Axially chiral thioamides of acrylic acid: correlated and uncorrelated internal rotations

Kinetics and activation parameter analysis for the prebiotic oligocytidylate formation on Na(+)-montmorillonite at 0-100 degrees C

The kinetic analysis of the temperature dependence of the formation of oligocytidylate (oligo(C)) from the 5'-monophosphorimidazolide moiety of cytidine (ImpC) in the presence of Na (+)-montmorillonite (Na (+)-Mont) catalyst has been carried out at 0-100 degrees C. The rate constants for the formation of oligo(C), hydrolysis of ImpC with and without Na (+)-Mont and degradation of oligo(C) were determined. The apparent activation parameters were 30.8 +/- 3.9 kJ mol (-1) ( Ea), 28.3 +/- 4.0 kJ mol (-1) (Delta H++), and -231 +/- 13 J mol (-1) K (-1) (Delta S++) for the formation of the 2-mer; 45.6 +/- 2.9 kJ mol (-1) ( Ea), 43.0 +/- 3.0 kJ mol (-1) (Delta H++), -164 +/- 10 J mol (-1) K (-1) (Delta S++) for the 3-mer; and 45.2 +/- 0.6 kJ mol (-1) ( Ea), 42.7 +/- 0.7 kJ mol (-1) (Delta H++), -159 +/- 2 J mol (-1) K (-1) (Delta S++) for the 4-mer in the presence of Na (+)-Mont. An increasing trend for the rate constants for the formation of oligo(C) in the order 2-mer << 3-mer <4-mer was observed at high temperatures, which is consistent with that observed at low temperatures. These analyses implied for the first time that the associate formation between an activated nucleotide monomer and an elongating oligonucleotide prior to the phosphodiester bond formation during the elongation of an oligonucleotide on a clay surface would be based on the interaction between the two reactants at the phosphoester and/or ribose moieties rather than at the nucleotide bases. The hydrolysis rate of ImpC at 25-100 degrees C was 5.3-10.6 times greater in the presence of Na (+)-Mont than in its absence. Although the degradation of oligo(C) in the presence of Na (+)-Mont was slower than the formation of the 3-mer and longer oligo(C) on Na (+)-Mont, its yield decreased with temperature. This is mainly because the ratios of the rate constant of the 2-mer formation to those of ImpC hydrolysis and the 3-mer and 4-mer formation decrease with an increase in temperature, which is attributed to the enthalpy and entropy changes for the formation of the 2-mer. This trend resembles the case of the template-directed formation of oligo(G) on a poly(C) template but is different from the Pb (2+)-ion-catalyzed oligo(C) formation. According to the kinetics and activation parameter analyses regarding the clay reaction and other prebiotic polymerase models, the possible pathways for the oligonucleotide formation are discussed and compared.

Synthetic molecular motors and mechanical machines

The widespread use of controlled molecular-level motion in key natural processes suggests that great rewards could come from bridging the gap between the present generation of synthetic molecular systems, which by and large rely upon electronic and chemical effects to carry out their functions, and the machines of the macroscopic world, which utilize the synchronized movements of smaller parts to perform specific tasks. This is a scientific area of great contemporary interest and extraordinary recent growth, yet the notion of molecular-level machines dates back to a time when the ideas surrounding the statistical nature of matter and the laws of thermodynamics were first being formulated. Here we outline the exciting successes in taming molecular-level movement thus far, the underlying principles that all experimental designs must follow, and the early progress made towards utilizing synthetic molecular structures to perform tasks using mechanical motion. We also highlight some of the issues and challenges that still need to be overcome.

A redox-mediated molecular brake: dynamic NMR study of 2-[2-(methylthio)phenyl]isoindolin-1-one and S-oxidized counterparts

A redox-mediated molecular brake based on the sulfide-sulfoxide redox cycle is illustrated by modulation of the rotation rate of an N-Ar "shaft" by varying the oxidation state of sulfur in 2-[2-(sulfur-substituted)phenyl]isoindolin-1-ones. N-Ar rotational barriers in methylsulfinyl (2) and methylsulfonyl (3) derivatives (13.6 kcal mol(-1)) are approximately 5 kcal mol(-1) higher than sulfide 1. Rate reduction for N-Ar rotation is approximately 10(4) s(-1) (280 K) upon oxidation. Correlated N-pyramidalization/N-Ar rotation reduces the effectiveness of the brake by decreasing the energy barrier to N-Ar bond rotation.

Chiroptical detection during liquid chromatography: Deconvolution of overlapping peaks of enantiomers and its applications

The peaks of enantiomers in liquid chromatography (LC) frequently overlap for different reasons. The experimental curve can be deconvolved, i.e., transformed into the two curves of the enantiomers, without any assumption concerning their peak shapes. Besides the usual photometric UV detection, resulting in absorbance A, polarimetric or circular dichroic detection is required, providing the rotation 90 degree angle alpha or the differential absorbance DeltaA, respectively. The accuracy of the ratio alpha/A or DeltaA/A for the pure enantiomers is essential for the quality of the deconvolution. The determination of these ratios, using the overlapping peaks, and the subsequent computer deconvolution of the latter are discussed in more detail than in the earlier publications, e.g. Ref. 1 concerning this particular method. The computer program developed for this purpose is characterized. A condition is given which limits the availability of ratios and, therefore, the possibility of deconvolution. Several novel examples are described which stem from the following fields of application of deconvolved peaks: actual optical purities during LC (on-line analysis), overall optical purity of a sample, purities of chromatographic peaks, and, finally, enantiomerization during LC.

Stereodynamics of bond rotation in tertiary aromatic amides

The degree to which the rotations about the C-N and Ar-CO bonds of aromatic amides occur in a concerted manner was investigated by a variety of NMR and kinetic techniques. Otherwise complex kinetic analyses were simplified by exploiting symmetry and asymmetry in the N-substituents of amides. In 2-unsubstituted 1-naphthamides bearing branched N-substituents, most conformational changes about the amide group were by correlated rotation, though uncorrelated Ar-CO rotation also occurred to some extent. In 2-substituted 1-naphthamides, correlated rotation accounted for all of the Ar-CO rotations, though a significant amount of uncorrelated C-N rotation also occurred. Naphthamides bearing branched N-substituents thus turn out to be efficient molecular gears: Compound 12 showed almost no gear slippage.

Can we predict the conformational preference of amides?

To what extent, if any, is the conformation of secondary amides revealed by theory? This question has now been addressed by computational methods using calculations at the B3LYP/6-31G level of theory and (1)H NMR spectroscopy. Both gas-phase and solvent studies predict a Z-anti conformation to be the lowest in energy for an evaluated series of acetamides. Moreover, Z-anti conformations may also be inferred from the chemical shifts of the N-CH alpha protons determined by NMR spectroscopy. Thus, a proton situated anti to the N-H proton consistently appears approximately 0.8 ppm further downfield than a proton situated gauche to the N-H proton. This finding, which could only be derived by using the DFT calculations of conformational preference as a guide to interpret the NMR data, might prove to be useful as a simple and convenient methodology for establishing amide conformation experimentally.

Using symmetry to monitor geared bond rotation in aromatic amides by dynamic NMR

Dynamic NMR proves that the fastest interconversion between conformers of simple tertiary aromatic amide 3 is racemization via a geared (correlated) rotation of both the Ar-CO and N-CO bonds. The symmetry of 3 is such that correlated and noncorrelated rotations are easily distinguishable, even without assignment of the NMR spectrum, simply by observing the number of peaks taking part in the exchange.