Low-energy states of a semiflexible polymer chain with attraction and the whip-toroid transitions

We establish a general model for the whip-toroid transitions of a semiflexible homopolymer chain using the path integral method and the O3 nonlinear sigma model on a line segment with the local inextensibility constraint. We exactly solve the energy levels of classical solutions and show that some of its classical configurations exhibit toroidal forms, and the system has phase transitions from a whip to toroidal states with a conformation parameter c = (W2l)(L2pi)2. We also discuss the stability of the toroid states and propose the low-energy effective Green's function. Finally, with the finite size effect on the toroid states, predicted toroidal properties are successfully compared to experimental results of DNA condensation.     

Semiflexible grafted polymers in poor solvents: toroidal, archway, and tower micelles

We study a system of grafted semiflexible polymers in a poor solvent which form toroidal or rodlike conformations in the bulk. However, because of the physical constraint of surface grafting, macrophase separation is inhibited and a number of different polymer aggregates (or micelles) form which can be related to the chains' stiffness and their affinity for each other. In contrast to the fully flexible Gaussian case, we observe a number of novel micelle structures, including tower micelles, archway micelles, and spider micelles. We also attempt to develop a phase diagram for the occurrence of these structures with respect to the variables of chain length, chain stiffness, and polymer grafting density.     

Rigidity effect on phase behavior of symmetric ABA triblock copolymers: A Monte Carlo simulation

The phase behavior of symmetric ABA triblock copolymers containing a semiflexible midblock is studied by lattice Monte Carlo simulation. As the midblock evolves from a fully flexible state to a semiflexible state in terms of increase in its persistence length, different phase behaviors are observed while cooling the system from an infinite high temperature to a temperature below T(ODT) (order-disorder transition temperature). Within the midblock flexibility range we studied (l(p)N(c)相似文献   

Association-dissociation equilibrium of loop structures in single-chain folding into a toroidal condensate

Recently, it has been revealed that a semiflexible polyelectrolyte chain can form a partially folded conformation stably as a result of an electrostatic interaction. Interestingly, there are cases where the appearance of this structure requires a high-salt condition of a solution. In order to solve this problem, we consider the double equilibrium of the formation of loops and their aggregation on a single-chain polymer. First, an aggregate with a typical surface energy is examined as a test case. The basic nature of the folding transition is discussed with regard to the chemical potential of loop structures. Next, we consider a charged aggregate for which the interior is completely neutralized by counter ions. In this model, a partially folded chain appears with a high-salt condition. Based on this model, screened interactions between surface charges and a toroidal shape of a folded structure are considered essential factors bihind this phenomenon.     

Morphological variation in a toroid generated from a single polymer chain

A single semiflexible polymer chain folds into a toroidal object under poor solvent conditions. In this study, we examined the morphological change in such a toroidal state as a function of the cross-sectional area and stiffness of the chain together with the surface energy, which characterizes the segmental interaction parameter. Changes in the thickness and outer/inner radius on a toroid are interpreted in terms of these parameters. Our theoretical expectation corresponds to the actual morphological changes in a single giant DNA molecule as observed by electron microscopy.     

Synthesis and In Vitro Antimicrobial Screening of New Azetidin‐2‐ones of 5‐Ethyl Pyridine‐2‐ethanol

A new series of azetidinones is described in this paper; Schiff base ( 4a , 4b , 4c , 4d , 4e , 4f , 4g , 4h , 4i , 4j , 4k , 4l , 4m , 4n , 4o ) were synthesized from 4‐[2‐(5‐ethylpyridin‐2‐yl)ethoxy]benzaldehyde, which was used to synthesize azetidinones ( 5a , 5b , 5c , 5d , 5e , 5f , 5g , 5h , 5i , 5j , 5k , 5l , 5m , 5n , 5o ), ( 6a , 6b , 6c , 6d , 6e , 6f , 6g , 6h , 6i , 6j , 6k , 6l , 6m , 6n , 6o ), and ( 7a , 7b , 7c , 7d , 7e , 7f , 7g , 7h , 7i , 7j , 7k , 7l , 7m , 7n , 7o ). The structures of the synthesized compounds were assigned on the basis of elemental analysis, IR, ¹H NMR, and ¹³C NMR spectral data. All the products were screened against different strains of bacteria and fungi. Most of the monosubstituted and disubstituted chloro groups are more effective to both bacterial and fungal species in comparison with the standard drugs.     

Stretching semiflexible polymer chains: evidence for the importance of excluded volume effects from Monte Carlo simulation

Semiflexible macromolecules in dilute solution under very good solvent conditions are modeled by self-avoiding walks on the simple cubic lattice (d = 3 dimensions) and square lattice (d = 2 dimensions), varying chain stiffness by an energy penalty ε(b) for chain bending. In the absence of excluded volume interactions, the persistence length l(p) of the polymers would then simply be l(p) = l(b)(2d - 2)(-1)q(b) (-1) with q(b) = exp(-ε(b)/k(B)T), the bond length l(b) being the lattice spacing, and k(B)T is the thermal energy. Using Monte Carlo simulations applying the pruned-enriched Rosenbluth method (PERM), both q(b) and the chain length N are varied over a wide range (0.005 ≤ q(b) ≤ 1, N ≤ 50,000), and also a stretching force f is applied to one chain end (fixing the other end at the origin). In the absence of this force, in d = 2 a single crossover from rod-like behavior (for contour lengths less than l(p)) to swollen coils occurs, invalidating the Kratky-Porod model, while in d = 3 a double crossover occurs, from rods to Gaussian coils (as implied by the Kratky-Porod model) and then to coils that are swollen due to the excluded volume interaction. If the stretching force is applied, excluded volume interactions matter for the force versus extension relation irrespective of chain stiffness in d = 2, while theories based on the Kratky-Porod model are found to work in d = 3 for stiff chains in an intermediate regime of chain extensions. While for q(b) ? 1 in this model a persistence length can be estimated from the initial decay of bond-orientational correlations, it is argued that this is not possible for more complex wormlike chains (e.g., bottle-brush polymers). Consequences for the proper interpretation of experiments are briefly discussed.     

Persistence lengths and structure factors of wormlike polymers under confinement

The behavior of semiflexible chains modeling wormlike polymers such as DNA and actin in confined spaces was explored by coarse-grained Monte Carlo simulations. The persistence length P, mean end-to-end distance R2, mean radius of gyration Rg2, and the size ratio R2/Rg2 were computed for chains in slits, cylinders, and spheres. It was found that the intrinsic persistence length of a free chain undergoes on confinement substantial alteration into the apparent persistence length. The qualitative differences were found in trends of the apparent persistence lengths between slits and cylinders on one side and spheres on the other side. The quantities P, R2, Rg2, and R2/Rg2 display similar dependences upon squeezing the chains in nanopores. The above quantities change nonmonotonically with confinement in slits and cylinders, whereas they drop smoothly with decreasing radius of a sphere. For elongation of a chain in a cylinder, two regimes corresponding to strong and moderate confinements were found and compared to experiments and predictions of the blob and Odijk theories. In a spherical cavity, the toroidal chain structure with a hole in the center was detected under strong confinements. The scattering form factor S(q) computed for semiflexible confined chains revealed three regimes of behavior in a slit and a cylinder that matched up well with the scaling theory. The complex form of the function S(q) computed for a sphere was interpreted as a sign of the toroidal structure. A reasonable agreement was found between the simulations and measurements of DNA and actin filaments, confined in nano- and microfluidic channels and spherical droplets, pertaining to the changes of the persistence lengths, chain elongation, and toroidal structure formation.     

Synthesis and Biological Activities of Some New Annulated Pyrazolopyranopyrimidines and Their Derivatives Containing Indole Nucleus

The key intermediate 6‐amino‐3‐methyl‐4‐aryl‐1‐(5′‐substituted‐3′‐phenyl‐1H‐indol‐2′‐carbonyl)‐1,4‐dihydropyrano[2,3‐c]pyrazol‐5‐carbonitriles 3a , 3b , 3c , 3d , 3e , 3f , 3g , 3h , 3i , 3j , 3k , 3l , 3m , 3n , 3o were prepared by cyclocondensation of 3‐methyl‐1‐(5′‐substituted‐3′‐phenyl‐1H‐indol‐2′‐carbonyl)‐5‐(4H)‐pyrazolones 1a , 1b , 1c with arylidine derivatives of malononitrile 2a , 2b , 2c , 2d , 2e . The compounds 3a , 3b , 3c , 3d , 3e , 3f , 3g , 3h , 3i , 3j , 3k , 3l , 3m , 3n , 3o were subjected to cyclocondensation reaction with formamide, formic acid, and carbon disulfide to afford the title compounds 4a , 4b , 4c , 4d , 4e , 4f , 4g , 4h , 4i , 4j , 4k , 4l , 4m , 4n , 4o , 5a , 5b , 5c , 5d , 5e , 5f , 5g , 5h , 5i , 5j , 5k , 5l , 5m , 5n , 5o , and 6a , 6b , 6c , 6d , 6e , 6f , 6g , 6h , 6i , 6j , 6k , 6l , 6m , 6n , 6o , respectively. The structures of all these previously unknown compounds were confirmed by their spectral studies and elemental analysis. These compounds were screened for their antimicrobial and antioxidant activities.     

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.     

(HAlNH)~n(n=1～6)簇的结构、红外光谱和热力学性 质的研究

用自洽场理论(HF)和密度泛函理论(DFT)的B3LYP方法,在6-31G水平上研究了HAlNH的低聚物(HAlNH)~n(n=1～6)簇的几何构型、电子结构、红外光谱和化学热力学性质,并比较了(HAlNH)~n和(ClAlNH)~n两种低聚物对应结构中化学键强弱,分析了引起(AlN)~n骨架结构发生变化的原因。结果表明,(HAlNH)~n簇的基态结构为C~s(n=1),D~2~h(n=2),D~3~h(n=3),T~d(n=4),C~s(n=5)和D~3~d(n=6)对称点群。HAlNH基态结构中,Al-N键是三重键。在D~2~h(n=2)和D~3~h(n=3)结构中,所有Al-N键均为二重键。在T~d(n=4)和D~3~d(n=6)中,Al-N键为正常单键,而在C~s(n=5)结构中含有三种Al-N键：单键、双键和混合键。振动频率计算表明,结构a～f均为基态稳定结构。热力学计算给出的稳定性顺序为：f>d>e>c>b>a。     

Role of chain stiffness on the conformation of single polyelectrolytes in salt solutions

Conformation of single polyelectrolytes in tetravalent salt solutions is investigated under the framework of a coarse-grained model, using Langevin dynamics simulations. The chain size, studied by the radius of gyration, shows three different variational behaviors with salt concentration, depending on the chain stiffness. According to the size variations, polyelectrolytes of fixed chain length are classified into three categories: (1) flexible chain, for which the variation shows a curve similar to a tilted L, (2) semiflexible chain, whose curve resembles U, and (3) rigid chain, for which the curve is a straight line. The wormlike chain model with persistence length predicted by the Odijk-Skolnick-Fixman theory is found to be able to qualitatively describe the end-to-end distance at low salt concentration not only for semiflexible and rigid chains but also for flexible chain. In a low salt region, a flexible polyelectrolyte extends more significantly than a semiflexible chain, in reference of the size of their uncharged counterparts, and in a high salt region, regardless of chain stiffness, a chain attains a dimension comparable to that of its neutral polymer. The chain stiffness influences both the local and the global chain structures. A flexible chain exhibits a zigzagged local structure in the presence of salt ions, and the condensed structure is a disordered, random globule. A semiflexible chain is locally smooth, and the condensed structure is orderly packed, taking a form such as hairpin or toroid. Moreover, the chain stiffness can also affect the nature of the coil-globule transition. The transition occurred in a discrete manner for semiflexible chain, whereas it occurred in a continuous way for flexible chain. This discrete feature happened not only at low salt concentration when a semiflexible chain collapsed but also at high salt concentration when the collapsed chain is reexpanded. At the end, the effects of chain stiffness and salt concentration on the conformation of single polyelectrolytes are summarized in a schematic state diagram.     

Structures of stiff macromolecules of finite chain length near the coil‐globule transition: A Monte Carlo simulation

Using a coarse‐grained model of a semiflexible macromolecule, the equilibrium shapes of the chain have been studied varying both the temperature and the chain stiffness. We have applied Monte Carlo techniques using the bond fluctuation model for a chain length of N = 80 effective monomers, and two different types of interactions: a potential depending on the angle between successive bonds along the chain to control the chain stiffness, and an attractive interaction between non‐bonded effective monomers to model variable solvent quality. In a diagram of states where chain stiffness and inverse temperature are used as variables, we find regions where the chain exists as coil, as spherical globule, and as toroidal globule, respectively. Some of these regions are not limited by sharply defined boundaries, but rather wide two‐state coexistence regions occur in between them, where also intermediate metastable structures (such as rods and disks) occur. Recording histograms of energy, orientational order parameters, etc., which exhibit a two‐peak structure in the two‐state coexistence regions, we perform a subensemble analysis of the individual structures corresponding to these peaks.     

Ejection dynamics of semiflexible polymers out of a nanochannel

Using theoretical analysis and three-dimensional Langevin dynamics simulations, we investigate the influence of chain rigidity on the ejection dynamics of polymers from a nanochannel. We find that there exist two distinct dynamical regimes divided by a critical chain length for both flexible and semiflexible chains. At the short chain regime, semiflexible chains eject faster than flexible chains of the same chain length due to the longer occupying length. In contrast, at the long chain regime, semiflexible chains eject slower than flexible ones as the effective entropic driving force decreases. Based on these results, we propose that the nanochannels could be used to separate flexible and semiflexible chains effectively.     

Design and synthesis of new imidazolinone derivatives as potential antifungal agents

A new series of chalcones, pyrimidines, and imidazolinone is described; chalcones ( 4a , 4b , 4c , 4d , 4e , 4f , 4g , 4h , 4i , 4j , 4k , 4l , 4m , 4n , 4o ) were prepared from the lead 4‐[2‐(5‐ethylpyridin‐2‐yl)ethoxy]benzaldehyde. Pyrimidines ( 5a , 5b , 5c , 5d , 5e , 5f , 5g , 5h , 5i , 5j , 5k , 5l , 5m , 5n , 5o ) were prepared from the reaction of chalcones and guanidine nitrate in alkali media. Imidazolinones ( 6a , 6b , 6c , 6d , 6e , 6f , 6g , 6h , 6i , 6j , 6k , 6l , 6m , 6n , 6o ) were synthesized from the reaction of pyrimidine and oxazolone derivatives (prepared by Erlenmeyer azlactone synthesis). The structures of the synthesized compounds were assigned on the basis of elemental analyses, IR, ¹H‐NMR, and ¹³C‐NMR spectral data. All the products were screened against different strains of bacteria and fungi. Most of these compounds showed better inhibitory activity in comparison with the standard drugs. J. Heterocyclic Chem., (2011).     

Systematic investigation of zinc aminoalkylphosphonates: influence of the alkyl chain lengths on the structure formation

With the high-throughput (HT) methodology, the bifunctional aminoalkylphosphonic acids (AAPA) linker molecules 2-aminoethyl- (AEPA), 3-aminopropyl- (APPA), and 4-aminobutylphosphonic acid (ABPA) [HO(3)P-C(n)H(2n)-NH(2) (n = 2-4)] and zinc nitrate were used to synthesize new metal phosphonates in order to investigate the influence of the alkyl chain length on the structure formation. The systematic investigations led to one known (ZnO(3)PC(2)H(4)NH(2)) and six new compounds: one using AEPA, three using APPA, and two using ABPA. The crystal structures of five compounds were determined by single crystal X-ray diffraction, using X-ray powder diffraction (XRPD) data as well as structure modeling employing force field methods. For compound 1, Zn(O(3)P-C(2)H(4)-NH(3))(NO(3))(H(2)O) (monoclinic, Cc, a = 4.799(1) ?, b = 29.342(6) ?, c = 5.631(1) ?, β = 91.59(3)°, V = 792.7(3) ?(3), Z = 4), and compound 2, Zn(2)(OH)(O(3)P-C(3)H(6)-NH(3))(NO(3)) (monoclinic, P2/c, a = 12.158(2) ?, b = 5.0315(10) ?, c = 13.952(3) ?, β = 113.23(3)°, V = 784.3(3) ?(3), Z = 2), the structures were determined using single crystal X-ray diffraction data. The crystal structures of [Zn(O(3)P-C(3)H(6)-NH(2))]·H(2)O (3) (monoclinic, P2(1)/c, a = 9.094(2) ?, b = 5.0118(7) ?, c = 16.067(4) ?, β = 90.38(2)°, V = 732.3(2) ?(3), Z = 4) and Zn(O(3)P-C(4)H(8)-NH(2)) (5) (monoclinic, P2(1)/c, a = 8.570(7) ?, b = 8.378(4) ?, c = 9.902(6) ?, β = 90.94(5)°, V = 710.9(8) ?(3), Z = 4) were determined using XRPD data. The structural model for compound 6, Zn(O(3)P-C(4)H(8)-NH(3))(NO(3))(H(2)O), was established using lattice parameters from XRPD data and following crystal structure modeling employing force field methods. The structures depend strongly on the alkyl chain length n. For n = 2 and 4 isoreticular compounds are observed, while n = 3 leads to new structures. Larger amounts of all compounds were obtained employing scale-up syntheses in a conventional oven as well as in a microwave reactor system. In addition, in situ energy dispersive X-ray diffraction (EDXRD) experiments at 130 °C were performed at beamline F3 at HASYLAB, DESY, Hamburg, to investigate the formation of compounds 2 and 3 as well as the phase transformation of 2 into 3 upon addition of NaOH. All compounds were characterized in detail using X-ray powder diffraction, IR/Raman spectroscopy, and thermogravimetric and elemental analysis.     

Surface structures of rutile TiO2 (011)

Surface structures of rutile TiO(2) (011) are determined by a combination of noncontact atomic force microscopy (NC-AFM), scanning tunneling microscopy (STM), and density functional calculations. The surface exhibits rowlike (n x 1) structures running along the [01] direction. Microfaceting missing-row structural models can explain the experimental results very well. Calculated images for NC-AFM and STM are in good agreement with the experimental results. A decrease of the density of dangling bonds stabilizes the surface energy, which results in the microfaceting missing-row reconstructions.     

Coordination networks with fluorinated backbones

Fluorine-containing ligands 2,3,5,6-tetrafluoro-1,4-bis(imidazol-1-yl-methyl)benzene (1) and 2,3,5,6-tetrafluoro-1,4-bis(2-methylimidazol-1-yl-methyl)benzene (2) were prepared and coordinated with AgNO3, Co(ClO4)2 x 6 H2O, and Cd(NO3)2 x 4 H2O, respectively, to form the following structures: 3D channel polymer [Ag2(1)2(NO3)2 x H2O x MeOH]n (3), 2D sheet polymer [Co(1)3(ClO4)2]n (4), 1D chain polymer [Cd(1)3(NO3)2 x 4 H2O]n (5), and a 2D herringbone sheet polymer [Ag(2)NO3 x 1.5 MeOH]n (6). The solid-state crystal structures of 3-6 were studied by single-crystal X-ray crystallography.     

A joint structural, kinetic, and thermodynamic investigation of substituent effects on host-guest complexation of bicyclic azoalkanes by beta-cyclodextrin.

Derivatives of the azoalkane 2,3-diazabicyclo[2,2,2]oct-2-ene (1a) with bridgehead 1,4-dialkyl (1b), 1,4-dichloro (1c), 1-hydroxymethyl (1d), 1-aminomethyl (1e), and 1-ammoniummethyl (1f) substituents form host-guest inclusion complexes with beta-cyclodextrin. They were employed as probes to assess substituent effects on the kinetics and thermodynamics of this complexation by using time-resolved and steady-state fluorimetry, UV spectrophotometry, induced circular dichroism (ICD) measurements, and (1)H NMR spectroscopy. The kinetic analysis based on quenching of the long-lived fluorescence of the azoalkanes by addition of host provided excited-state association rate constants between 2.6 x 10(8) and 7.0 x 10(8) M(-)(1) s(-)(1). The binding constants for 1a (1100 M(-1)), 1b (900 M(-1)), 1c (1900 M(-1)), 1d (180 M(-1)), 1e (250 M(-1)), and 1f (ca. 20 M(-1)) were obtained by UV, NMR, and ICD titrations. A positive ICD signal of the azo absorption around 370 nm was observed for the beta-cyclodextrin complexes of 1a, 1d, and 1f with the intensity order 1a > 1d approximately 1f, and a negative signal was measured for those of 1b, 1c, and 1e with the intensity order 1c < 1b approximately 1e. The ICD was employed for the assignment of the solution structures of the complexes, in particular the relative orientation of the guest in the host (co-conformation).