Chemistry Commons^™

A Polarizable Force-Field Model For Quantum-Mechanical-Molecular-Mechanical Hamiltonian Using Expansion Of Point Charges Into Orbitals, P. K. Biswas, Valentin Gogonea

Chemistry Faculty Publications

We present an ab initio polarizable representation of classical molecular mechanics (MM) atoms by employing an angular momentum-based expansion scheme of the point charges into partial wave orbitals. The charge density represented by these orbitals can be fully polarized, and for hybrid quantum-mechanical-molecular-mechanical (QM/MM) calculations, mutual polarization within the QM/MM Hamiltonian can be obtained. We present the mathematical formulation and the analytical expressions for the energy and forces pertaining to the method. We further develop a variational scheme to appropriately determine the expansion coefficients and then validate the method by considering polarizations of ions by the QM system employing the …

Spectroscopy Is Applied Quantum Mechanics. Part 2: The Quantum Revolution, David W. Ball

Chemistry Faculty Publications

The article presents several theories relative to the nature of matter. The quantum theory of German theoretical physicist Max Planck proposes that the energy of a vibrating atom was related to its frequency. Albert Einstein's quantum theory of light hypothesizes that light itself had an energy that was directly proportional to its frequency. Danish physicist Niels Bohr develops an equation that could help explain the lines that appeared in the spectrum of the hydrogen atom.

Wet Etching Of Pillar-Covered Silicon Surfaces: Formation Of Crystallographically Defined Macropores, M E. Dudley, Kurt Kolasinski

Chemistry Faculty Publications

Silicon substrates exposed to laser ablation in a chemically reactive environment such as SF6 or HCl can experience spontaneous formation of conical pillars. We use these pillars as a template to define the dimensions and order of macropores produced by etching such substrates in aqueous solutions of KOH or tetramethylammonium hydroxide. The pillars anchor the sidewalls of the pores during etching, and the interpillar spacing controls the width of the pores. The macropores have crystallographically defined shapes for which we develop an explanation based on the kinetics of etching. Si(001) macropores can be etched such that they are rectangular with …

Suppression Of Aromatase In Human Breast Cells By A Cyclooxygenase-2 Inhibitor And Its Analog Involves Multiple Mechanisms Independent Of Cyclooxygenase-2 Inhibition, Bin Su, Edgar S. Diaz-Cruz, Serena Landini, Robert W. Brueggemeier

Chemistry Faculty Publications

Previous studies have demonstrated that cyclooxygenase-2 (COX-2) inhibitor NS-398 decrease aromatase activity at the transcript level in breast cancer cells. However, N-Methyl NS-398, which does not have COX-2 inhibitory activity but has very similar structure to NS-398, decreases aromatase activity and transcription in MCF-7 and MDA-MB-231 breast cells to the same extent as NS-398. This suggests that NS-398 decrease aromatase expression in breast cancer cells via other mechanism(s). Further investigations find that both compounds only decrease aromatase activity stimulated by forskolin/phorbol ester at the transcript level in both breast cancer cell lines and in breast stromal cells from patients. They …

High-Purity White Light From A Simple Single Dopant Host-Guest White Organic Lightemitting Diode Architecture, Pavel Anzenbacher Jr., Victor A. Montes, Shin-Ya Takizawa

Chemistry Faculty Publications

White light with good color properties color rendering index=82–87 is generated in a simple organic light-emitting diode comprising an emissive layer, composed of an undoped tris 4-methyl-8-quinolinato aluminum Almq3 sublayer and region doped with an orange-red phosphorescent dopant, bis 2-phenyl-1-quinoline iridium acetylacetonate Ir pq 2acac . Electron-hole recombination in a thin spacing Almq3 layer results in blue-green fluorescence, while the formed triplet excitons diffuse to the doped region and are harvested by the dopant to emit orange-red phosphorescence. The combination of blue-green and orange lights results in warm white light. This approach takes advantage of efficient migration of triplet excitons …

Specific Rna Self-Assembly With Minimal Paranemic Motifs, Kirill A. Afonin, Dennis J. Cieply, Neocles B. Leontis

Chemistry Faculty Publications

The paranemic crossover (PX) is a motif for assembling two nucleic acid molecules using Watson-Crick (WC) basepairing without unfolding preformed secondary structure in the individual molecules. Once formed, the paranemic assembly motif comprises adjacent parallel double helices that crossover at every possible point over the length of the motif. The interaction is reversible as it does not require denaturation of basepairs internal to each interacting molecular unit. Paranemic assembly has been demonstrated for DNA but not for RNA and only for motifs with four or more crossover points and lengths of five or more helical half-turns. Here we report the …

Pentadienyl Complexes Of Alkali Metals: Structure And Bonding, Erick Cerpa, Francisco J. Tenorio, Maryel Contreras, Manuel Villanueva, Hiram I. Beltran, Thomas Heine, Kelling J. Donald, Gabriel Merino

Chemistry Faculty Publications

A systematic density functional study of the structure and bonding in the alkali-metal pentadienyl complexes C₅H₇E (E = Li-Cs) and their analogues derived from the 2,4-dimethylpentadienyl ligand is performed. The bonding in these structures has been analyzed in some detail with reference to molecular orbital analysis, and energy partition analysis, obtained by density functional calculations. An energy decomposition analysis indicates that the electrostatic interaction is the main factor to be considered in the stabilization of the gas-phase complexes we have studied. The stability of the U-shaped minimum energy structure decreases (the potential energy surface becomes more …

Excited-State Equilibration Over 30 Å In A Platinum(Ii) Quinolinolate−Bridge−Platinum(Ii) Porphyrin Complex, Victor A. Montes, Michael A. J. Rodgers, Pavel Anzenbacher Jr.

Chemistry Faculty Publications

Long-range triplet excited-state equilibration occurs over a nanometric distance between platinum(II) 8-quinolinolate ((3)Ptq(2) = 1.87 eV) and platinum(II) tetraphenylporphyrin ((PtTPP)-Pt-3 = 1.89 eV). The equilibrium is mediated by a fluorene-thiophene-fluorene bridge ((FTF)-F-3 = 1.92 eV) and is characterized by a double-exponential decay (tau(1) = 39 +/- 4 ps; tau(2) = 351 +/- 15 ps) that suggests the participation of three separate excited states : (3)Ptq(2), (FTF)-F-3, and 3PtTPP, respectively. Numerical simulation of the dual equilibrium allowed for estimation of the individual rate constants for each of the reversible steps (k(ET) = 3.9 x 10(9)-4.1 x 10(10) s(-1)). As a result …

Formation Of Peptide Nanospheres And Nanofibrils By Metal Coordination, Mikhail V. Tsurkan, Michael Y. Ogawa

Chemistry Faculty Publications

Two amphipathic polypeptides were coordinated to the cis positions of a square planar Pt(II) complex in order to provide the metal center with two noncovalent oligomerization domains. This resulted in the formation of new metal-peptide nanoassemblies which are shown to exist as nanometer-sized spheres and fibrils. Construction of these assemblies was based on the 30-residue polypeptide AQ-Pal14 which was designed for its ability to self-assemble into the common protein oligomerization motif of a noncovalent coiled-coil, and modified to contain a metal-binding 4-pyridylalanine residue at its surface. When AQ-Pal14 was reacted with Pt(en)(NO3)(2), a new metal-peptide complex was formed in which …

Reactivity Of Iso-Diiodomethane And Iso-Iodoform, Isomers Of Ch2i2 And Chi3, Toward The Double Bond Of A Variety Of Cycloalkenes, Alexander N. Tarnovsky, Irmin Pascher, Torbjorn Pascher

Chemistry Faculty Publications

The metastable CH2I-I and CHI2-I isomers formed by UV photolysis of CH2I2, and CHI3 transfer methylene and iodomethylene groups, respectively, to a variety of cycloalkenes, leading to their cyclopropanation. More than a 100-fold increase of the reaction rate with increasing solvent polarity suggests a dipolar transition state. The fastest second-order rates observed were in CH3CN. However, CH2Cl2 will be the more appropriate reaction medium because the isomer thermal stability is greater in CH2Cl2 than in the more polar CH3CN.

Optimization Of Non-Natural Nucleotides For Selective Incorporation Opposite Damaged Dna, Diana Vineyard, Xuemei Zhang, Alison Donnelley, Irene Lee, Anthony J. Berdis

Chemistry Faculty Publications

The promutagenic process known as translesion DNA synthesis reflects the ability of a DNA polymerase to misinsert a nucleotide opposite a damaged DNA template. To study the underlying mechanism of nucleotide selection during this process, we quantified the incorporation of various non-natural nucleotide analogs opposite an abasic site, a non-templating DNA lesion. Our kinetic studies using the bacteriophage T4 DNA polymerase reveal that the π-electron surface area of the incoming nucleotide substantially contributes to the efficiency of incorporation opposite an abasic site. A remaining question is whether the selective insertion of these non-hydrogen-bonding analogs can be achieved through optimization of …

Luminescent Charge-Transfer Platinum(Ii) Metallacycle, Fei Hua, Solen Kinayyigit, Aaron A. Rachford, Elena A. Shikhova, Sebastien Goeb, John R. Cable, Christopher J. Adams, Kristin Kirschbaum, A. Alan Pinkerton, Felix N. Castellano

Chemistry Faculty Publications

The photophysical and electrochemical properties of a platinum(II) diimine complex bearing the bidentate diacetylide ligand tolan-2,2'-diacetylide (tda), Pt(dbbpy)(tda) [dbbpy = 4,4'-di-tert-butyl-2,2'-bipyridine] (1), are compared with two reference compounds, Pt(dbbpy)(C CPh)(2) (2) and Pt(dppp)tda [dppp = 1,3-bis(diphenylphosphino)propane] (3), respectively, The X-ray crystal structure of 1 is reported, which illustrates the nearly perfect square planarity exhibited by this metallacycle. Chromophore 2 possesses low-lying charge-transfer excited states analogous to 1, whereas structure 3 lacks such excited states but features a low-lying platinum-perturbed tda intraligand triplet manifold. In CH2Cl2, 1 exhibits a broad emission centered at 562 nm at ambient temperature, similar to 2, …

Ultrafast Dynamics Of Triplet Excitons In Alq3-Bridge-Pt(Ii)Porphyrin Electroluminescent Materials, Victor A. Montes, Cesar Perez-Bolivar, Leandro A. Estrada, Joseph Shinar, Pavel Anzenbacher Jr.

Chemistry Faculty Publications

Excited-state dynamics are crucial for maximizing the performance of organic light-emitting diodes (OLEDs). Because electron-hole recombination yields singlet and triplet excited states in a 3:1 ratio, it is important to harvest the energy of triplets in light-emitting processes. Self-assembled multichromophore electroluminescent materials consisting of a trisquinolinolate aluminum(III) (Alq(₃)) donor, fluorene-based conjugated oligomers; as a bridge, and Pt(II)tetraphenylporphyrin as an acceptor and phosphorescent emitter are described. In these materials, the energy of singlet as well as triplet states is harvested and emitted as red phosphorescence from the porphyrin acceptor. Attention was devoted to the triplet exciton dynamics, which was …

Ovarian Cancer G Protein–Coupled Receptor 1, A New Metastasis Suppressor Gene In Prostate Cancer, Lisam Shanjukumar Singh, Michael Berk, Rhonda Oates, Zhenwen Zhao, Haiyan Tan, Ying Jiang, Aimin Zhou, Kashif Kirmani, Rosemary Steinmetz, Daniel Lindner, Yan Xu

Chemistry Faculty Publications

Background

Metastasis is a process by which tumors spread from primary organs to other sites in the body and is the major cause of death for cancer patients. The ovarian cancer G protein–coupled receptor 1 (OGR1) gene has been shown to be expressed at lower levels in metastatic compared with primary prostate cancer tissues.

Methods

We used an orthotopic mouse metastasis model, in which we injected PC3 metastatic human prostate cancer cells stably transfected with empty vector (vector-PC3) or OGR1-expressing vector (OGR1-PC3) into the prostate lobes of athymic or NOD/SCID mice (n = 3–8 mice per group). Migration of PC3 …

Aromatase And Cox In Breast Cancer: Enzyme Inhibitors And Beyond, Robert W. Brueggemeier, Bin Su, Yasuro Sugimoto, Edgar S. Diaz-Cruz, Danyetta D. Davis

Chemistry Faculty Publications

Aromatase expression and enzyme activity in breast cancer patients is greater in or near the tumor tissue compared with the normal breast tissue. Complex regulation of aromatase expression in human tissues involves alternative promoter sites that provide tissue-specific control. Previous studies in our laboratories suggested a strong association between aromatase (CYP19) gene expression and the expression of cyclooxygenase (COX) genes. Additionally, nonsteroidal anti-inflammatory drugs (NSAIDs) and COX selective inhibitors can suppress CYP19 gene expression and decrease aromatase activity. Our current hypothesis is that pharmacological regulation of aromatase and/or cyclooxygenases can act locally to decrease the biosynthesis of estrogen and may …

Magnetic Properties Of Variable-Sized Fe3o4 Nanoparticles Synthesized From Non-Aqueous Homogeneous Solutions Of Polyols, D. Caruntu, Gabriel Caruntu, Charles J. O'Connor

Chemistry Faculty Publications

The magnetic behaviour of well-dispersed monodisperse Fe3O4 nanoparticles with sizes varying between 6.6 and 17.8 nm prepared in a non-aqueous medium was investigated. The smaller nanocrystals exhibit superparamagnetism with the blocking temperatures increasing with the particle size, whereas the biggest particles are ferromagnetic at room temperature. The saturation magnetization values are slightly smaller than that of the bulk material, suggesting the existence of a disordered spin configuration on their surface. The thickness of the magnetically inert shell was estimated from the size variation of the magnetization at 1.9 Å. The dipole–dipole interactions between the particles were tuned by changing the …

The Use Of Non-Natural Nucleotides To Probe Template-Independent Dna Synthesis, Anthony J. Berdis, David Mccutcheon

Chemistry Faculty Publications

The vast majority of DNA polymerases use the complementary templating strand of DNA to guide each nucleotide incorporation. There are instances, however, in which polymerases can efficiently incorporate nucleotides in the absence of templating information. This process, known as translesion DNA synthesis, can alter the proper genetic code of an organism. To further elucidate the mechanism of template-independent DNA synthesis, we monitored the incorporation of various nucleotides at the “blunt-end” of duplex DNA by the high-fidelity bacteriophage T4 DNA polymerase. Although natural nucleotides are not incorporated at the blunt-end, a limited subset of non-natural indolyl analogues containing extensive π-electron surface …

Metal-Mediated Peptide Assembly: Use Of Metal Coordination To Change The Oligomerization State Of An Α-Helical Coiled-Coil, Mikhail V. Tsurkan, Michael Y. Ogawa

Chemistry Faculty Publications

Metal coordination is used to alter the oligomerization state of a designed peptide structure. The 30-residue polypeptide AQ-Pal21 4Pal21 contains two metal-binding 4-pyridylalanine (Pal) residues on its solvent-exposed surface and exists as a very stable two-stranded a-helical coiled-coil. Upon the addition of Pt(en)(NO3)(2), a significant conformational change to a metal-bridged, four-helix bundle is seen.

Stable Aqueous Nanoparticle Film Assemblies With Covalent And Charged Polymer Linking Networks, Lesley E. Russell, Anne A. Galyean, Sherilyn M. Notte, Michael C. Leopold

Chemistry Faculty Publications

The construction of highly stable and efficiently assembled multilayer films of purely water soluble gold nanoparticles is reported. Citrate-stabilized nanoparticles (CS-NPs) of average core diameter of 10 nm are used as templates for stabilization-based exchange reactions with thioctic acid to form more robust aqueous NPs that can be assembled into multilayer films. The thioctic acid stabilized nanoparticles (TAS-NPs) are networked via covalent and electrostatic linking systems, employing dithiols and the cationic polymer poly(l-lysine), respectively. Multilayer films of up to 150 nm in thickness are successfully grown at biological pH with no observable degradation of the NPs within the film. The …

A Series Of Vertically Integrated Nanotechnology Experiments For The Undergraduate Curriculum, Kevin W. Kittredge, Lesley E. Russell, Michael C. Leopold

Chemistry Faculty Publications

We have designed three nanotechnology experiments that are vertically integrated for an undergraduate chemistry curriculum. They are an evolving set of experiments for sequential courses in an undergraduate chemistry program. These experiments are designed to match the student's level of understanding for each particular course. The participating student is involved in a "research" project that progresses in both theory and experimental technique. Students benefit from these vertically integrated experiments by being involved in multiple facets of a simulated research project. This mimics a traditional research project under an advisor's supervision without the undesired drawback of an unknown outcome.

Fluctuating Two-State Light Harvesting In A Photosynthetic Membrane, Duohai Pan, Dehong Hu, Ruchuan Liu, Xiaohua Zeng, Samuel Kaplan, H. Peter Lu

Chemistry Faculty Publications

The mechanism by which light is converted into chemical energy in a natural photosynthetic system has drawn considerable research interest. Using fluorescence spectroscopy and microscopic imaging, we have observed fluctuating intermolecular protein fluorescence resonant energy transfers (FRET) among light-harvesting proteins I and II (LH1 and LH2) in bacterial photosynthetic membranes. Using two-channel, FRET, photon-counting detection and a novel, two-dimensional cross-correlation function amplitude-mapping analysis, we revealed fluorescence intensity and spectral fluctuations of donor (LH2) and acceptor (LH1) fluorescence involving FRET. Our results suggest that there are dynamic coupled and noncoupled states of the light-harvesting protein assemblies in photosynthetic membranes. The light-harvesting …

Triplet Energy Studies Of Thiophene And Para-Phenylene Based Oligomers, Leandro A. Estrada, Victor A. Montes, Grigory Zyryanov, Pavel Anzenbacher Jr.

Chemistry Faculty Publications

A series of conjugated materials based on oligomers of the para-phenylene type and oligothiophenes was prepared, and their phosphorescence spectra were recorded at 77 K using a pulsed flash-lamp as a light source and gated detection. The triplet energies of the oligomers were estimated and correlated with their chemical structure. It was found that simple changes in the building block sequence in the thiophene-containing oligomers allowed for tuning the triplet energy from 1.86 to 2.35 eV (530-670 nm). Hypsochromic shifts and little variation of the triplet energy were obtained with increasing length of the pi-system for thiophene end-capped oligomers, contrary …

Supramolecular Chemistry Approach To The Design Of A High-Resolution Sensor Array For Multianion Detection In Water, Manuel A. Palacios, Ryuhei Nishiyabu, Manuel Marquez, Pavel Anzenbacher Jr.

Chemistry Faculty Publications

Reliable sensing of structurally similar anions in water is a difficult problem, and analytical tests and sensor devices for reliable sensing of multiple anions are very rare. This study describes a method for fabrication of simple colorimetric array-based assays for aqueous anion solutions, including complex analytes encountered in real-life applications. On the fundamental level, this method shows how the discriminatory capacity of sensor arrays utilizing pattern recognition operating in multianalyte environments may be dramatically improved by employing two key features. The synergy between the sensor and hydrogel host resembles the cooperative effects of an apoenzyme and cofactor: the host hydrogel …

1,4-Di-9-Anthrylbutane, Mustafa Arslan, Erol Asker, John Masnovi, Ronald J. Baker

Chemistry Faculty Publications

In the title compound, C₃₂H₂₆, the molecule has an inversion centre at the mid-point of the central C—C bond. Weak intermolecular C—H...π interactions help to stabilize the crystal structure.

A Tandem Enol Silane Formation-Mukaiyama Aldol Reaction Mediated By Tmsotf, C. Wade Downey, Miles W. Johnson

Chemistry Faculty Publications

A slight excess of silyl trifluoromethanesulfonate mediates a tandem enol silane formation-Mukaiyama aldol reaction in the presence of Hunig’s base. Preformation of the enol silane is unnecessary for efficient reactions, which proceed in 75–97% yield for the addition of aryl methyl ketones and acetate esters to non-enolizable aldehydes. Mechanistic data suggests that free amine is crucial for full conversion.

Watching Ultrafast Barrierless Excited-State Isomerization Of Pseudocyanine In Real Time, Benjamin Dietzek, Arkady Yartsev, Alexander N. Tarnovsky

Chemistry Faculty Publications

The photoinduced excited-state processes in 1,1'-diethyl-2,2'-cyanine iodine are investigated using femtosecond time-resolved pump-probe spectroscopy. Using a broad range of probe wavelengths, the relaxation of the initially prepared excited-state wavepacket can be followed down to the sink region. The data directly visualize the directed downhill motion along the torsional reaction coordinate and suggest a barrierless excited-state isomerization in the short chain cyanine dye. Additionally, ultrafast ground-state hole and excited-state hole replica broadening is observed. While the narrow excited-state wavepacket broadens during pump-probe overlap, the ground-state hole burning dynamics takes place on a significantly longer time-scale. The experiment reported can be considered …

1,3-Bi-9-Anthrylpropane, Mustafa Arslan, Erol Asker, John Masnovi, Ronald J. Baker

Chemistry Faculty Publications

The title compound, C₃₁H₂₄, with three molecules in the asymmetric unit. The crystal packing is mainly stabilized by weak C—H⋯π inter­actions in addition to van der Waals forces.

Biophysical Characterization Of A Beta-Peptide Bundle: Comparison To Natural Proteins, E. James Petersson, Cody J. Craig, Douglas S. Daniels, Jade X. Qiu, Alanna S. Schepartz

Chemistry Faculty Publications

We recently described the high-resolution X-ray structure of a helical bundle composed of eight copies of the β-peptide Zwit-1F. Like many proteins in Nature, the Zwit-1F octamer contains parallel and antiparallel helices, extensive inter-helical electrostatic interactions, and a solvent-excluded hydrophobic core. Here we explore the stability of the Zwit-1F octamer using circular dichroism (CD) spectroscopy, analytical ultracentrifugation (AU), differential scanning calorimetry (DSC), and NMR. These studies demonstrate that the thermodynamic and kinetic properties of Zwit-1F closely resemble those of α-helical bundle proteins. Together these studies should provide a model for the design of β-peptide proteins with biological functions.

The Role Of The Intersection Space In The Photochemistry Of Tricyclo[3.3.0.02,6]Octa-3,7-Diene, Luis Manuel Frutos, Unai Sancho, Marco Garavelli, Massimo Olivucci, Obis Castano

Chemistry Faculty Publications

CASSCF and CASPT2 methods were used to study the photochemistry of tricyclo[3.3.0.0(2,6)]octa-3,7-diene (TOD). The analysis of different S-1 reaction paths as well as the topology of the S-1/S-0 intersection space allows us to establish two novel properties associated with the photochemical behavior of this compound: (i) simple low-lying intersection space domains can mediate different photoproducts, and (ii) TOD photochemistry is probably mediated by two disconnected intersection space domains, related to the formation of cyclooctatetraene and semibulvalene in different time-scales. It is shown that these domains are chemically distinct since the first, leading to COT, mediates barrierless pericyclic reactions while the …

Replica Exchange With Dynamical Scaling, Steven W. Rick

Chemistry Faculty Publications

A replica exchange method is presented which requires fewer replicas and is designed to be used for large systems. In this method, dynamically scaled replicas are placed between conventional replicas at broadly spaced temperatures. The potential of the scaled replicas is linearly scaled by a dynamicalvariable which varies between 0 and 1. When the variable is near either end point the replica can undergo exchanges with one of its neighboring replicas. Two different versions of the method are presented for a model system of a small peptide in water. The scaled replica can replace manyreplicas and the method can be …