Saturday May 6th – Presentations

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Strategies for Success in STEM Majors – Implementation and Evaluation of a Pilot Course

Emily C. Heider, Jamil Johnson

University of Central Florida

08:35 AM
to 09:00 AM
Chemistry Education

Demand for a highly-trained STEM workforce is garnering increasingly urgent notice, and national efforts call on the development of talent from all sectors, including underrepresented minorities. According to the National Research Council (NRC) panel, the ingredients for inclusive success in STEM are the “acquisition of knowledge, skills, and habits of mind; opportunities to put these into practice; a developing sense of competence and progress; motivation to be in, a sense of belonging to, or self-identification with the field; and information about stages, requirements, and opportunities.” Addressing these requirements for freshmen STEM majors in a first-year experience course has potential to staunch the outflow of students from STEM fields. Strategies for Success (SLS 1501) is 3-credit elective cours, with the focus on helping students transition to collegiate life. Recently, a pilot section of SLS-1501 was offered exclusively to STEM majors to focus more narrowly on strategies for success in STEM majors and aimed to achieve the goals set by the NRC for inclusive success in STEM. The focus of this research is to evaluate the merit of the course – through analysis of the scientific reasoning exams administered in the course, surveys of the students who completed the course, and through following the progress of the students in their chosen majors over time.

G-Quadruplex Formation from H8 Modified Guanosine Derivatives: From Structure to Function

Ying He, Xiaodong Shi*

Department of Chemistry, University of South Florida, Tampa, FL 33620, USA

08:50 AM
to 09:10 AM
Biochemistry / Chem Bio.

G-quadruplex (GQ) has been developed extensively over the past decades. It has been reported that GQs could be used in many directions of chemical, material and biological researches, including supramolecular hydrogel, molecular switch and ionophores. To form a controllable G-quadruplex, one general consideration of self-assembly process is the competition between ΔH formed by hydrogen bonding and the ΔS generated from formation of highly organized structure. It is reasonable to assume that structurally more rigid monomer will lead to the formation of more stable G-quartet due to the reduction of conformation flexibility. One general approach to achieve structurally rigid G-monomer is the modification of C-8 position by fixing the sugar syn/anti conformation. However, according to literature, the studies of C-8-modified G-quadruplexes are rare, mainly due to the challenges associated with the substrate synthesis.

Taking advantage of the electron deficiency of 1,2,3-triazole and electron rich guanosine, we designed a triazole substituted guanosine and successfully achieved high fluorescent intensity which can be used in the application of molecular switch. Herein, we report the new synthesis of 8-aryl guanosine and fluorescent active 8-triazole guanosine and their selfassembly property in solid state and in solution. Through cation templation (Mn+= Na+, K+, Ba2+, Pb2+, Sr2+, La3+), discrete self-assembled G-quartet structures were formed. Both structurally novel and functional enriched G-quartets are achieved using this new system. Potential applications in molecular sensing and biological target recognition are expected with this new system.

CONDUCTING CHARGE TRANSFER SALTS of Fe(II) COMPLEXES WITH TCNQ RADICALS

Okten Ungor, Hoa Phan, and Michael Shatruk

Department of Chemistry and Biochemistry, Florida State University, Tallahassee, Florida 32306, USA

08:50 AM
to 09:10 AM
Inorganic Chemistry

Fe(II) complexes with ligands of an intermediate ligand field strength show magnetic bistability, i.e. switching between the high-spin and low-spin electronic configurations driven by changes in temperature, pressure, or photoexcitation. We are interested in designing multi functional materials that exhibit both spin crossover (SCO) and conductivity by combining para-magnetic Fe(II) cationic complexes and TCNQ· anion radicals. It is expected that the latter should provide conducting pathways via the formation of p-p interacting stacks in the solid state structure. The synthetic strategy toward such hybrid materials is two-pronged: first, the TCNQ· anions can coordinate to Fe(II) ions that are partially protected by blocking ligands, in order to limit fast precipitation of extended structures; second, these anions can be co-crystallized with completely blocked Fe(II) centers. In both approaches, the goal is to obtain a hybrid crystal structure that features both conducting stacks of fractionally charged organic radicals and SCO Fe(II) complexes. We report the synthesis of several such complexes, which demonstrate significant conductivity values and, in some cases, SCO behavior.

HALOGEN BONDING INDUCED SUPRAMOLECULAR ASSEMBLY OF A LOW-ENERGY-GAP π-CONJUGATED OLIGOMER AND THERMAL ACTIVATION OF COMPLEMENTARY HYDROGEN BONDING SITES TO FURTHER TUNE THE ASSEMBLY

Asmerom O. Weldeab,1 Suong T. Nyguen,2 Daken J. Starkenburg,3 Jiangeng Xue,3 Ronald K. Castellano1, and Davita L. Watkins2

1 Department of Chemistry, University of Florida, P.O.Box 117200, Gainesville, FL 32611-7200, USA
2 Department of Chemistry and Biochemistry, University of Mississippi, Oxford, MS 38677, USA
3 Department of Materials Science and Engineering, University of Florida, P.O.Box 116400, Gainesville, FL 32611-6400, USA

08:50 AM
to 09:10 AM
Organic Chemistry

Significant effort has been made in the recent decade towards developing organic semiconductors. Despite improvements in molecular design, currently available organic semiconductors still suffer lower device efficiencies and mechanical stabilities compared to their inorganic counterparts. The poorly controllable and often random solid state arrangements of the molecules affects device efficiency (i.e., charge mobility). Increasing in the literature are supramolecular approaches which utilize hydrogen bonding (HB) to control the nanoscale to microscale arrangement of molecules in thin films. Also arising are approaches exploiting halogen bonding (XB) for similar applications.

Prepared here is a halogen bond capable C2-symmetric π-conjugated oligomeric moiety (II_Boc) with a general Donor-Acceptor-Donor design. Isoindigo and thiophenes are used as electron accepting and donating units, respectively. The molecule is end- capped with pyridine units, also part of the conjugated system, as halogen bond acceptors. The halogen bonding driven assembly of II_Boc with 1,4-diiodotetrafluorobenzene (DITFB) is confirmed experimentally by X-ray crystallography. This noncovalent interaction guides the ordering of the molecules to yield highly directional halogen bond induced 2D assemblies which stack via π-π interactions. Pyrolytic cleavage and removal of t-butyloxycarbonyl (Boc) groups, installed for solubility purposes, and subsequent exposure of the complementary hydrogen bonding sites in II_NH was also confirmed by TGA and IR. Overall, the data is consistent with 3D assembly of the molecule through synergetic halogen bonding, hydrogen bonding, and π-stacking.

Design Principles for High H2 Storage Using Chelation of Abundant Transition Metals in Covalent Organic Frameworks for 0-700 bar at 298 K

Jose L. Mendoza-Cortes

†Department of Chemical & Biomedical Engineering, FAMU-FSU College of Engineering and ‡Scientific Computing Department, Materials Science and Engineering Program, High Performance Material Institute, Condensed Matter Theory-National High Magnetic Field Laboratory, Florida State University, Tallahassee Florida 32310, United States

09:00 AM
to 09:30 AM
Computational Chemistry

Physisorption is an effective route to meet hydrogen gas (H2) storage and delivery requirements for transportation because it is fast and fully reversible under mild conditions. However, most current candidates have too small binding enthalpies to H2 which leads to volumetric capacity less than 10 g/L compared to that of the system target of 40 g/L at 298 K. Accurate quantum mechanical (QM) methods were used to determine the H2 binding enthalpy of 5 linkers which
were chelated with 11 di
fferent transition metals (Tm), including abundant first-row Tm (Sc through Cu), totaling 60 molecular compounds with more than 4 configurations related to the different number of H2 that interact with the molecular compound. It was found that first-row Tm gave similar and sometimes superior van der Waals interactions with H2 than precious Tm. Based on these linkers, 30 new covalent organic frameworks (COFs) were constructed. The H2 uptakes of these new COFs were determined using quantum mechanics (QM)-based force fields and grand canonical Monte Carlo (GCMC) simulations. For the first time, the range for the adsorption pressure was explored for 0-700 bar and 298 K. It was determined that Co-, Ni-, and Fe-based COFs can give high H2 uptake and delivery when compared to bulk H2 on this unexplored range of pressure.

ELECTRODEPOSITION AND CHARACTERIZATION OF MANGANESE DIOXIDE ON GOLD NANOTUBES

Juliette Experton, Xiaojian (James) Wu, Charles R. Martin

Department of Chemistry, University of Florida, Gainesville, FL 32611

09:05 AM
to 09:25 AM
Analytical Chemistry

Bipolar electrochemistry is a powerful tool capable of localized and asymmetric electrodeposition on nano-objects in the absence of electrical contact. It offers a precise way to grow oxide nanoparticles on 3D substrates. We have developed a technique to synthesize MnO2 particles using bipolar electrochemistry at a low voltage (3.5 V). This voltage is applied across a gold nanotube membrane forming redox reactions, one cathodic and one anodic, at either end of the nanotube. The anodic reaction is chosen such that it forms MnO2 at the pore orifice. The resulting capped pores were used for the electrochemical analysis of MnO2 to determine its conductivity, surface charge and permselectivity. In this presentation, we will address the performance of this material for applications in batteries and catalysis.

EXAMINING THE GAS ADSORPTION PROPERTIES IN MOLECULAR POROUS MATERIALS BASED UPON COPPER–ADENINE PADDLEWHEEL COMPLEXES

Tony Pham,1 Katherine A. Forrest,1 Patrick S. Nugent,1 Michael J. Zaworotko,2 and Brian Space1

 

1.) Department of Chemistry, University of South Florida, 4202 East Fowler Avenue, CHE205, Tampa, FL 33620-5250, United States
2.) Department of Chemical & Environmental Sciences, University of Limerick, Limerick, Republic of Ireland

09:05 AM
to 09:25 AM
Materials Chemisry

Experimental and theoretical gas adsorption studies were performed in MPM-1-Cl and MPM-1-TIFSIX, two robust molecular porous materials (MPMs) with the empirical formula [Cu2(adenine)4Cl2]Cl2 and [Cu2(adenine)4(TiF6)2], respectively. Both MPMs consist of a hydrogen-bonding network that is self-assembled by dinuclear copper–adenine paddlewheel complexes. The difference between the two structures is simply the axial ligand. Experimental measurements revealed that MPM-1-TIFSIX displays higher CO2 uptake, isosteric heat of adsorption (Qst), and selectivity than MPM-1-Cl. These findings have been verified through molecular simulations. The zero-loading Qst for CO2 in MPM-1-TIFSIX is actually comparable to that for the top-performing metal–organic frameworks (MOFs). MPM-1-TIFSIX was also shown to exhibit high H2 uptake and Qst for H2 through experimental studies, which were subsequently supported by simulation. Modeling studies have also yielded insights into the adsorption sites in both MPMs.

The Revolution will be Compartmentalized: Technology for Distributed Drug Discovery

Brian M Paegel

The Scripps Research Institute, Department of Chemistry, Jupiter, FL 33458

09:10 AM
to 09:35 AM
Biochemistry / Chem Bio.

The NIH Molecular Libraries Program (MLP) was founded to translate the discoveries of the Human Genome Project into therapeutics through a network of high-throughput screening (HTS) centers. A decade of discovery produced hundreds of probes — highly selective small molecules that modulate cellular function — but centralized compound screening bears the same cost and infrastructure burdens of millennial DNA sequencing centers, which has limited access to the technology and, more significantly, the rate of small molecule discovery. We are building a next-generation distributable drug discovery platform analogous to next-generation DNA sequencing. We have developed DNA-encoded solid-phase synthesis strategies to produce ultra-miniaturized compound libraries where each microscopic bead displays many copies of a small molecule library member and a corresponding amplifiable DNA that that encodes the structure. In parallel, we engineered microfluidic instrumentation for miniaturizing automated screening. The integrated microfluidic compound screening circuit loads individual compound library beads into picoliter-scale droplets of assay reagent. Compound, which is attached to the bead via photolabile linker, is released into the droplet in a UV dose-dependent fashion (0.01–10 µM compound) using an integrated UV fiber optic, the dosed droplets are then incubated, evaluated for activity using laser-induced confocal fluorescence detection, and sorted for PCR amplification and high-throughput sequencing. To demonstrate the feasibility of the platform, we synthesized a modest (~50k compounds) DNA-encoded combinatorial protease inhibitor library and developed droplet-scale biochemical assays of HIV-1 protease, ZIKV NS2B-NS3 protease, and cathepsin D. Library screening of HIV-1 protease is under way. Not only are the molecular libraries and screening technology deployable in any laboratory setting, but dose-response screening will generate whole-library structure activity relationship profiles. The unprecedented molecular detail of these data will yield portfolios of new leads and replenish the pipeline of therapeutics, especially those targeting rapidly-evolving bacterial and viral pathogens.

Preparation of New Akoxy-Derivatives of the Carborane Anion, CB11H12

Christos Douvris, Austin Harris, Phoenix Sconzert, Kiran Boggavarapu

Department of Chemistry, McNeese State University

09:10 AM
to 09:45 AM
Inorganic Chemistry

The carborane anion CB11H12 and its derivatives have received widespread attention in the recent years due to its weakly coordinating nature. This allows it to support highly reactive counterions such as H+, CH3+, R3Si+, and also make it able to mask empty coordination sites in the coordination sphere of transition metals. With this work, we report synthetic routes for the preparation of alkoxy derivatives, RO- with R = Me, Et, Pr, Bu, of the carborane anion and we explore the possibility for their application in non-coordination chemistry

Recent Advances in Homogenous Gold Catalysis: Accessing Heterocycles Containing Nitrogen Boron Bonds

Stephen Motika; Xiaodong Shi

University of South Florida

09:10 AM
to 09:30 AM
Organic Chemistry

The combination of triazole/gold (TA-Au) and Cu(OTf)2 is identified as the optimal catalytic system for promoting intramolecular hydroboration for the synthesis of a six-membered cyclic amine–borane. Excellent yields (up to 95 %) and regioselectivities (5-exo vs. 6-endo) were achieved through catalyst control and sequential dilution. Good functional-group tolerance was attained, thus allowing the preparation of highly functionalized cyclic amine–borane substrates, which could not be achieved using other methods. Deuterium-labeling studies support the involvement of a hydride addition to a gold-activated alkyne with subsequent C−B bond formation

Discovery and Targeted Monitoring of Lipids Under Different Cell Conditions using a Multidimensional Analytical Approach

Kendra J. Adams1, Cesar E. Ramirez1Richard H. Gomer2, Francisco Fernandez-Lima1,3

 

1. Department of Chemistry & Biochemistry, Florida International University, Miami, FL
2. Department of Biology, Texas A&M University, College Station, TX
3. Biomolecular Sciences Institute, Florida International University, Miami, FL

09:25 AM
to 09:45 AM
Analytical Chemistry

The complexity of biological matrices demands the use of complementary analytical tools for separation, identification and quantitation of single components. For example, traditional lipid analysis is based on the use of liquid chromatography coupled to mass spectrometry (LC-MS/MS) for separation and identification based on the molecular mass and fragmentation pattern; however, reproducibility and the need for long separation times reduces the throughput of this technique. In order to overcome these challenges, a multidimensional separation technique is proposed based on the use of trapped ion mobility spectrometry coupled to mass spectrometry (TIMS-MS/MS) as a screening and quantification tool. In the present work, we compare traditional LC-MS/MS with TIMS-MS/MS workflows for the separation and detection of lipids from Dictyostelium discoideum cells at different developmental stages. TIMS-MS/MS provides a faster and more comprehensive lipid profile of Dictyostelium discoideum cells and has the potential to be further applied to other biological problems. Over 100 lipids have been identified from a wide variety of lipid classes (e.g., phosphoglycerols and ceramides) and levels of expression. Challenges and future trends are discussed for the development of discovery and targeted monitoring strategies using TIMS-MS/MS and LC-TIMS-MS/MS.

Growth of Fluorescent Noble Metal Nanoclusters Protected with Dithiolate Ligands

Dinesh Mishra, Fadi Aldeek, Goutam Palui, and Hedi Mattoussi

Department of Chemistry and Biochemistry, Florida State University, Tallahassee, FL 32306, USA.

09:25 AM
to 09:45 AM
Materials Chemisry

We describe the use of Lipoic Acid modified with poly(ethyleneglycol) and zwitterion group in the aqueous growth of fluorescent gold and silver nanoclusters.  The conventional growth method, i.e., borohydride reduction of metal precursors in the presence of thiol ligand produces red/NIR emitting clusters with PL efficiency up to 14%. These clusters exhibit long term stability in buffer and other biologically relevant conditions. To attain tunable emission, we rely on the photochemical reducing property of thiolates. Lipoic acid has a strained  ring with a disulfide bond, which is cleaved by UV radiation to generate thiols and other byproducts. When this mixture of photochemically generated compounds and gold(III) compounds is refluxed in basic condition, luminescent gold clusters are formed. By varying the cluster growth conditions, we could tune the optical emission of gold clusters from blue to red. Growth of bimetallic nanoclusters made of  gold and silver is also presented. We followed two different approaches: a) growth by co-reduction of the mixture of gold and silver precursors and (b) reaction of silver(I)-thiolate complexes with pre-synthesized Au11clusters, which results in the formation of luminescent Au/Ag nanoclusters with unique optical properties. The characterization of these materials using various techniques is also described.

3D printing in chemical education

Neelam Bharti

University of Florida

09:00 AM
to 09:25 AM
Chemistry Education

As an emerging technology, three-dimensional (3D) printing has gained much attention as a rapid prototyping and small-scale manufacturing technology around the world. 3D printing provides a new creative and innovative platform for almost every discipline in education and research including STEM disciplines. Engineering disciplines use 3D printing to make models of new machines, robots, and other prototypes. 3D printing has a substantial impact on the field of chemical education as well. 3D printed interactive models of the Bohr Model of the atom, bond polarity, and hybridization is a great learning tool for students to explore the atomic theory. 3D models also have been used to teach orbital theory as well as VSEPR theory in the classroom and laboratory. 3D printed crystal structures became valuable teaching tools for the instructors. This presentation will include basics of 3D printing and their applications in chemical education as well as emerging benefits and risks involved.

Incorporating Green Chemistry experiments in the IB Chemistry curriculum

Karen Loweke

Bartow International Baccalaureate High School, Bartow, FL 33830

09:25 AM
to 09:45 AM
Chemistry Education

This presentation will share examples on how to incorporate green chemistry experiments in the IB curriculum.

ANALYTIC GRADIENTS FOR V2RDM-CASSCF METHODS

Elvis Maradzike and A. E. DePrince III

Florida State University, Tallahassee, FL 32306

09:30 AM
to 09:45 AM
Computational Chemistry

The CASSCF approach enables an accurate description of the electronic structure of many-electron systems where non-dynamical correlation effects are important. Variational two-electron reduced-density-matrix (v2RDM) methods provide a route to polynomial-scaling implementations of CASSCF enabling the description of active-spaces larger than those that can be considered using configuration interaction-(CI-) based CASSCF. In this work, we present an implementation of analytic energy gradients for (v2RDM)-driven CASSCF. Expressions for analytic gradients are simplified by the fact that the Lagrangian for the active-space energy is stationary with respect to variations in the active-space reduced-density matrices. We assess the relative performance of v2RDM-CASSCF relative to CI-based CASSCF in the geometry optimization of 20 molecules. For these molecules, bond lengths from geometry optimization with v2RDM-driven CASSCF are in good agreement with those from (CI)-driven CASSCF. When enforcing two-particle N-representability conditions, v2RDM-CASSCF-optimized bond lengths display a mean unsigned error of 0.006 Å and a maximum unsigned error of 0.0265 Å, relative to those obtained with CI-CASSCF. When enforcing partial three-particle N-representability conditions, the mean and maximum errors are reduced to 0.0006 Å and 0.0054 Å, respectively.

MULTIFUNCTIONALIZED MOLECULES AND MATERIALS FROM BENZOTRIFURAN(ONE)

Ronald K. Castellano

Department of Chemistry, University of Florida, P.O. Box 117200, Gainesville, FL 32611-7200, USA

09:30 AM
to 09:50 AM
Organic Chemistry

Benzotrifuranone (BTF) is a deceptively simple looking heterocycle bearing three lactone rings that our lab introduced to the community in 2009.  Since this time we have come to appreciate its structure, reactivity, and more recently, potential for applications.  The story begins with BTF’s unique ability to undergo selective and sequential aminolysis reactions, behavior we now confidently understand to arise from a synergism of electronic effects and a "ring strain gradient". The reactivity has recently leveraged the mild and efficient preparation of both heterodifunctionalized polymers and a molecular FRET relay system.  Acylation of BTF provides access to benzotrifurans, attractive but otherwise difficultly prepared heterocycles.  Described will be the first preparation and structural analysis of parent benzotrifuran (BTFuran), as well as its usefulness for accessing π-conjugated materials.

Simple Strategies for Complex Terpenoid Natural Product Synthesis

Alex Grenning

Department of Chemistry, University of Florida

09:35 AM
to 09:55 AM
Biochemistry / Chem Bio.

Structurally-complex terpenoid natural products (NPs), are used in the treatment of various diseases including cancer. NP drugs and leads are procured most commonly by isolation and semisynthesis from the natural source. Terpenoid total-synthesis is an alternative strategy to access terpenoid derived drug candidates. Although significant progress has been made in chemical synthesis, there is immediate need improve synthetic efficiency and devise routes that produce medicinally relevant NPs and NP-analogs rapidly. We are attempting to develop a operationally simple, unified route to various "terpenoid building blocks" for processing into terpenoid natural products and analogs for application in the drug discovery process. Our progress toward frondosin-, guaianolide-, tigliane-, and dolastane-terpenoid NP families is presented.

UNRAVELING THE STRUCTURAL COMPLEXITY OF CRUDE OILS USING TIMS-FT-ICR MS

Paolo Benigni1, Francisco Fernandez-Lima1,2

 

1Department of Chemistry and Biochemistry, Florida International University, Miami, USA
2Biomolecular Sciences Institute, Florida International University, Miami, USA

10:15 AM
to 10:35 AM
Analytical Chemistry

Crude oil is one of the most complex mixtures in the world, with over 100,000 estimated number of unique molecular components. Characterization of a crude oil is particularly difficult because current analytical techniques are only able to identify a small fraction of the molecular components in a crude oil. Therefore, our knowledge of crude oil, at the molecular level, has been limited to the molecular species that can be separated by Gas Chromatography MS; However, this greatly limits the molecular species that can be analyzed, primarily due to the volatility requirements of the GC separation. In this work, for the first time, Trapped Ion Mobility Spectrometry is coupled to FT-ICR MS for the analysis of standard crude oils. When utilizing TIMS-FT-ICR MS we are able to separate isomeric molecular species using high resolution ion mobility spectrometry (R>150). These two dimensions of analysis increases the peak capacity, allowing for a greater number of identifications compared to MS alone. Another advantage of TIMS is that is it a time independent separation, therefore the FT-ICR MS analysis step does not have to be reduced in order to have an analytical number of points characterizing the peak. An unsupervised candidature structure workflow was developed to proposed candidate structures based on their chemical formula and mobility measurements.

Exploration of New Opioid Macrocyclic Tetrapeptides as Potential Analgesics

Jane V. Aldrich,1 Sanjeewa Senadheera,3 and Jay McLaughlin2

Departments of 1Medicinal Chemistry and 2Pharmacodynamics, University of Florida, Gainesville, FL 32610 USA; 3Department of Medicinal Chemistry, the University of Kansas, Lawrence, KS 66045

10:15 AM
to 10:40 AM
Biochemistry / Chem Bio.

The macrocyclic tetrapeptides CJ-15,208 (cyclo[Phe-D-Pro-Phe-Trp]) and its D-Trp isomer both bind to kappa opioid receptors (KOR) and exhibit KOR antagonist activity. The change in the tryptophan stereochemistry, however, changes the in vivo opioid activity profile; while the D-Trp isomer exhibits KOR antagonism with minimal agonist activity, CJ-15,208 containing L-Trp exhibits mixed agonist/KOR antagonist activity in a mouse antinociceptive assay (Ross et al., 2012). Therefore we explored the effects of changing the stereochemistry of the phenylalanine residues on opioid activity. The peptides were synthesized by a combination of solid phase synthesis of the linear precursors followed by cyclization of the peptides in dilute solutions using optimized reaction conditions. All of the new stereoisomers examined exhibited antinociceptive (agonist) activity in vivo in the mouse 55 oC warm-water tail-withdrawal assay, with multiple opioid receptors contributing to the antinociceptive activity. However, unlike the lead peptides most of the stereoisomers did not exhibit KOR antagonism. Several of the stereoisomers were also active after oral administration and some exhibited promising results in tests for liabilities associated with standard narcotic analgesics (sedation, tolerance). Thus these peptides represent new lead compounds for the potential development of novel analgesics. Research supported by NIDA grants R01 DA18832 and R01 DA023924.

HIGH-PERFORMANCE MOLECULAR DYNAMICS AT CONSTANT PH AND CONSTANT REDOX POTENTIAL USING AMBER

Vinicius Wilian D. Cruzeiro 1,Marcos Amaral 2, Adrian E. Roitberg 1

1. Chemistry Department, University of Florida, Gainesville, FL, United States.
2. Univ. Federal de MS, Campo Grande, Brazil.

10:15 AM
to 10:30 AM
Computational Chemistry

The protonation/oxidation state of proteins and other biomolecules can be related to their structure and function, and it can affect properties like stability, ligand binding, catalysis, absorption spectrum, among others. This happens because pH and/or the redox potential affect the charge distribution on the biomolecules due to changes in the predominant protonation/oxidation state of the relevant groups. Also, ligands can change their protonation/oxidation state upon protein binding process or during an enzymatic reaction. Therefore, theoretical methods that can correctly describe the protonation/reduction state at constant pH and/or at constant redox potential are very important.
On this presentation, we show the implementation on AMBER of an extension to constant redox potential of codes already implemented: constant pH Molecular Dynamics (CpHMD) and Replica Exchange Molecular Dynamics along the pH-dimension (pH-REMD). Due to the similarity between the Henderson-Hasselbalch equation (applied to acid-base reactions) and the Nernst equation (applied to electrochemistry, reduction reactions), the mathematical derivations used for CpHMD and pH-REMD can be extended to the redox potential. By making use of CUDA implementation, we obtain a high-performance code that can be used on simulations of large systems. REMD is an important technique that enhances the statistical ensemble of a simulation while takes advantage of parallelism. The REMD implementation along both the pH and redox potential dimensions (pH,E-REMD) is important because several experimental measures are done both at constant pH and at constant redox potential.
We also show how our results are in agreement with theoretical/experimental expectations, and how computational benchmarks show the high-performance of calculations using GPU in comparison with serial or MPI calculations for large systems.

Investigation of Magnetic Phase Transitions in CuFe2–xCoxGe2

Zachary P. Tener1, Sebastian Stoian2, Michael Shatruk1

1Department of Chemistry and Biochemistry, Florida State University, Tallahassee, FL 32306, USA
2National High Magnetic Field Laboratory, E. Paul Dirac Dr, Tallahassee FL, USA

10:15 AM
to 10:35 AM
Inorganic Chemistry

A recent experimental investigation of CuFe2Ge2 revealed that this compound exhibits weak itinerant antiferromagnetism,1 in agreement with the earlier theoretical prediction.2 Based on the similarity of the electronic band structure of CuFe2Ge2  and recently discovered superconductor, YFe2Ge2,3 it has been suggested that proper doping into the former structure might suppress the antiferromagnetic ordering and lead to the superconducting state.2 Guided by the electronic structure calculations performed at the DFT level of theory, we pursued electron doping by exploring the entire range of isostructural solid solutions, CuFe2–xCoxGe2, with an incremental (0.2) increase in the Co content across the series. Magnetic measurements do reveal a gradual suppression of the AFM behavior with the increase in the Co content (x). The low-temperature investigation of the materials that appear at the borderline of AFM ordering might result in the discovery of a superconducting phase transition.

References

  1. May, A. F.; Calder, S.; Parker, D. S.; Sales, B. C.; McGuire, M. A. Sci. Rep. 2016, 6, 35325.
  2. Shanavas, K. V.; Singh, D. J. PLoS One 2015, 10, 1.
  3. Zou, Y.; Feng, Z.; Logg, P. W.; Chen, J.; Lampronti, G.; Grosche, F. M. Phys. Status Solidi - Rapid Res. Lett. 2014, 8, 928.

SYNTHESIS, STRUCTURE, AND PROPERTIES OF BISMUTH CONTAINING MIXED METAL OXIDES

Michael Lufaso1, Daniel Chica1, Jessica Wilson1, Eric Hearn1, Jeffrey Auletta1

1 Department of Chemistry, University of North Florida, Jacksonville, FL 32224, USA

10:15 AM
to 10:35 AM
Materials Chemisry

Solid-state chemistry is aligned with emerging and potential technologies, which require materials with improved properties to meet the desired and stringent requirements for many applications. Advances in the physical sciences benefit from synthesis of new materials and their characterization, and also an understanding of the extent of chemical substitutions to alter their physical properties. Exploratory and targeted methods each have unique advantages in the synthesis of new materials. These methods were used to prepare well-characterized bismuth containing mixed-metal oxides, which exhibit structural variety and diverse physical properties. The phase compositions and crystal structures were determined using diffraction techniques. The influence of synthesis temperature and limits of chemical substitution on the crystal structure and unit cell volume were explored. To pursue structure-property relationships, variable temperature electrical and dielectric property measurements were performed and indicate tunable activation energies of conduction, tunable dielectric properties, and promising responses for gas sensing.

Highly efficient cellular entry and intracellular organelle targeting of

conjugated polymer nanoassembly

Md. Salauddin Ahmed, Rajeshkumar Manian, Joong Ho Moon

Department of Chemistry and Biochemistry, Biomolecular Sciences Institute, Florida International University

10:15 AM
to 10:40 AM
Organic Chemistry

Although various nanomaterials offer improved payloads delivery to the diseased tissues, poor intracellular entry and lack of organelle targeting are still big huddles that substantially decrease the therapeutic effects. In this presentation, our recent efforts to achieve high cellular entry and organelle targeting using p-electron conjugated polymer nanoassembly (CPNs) will be discussed. CPNs are formed by self-assembly of non-aqueous soluble luminescent conjugated polymers (CPs), and have been used for labeling, sensing, and delivery of biological substances. By modulating the chemical structures of rigid aromatic backbone and flexible side chains, we have successfully fabricated various self-assembly structures and demonstrated modulated cellular interaction, entry, and intracellular targeting. The structure-function relationship obtained from our research will lead to novel design concepts for multifunctional cellular nanomaterials with high cellular entry and targeting efficiency.

American Association of Chemistry Teachers (AACT):  Overview and Invitation

Jenn Parsons

American Association of Chemistry Teachers, ACS

10:15 AM
to 10:40 AM
Chemistry Education

AACT Education Resource Specialist Jenn Parsons will introduce the national membership organization by and for K–12 teachers of chemistry, while highlighting its goals, member benefits, and opportunities to get involved.

pH-DEPENDENT CONFORMATIONAL CHANGES AND ITS IMPACT ON E.coli GLYCINAMIDE RIBONUCLEOTIDE TRANSFORMYLASE (GAR-Tfase) CATALYSIS

Pancham Lal Gupta, Adrian E. Roitberg

Department of Chemistry, University of Florida, Gainesville FL 32611-7200, USA

10:30 AM
to 10:45 AM
Computational Chemistry

Human GAR-Tfase is a regulatory enzyme in de-novo purine biosynthesis which has been proven to be an anti-cancer target. Drugs such as Lometrexol, AG-2034 and pemetrexed have been designed using GAR-Tfase as a target enzyme. Folylpolyglutamate synthetase (FPGS) adds charged glutamates to these drugs which improves their binding affinities. However, the added charge leads to excessive cell retentivity and toxicity. E.coli GAR-Tfase, a well studied system, is sequentially similar to Human GAR-Tfase and most of its functional residues remain conserved. In the present work, we use E.coli GAR-Tfase to study pH-dependent conformational changes, ligand-binding and catalysis. We use pH replica exchange molecular dynamics (pH-REMD) simulations implemented in the AMBER suite to run in GPUs. We find that conformational changes in GAR-Tfase take place at low pH, which are consistent with experimental and previous theoretical studies. We propose refinements to the existing GAR-Tfase catalytic mechanism which has the potential to design effective inhibitors. To explain the effect of pH on catalysis, we present a pH-activity curve combining the population of catalytically competent protonation states and pH-dependent ligand-binding; which is consistent with experiments. This work can be applied to identify and extend the pH-range of drug molecules’ inhibition.