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Articles 1 - 23 of 23
Full-Text Articles in Physical Sciences and Mathematics
A Molecular Chemodosimeter To Probe “Closed Shell” Ions In Kidney Cells, Rashid Mia
A Molecular Chemodosimeter To Probe “Closed Shell” Ions In Kidney Cells, Rashid Mia
Faculty Publications
Two quinidine-functionalized coumarin molecular probes have been synthesized and have been found to bind metal cations (Cd2+, Co2+, Cu2+, Fe2+, Hg2+, Ni2+, and Zn2+) with high affinity in organic–aqueous media (DMSO–HEPES). The chemodosimeters coordinate with the Zn2+ ions in a two-to-one ratio (molecular probe : Zn2+) with a log β of 10.0 M−2. Upon the addition of the closed-shell metal ions studied, a fluorescence turn-on via an excimer formation is seen at 542 nm due to the quinaldine moiety adopting a syn arrangement when coordinated to the metal Zn2+ ions. Confocal microscopy monitored free Zn2+ ions in the Human Embryonic …
Mechanism For Selective Binding Of Aromatic Compounds On Oxygen-Rich Graphene Nanosheets Based On Molecule Size/Polarity Matching, Heyun Fu, Bingyu Wang, Dongqiang Zhu, Zhicheng Zhou, Shidong Bao, Xiaolei Qu, Yong Guo, Lan Ling, Shourong Zheng, Pu Duan, Jingdong Mao, Klaus Schmidt-Rohr, Shu Tao, Pedro J.J. Alvarez
Mechanism For Selective Binding Of Aromatic Compounds On Oxygen-Rich Graphene Nanosheets Based On Molecule Size/Polarity Matching, Heyun Fu, Bingyu Wang, Dongqiang Zhu, Zhicheng Zhou, Shidong Bao, Xiaolei Qu, Yong Guo, Lan Ling, Shourong Zheng, Pu Duan, Jingdong Mao, Klaus Schmidt-Rohr, Shu Tao, Pedro J.J. Alvarez
Chemistry & Biochemistry Faculty Publications
Selective binding of organic compounds is the cornerstone of many important industrial and pharmaceutical applications. Here, we achieved highly selective binding of aromatic compounds in aqueous solution and gas phase by oxygen-enriched graphene oxide (GO) nanosheets via a previously unknown mechanism based on size matching and polarity matching. Oxygen-containing functional groups (predominately epoxies and hydroxyls) on the nongraphitized aliphatic carbons of the basal plane of GO formed highly polar regions that encompass graphitic regions slightly larger than the benzene ring. This facilitated size match–based interactions between small apolar compounds and the isolated aromatic region of GO, resulting in high binding …
Synthesis Of Carbohydrate Based Macrolactones And Their Applications As Receptors For Ion Recognition And Catalysis, Surya B. Adhikari, Anji Chen, Guijun Wang
Synthesis Of Carbohydrate Based Macrolactones And Their Applications As Receptors For Ion Recognition And Catalysis, Surya B. Adhikari, Anji Chen, Guijun Wang
Chemistry & Biochemistry Faculty Publications
Glycomacrolactones exhibit many interesting biological properties, and they are also important in molecular recognitions and for supramolecular chemistry. Therefore, it is important to be able to access glycomacrocycles with different sizes and functionality. A new series of carbohydrate-based macrocycles containing triazole and lactone moieties have been designed and synthesized. The synthesis features an intramolecular nucleophilic substitution reaction for the macrocyclization step. In this article, the effect of some common sulfonate leaving groups is evaluated for macrolactonization. Using tosylate gave good selectivity for monolactonization products with good yields. Fourteen different macrocycles have been synthesized and characterized, of which eleven macrocycles are …
Molecular Recognition Of Methionine-Terminated Peptides By Cucurbit[8]Uril, Zoheb Hirani, Hailey F. Taylor, E. F. Babcock, Andrew T. Bockus, C. D. Varnado Jr., Christopher W. Bielawski, Adam R. Urbach
Molecular Recognition Of Methionine-Terminated Peptides By Cucurbit[8]Uril, Zoheb Hirani, Hailey F. Taylor, E. F. Babcock, Andrew T. Bockus, C. D. Varnado Jr., Christopher W. Bielawski, Adam R. Urbach
Adam R Urbach
This Article describes the molecular recognition of peptides containing an N-terminal methionine (Met) by the synthetic receptor cucurbit[8]-uril (Q8) in aqueous solution and with submicromolar affinity. Prior work established that Q8 binds with high affinity to peptides containing aromatic amino acids, either by simultaneous binding of two aromatic residues, one from each of two different peptides, or by simultaneous binding of an aromatic residue and its immediate neighbor on the same peptide. The additional binding interface of two neighboring residues suggested the possibility of targeting nonaromatic peptides, which have thus far bound only weakly to synthetic receptors. A peptide library …
A Study In Molecular Recognition: Synthesis Of A Β-Sheet Mimic & Quantitation Of Metal Ions In Aqueous Solutions Through Solid Supported Semi-Selective Chemosensors, Tyler G. Fenske
Theses and Dissertations
From the hydrophobic effect, which is responsible for the organization of amphipathic molecules into cellular membranes, to the highly specific hydrogen binding patterns found in DNA base pairs that keeps our genetic material “zipped up”, non-covalent and reversible interactions are critical to properly functioning biological processes. Molecular recognition is an area of study that seeks to better understand these observed phenomena. In a general sense, association of “Host” and “Guest” molecules are based on ionic forces, hydrophobic interactions, cation-π effects, π-π stacking, conformational restriction, and many others. This dissertation will primarily focus on two projects that have an emphasis on …
Molecular Recognition Of Methionine-Terminated Peptides By Cucurbit[8]Uril, Zoheb Hirani, Hailey F. Taylor, E. F. Babcock, Andrew T. Bockus, C. D. Varnado Jr., Christopher W. Bielawski, Adam R. Urbach
Molecular Recognition Of Methionine-Terminated Peptides By Cucurbit[8]Uril, Zoheb Hirani, Hailey F. Taylor, E. F. Babcock, Andrew T. Bockus, C. D. Varnado Jr., Christopher W. Bielawski, Adam R. Urbach
Chemistry Faculty Research
This Article describes the molecular recognition of peptides containing an N-terminal methionine (Met) by the synthetic receptor cucurbit[8]-uril (Q8) in aqueous solution and with submicromolar affinity. Prior work established that Q8 binds with high affinity to peptides containing aromatic amino acids, either by simultaneous binding of two aromatic residues, one from each of two different peptides, or by simultaneous binding of an aromatic residue and its immediate neighbor on the same peptide. The additional binding interface of two neighboring residues suggested the possibility of targeting nonaromatic peptides, which have thus far bound only weakly to synthetic receptors. A peptide library …
Ligand Binding Constants Of The Cucurbit[7]Uril Predicted With Molecular Docking: A Theoretical Study, Balázs Roósz, Tamás Körtvélyesi, Béla Viskolcz
Ligand Binding Constants Of The Cucurbit[7]Uril Predicted With Molecular Docking: A Theoretical Study, Balázs Roósz, Tamás Körtvélyesi, Béla Viskolcz
Turkish Journal of Chemistry
A binding stability order predicting, molecular docking based fast technique was developed for host--guest complexes. Molecular descriptors were applied to ligand molecules to make the binding energy based docking scoring functions more efficient and reach the $\pm $0.50 log K unit theoretical precision for predictions. The goal of this work was to model complexes of cucurbit[7]uril (CB7) as a host molecule with different local anesthetics and choline and phosphonium choline molecules. The guest molecules were docked into the cavity of CB7. The binding free energy maps were correlated by Contact, Grid-Based, Hawkins GB/SA, and AMBER docking scores obtained from UCSF …
Scope Of Amino Acid Recognition By Cucurbit[8]Uril, Preetika Rajgariah, Adam Urbach
Scope Of Amino Acid Recognition By Cucurbit[8]Uril, Preetika Rajgariah, Adam Urbach
Adam R Urbach
This paper describes the molecular recognition of amino acids by cucurbit[8]uril (Q8) and by the 1:1 complex between Q8 and methyl viologen (MV) in purely aqueous solution. These hosts are known to bind aromatic peptides with high affinity and sequence specificity, but prior work has focused on only a small subset of amino acids. In an effort to elucidate the scope and limitations of amino acid recognition by Q8 and Q8•MV, a comprehensive examination of the 20 genetically encoded amino acids was carried out by 1H NMR spectroscopy and isothermal titration calorimetry. We find that both Q8 and Q8•MV …
Nanomolar Binding Of Peptides Containing Noncanonical Amino Acids By A Synthetic Receptor, Leigh Logsdon, Christopher Schardon, Vijayakumar Ramalingam, Sharon Kwee, Adam Urbach
Nanomolar Binding Of Peptides Containing Noncanonical Amino Acids By A Synthetic Receptor, Leigh Logsdon, Christopher Schardon, Vijayakumar Ramalingam, Sharon Kwee, Adam Urbach
Adam R Urbach
This paper describes the molecular recognition of phenylalanine derivatives and their peptides by the synthetic receptor cucurbit[7]uril (Q7). The 4-tert-butyl and 4-aminomethyl derivatives of phenylalanine (tBuPhe and AMPhe) were identified from a screen to have 20–30-fold higher affinity than phenylalanine for Q7. Placement of these residues at the N-terminus of model tripeptides (X-Gly-Gly), resulted in no change in affinity for tBuPhe-Gly-Gly, but a remarkable 500-fold increase in affinity for AMPhe-Gly-Gly, which bound to Q7 with an equilibrium dissociation constant (Kd) value of 0.95 nM in neutral phosphate buffer. Structure–activity studies revealed that three functional groups work in a positively cooperative …
Molecular Probes For The Detection Of Zn2+ And Fe3+ Ions, Erendra Manandhar
Molecular Probes For The Detection Of Zn2+ And Fe3+ Ions, Erendra Manandhar
Dissertations
A number of molecular probes have been designed and synthesized for the detection of Zn2+ and Fe3+ ions. Two types of functional groups have been incorporated into the molecular scaffolds to utilize different fluorescent mechanisms. The first class of receptors contains a pyrene moiety. These molecular probes use the excimer mechanism for the detection of Zn2+ ion. The probes work well in an organic solvent with a detection limit of 20 nM (one ppb). Alternatives are made to make them water soluble, but this proved to be difficult. An interesting ion-induced self-assembly system will also be discussed. …
Bio-Imprinted Hydro-Gels (Bigs) For Protein And Virus Detection, Wei Bai
Bio-Imprinted Hydro-Gels (Bigs) For Protein And Virus Detection, Wei Bai
LSU Doctoral Dissertations
Detection of bio-markers at low concentration is becoming a more and more important topic in scientific research due to its importance in applications crucially related to people’s life like medical diagnosis, environment protection and national security. In the past decades, as the improvement of the modern analytical technologies progressed, plenty of methodologies have been developed to realize the fast and accurate detection of bio-markers in liquid media. However, some drawbacks still remain like the expensive cost, high requirement of operational environment, and need for skilled operators. Here, a new kind of aptamer-based bio-imprinted hydrogel sensor (BIG) with specific macroscopic volume …
Selective Fluorescence Sensing Of Salicylic Acid Using A Simple Pyrene Appended Imidazole Receptor, Md Wasi Ahmad, Bo Yeon Kim, Hong Seok Kim
Selective Fluorescence Sensing Of Salicylic Acid Using A Simple Pyrene Appended Imidazole Receptor, Md Wasi Ahmad, Bo Yeon Kim, Hong Seok Kim
Dr. Mohammad Wasi Ahmad (Md Wasi Ahmad)
A simple salicylic acid selective fluorescence receptor 1 was designed by combining 1-pyrenecarboxaldehyde and 1-(3-aminopropyl)imidazole. The selective sensing of salicylic acid resulted in a significant increase in monomer emissions due to the p–p interactions between the benzene and pyrene rings. The nature of the interactions between receptor 1 and salicylic acid was investigated further by 1H NMR spectroscopy, and the energy minimised structure of the complex between receptor 1 and salicylic acid was optimised. Receptor 1 showed the highest binding constant with 5-nitrosalicylic acid among all the aromatic carboxylic acids tested. 5-Nitrosalicylic acid formed a complex with receptor 1 at …
Selective Recognition Of H2po4 By A Cholestane-Imidazole-Zinc Ensemble, Jyoti Ramesh Jadhav, Md Wasi Ahmad, Hong Seok Kim
Selective Recognition Of H2po4 By A Cholestane-Imidazole-Zinc Ensemble, Jyoti Ramesh Jadhav, Md Wasi Ahmad, Hong Seok Kim
Dr. Mohammad Wasi Ahmad (Md Wasi Ahmad)
A new facile amphiphile cholestane-based zinc complex 4 containing a 3-aminopropylimidazole moiety at the 3a and 7a positions of cholestane was designed and synthesized. Recognition selectivity of the new receptor 4 with various anions was assessed by 1H NMR titration. Dihydrogen phosphate showed the highest binding affinity among all the tested anions
Nanomolar Binding Of Peptides Containing Noncanonical Amino Acids By A Synthetic Receptor, Leigh A. Logsdon, Christopher L. Schardon, Vijayakumar Ramalingam, Sharon K. Kwee, Adam R. Urbach
Nanomolar Binding Of Peptides Containing Noncanonical Amino Acids By A Synthetic Receptor, Leigh A. Logsdon, Christopher L. Schardon, Vijayakumar Ramalingam, Sharon K. Kwee, Adam R. Urbach
Chemistry Faculty Research
This paper describes the molecular recognition of phenylalanine derivatives and their peptides by the synthetic receptor cucurbit[7]uril (Q7). The 4-tert-butyl and 4-aminomethyl derivatives of phenylalanine (tBuPhe and AMPhe) were identified from a screen to have 20–30-fold higher affinity than phenylalanine for Q7. Placement of these residues at the N-terminus of model tripeptides (X-Gly-Gly), resulted in no change in affinity for tBuPhe-Gly-Gly, but a remarkable 500-fold increase in affinity for AMPhe-Gly-Gly, which bound to Q7 with an equilibrium dissociation constant (Kd) value of 0.95 nM in neutral phosphate buffer. Structure–activity studies revealed that three functional groups …
Enantioselective Complexation Of Chiral Lariat Crown Ethers And Chiral Primary Alkylammonium Perchlorates, Mehmet Zafer Köylü, Tarik Aral, Mehmet Karakaplan, Şafak Özhan Kocakaya, Hali̇l Hoşgören
Enantioselective Complexation Of Chiral Lariat Crown Ethers And Chiral Primary Alkylammonium Perchlorates, Mehmet Zafer Köylü, Tarik Aral, Mehmet Karakaplan, Şafak Özhan Kocakaya, Hali̇l Hoşgören
Turkish Journal of Chemistry
In order to investigate the enantiomeric recognition abilities toward 2 chiral alkylammonium perchlorates (AmI, AmII) by ^1H-NMR titration method in CDCl_3, 4 chiral lariat ethers 8-11 with a (p-methoxyphenoxy) methyl flexible side arm were used. The most effective enantiomeric recognition was obtained by LCEs 9 and 11 toward AmII, by K_R/K_S 6.58 and K_S/K_R 6.63, respectively. The effect of macroring size, subunit of macroring, and side arm appeared to have strong influence on the binding ability of these alkylammonium ions.
New 2-Aminoethylimidazole-Based Dicarboxylic Acid Receptor Derived From Cholestane, Jyoti Ramesh Jadhav, Md Wasi Ahmad, Hong Seok Kim
New 2-Aminoethylimidazole-Based Dicarboxylic Acid Receptor Derived From Cholestane, Jyoti Ramesh Jadhav, Md Wasi Ahmad, Hong Seok Kim
Dr. Mohammad Wasi Ahmad (Md Wasi Ahmad)
A new facial amphiphile cholestane-based receptor 1 containing a 2-imidazolylethylamino moiety at the 3a and 7a positions of cholestane was synthesized. Recognition selectivity of the new receptor 1 with various dicarboxylic acids was assessed by 1H NMR titration. Maleic acid showed the highest binding constant among all the tested acids
A Photochemically Initiated Chemistry For Coupling Underivatized Carbohydrates To Gold Nanoparticles, Xin Wang, Olof Ramström, Mingdi Yan
A Photochemically Initiated Chemistry For Coupling Underivatized Carbohydrates To Gold Nanoparticles, Xin Wang, Olof Ramström, Mingdi Yan
Chemistry Faculty Publications and Presentations
The sensitive optoelectronic properties of metal nanoparticles make nanoparticle-based materials a powerful tool to study fundamental biorecognition processes. Here we present a new and versatile method for coupling underivatized carbohydrates to gold nanoparticles (Au NPs) via the photochemically induced reaction of perfluorophenylazide (PFPA). A one-pot procedure was developed where Au NPs were synthesized and functionalized with PFPA by a ligand-exchange reaction. Carbohydrates were subsequently immobilized on the NPs by a fast light activation. The coupling reaction was efficient, resulting in high coupling yield as well as high ligand surface coverage. A colorimetric system based on the carbohydrate-modified Au NPs was …
Structural Basis For Binding Specificity Between Subclasses Of Modular Polyketide Synthase Docking Domains, Tonia Buchholz, Todd W. Geders, Frank E. Bartley Iii, Kevin A. Reynolds, Janet L. Smith, David H. Sherman
Structural Basis For Binding Specificity Between Subclasses Of Modular Polyketide Synthase Docking Domains, Tonia Buchholz, Todd W. Geders, Frank E. Bartley Iii, Kevin A. Reynolds, Janet L. Smith, David H. Sherman
Chemistry Faculty Publications and Presentations
Bacterial type I polyketide synthases (PKSs) assemble structurally diverse natural products of significant clinical value from simple metabolic building blocks. The synthesis of these compounds occurs in a processive fashion along a large multiprotein complex. Transfer of the acyl intermediate across interpolypeptide junctions is mediated, at least in large part, by N- and C-terminal docking domains. We report here a comprehensive analysis of the binding affinity and selectivity for the complete set of discrete docking domain pairs in the pikromycin and erythromycin PKS systems. Despite disconnection from their parent module, each cognate pair of docking domains retained exquisite binding selectivity. …
The Design And Evaluation Of Boronic Acid Derivatives For The Recognition Of Cell Surface Carbohydrates For Medicinal Applications, Sandra Navonne Craig
The Design And Evaluation Of Boronic Acid Derivatives For The Recognition Of Cell Surface Carbohydrates For Medicinal Applications, Sandra Navonne Craig
Chemistry Dissertations
ABSTRACT Carbohydrates in various forms play vital roles in numerous critical biological processes including cell-cell adhesion and communication, embryo development, immune response, etc. Fluorescent sensors for such carbohydrates have a wide range of potential applications including glucose concentration determination, cell labeling and targeting based on carbohydrate biomarkers, as in vitro diagnostic tools, and biomarker-directed cellular imaging. Our group has been interested in the design and synthesis of multi-boronic acid compounds with well-defined three-dimensional scaffolding for the specific recognition of selected carbohydrate biomarkers. Aberrant expression of carbohydrate antigens such as sialyl Lewis X (sLex), sialyl Lewis A (sLea), Lewis X (Lex), …
Chemomechanical Polymers As Sensors And Actuators For Biological And Medicinal Applications, Hans-Jörg Schneider, Kazuaki Kato, Robert M. Strongin
Chemomechanical Polymers As Sensors And Actuators For Biological And Medicinal Applications, Hans-Jörg Schneider, Kazuaki Kato, Robert M. Strongin
Chemistry Faculty Publications and Presentations
Changes in the chemical environment can trigger large motions in chemomechanical polymers. The unique feature of such intelligent materials, mostly in the form of hydrogels, is therefore, that they serve as sensors and actuators at the same time, and do not require any measuring devices, transducers or power supplies. Until recently the most often used of these materials responded to changes in pH. Chemists are now increasingly using supramolecular recognition sites in materials, which are covalently bound to the polymer backbone. This allows one to use a nearly unlimited variety of guest (or effector) compounds in the environment for a …
A Chloride Selective Calix[4]Arene Optical Sensor Combining Urea Functionality With Pyrene Excimer Transduction, Benjamin Schazmann, Dermot Diamond
A Chloride Selective Calix[4]Arene Optical Sensor Combining Urea Functionality With Pyrene Excimer Transduction, Benjamin Schazmann, Dermot Diamond
Articles
A neutral 2-site chloride selective compound has been developed (3), based on a 1,3- alternate tetrasubstituted calix[4]arene providing a preorganised supramolecular scaffold. The resultant supramolecular cavity is amongst the first to combine urea functional groups bridged with single methylene spacers to pyrene moieties. It combines a naturally and synthetically proven H-bonding system with the elegant ratiometric fluorescent signalling properties of an intramolecular pyrene excimer system, triggered by conformational changes upon anion coordination. The excimer emission of 3 is quenched, with a simultaneous rise in the monomer emission solely by the chloride anion amongst a wide variety of anions tested. 3 …
Molecular Recognition And Its Underlying Mechanisms In Molecularly Imprinted Polymers, Ryan Simon
Molecular Recognition And Its Underlying Mechanisms In Molecularly Imprinted Polymers, Ryan Simon
LSU Doctoral Dissertations
Molecular recognition in molecularly imprinting polymers (MIPs) is governed by two mechanisms: pre-organization of functional groups and shape specificity of the binding site. While pre-organization of functional groups has been studied extensively, shape specificity of the binding site has not been rigorously explored. The goal of this research is to determine the influence of shape specificity on molecular recognition in MIPs (Chapter 2). Once shape selectivity was proven to play a vital role in molecular recognition, it was important to determine if pre-organization of functional groups or shape specificity was the dominating factor in determining molecular recognition in the binding …
Design, Synthesis, And Applications Of Bio-Derived Crosslinking Monomers For Molecular Imprinting, Martha Sibrian-Vazquez
Design, Synthesis, And Applications Of Bio-Derived Crosslinking Monomers For Molecular Imprinting, Martha Sibrian-Vazquez
LSU Doctoral Dissertations
Most of the research in the field of molecular imprinting has been focused on the development of new functional monomers, in order to improve the molecular recognition properties afforded by these materials. The role of the crosslinking monomer has often been overlooked, since it is considered an inert component that only provides a scaffold to support the binding sites. However, the crosslinking monomer represents a high percent (80-90%) of the composition of molecularly imprinted polymers (MIPs), which can have a large influence on the MIPs properties. This research addresses the design, synthesis, and applications of new crosslinking monomers for molecular …