise not observed. 50+ mg of the pure Au₆₇ was isolated for the first time¹ using the above designed protocols. The high yields of the product has enabled its complete characterization using mass spectrometry, optical spectroscopy, NMR, powder-XRD and electrochemistry. 2) The isolation and purification nanomolecules using size exclusion chromatography (SEC) which proved to be highly reproducible and less laborious. 3) Protocols of “etching” and “core size conversion” as a way to minimize the polydispersity of nanomolecules.² These protocols can be used to exclusively synthesize highly stable Au₃₈ and Au₄₀ sizes. 4) The role of capping ligands in determining size, geometry and properties of nanomolecules; a factor which typically overlooked in this field was investigated.^3,4

References:

(1)          Nimmala, P. R.; Yoon, B.; Whetten, R. L.; Landman, U.; Dass, A. The Journal of Physical Chemistry A 2013, 117, 504.

(2)          Nimmala, P. R.; Jupally, V. R.; Dass, A. Langmuir 2014, 30, 2490.

(3)          Nimmala, P. R.; Dass, A. Journal of the American Chemical Society 2011, 133, 9175.

(4)          Nimmala, P. R.; Knoppe, S.; Jupally, V. R.; Delcamp, J. H.; Aikens, C. M.; Dass, A. The Journal of Physical Chemistry B 2014, 118, 14157.

Dr. Anne Gorden from Auburn University will present “Taking Advantage of the Chemistry of Heterocycles in Ligands for Sensors and Catalyst Supports” to the department.

Abstract:
In an effort to develop inexpensive ligands for colorimetric selective sensing of actinides, we have developed ligands incorporating quinoxalines or imine aza-donors. These have been characterized for selectivity in distinguishing metals. The addition of a quinoxaline to the salen imparts the fluorescence to the quinoxaline and alters the coordination site. We have used these complexes to probe the contributing factors toward selectivity, signal intensity, and the differentiation between actinides (like uranium and thorium) and first row transition metals These are the basis of new chemosensors to allow for rapid in-the-field visual identification. The complexes with early transition metals originally prepared for comparison were also found to be useful as catalyst supports in oxidation reactions, and we have explored using the 2-quinoxalinol salen ligand – abbreviated salqu – as a catalyst support for Cu(II). Simple olefin substrates can be oxidized using the salqu catalyst with tert-butyl hydroperoxide TBHP (up to 99% yield) within a very short reaction time and improved selectivity.

Dr. Sarah Bondos from Texas A&M University will present “Functionalizing protein-based materials  with biomolecules” to the department.

Abstract:

A major challenge in the materials field is the development of bioactive materials that can manipulate or respond to their environment.  Theoretically, materials composed of proteins have an enormous advantage, since most of the desired functions can be imparted by proteins.  By fusing the gene that encodes the functional protein to the gene that encodes a self-assembling protein, a fusion protein can be easily produced in bacteria that should both mediate the function of interest and self-assemble into useful materials.  The gene fusion approach bypasses common problems, such as loss due to diffusion for non-covalent attachment, or protein inactivation and toxic residues for chemical crosslinking approaches.  However, the success of this approach has been limited because self-assembling proteins, when artificially produced, often require harsh (denaturing) conditions to trigger materials formation.  These conditions unfold and inactivate any appended functional proteins.  In contrast, we have accidentally discovered that the Drosophila Hox transcription factor Ultrabithorax (Ubx) will hierarchically self-assemble in vitro into mechanically robust, biocompatible materials spanning the nanoscale to macroscale size regimes.  Materials assembly occurs rapidly in mild aqueous buffers, and thus proteins appended by gene fusion retain their activity.  Conversely, the appended proteins do not alter Ubx materials assembly.

As a Hox transcription factor, the Ubx protein contains a homeodomain, which binds DNA with remarkably high affinity.  This homeodomain remains intact in the materials, and the materials bind DNA in a sequence-specific manner.  Thus the DNA can be oriented on the surface of Ubx materials based on the placement of Ubx binding sites.  Materials binding also helps protect the DNA from degradation.  Thus Ubx provides a remarkably facile system for creating materials functionalized with two key types of biomolecules: protein and DNA.

Dr. Angela Wilson from the University of North Texas will present “Energetic and Spectroscopic Properties Across the Periodic Table” to the department.

Abstract:

In the rational analysis and design of molecular species, energetic data is often the most critical information needed. One of the longstanding challenges in computational chemistry, however, is in achieving accurate energetics (i.e., enthalpies of formation, ionization energies) for molecules species across the periodic table, and for molecules of increasing size. Challenges that can be encountered include limited experimental gauges for calculations, computational (i.e., computer memory, disk space, and CPU time) limitations, and, often, increasing atomic and molecular complexity beyond the first rows of the periodic table. Strategies for addressing these challenges and predicting quantitatively accurate energies will be discussed.  The importance of the choice of thermochemical pathway, effective gauges and insight into density functional theory, particularly for transition metal species, and effective ab initio composite schemes are routes that are considered.