Relativistic Dynamics in Basic Chemistry

This paper revisits the historical sequence in which some of the major developments of 20th-century physics occurred, and explores how theories could have turned out differently, if the sequence of developments had been different. It shows how a delay in founding special relativity theory until after (1) at least one puzzling problem in electromagnetic theory could be acknowledged, and (2) sat least some of the experimental observations pertinent to the development of quantum mechanics had become well known, could have resulted in a larger theory that covers both domains in a manner quite different from that of any of the theories we use today. The revised theory dispenses with a separate postulate introducing Planck’s constant h, identifying instead a physical mechanism that implies the constant. Some important aspects of quantum chemistry then follow. Editor, Galilean Electrodynamics, Proceedings of the Natural Philosophy Alliance; Visiting Industry Professor, Tufts University, retired     

Site-specific cleavage of human telomerase RNA using PNA-neocuproine.Zn(II) derivatives

Here we report the synthesis of a novel PNA based neocuproine.Zn RNA cleaving agent; we demonstrate that such agents sequence specifically cleave a synthetic RNA target and in particular the RNA component of human telomerase.     

The effect of crown ethers on the alkylation of a cyclic β-keto ester

The effects of crown ethers (6 and 7) on the reactions of sodium (2a) and potassium enolates (2b) of 2-ethoxycarbonylcyclohexanone (1) with isopropyl iodide in dimethylsulfoxide and dimethoxyethane have been investigated. When the addition of crown ether promoted dissociation of ion pair 2 in either of the two solvents, the total rate of reaction (k_t) increased and the ratio of carbon- (3) to oxygen-alkylation (4 and 5) products decreased. The results are consistent with the involvement of both the ion pair and more dissociated species in alkylation and with greater reactivity for the latter.     

X-ray diffraction and morphology of crystalline,hard, elastic materials

Summary X-ray diffraction and electron microscopic results on several crystalline polymers which demonstrate elastic properties (polypropylene, Celcon^®, poly-4-methyl-pentene) are reported. Photographic small angle X-ray diffraction techniques provided considerable qualitative information, concerning the morphological features of these elastic materials both as extruded, annealed and during extension. Lamellar thickness, thickness distribution and perfection of lamellae could be estimated. Lateral order features and orientation of the lamellar structures were obtainable from the sharpness and length of the equatorial wide angle diffraction arcs. Electron microscopic results essentially confirm the morphological features postulated on the basis of the X-ray results. These morphological features are discussed in terms of a general structural model which appears consistent with the mechanical properties of these materials.

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Zusammenfassung Röntgenbeugung und elektronenmikroskopische Daten von einigen kristallinen Polymerprodukten mit elastischen Eigenschaften (Polypropylen, Celcon, Poly-4-methylpenten) werden berichtet. Die photographische Röntgen-Kleinwinkelmethode liefert wichtige qualitative Messungen der morphologischen Struktur dieser elastischen Materialien in den Zuständen sowohl wie hergestellt als auch nach Tempern und während des Dehnungsprozesses. Die Dicke der Lamellen, ihre Dikkenverteilung und die Güte der Lamellen konnten abgeschätzt werden. Die laterale Ordnung und die Orientierung der Lamellen kann aus Weitwinkelbeugungsdaten abgeleitet werden. Die Elektronenmikroskopie bestätigt die Morphologie, die aus Röntgendaten folgt. Ein allgemeines Strukturmodel dieser Morphologie, das im Einklang mit den mechanischen Eigenschaften dieser Produkte steht, wird diskutiert.

     

General deoxyribozyme-catalyzed synthesis of native 3'-5' RNA linkages

An elusive goal for nucleic acid enzymology has been deoxyribozymes that ligate RNA rapidly, sequence-generally, with formation of native 3'-5' linkages, and in preparatively useful yield. Using in vitro selection, we have identified Mg2+- and Zn2+-dependent deoxyribozymes that simultaneously fulfill all four of these criteria. The new deoxyribozymes operate under practical incubation conditions and have modest RNA substrate sequence requirements, specifically D downward arrowRA for 9DB1 and A downward arrowR for 7DE5 (D = A, G, or U; R = A or G). These requirements are comparable to those of deoxyribozymes such as 10-23 and 8-17, which are already widely used as biochemical tools for RNA cleavage. We anticipate that the 9DB1 and 7DE5 deoxyribozymes will find immediate practical application for RNA ligation.     

Principles of rapid polymerase chain reactions: mathematical modeling and experimental verification

Polymerase chain reaction (PCR) is an important diagnostic tool for the amplification of DNA. The PCR process can be treated as a problem in biochemical engineering. This study focuses on the development of a mathematical model of the polymerase chain reaction. The PCR process consists of three steps: denaturation of target DNA, annealing of sequence-specific oligonucleotide primers and the enzyme-catalyzed elongation of the annealed complex (primer:DNA:polymerase). The denaturation step separates the double strands of DNA; this model assumes denaturation is complete. The annealing step describes the formation of a primer-fragment complex followed by the attachment of the polymerase to form a ternary complex. This step is complicated by competitive annealing between primers and incomplete fragments including primer-primer reactions. The elongation step is modeled by a stochastic method. Species that compete during the elongation step are deoxynucleotide triphosphates dCTP, dATP, dTTP, dGTP, dUTP, and pyrophosphate. Thermal deamination of dCTP to form dUTP is included in the model. The probability for a species to arrive at the active site is based on its molar fraction. The number of random insertion events depends on the average processing speed of the polymerase and the elongation time of the simulation. The numerical stochastic experiment is repeated a sufficient number of times to construct a probability density distribution (PDF). The moment of the PDF and the annealing step products provide the product distribution at the end of the elongation step. The overall yield is compared to six experimental values of the yield. In all cases the comparisons are very good.     

Synthesis and antimalarial effects of N,N-dialkyl-6-(substituted phenyl)-1,2,4,5-tetrazin-3-amines

The synthesis of a series of N,N-dialkyl-6-(substituted phenyl)-1,2,4,5-tetrazin-3-amines (IV) by two routes is described. The first route (Scheme I) involved the oxidative cyclization of formazans (II) to 3-bromo-6-(substituted phenyl)-1,2,4,5-tetrazines (III), followed by treatment with amines. The second (Scheme II) utilized the treatment of 3-(methylthio)-6-(substituted phenyl)-1,2,4,5-tetrazines (VII) with amines to provide the desired products. The intermediate 3-(methylthio)-6-(substituted phenyl)-1,2,4,5-tetrazines (VII) were obtained by thiobenzoylation of hydrazinecarbohydrazonothioic acid methyl ester with [[(substituted phenyl)thioxomethyl]thio]-acetic acids (V) to afford the 1,2-dihydro-3-(methylthio)-6-(substituted phenyl)-1,2,4,5-tetrazines (VI). Oxidation with bromine in acetic acid provided the desired intermediates. The target 6-(substituted phenyl)-1,2,4,5-tetrazin-3-amines (IV) displayed modest antimalarial activity.     

Novel Copolymers of Styrene and Some Ring‐Substituted 2‐Cyano‐N,N‐Dimethyl‐3‐Phenyl‐2‐Propenamides

Electrophilic trisubstituted ethylene monomers, ring‐substituted 2‐cyano‐N,N‐dimethyl‐3‐phenyl‐2‐propenamides, RC₆H₄CH?C(CN)CON(CH₃)₂ (where R is 4‐(CH₃)₂N, 4‐CH₃CO₂, 4‐CH₃CONH, 2‐CN, 3‐CN, 4‐CN, 4‐(C₂H₅)₂N) were synthesized by potassium hydroxide catalyzed Knoevenagel condensation of ring‐substituted benzaldehydes and N,N‐dimethyl cyanoacetamide, and characterized by CHN elemental analysis, IR, ¹H‐ and ¹³C‐NMR. Novel copolymers of the ethylenes and styrene were prepared at equimolar monomer feed composition by solution copolymerization in the presence of a radical initiator, ABCN at 70°C. The composition of the copolymers was calculated from nitrogen analysis, and the structures were analyzed by IR, ¹H and ¹³C NMR, GPC, DSC, and TGA. High T_g of the copolymers in comparison with that of polystyrene indicates a substantial decrease in chain mobility of the copolymer due to the high dipolar character of the trisubstituted ethylene monomer unit. The gravimetric analysis indicated that the copolymers decompose in the 300–450°C range.