New method for determining size of critical nucleus of fibril formation of polypeptide chains

A new method for determining the size of critical nucleus of fibril formation of polypeptide chains is proposed. Based on the hypothesis that the fibril grows by addition of a nascent peptide to the preformed template, the nucleus size N(c) is defined as the number of forming template peptides above which the time to add a new monomer becomes independent of the template size. Using lattice models one can show that our method and the standard method which is based on calculation of the free energy, provide the same result for N(c).     

On the origin of the unusual behavior in the stretching of single-stranded DNA

Force-extension curves (FECs), which quantify the response of a variety of biomolecules subject to mechanical force (f), are often quantitatively fit using worm-like chain (WLC) or freely jointed chain (FJC) models. These models predict that the chain extension, x, normalized by the contour length increases linearly at small f and at high forces scale as x ~ (1 - f(-α)), where α = 0.5 for WLC and unity for FJC. In contrast, experiments on single-stranded DNA (ssDNA) show that over a range of f and ionic concentration, x scales as x ~ ln f, which cannot be explained using WLC or FJC models. Using theory and simulations we show that this unusual behavior in FEC in ssDNA is due to sequence-independent polyelectrolyte effects. We show that the x ~ ln f arises because in the absence of force the tangent correlation function, quantifying chain persistence, decays algebraically on length scales on the order of the Debye length. Our theory, which is most appropriate for monovalent salts, quantitatively fits the experimental data and further predicts that such a regime is not discernible in double-stranded DNA.     

Synthesis and NMR Spectroscopic Characteristics of a Series of Hydrazide‐Hydrazones Containing Furoxan Ring Derived from Isoeugenoxyacetic Acid

A novel hydrazide, 2‐methoxy‐4‐(3‐methyfuroxan‐4‐yl)‐5‐nitrophenoxyacetylhydrazine, was prepared from isoeugenoxyacetic acid. The hydrazide was condensed with aromatic aldehydes to give a series of 20 hydrazide‐hydrazones incorporating the furoxan ring. The structure of obtained compounds was determined by analytical and spectral data. It was demonstrated that the two sets of resonance signals in the ¹H‐NMR and ¹³C‐NMR spectra of the examined hydrazide‐hydrazones are caused by E_N–C(O) and Z_N–C(O) conformers. The energy barriers for the conformation exchange were determined by ¹H‐NMR‐measurement at various temperatures. Among seven tested hydrazide‐hydrazones, four compounds exhibit inhibition activities in vitro on human epidermis carcinoma (KB‐cell) with IC₅₀ = 47, 68, 79, and 103 μg/mL.     

Electronic structure and thermochemical properties of silicon-doped lithium clusters Li(n)Si0/+, n = 1-8: new insights on their stability

A theoretical investigation on small silicon-doped lithium clusters Li(n)Si with n = 1-8, in both neutral and cationic states is performed using the high accuracy CCSD(T)/complete basis set (CBS) method. Location of the global minima is carried out using a stochastic search method and the growth pattern of the clusters emerges as follows: (i) the species Li(n)Si with n ≤ 6 are formed by directly binding one Li to a Si of the smaller cluster Li(n-1)Si, (ii) the structures tend to have an as high as possible symmetry and to maximize the coordination number of silicon. The first three-dimensional global minimum is found for Li(4)Si, and (iii) for Li(7)Si and Li(8)Si, the global minima are formed by capping Li atoms on triangular faces of Li(6)Si (O(h)). A maximum coordination number of silicon is found to be 6 for the global minima, and structures with higher coordination of silicon exist but are less stable. Heats of formation at 0 K (Δ(f)H(0)) and 298 K (Δ(f)H(298)), average binding energies (E(b)), adiabatic (AIE) and vertical (VIE) ionization energies, dissociation energies (D(e)), and second-order difference in total energy (Δ(2)E) of the clusters in both neutral and cationic states are calculated from the CCSD(T)/CBS energies and used to evaluate the relative stability of clusters. The species Li(4)Si, Li(6)Si, and Li(5)Si(+) are the more stable systems with large HOMO-LUMO gaps, E(b), and Δ(2)E. Their enhanced stability can be rationalized using a modified phenomenological shell model, which includes the effects of additional factors such as geometrical symmetry and coordination number of the dopant. The new model is subsequently applied with consistency to other impure clusters Li(n)X with X = B, Al, C, Si, Ge, and Sn.     

Singly and doubly lithium doped silicon clusters: geometrical and electronic structures and ionization energies

The geometric structures of neutral and cationic Si(n)Li(m)(0/+) clusters with n = 2-11 and m = 1, 2 are investigated using combined experimental and computational methods. The adiabatic ionization energy and vertical ionization energy (VIE) of Si(n)Li(m) clusters are determined using quantum chemical methods (B3LYP/6-311+G(d), G3B3, and CCSD(T)/aug-cc-pVxZ with x = D,T), whereas experimental values are derived from threshold photoionization experiments in the 4.68-6.24 eV range. Among the investigated cluster sizes, only Si(6)Li(2), Si(7)Li, Si(10)Li, and Si(11)Li have ionization thresholds below 6.24 eV and could be measured accurately. The ionization threshold and VIE obtained from the experimental photoionization efficiency curves agree well with the computed values. The growth mechanism of the lithium doped silicon clusters follows some simple rules: (1) neutral singly doped Si(n)Li clusters favor the Li atom addition on an edge or a face of the structure of the corresponding Si(n)(-) anion, while the cationic Si(n)Li(+) binds with one Si atom of the bare Si(n) cluster or adds on one of its edges, and (2) for doubly doped Si(n)Li(2)(0/+) clusters, the neutrals have the shape of the Si(n+1) counterparts with an additional Li atom added on an edge or a face of it, while the cations have both Li atoms added on edges or faces of the Si(n)(-) clusters.     

Fourteen-electron ring model and the anomalous magnetic circular dichroism of meso-triarylsubporphyrins

The MCD spectra of meso-triarylsubporphyrins show a sign anomaly which is correlated with the acceptor properties of the aryl substituent. From the spectra, magnetic moments of the excited states are determined. In the context of a simplified orbital model, the sign change is attributed to the quenching of the magnetic moment of the LUMO by acceptor orbitals of the substituent. The actual calculation of this moment presents a major challenge to computational methods. It is shown that wave function techniques based on CASSCF underestimate the covalency effects that are responsible for the quenching. In contrast, a CI method based on DFT orbitals yields excellent results, which fully support the orbital model.     

Generalized Cauchy problems involving nonlocal and impulsive conditions

We study the abstract Cauchy problem involving a class of nonlinear differential inclusions, with impulsive and nonlocal conditions. By using MNC estimates, the existence result and continuous dependence on initial data of the solution set are proved.     

A New Invariant of Quadratic Lie Algebras

We define a new invariant of quadratic Lie algebras and give a complete study and classification of singular quadratic Lie algebras, i.e. those for which the invariant does not vanish. The classification is related to O(n)-adjoint orbits in $\mathfrak{o}(n)$ .     

Identification of a TGBA liquid crystal phase via its defects

We have shown that cholesteryl nonanoate, a thermotropic compound which is well known to exhibit pretransitional effects at the smectic A (SmA) cholesteric (N*) transition (W.L. McMillan, Phys. Rev. A 4, 1238 (1971); 6, 936 (1972)), has in fact a TGBA phase in between. Our arguments rely on the observation of new TGBA defects, either in Robinson spherulites cooled from the N* phase or in free-standing films. The same new defects can be obtained in a well-documented TGBA phase of a tolane compound. We analyze qualitatively the TGBA defects in both geometries, in particular their relation to the disclination radius of the N* Robinson spherulites. Received 12 February 2001     

Commensurate and incommensurate hydrogen bonds. An exercise in crystal engineering.

Ureas characteristically form one-dimensional hydrogen-bonded alpha-networks with a repeat distance of about 4.60 A. Oxamides form similar alpha-networks with a longer 5.05 A repeat distance. The urea of glycine and the oxamide of glycine were each cocrystallized with a series of four bipyridines, including two urea derivatives and two oxamide derivatives. This series of eight cocrystals was studied by X-ray diffraction in order to see what would happen when molecules that would normally form alpha-networks with incommensurate distances were forced into the same crystal. The two all-urea crystals and the two all-oxamide crystals contained the expected alpha-networks with repeat distances in accordance with normal urea or oxamide values. Four of the crystals were mixed, containing both oxamide and urea molecules. Three consisted of two-dimensional beta-networks with alternating parallel urea and oxamide subnetworks. The repeat distances averaged 4.87 A, a value close to the value expected for oxamides, but shorter than any previously observed examples. In the fourth mixed crystal, the urea alpha-network formed with a normal urea repeat distance, but the oxamide network did not form, the oxamide adopting an unusual molecular conformation that maximizes intramolecular hydrogen bonds instead.