Physical Sciences and Mathematics Commons^™

The Effect Of Frictional And Adhesion Forces Attributed To Slurry Particles On The Surface Quality Of Polished Copper, Yi-Koan Hong, Ja-Hyung Han, Tae-Gon Kim, Jin-Goo Park, Ahmed A. Busnaina

Ahmed A. Busnaina

The effect of frictional and adhesion forces attributed to slurry particles on the quality of copper surfaces was experimentally investigated during copper chemical mechanical planarization process. The highest frictional force of 9 Kgf and adhesion force of 5.83 nN were observed in a deionized water-based alumina slurry. On the other hand, the smallest frictional force of 4 Kgf and adhesion force of 0.38 nN were measured in an alumina slurry containing citric acid. However, frictional (6 Kgf) and adhesion (1 nN) forces of silica particles in the slurry were not significantly changed regardless of the addition of citric acid. These …

The Effect Of Frictional And Adhesion Forces Attributed To Slurry Particles On The Surface Quality Of Polished Copper, Yi-Koan Hong, Ja-Hyung Han, Tae-Gon Kim, Jin-Goo Park, Ahmed A. Busnaina

Ahmed A. Busnaina

The effect of frictional and adhesion forces attributed to slurry particles on the quality of copper surfaces was experimentally investigated during copper chemical mechanical planarization process. The highest frictional force of 9 Kgf and adhesion force of 5.83 nN were observed in a deionized water-based alumina slurry. On the other hand, the smallest frictional force of 4 Kgf and adhesion force of 0.38 nN were measured in an alumina slurry containing citric acid. However, frictional (6 Kgf) and adhesion (1 nN) forces of silica particles in the slurry were not significantly changed regardless of the addition of citric acid. These …

Controlling Microbial Contamination During Hydrolysis Of Afex-Pretreated Corn Stover And Switchgrass: Effects On Hydrolysate Composition, Microbial Response And Fermentation, Jose Serate, Dan Xie, Edward Pohlmann, Charles Donald Jr., Mahboubeh Shabani, Li Hinchman, Alan Higbee, Mick Mcgee, Alex La Reau, Grace E. Klinger, Sheena Li, Chad L. Myers, Charles Boone, Donna M. Bates, Dave Cavalier, Dustin Eilert, Lawrence G. Oates, Gregg Sanford, Trey K. Sato, Bruce Dale, Robert Landrick, Jeff Piotrowski, Rebecca G. Gong, Yaoping Zhang

Rebecca Ong

Characterization Of Physical, Spectroscopic And Thermal Properties Of Biofield Treated Biphenyl, Mahendra Kumar Trivedi, Rama Mohan Tallapragada, Alice Branton, Dahryn Trivedi, Gopal Nayak, Rakesh K. Mishra, Snehasis Jana

Mahendra Kumar Trivedi

Characterization Of Physical, Thermal And Spectral Properties Of Biofield Treated 2,6-Dichlorophenol, Mahendra Kumar Trivedi, Rama Mohan Tallapragada, Alice Branton, Dahryn Trivedi, Gopal Nayak, Rakesh K. Mishra, Snehasis Jana

Mahendra Kumar Trivedi

Interference-Free Gas-Phase Thermometry At Elevated Pressure Using Hybrid Femtosecond/Picosecond Rotational Coherent Anti- Stokes Raman Scattering, Joseph D. Miller, Chloe Elizabeth Dedic, Sukesh Roy, James R. Gord, Terrence R. Meyer

Terrence R Meyer

Rotational-level-dependent dephasing rates and nonresonant background can lead to significant uncertainties in coherent anti-Stokes Raman scattering (CARS) thermometry under high-pressure, lowtemperature conditions if the gas composition is unknown. Hybrid femtosecond/picosecond rotational CARS is employed to minimize or eliminate the influence of collisions and nonresonant background for accurate, frequency-domain thermometry at elevated pressure. The ability to ignore these interferences and achieve thermometric errors of <5% is demonstrated for N2 and O2 at pressures up to 15 atm. Beyond 15 atm, the effects of collisions cannot be ignored but can be minimized using a short probe delay (~6.5 ps) after Raman excitation, …

Peroxide Content Of Secondary Organic Aerosol, Ryan Caylor, Matthew E. Wise, John Shilling

Matthew E. Wise

C–N Bond Rotation And E–Z Isomerism In Some N-Benzyl-N-Methylcarbamoyl Chlorides: A Dft Study, Michael Horwath, Vladimir Benin

Vladimir Benin

The current report presents the first theoretical study of the restricted CN bond rotation in carbamoyl chlorides. Several N-benzyl-N-methylcarbamoyl chlorides were investigated, with varying pattern of substitution in the aromatic ring. Optimizations and frequency calculations were conducted employing DFT at the B3LYP/6-31+G(d) level of theory. Each of the studied structures exhibits a pair of rotamers (s-Z and s-E), generated upon rotation around the C(O)N bond. The s-E isomer is the global minimum in every case, but the preference for it is usually less than 1 kcal/mol. Two possible transition state structures were identified for the rotamer interconversion: TSsyn and TSanti, …

Preparation And Characterization Of Some Substituted Benzyl N-Nitrosocarbamates Containing An N-2-(Methylthio)Ethyl Or A Bis(2-Aminoethyl)Sulfide Functionality, Satya Venkata, Eric Shamo, Vladimir Benin

Vladimir Benin

The synthesis and characterization of some substituted benzyl N-nitrosocarbamates with an N-2-(methylthio)ethyl or a bis(2-aminoethyl)sulfide functionality is reported, as a part of a long-term goal to design and prepare novel photolabile structures that could be used as substances for controlled release of alkylating and/or crosslinking agents. The synthesis was accomplished by reaction of benzyl chloroformates with the corresponding amines, resulting in the preparation of carbamates. The latter were subsequently nitrosated, utilizing two different N-nitrosation methods, to yield the target structures.

The Tetrafluoroborate Salt Of 4-Methoxybenzyl N-2-(Dimethylamino)Ethyl-N-Nitrosocarbamate: Synthesis, Crystal Structure And Dft Calculations, Helene Hedian, Vladimir Benin

Vladimir Benin

The tetrafluoroborate salt of 4-methoxybenzyl N-2-(dimethylamino)ethyl-N-nitrosocarbamate was prepared in two steps, via the corresponding carbamate. Its crystal structure is monoclinic, space group P21/c. The unit cell dimensions are: a = 19.499(8) Å, b = 5.877(3) Å, c = 15.757(7) Å, α = 90°, β = 110.019(7)°, γ = 90°, V = 1696.5(12) Å3, Z = 4. The structure exhibits an unexpected, pseudo-gauche conformation with respect to the C2–C3 bond, due to a stabilizing hydrogen bond between the carbonyl oxygen (O1) and the hydrogen atom at the trialkylammonium center (H3n), with a distance between them of 2.37 Å. DFT calculations on …

A Sodium Salt Of The Dimer Of Boronoterephthalic Acid Anhydride, Scott Simmons, Albert Fratini, Vladimir Benin

Vladimir Benin

The title compound, sodium bis­(6-carb­oxy-1-hy­droxy-3-oxo-1,3-dihydro-2,1-benzoxaborol-1-yl)oxidanium, Na+·C16H15B2O13-, was prepared in two steps from 2-bromo-p-xylene. Its crystal structure was determined at 140 K and has triclinic (P) symmetry. The compound presents a unique structural motif, including two units of the cyclic anhydride of boronoterephthalic acid, joined by a protonated, and thereby trivalent, oxonium center. Association in the crystal is realized by complementary hydrogen bonding of the carboxyl groups, as well as by coordination of the sodium cations to the oxygen centers on the five-membered rings.

Secondary N-Nitrosocarbamate Anions: Structure And Alkylation Reactions. A Dft Study, Vladimir Benin

Vladimir Benin

The current article reports theoretical studies (DFT: B3LYP/6-31+G(d)) on the structure and alkylation reactions of the anions of some secondary N-nitrosocarbamates, a class of ambident nucleophiles whose chemistry has been little explored. Several anions (1–4), with an increasing size of the carbamate alkyl (aryl) group were investigated, in an attempt to establish the influence of the size of that group on the thermal stability and regioselectivity of alkylation of the title anions. The conclusion is that thermal stability and the mode of reaction are affected significantly only in the presence of very large and branched carbamate groups. The thermal decomposition …

Preparation Of Phosphonoterephthalic Acids Via Palladium-Catalyzed Coupling Of Aromatic Iodoesters, Nathaniel Ivan, Vladimir Benin, Alexander Morgan

Vladimir Benin

The current article reports in detail the preparation of two phosphonoterephthalic acids: 2-phosphonoterephthalic acid (1) and 2,5-diphosphonoterephthalic acid (2). Efficient, scalable syntheses have been developed for both compounds based on Pd-catalyzed coupling reactions of iodinated terephthalate esters. Phosphonoterephthalic acids are potentially useful as flame-retardant additives or as monomers for the construction of acid-pendant polymer chains.

Preparation Of Some Substituted Terephthalic Acids, Susanna Branion, Vladimir Benin

Vladimir Benin

We report in detail the preparation of two substituted terephthalic acids: 2‐sulfomethylterephthalic acid (1) and 2‐phosphonoterephthalic acid (2). Efficient, short syntheses have been developed for both compounds. They are potentially useful monomers for construction of acid‐pendant polymer chains.

Theoretical Investigation Of A Reported Antibiotic From The 'Miracle Tree' Moringa Oleifera, Michael Horwath, Vladimir Benin

Vladimir Benin

Moringa oleifera, sometimes called the “Miracle Tree,” has received international attention for its potential to improve health in impoverished tropical areas. In addition to high vitamin content in the leaves and pods, the tree contains compounds with antioxidant and antibacterial properties. This study focused on the theoretical investigation of the suggested structure of one antibacterial compound, “pterygospermin,” whose existence was proposed after some studies of the roots of M. oleifera. The structure of pterygospermin was first proposed by a research group working in the 1950s, but later studies have not found evidence of this compound and have instead attributed the …

Synthesis And Flame Retardant Testing Of New Boronated And Phosphonated Aromatic Compounds, Vladimir Benin, Sravanthi Durganala, Alexander Morgan

Vladimir Benin

The present report describes the preparation and use of some dimethyl terephthalate derivatives in transition metal-catalyzed coupling reactions to produce new reactive flame retardants. Dimethyl iodoterephthalate and dimethyl 2,5-diiodoterephthalate were successfully employed in the preparation of phosphonic and boronic esters and acids. The latter were tested for heat release with a microcombustion calorimeter (ASTM D7309) to determine the potential for heat release reduction of these flame retardant molecules. The results showed that the addition of boronic or phosphonic acids greatly lowered the heat release, due to a condensed phase (char formation) mechanism. Adding ester groups to the boronic acids or …

Heat Release Of Polyurethanes Containing Potential Flame Retardants Based On Boron And Phosphorus Chemistries, Vladimir Benin, Bastien Gardelle, Alexander Morgan

Vladimir Benin

Using a polyurethane of methylene diphenyl isocyanate and 1,3-propane diol, several new non-halogenated aromatic boron and phosphorus flame retardants were evaluated for heat release reduction potential using the pyrolysis combustion flow calorimeter (PCFC). The polyurethanes were prepared in the presence of the potential flame retardants via solvent mixing and copolymerization methods, and were then analyzed via spectroscopic methods to determine if the flame retardant was still present in the final product. PCFC testing on the resulting products showed that the flame retardant molecule can have different effects on heat release depending upon how it is mixed into the polyurethane. Some …

Preparation, Characterization And Dft Studies Of Some New N-Nitrosocarbamates And N-Nitrosoureas, Ragavan Narayanan, Helene Hedian, Eric Shamo, Vladimir Benin

Vladimir Benin

We are presenting the preparation, characterization and density functional theory (DFT) studies {B3LYP/6-31+G(d)) of several reiated classes of N-nitrosocarbamates and N-nitrosoureas. The iong-range goal is the design and preparation of compounds, which would undergo photochemical or hydrolytic decomposition, to yield stabilized cyclic cations that can serve as alkylating agents at various nucleophilic centers, including DNA bases.

Reactions Of Methyl Perfluoroalkyl Ethers With Isopropyl Alcohol: Experimental And Theoretical Studies, Howard Knachel, Vladimir Benin, Chadwick Barklay, Janine C. Birkbeck, Billy D. Faubion, William E. Moddeman

Vladimir Benin

The reaction of an isomeric mixture of the methyl perfluoroalkyl ether, C4F9OCH3 (Novec-7100), in the presence of isopropyl alcohol (IPA) and/or water has been studied by measuring the rate of product formation using an ion-selective electrode (ISE) for fluoride ion, Karl Fisher coulometric titrations for water, and 1H and 19F NMR spectroscopy for product identification and rate studies. The results showed the methyl perfluoroalkyl ether to be very stable with products forming at the rate of ∼1 ppm per year at a laboratory temperature of 20 °C. Measurements over the temperature range of 6° to 100 °C were made on …

Preparation Of Halogenated Derivatives Of Thiazolo[5,4-D]Thiazole Via Direct Electrophilic Aromatic Substitution, Vladimir Benin, Alan T. Yeates, Douglas Dudis

Vladimir Benin

Chlorination and bromination reactions of thiazolo[5,4-d]thiazole led to the generation of its mono- and dihalogenated derivatives. These are the first instances of successful direct electrophilic aromatic substitution in the thiazolo[5,4-d]thiazole ring system. X-ray analysis demonstrates that both 2-bromothiazolo[5,4-d]-thiazole and 2,5-dibromothiazolo[5,4-d]thiazole are planar structures, with strongly manifested π-stacking in the solid state. Theoretical analysis of the pyridine-catalyzed halogenation (MP2/6-31+G(d) and B3LYP/6-31+G(d)calculations) reveals that introduction of one halogen actually leads to a slightly enhanced reactivity towards further halogenation. Several halogenation mechanisms have been investigated: 1) The direct C-halogenation with N-halopyridine as electrophile; 2) C-halogenation viaintermediate N-halogenation, and 3) C-halogenation following an addition …

Structure, Theoretical Studies And Coupling Reactions Of Some New Cyclic Boronic Esters, Andrew Kuttler, Sravanthi Durganala, Albert Fratini, Alexander Morgan, Vladimir Benin

Vladimir Benin

The present report describes the X-ray structural and theoretical studies of some new pinacolboronate esters, and it also outlines the use of the target structures in Suzuki coupling reactions to produce new aromatic or heteroaromatic esters and amides. X-ray structural analysis of the studied compounds revealed that the pinacolborane ring's position with respect to the benzene ring varies, depending on the particular environment. An ortho-positioned carboxylic ester (methyl ester) causes a nearly perpendicular orientation of the pinacolborane unit with respect to the benzene ring, whereas an ortho-positioned amide (N,N-dimethylamide) causes the pinacolborane unit to orient itself nearly coplanar. A plausible …

Determining Protease Substrate Selectivity And Inhibition By Label-Free Supramolecular Tandem Enzyme Assays, Garima Ghale, Vijayakumar Ramalingam, Adam R. Urbach, Werner M. Nau

Adam R Urbach

An analytical method has been developed for the continuous monitoring of protease activity on unlabeled peptides in real time by fluorescence spectroscopy. The assay is enabled by a reporter pair comprising the macrocycle cucurbit[7]uril (CB7) and the fluorescent dye acridine orange (AO). CB7 functions by selectively recognizing N-terminal phenylalanine residues as they are produced during the enzymatic cleavage of enkephalin-type peptides by the metalloendopeptidase thermolysin. The substrate peptides (e.g., Thr-Gly-Ala-Phe-Met-NH₂) bind to CB7 with moderately high affinity (K ≈ 10⁴ M^–1), while their cleavage products (e.g., Phe-Met-NH₂) bind very tightly (K …

Sequence-Specific, Nanomolar Peptide Binding Via Cucurbit[8]Uril-Induced Folding And Inclusion Of Neighboring Side Chains, Lauren C. Smith, David G. Leach, Brittney E. Blaylock, Omar A. Ali, Adam R. Urbach

Adam R Urbach

This paper describes the molecular recognition of the tripeptide Tyr-Leu-Ala by the synthetic receptor cucurbit[8]uril (Q8) in aqueous buffer with nanomolar affinity and exceptional specificity. This combination of characteristics, which also applies to antibodies, is desirable for applications in biochemistry and biotechnology but has eluded supramolecular chemists for decades. Building on prior knowledge that Q8 binds to peptides with N-terminal aromatic residues, a library screen of 105 peptides was designed to test the effects of residues adjacent to N-terminal Trp, Phe, or Tyr. The screen used tetramethylbenzobis(imidazolium) (MBBI) as a fluorescent indicator and resulted in the unexpected discovery that MBBI …

Blind Prediction Of Host-Guest Binding Affinities: A New Sampl3 Challenge, Hari S. Muddana, C Daniel Varnado, Christopher W. Bielawski, Adam R. Urbach, Lyle Isaacs, Matthew T. Geballe, Michael K. Gilson

Adam R Urbach

The computational prediction of protein–ligand binding affinities is of central interest in early-stage drug-discovery, and there is a widely recognized need for improved methods. Low molecular weight receptors and their ligands—i.e., host–guest systems—represent valuable test-beds for such affinity prediction methods, because their small size makes for fast calculations and relatively facile numerical convergence. The SAMPL3 community exercise included the first ever blind prediction challenge for host–guest binding affinities, through the incorporation of 11 new host–guest complexes. Ten participating research groups addressed this challenge with a variety of approaches. Statistical assessment indicates that, although most methods performed well at predicting some …

Molecular Recognition Of Amino Acids, Peptides, And Proteins By Cucurbit[N]Uril Receptors, Adam R. Urbach, Vijayakumar Ramalingam

Adam R Urbach

At the forefront of the endeavor to understand and manipulate living systems is the design and study of receptors that bind with high affinity and selectivity to specific amino acids, peptides, and proteins. Cucurbit[n]urils are among the most promising class of synthetic receptors for these targets due to their high affinities and selectivities in aqueous media and to the unique combination of electrostatic and hydrophobic interactions that govern binding. The fundamental supramolecular chemistry in this area has been explored in depth, and novel, useful applications are beginning to emerge.

Physicochemical And Spectroscopic Characterization Of P-Chlorobenzaldehyde: An Impact Of Biofield Energy Treatment, Mahendra Kumar Trivedi, Alice Branton, Dahryn Trivedi, Gopal Nayak, Khemraj Bairwa, Snehasis Jana

Mahendra Kumar Trivedi

Physical, Thermal And Spectral Properties Of Biofield Treated 3-Nitroacetophenone, Mahendra Kumar Trivedi, Rama Mohan Tallapragada, Alice Branton, Dahryn Trivedi, Gopal Nayak, Rakesh K. Mishra, Snehasis Jana

Mahendra Kumar Trivedi

Constructing Explicit Magnetic Analogies For The Dynamics Of Glass Forming Liquids, Jacob D. Stevenson, Aleksandra M. Walczak, Randall W. Hall, Peter G. Wolynes

Randall W. Hall

By defining a spatially varying replica overlap parameter for a supercooled liquid referenced to an ensemble of fiducial liquid state configurations, we explicitly construct a constrained replica free energy functional that maps directly onto an Ising Hamiltonian with both random fields and random interactions whose statistics depend on the liquid structure. Renormalization group results for random magnets when combined with these statistics for the Lennard-Jones glass suggest that discontinuous replica symmetry breaking would occur if a liquid with short range interactions could be equilibrated at a sufficiently low temperature where its mean field configurational entropy would vanish, even though the …

An Adaptive, Kink-Based Approach To Path Integral Calculations, Randal W. Hall

Randall W. Hall

A kink-based expression for the canonical partition function is developed using Feynman’s path integral formulation of quantum mechanics and a discrete basis set. The approach is exact for a complete set of states. The method is tested on the 3×3 Hubbard model and overcomes the sign problem seen in traditional path integral studies of fermion systems. Kinks correspond to transitions between different N-electron states, much in the same manner as occurs in configuration interaction calculations in standard ab initio methods. The different N-electron states are updated, based on which states occur frequently during a Monte Carlo simulation, giving better estimates …

Divergence, Recombination And Retention Of Functionality During Protein Evolution, Yanong O. Xu, Randall W. Hall, Richard A. Goldstein, David D. Pollock

Randall W. Hall

We have only a vague idea of precisely how protein sequences evolve in the context of protein structure and function. This is primarily because structural and functional contexts are not easily predictable from the primary sequence, and evaluating patterns of evolution at individual residue positions is also difficult. As a result of increasing biodiversity in genomics studies, progress is being made in detecting context-dependent variation in substitution processes, but it remains unclear exactly what context-dependent patterns we should be looking for. To address this, we have been simulating protein evolution in the context of structure and function using lattice models …