Conformations of cycloundecane

Cycloundecane (1) was shown to exist at -183.1 degrees C as a mixture of the [12323] (approximately 59%) and [335] (approximately 41%) conformations. Populations were determined from the (13)C NMR spectrum, and assignments were based on the (13)C spectra, calculated free energies and chemical shifts, and information from the literature, including X-ray studies of solid derivatives and calculated barriers.     

Conformations of Biopolymers

Discussion of the history of biopolymers is focused on proteins and polypeptides. Rubber elasticity is discussed from the early days onward, when the first and second laws of thermodynamics were established. Insight in the elasticity of elastin, an amorphous protein occurring in ligaments and arteries, is followed against this background. Denatured proteins also fit in this category. At present, the random-coil state that underlies the elasticity is rather well understood as a result of the new methods of analyzing the dimensions in terms of the conformations of the residues. Subsequently, the discovery of the α-helix, as well as that of the other helical structures of DNA and collagen, is described. The conversion to random coils is followed with emphasis on our insight into the cooperative nature of the transition. Finally, the least understood globular proteins are considered. Major progress was made with the successful analysis of x-ray patterns. The native state is characterized by closely packed residues in complicated, but unique, patterns. The conversion to random coils (denaturation) is sharp, not unlike a phase transition. Although the native state is rather closely packed, some mobility still exists. The implication of this mobility for enzymatic action is hinted at.     

Conformations of antipyrines

Reliable conformational energetics is essential in interpreting and predicting structures of molecular crystals. We provide a combined density functional theory (DFT)-structural database study, demonstrating that this combination can be used as a foundation for this purpose. A subtle problem of nitrogen pyramidalization is used as the example in antipyrines, a group of bioactive molecules. Nitrogen pyramidalization on the two adjacent sp(3) nitrogens directly affects the orientation of the methyl and phenyl substituents, which tend toward opposite sides of the heteroaromatic ring, affecting crystal packing. Accordingly, the overwhelming majority of the structures of antipyrines in the Cambridge Structural Database (CSD) are either nearly planar or have substituents on the opposite sides of the ring. Recent powder X-ray structures by Lemmerer et al. identified propyphenazone, an antipyrine, to have two substituents on the same side in an apparently sterically crowded conformation. We show that the new structure, although counterintuitive, is not an outlier on the conformational map. A distribution of the conformations of all antipyrines listed in the CSD is in good agreement with the computed conformational map. We also examine the role of the hysteretic property of the phenyl torsion in propyphenazone and its indirect effects on its overall conformation.     

Synthesis of cyclobutane serine analogues

In this paper, we describe a thermal [2 + 2] cycloaddition involving 2-acylaminoacrylates as electron-poor acceptor alkenes, a reaction that involves a Michael-Dieckmann-type process. The reaction gives rise to a new substituted cyclobutane skeleton that can be transformed into amino acid derivatives. For example, a number of transformations were carried out to give the two pairs of stereoisomers of the 2-hydroxycyclobutane-alpha-amino acid serine analogue (c(4)Ser); compounds 22 and 23. This synthesis covers a gap in knowledge in the broad field of restricted amino acids.     

Isoxazolidines with a cyclobutane link

N-(Phenacylidene)- and N-(arylaminooxoethylidene)aniline N-oxides form 11 adducts with methylenecyclobutane. The addition of the nitrones proceeds specifically and leads to substituted isoxazolidines in high yields. In the case of N-(phenylaminooxoethylidene)aniline N-oxide it was shown that 1-methylcyclobutene and bicyclobutylidene also undergo cycloaddition to give isoxazolidines.Translated from Khimiya Geterotsiklicheskikh Soedinenii, No. 10, pp. 1316–1318, October, 1982.     

Conformations of hydrophobic polyelectrolytes

Recent studies on the (hypercoiled) compact conformation and the pH-induced conformational transition to the extended coil of the hydrophobic poly(acids or bases), which have been well used in industrial and medical circles, are summarized, especially on the basis of our studies on poly(α-alkyl acrylic acids) and maleic acid copolymers with hydrophobic aromatic monomers. The stability of the compact conformation and values of various thermodynamic parameters of the transition of the hydrophobic polyelectrolytes suggest the importance of hydrophobic interaction among the side chains to form the compact conformation. Characterization of various physicochemical methods, including ¹H-NMR measurements, gives a model of the compact conformation with a more expanded structure than in globular proteins, a free-draining property of the solvent, the conformation fluctuation, etc. Also, the apparent two-state character of each segment in the transition region, a life-time in each state and the cooperative parameter for the compact form formation are discussed.A review of our conformational studies on the hydrophobic-hydrophilic polypeptides is also given. For the anion-induced conformation transition in basic homopoly(α-amino acids), hydrophobic characters of the anion and the side chain in the polypeptide are shown to be important, especially in terms of solvation. The difference in the induced conformation by the anion between random and alternating basic copolypeptides is explained by introducing a model which shows the importance of the sequence of hydrophobic and hydrophilic residues in the polypeptide to induce the ordered conformation of the anions. Also, we attempt to explain the difference between the induction of ordered conformation in the basic homo- or copolypeptide in reversed micelles with a large sulfonate (AOT) vs. that in aqueous AOT in terms of the hydrophobic character of the side chains in the polypeptides, AOT and the medium.     

Conformations of hydrophobic polyelectrolytes

Recent studies on the (hypercoiled) compact conformation and the pH-induced conformational transition to the extended coil of the hydrophobic poly(acids or bases), which have been well used in industrial and medical circles, are summarized, especially on the basis of our studies on poly(alpha-alkyl acrylic acids) and maleic acid copolymers with hydrophobic aromatic monomers. The stability of the compact conformation and values of various thermodynamic parameters of the transition of the hydrophobic polyelectrolytes suggest the importance of hydrophobic interaction among the side chains to form the compact conformation. Characterization of various physicochemical methods, including 1H-NMR measurements, gives a model of the compact conformation with a more expanded structure than in globular proteins, a free-draining property of the solvent, the conformation fluctuation, etc. Also, the apparent two-state character of each segment in the transition region, a life-time in each state and the cooperative parameter for the compact form formation are discussed. A review of our conformational studies on the hydrophobic-hydrophilic polypeptides is also given. For the anion-induced conformation transition in basic homopoly(alpha-amino acids), hydrophobic characters of the anion and the side chain in the polypeptide are shown to be important, especially in terms of solvation. The difference in the induced conformation by the anion between random and alternating basic copolypeptides is explained by introducing a model which shows the importance of the sequence of hydrophobic and hydrophilic residues in the polypeptide to induce the ordered conformation of the anions. Also, we attempt to explain the difference between the induction of ordered conformation in the basic homo- or copolypeptide in reversed micelles with a large sulfonate (AOT) vs. that in aqueous AOT in terms of the hydrophobic character of the side chains in the polypeptides, AOT and the medium.     

Positive photosensitive polyimides with cyclobutane structure

A new family of positive photosensitive polyimide (PPI) systems composed of solvent soluble polyimides (Pls) with cyclobutane (CBDA) structures and diazonaphthoquinone compounds (DNQ) has been prepared. Heat and catalytic imidizations were carried out to obtain CBDA Pls; the former was better than the latter in controlling the molecular weight of the Pl. The ? OH groups in the Pls were easily acetylated during catalytic imidization, so ? COOH groups were selected as weak acidic groups in the Pls. The ? COOH groups were also effective in giving the Pls an alkaline solubility. Therefore, Pls having ? COOH groups were superior to those having ? OH groups for PPI systems. The photosensitive properties of various PPl systems containing ? COOH were found to vary with the fraction of ? COOH groups in the Pls, the content of DNQ in the systems, and the molecular weight of the Pls.     

Population Shuffling of Protein Conformations

Motions play a vital role in the functions of many proteins. Discrete conformational transitions to excited states, happening on timescales of hundreds of microseconds, have been extensively characterized. On the other hand, the dynamics of the ground state are widely unexplored. Newly developed high‐power relaxation dispersion experiments allow the detection of motions up to a one‐digit microsecond timescale. These experiments showed that side chains in the hydrophobic core as well as at protein–protein interaction surfaces of both ubiquitin and the third immunoglobulin binding domain of protein G move on the microsecond timescale. Both proteins exhibit plasticity to this microsecond motion through redistribution of the populations of their side‐chain rotamers, which interconvert on the picosecond to nanosecond timescale, making it likely that this “population shuffling” process is a general mechanism.     

Detailed dynamics of the photodissociation of cyclobutane

Semiclassical electron-radiation-ion dynamics simulations are reported for the photodissociation of cyclobutane into two molecules of ethylene. The results clearly show the formation of the tetramethylene intermediate diradical, with dissociation completed in approximately 400 fs. In addition, the potential energy surfaces of the electronic ground state and lowest excited-state were calculated at the complete-active-space self-consistent-field/multireference second-order perturbation theory (CASSCF/MRPT2) level with 6-31G* basis sets, along the reaction path determined by the dynamics simulations. There are well-defined energy minima and maxima in the intermediate state region. It is found that both C-C-C bond bending and rotation of the molecule (around the central C-C bond) have important roles in determining the features of the potential energy surfaces for the intermediate species. Finally, the simulations and potential energy surface calculations are applied together in a discussion of the full mechanism for cyclobutane photodissociation.     

Biological consequences of cyclobutane pyrimidine dimers.

In the skin many molecules may absorb ultraviolet (UV) radiation upon exposure. In particular, cellular DNA strongly absorbs shorter wavelength solar UV radiation, resulting in various types of DNA damage. Among the DNA photoproducts produced the cyclobutane pyrimidine dimers (CPDs) are predominant. Although these lesions are efficiently repaired in the skin, this CPD formation results in various acute effects (erythema, inflammatory responses), transient effects (suppression of immune function), and chronic effects (mutation induction and skin cancer). The relationships between the presence of CPD in skin cells and the subsequent biological consequences are the subject of the present review.     

Structure-mechanochemical activity relationships for cyclobutane mechanophores

Ultrasound activation of mechanophores embedded in polymer backbones has been extensively studied of late as a method for realizing chemical reactions using force. To date, however, there have been few attempts at systematically investigating the effects of mechanophore structure upon rates of activation by an acoustic field. Herein, we develop a method for comparing the relative reactivities of various cyclobutane mechanophores. Through the synthesis and ultrasonic irradiation of a molecular weight series of poly(methyl acrylate) polymers in which each macromolecule has a single chain-centered mechanophore, we find measurable and statistically significant shifts in molecular weight thresholds for mechanochemical activation that depend on the structure of the mechanophore. We also show that calculations based on the constrained geometries simulate external force method reliably predict the trends in mechanophore reactivity. These straightforward calculations and the experimental methods described herein may be useful in guiding the design and the development of new mechanophores for targeted applications.