Translocation of compact polymer chains through a nanopore

We perform dynamical Monte Carlo simulation to study the forced translocation of compact polymer chains in three-dimensional lattices. The chains are driven through a nanopore connecting two infinite channels by an external field. The scaling properties of average translocation time τ and translocation time distribution (TTD) are studied. The effects of contact energy (?_C), electric field strength (E), and nanopore width (L) on the scaling exponent (α) of average translocation time τ ∼ N^α and the TTD are investigated. For the scaling behavior of τ ∼ N^α, we have found that there is no crossover behavior with weak field strength when the nanopore width is one lattice spacing, which is less than average bond length, while crossover behaviors are observed for larger nanopore widths. The scaling exponent α also depends on contact energy ?_C and electric field strength E. For the TTD, it shifts from the Gaussian to a right-skew distribution with the electric field E increasing for short chains; while for long chains, multi-peak distributions are observed. As a primary and simple model, compact polymer chains are extensively used to capture the structure and thermodynamic properties of proteins, therefore we can investigate the protein translocation by simulating compact chain translocation, and this study will be useful for exploring the complex translocation behaviors of proteins.     

Elastic behavior of compact polymer chain transporting through an infinite adsorption channel

The elastic behavior of a single compact chain transporting through an infinite adsorption channel is investigated using the pruned-enriched-Rosenbluth method (PERM). In our model, single compact chain is fixed with one of its first monomer at a position in an infinite adsorption channel, is then pulled slowly along the direction of z-axis. We first calculate the chain size and shape of compact chains transporting through an infinite channel, such as mean-square end-to-end distance per bond 〈R²〉/N, mean-square radii of gyration per bond 〈S²〉/N, 〈S²〉_xy/N and 〈S²〉_z/N, and shape factor 〈δ〉 for the changes in the size and shape of compact chains during the translocation process. If there are strong adsorption interactions between the monomers and the channel, some special behaviors for the size and shape of compact chains are obtained during the process. On the other hand, some thermodynamics properties are also investigated, such as average energy bond, average Helmholtz free energy per bond, elastic force per bond f and energy contribution to elastic force per bond f_E. During the translocation process, elastic force f is less than zero, and has some plateaus in some special regions for strong adsorption interaction, which may explain how the adsorption interaction drives chains through narrow channels or pores in many biological systems because f<0 means that the translocation process need no external force on the chains. These investigations can provide some insights into the mechanics of proteins infiltrating through membrane. In the meantime, by recording and comparing these force-extension curves, we may also investigate the complex interactions between biopolymers (such as protein, RNA, and DNA) and the membranes, and determine indirectly the complicated structure of the channel.     

Preparation of a Novel Class of Cationic Gemini Imidazolium Surfactants Containing Amide Groups as the Spacer: Their Surface Properties and Antimicrobial Activity

A class of novel cationic Gemini imidazolium surfactants containing amide groups as the spacer were synthesized from ethylenediamine and 1-bromoalkane(C₈, C₁₀, C₁₂, C₁₄, C₁₆) by N-alkylation to get N,N′-dialkyl ethylenediamine (1a–e), 1a–e was further reacted with chloroacetyl chloride by N-acylation to get N,N′-(ethane-1,2-diyl)bis(2-chloro-N-alkylacetamide) (2a–e), which was further reacted respectively with 1-methyl imidazole by quaternized to form the surfactant molecule, N,N′-((ethane-1,2-diyl)bis(alkyl-azanediyl)bis(2-oxoethane-2,1-diyl)) bis(1-methyl-1H-imidazol-3-ium) dichloride. The structures of intermediates (1a–e) and (2a–e) were characterized by IR and ¹H NMR. The structures of the surfactants (3a–e) were characterized by IR, ¹H-NMR and ¹³C-NMR and element analysis. The critical micelle concentrations (CMC) of 3a–e were determined by the conductivity method at 25 °C. The CMC values decreased with increasing the length of the hydrophobic chain. The surfactants (3a–e) showed good foaming stability, emulsion ability and wetting ability. The surfactants (3a–e) also have good antimicrobial activity against Staphylococcus aureus, Escherichia coli and Bacillus subtilis.     

Crystal Structures and Luminescent Properties of Two Lanthanide(III) Complexes Featuring Double-Stranded Helical Chains of Based on 2-Sulfoterephthalate

Hydrothermal reaction of Eu³⁺ and Dy³⁺ salts with monosodium 2-sulfoterephthalate (NaH₂stp) gives two 2D lanthanide coordination polymers, [Ln(stp)(H₂O)₂] _n (Ln = Eu (1) and Dy (2)). Single-crystal X-ray diffraction of the complexes reveal that both 1 and 2 crystallize in the triclinic crystal system of Pī space group. For 1, each Eu³⁺ ion lies in a 9-coordinated slightly distorted tri-capped triangle pyramidal configuration. The stp ligands adopt a μ ₄-type link to the metal ions to form a 2D layer-like structure, of which there exist the left- and right-handed double-stranded helical chains. For 2, each Dy³⁺ ion is in a 8-coordinated distorted bi-capped triangle pyramidal geometry. The double-stranded helical chains in 2 differ from those in 1. The thermal stabilities of the two compounds are studied by TGA. The solid state photoluminescence of 1 and 2 are reported. The fluorescent decay curves of the ligand and compounds indicate that 1 has the lifetime of 286.7 μs, τ ₁ = 0.51 ns and τ ₂ = 3.07 ns for the ligand, and for 2, τ ₁ = 0.53 ns and τ ₂ = 2.71 ns.     

Synthesis, Analysis, and Field Activity of Sordidin, a Male-Produced Aggregation Pheromone of the Banana Weevil, Cosmopolites sordidus

An efficient synthesis of the diastereoisomers of sordidin (1), a male-produced aggregation pheromone of Cosmopolites sordidus, has been developed from commercially available 4-methylpent-4-en-2-ol (2). Preparation of exo-β-sordidin (1a) and endo-β-sordidin (1b) is via the anti epoxide, 4d, which is derived via iodocarbonation of 2. The endo-α-sordidin (1c) and exo-α-sordidin (1d) are prepared from the corresponding syn epoxide, which is available via stereo-controlled epoxidation of the triisopropylsilyloxy derivative, 3b. Silyloxy derivatives of the epoxides, 4, efficiently alkylate the anions of N-cyclohexyldiethylketimine (6a) and 3-pentanone N,N-dimethylhydrazone (6b). Acidic work-up of these alkylation reactions promotes cyclization to give 1. Gram quantities of 1a?1d, 1a + 1b and 1c + 1d have been prepared by this route. In field tests in a banana plantation in Costa Rica, compounds 1a?1d significantly increased capture rates of standard pseudostem traps. Comparable numbers of adults were attracted to pseudostem traps baited with the major naturally occurring isomers of sordidin 1c + 1d or 1a?1d. Although addition of the minor naturally occurring isomers of sordidin (1a and 1b) to pseudostem traps increased capture rates above controls, these compounds did not increase attraction of pseudostem traps to the same extent as 1a?1d. In comparison tests with conventional pseudostem traps, significantly more adults were trapped in water-containing pitfall traps baited with 1a?1d.     

Revisiting of dimensional scaling of linear chains in dilute solutions

The dimensions of linear polymer chains are scaled to their molar mass (M) as R = kM^α with α = 1/2 and 3/5 in a theta and an athermal solvent, respectively. In a good solvent, both k and α are a function of the solvent quality and chain length range. A high-temperature laser light-scattering spectrometer was used to measure the average radius of gyration (〈R_g〉) and hydrodynamic radius (〈R_h〉) of a set of narrowly distributed linear polystyrene chains in decalin over a wide temperature range. k and α in the scaling experimentally varying with T over a chain length range was analyzed. The results reveal that for 〈R_g〉, α = 0.59 − 0.09exp(−τ/0.066) and k = 0.60τ^2α−1, reasonably agreeing with the thermal blob theory. For 〈R_h〉, α = 0.59 − 0.09exp(−τ/0.106), but k deviates from the relationship of k ∝ τ^2α−1, reflecting that the hydrodynamic interaction and chain draining are not considered in the thermal blob theory.     

Copper(II) azide complexes of [Cu(acac)(N3)(dpyam)] and [Cu(μ-N3-κN1)(C2N3-κN1)(dpyam)]2: Synthesis,crystal structure and magnetism

Two new compounds, [Cu(acac)(N₃)(dpyam)] (1), (acac = acetylacetonate; dpyam = di-2-pyridylamine) and [Cu(μ-N₃-κ^N1)(C₂N₃- κ^N1) (dpyam)]₂ (2), have been synthesized and characterized by single-crystal X-ray diffraction and magnetic analyses. Compound 1 is a mononuclear compound in which each of two independent Cu(II) ions is penta-coordinated with a distorted square pyramidal geometry with distortion parameters τ = 0.21 and 0.16. In contrast, compound 2 is an azido-bridged dinuclear compound with monodentate dicyanamide anions and the Cu(II) ions display a distorted trigonal bipyramidal geometry with τ = 0.73 and end-on azido bridges providing an equatorial–axial position between the metal ions. The EPR spectra of powdered samples for 1 and 2 have also been investigated. Magnetic susceptibility measurements of compound 2 reveal a very weak ferromagnetic interaction between the Cu(II) ions with a J value of +5.8 cm⁻¹.     

Free energy barrier for compact chains escaping from a small sphere

In this paper, the process of compact polymer chains escaping from a small sphere to a large one in the view of thermodynamics is investigated in detail based on the pruned-enriched-Rosenbluth method (PERM), which is quite efficient for the three-dimensional polymers on the simple-cubic lattice. In our simulation, three representative states of a polymer chain during the escaping process are studied, and some statistical properties of the chain size and the chain shape, such as mean-square radius of gyration per bond 〈S²〉/N and the shape factor 〈δ^∗〉 are investigated. Our aim is to illuminate how the size and shape of the compact chains change during the escaping process. The changes of 〈S²〉/N and 〈δ^∗〉 are not monotone and it is due to the fact that the chain should stretch itself in the escaping process. In the meantime, some thermodynamic properties are also calculated here. The hole is designed to be small enough to allow only one monomer at a time and it thus reduces the number of allowed chain conformations and breaks contacts between monomers at the beginning of the process. Additionally, we discuss the free energy barrier per bond H₂ − H₁ = ΔH of a compact chain, and here H₂ is the maximum free energy per bond during the process and H₁ is the minimum one when the compact chain is within the small sphere. Averaging free energy barrier over chain length N is convenient for the comparison with different chain lengths. ΔH as a function of chain length N and radius r₁ of the small sphere is also studied and our result shows that ΔH for longer chains is lower means that it is relatively easier for each bond in longer chains to surmount the free energy barrier to escape. Some discussions about the self-avoiding walk (SAW) and swollen chains are also made for the comparison, and our results also show that the restriction of the small sphere on the SAW and the swollen chains is more effective because of their relatively looser intrinsic structure.     

Stereoselective synthesis of trans N/O dispirocyclic cyclotriphosphazenes based on the steric demands of the constrained 2-pyridyl group

Monospiro- and dispirocyclic cyclotriphosphazenes, 2a and 2b, were synthesized by the reaction of hexachlorocyclotriphosphazene, N₃P₃Cl₆ (1), with 2-(2-pyridylamino)phenol in the presence of base. The reactions of phosphazenes 2a and 2b with sodium (4-methyl-2-pyridyl)oxide afforded tetrakis- and bis(4-methyl-2-pyridyloxy)cyclotriphosphazenes, 3a and 3b, respectively. ³¹P NMR spectroscopy of 2b and 3b using d-camphorsulfonic acid as a chiral solvating agent indicated that they were racemates of the trans isomers. The trans configuration of trans-3b could also be elucidated by X-ray crystal structural analysis, which suggested that the steric demand of the 2-pyridyl group was responsible for the stereoselective formation of trans-2b. The steric demand of the 2-pyridyl group was supported by the reaction of N₃P₃Cl₆ (1) with N,N′-bis(2-pyridyl)benzene-1,2-diamine, which only gave monospirocyclic cyclotriphosphazene 4a.     

Polymer translocation through a nanopore in mesoscopic simulations

Dissipative particle dynamics (DPD) simulations are carried out to study the translocation of a single polymer chain through a pore under fluid field. The influences of the field strength E, the chain length N, the solvent quality α_sp, and the pore size h on the translocation time are evaluated. The translocation time τ, which is defined as the time that the chain moves through the pore completely in the direction of the driving force, scales with the field strength E as τ ∼ E^{−0.48±0.01}. We find that the translocation time is proportional to the chain length, which is in agreement with the experimental results and theoretical predictions. Tracing the variation of the square radius of gyration, , and the polymer configuration during translocation, we observe that the chain is elongated when it is passing through the pore, which manifests that the chain is not in equilibrium during the translocation process. We also find that the worse the solvent quality is, the less time it will take to translocate, no matter what the size of the pore is. If the size of the pore is enlarged, the translocation time will be shorter. The information we gain from this study may benefit to the DNA sequencing.     

Coordination modes in zirconium β-diketiminate complexes

Reaction of β-diketiminate lithium salts, nacnac^RLi(THF) (R = 2,6-xylyl (1a), R-CH(Me)Ph (1b)), with ZrCl₄ or ZrCl₄·THF yielded the mono-diketiminate complexes nacnac^RZrCl₃(THF), 2a and 2b. Complex 2a did not react further with a second equivalent of 1a, but with CpLi or IndLi to form pseudo-tetrahedral complexes 3 and 4. No product could be isolated from reaction of 2b with CpLi. Coordination of the diketiminate ligand in 2a is best described as a distorted κ²-, in-plane coordination. Complexes 3 and 4, however, display a haptotropic shift of the diketiminate ligand and its coordination is best described as κ²,η²-coordination. Although not previously described, analyses of available structures in the literature reveal that non-symmetric κ²,η²-coordination is an independent coordination mode, which exists next to the previously described “η⁵-like” coordination.     

Fast transient fluorescence (FTRF) technique to study swelling of densely and loosely formed gels

A Strobe Master System (SMS) is introduced for studying the swelling of cylindrical densely (DG) and loosely (LG) formed gels. Gels were prepared by free radical copolymerization of methyl (methacrylate) (MMA) and ethylene glycol dimethacrylate (EGDM). Pyrene (P) was introduced as a fluorescence probe during polymerization, and the lifetimes of P were measured using (SMS) during in situ swelling processes. Chloroform was used as a swelling agent. A model is derived for low quenching efficiencies to measure mean lifetimes 〈τ〉 of P, and it was observed that 〈τ〉 values decreased as the swelling proceeded. The Li‐Tanaka equation was employed to determined the time constants, τ_c, and cooperative diffusion coefficients, D_c, which were found to be around 400 min and 10⁻⁵ cm²s⁻¹, respectively. No differences were detected in τ_c and D_c values of DG and LG gels. Quenching rate constants, κ, and the mutual diffusion coefficient, D_m, were measured and found to be around 10⁵ M⁻¹s⁻¹ and 10⁻¹⁰ cm²s⁻¹ for DG and LG gel samples. © 2000 John Wiley & Sons, Inc. J Appl Polym Sci 76: 1494–1502, 2000     

Dielectric and dynamic Kerr effect studies of poly(n-butyl isocyanate) and poly(n-octyl isocyanate) in solution

Static and dynamic Kerr effect studies on poly(n-butyl isocyanate) (PBIC) and poly(n-octyl isocynate) (POIC) in CCl₄ solution are reported and are compared with dielectric studies. The variation of dipole moment μ and Kerr constant factors θ₁ and θ₂ with temperature suggest the chains for M_W ～ 10⁵ depart from a rod-like conformation, and this is also indicated by a detailed analysis of the dynamic Kerr effect and dielectric data. It is shown that the ratio of areas for the rise and decay transients for the Kerr effect are inconsistent with the simple model for rotational diffusion. In addition the averaging process involved in the apparent dielectric relaxation time 〈τ_D〉 and the Kerr effect decay average relaxation time 〈τ_K,d〉 is examined and it is shown that for rigid-rod, coil and Kratky-Porod behaviour that $\text{〈τ}{}_{\mathrm{D}}\text{〉}\text{〈τ}{}_{\mathrm{K,d}}\text{〉}\text{? 〈}\text{A}{}_{\mathrm{D}}\text{A}{}_{\mathrm{K}}\text{〉}$ a factor which would be 3 for rotational diffusion, and is found to be ～1 for PBIC and POIC again indicating the departure from simple rotational diffusion for the present samples.     

Syntheses of well-defined poly(siloxane)-b-poly(styrene) and poly(norbornene)-b-poly(styrene) block copolymers using functional alkoxyamines

Functional alkoxyamines, 1-[4-(4-lithiobutoxy)phenyl]-1-(2,2,6,6-tetramethylpiperidinyl-N-oxyl)ethane (2) and 1-[4-(2-vinyloxyethoxy)phenyl]-1-(2,2,6,6-tetramethylpiperidinyl-N-oxyl)ethane (3) were prepared, and well-defined poly(hexamethylcyclotrisiloxane)-b-poly(styrene)[poly(D₃)-b-poly(St)] and poly(norbornene)-b-poly(St) [poly(NBE)-b-poly(St)] were prepared using the alkoxyamines. The first step was preparation of poly(D₃) and poly(NBE) macroinitiators, which were obtained by the ring-opening anionic polymerization of D₃ using 2 as an initiator and the ring-opening metathesis polymerization of NBE using 3 as a chain transfer. The radical polymerization of St by the poly(D₃) and poly(NBE) macroinitiators proceeded in the ‘living’ fashion to give well-defined poly(D₃)-b-poly(St) and poly(NBE)-b-poly(St) block copolymers.     

Double helix of Agrobacterium tumefaciens succinoglycan in dilute solution

Succinoglycan samples ranging in weight-average molecular weight from 1.4×10⁵ to 10.5×10⁵ (in 0.1 M aqueous NaCl at 25°C), prepared from native succinoglycan by sonication, were investigated by static light scattering and viscometory in 0.1 M aqueous NaCl. It is well known that the conformation of the polysaccharide changes at around 65°C. In order to confirm the conformation of the polysaccharide, the property of the polysaccharide in dilute solution was studied at both 25 and 75°C. The molecular weight of a sample at 25°C is the double of the value at 75°C. The molecular weight dependence of 〈s²〉_Z and [η] for succinoglycan shows that the polysaccharide is a rod-like polymer at 25°C and behaves like a semi-flexible polymer at 75°C in 0.1 M aqueous NaCl. Moreover, the linear mass density of the polysaccharide was almost twice that expected for single succinoglycan molecules. These results indicate that the conformation of the polysaccharide would be a double helix at 25°C and the helix melts to a single strand behaving as a semi-flexible chain above 65°C.     

1D Ladder-Like Structure Motif Assembled from Edge-Sharing Rhombic Squares of Sm2Mo2 Based on [Mo(CN)8]4− and Sm3+ Ions as Building Blocks

Novel bimetallic 4d–4f complex, {Cs[Sm(MeOH)₃(DMF)(H₂O)Mo(CN)₈] · H₂O} _n (1) (DMF = N,N′-dimethylformamide) has been synthesized and structurally characterized. The crystal analyses shown that 1 exhibit a one-dimension (1D) infinite chain structure, which adopts a 1D ladder-like structure motif assembled from edge-sharing rhombic squares of Sm₂Mo₂, and that is the first structurally characterized example of a 1D ladder structure based on the [Mo(CN)₈]^4? and Sm³⁺ building blocks. The complex 1 crystallizes in triclinic, space group P-1, with a = 9.905(2), b = 10.333(2), c = 13.562(3) Å, α = 82.00(3)°, β = 86.62(3)°, γ = 65.76(3)°, V = 1253.5(4) Å³ and Z = 2. The magnetic behavior of 1 has also been studied in this paper.     

Cyclization dynamics of polymers: 7. Applications of the pyrene excimer technique to the internal dynamics of poly(dimethylsiloxane) chains

Poly(dimethylsiloxane) (PDMS) polymers end-capped on both ends with pyrene chromophores have been synthesized. Rate constants for end-to-end cyclization 〈 k₁ 〉 have been determined for dilute solutions of these polymers in toluene solution using a combination of fluorescence decay and steady-state fluorescence measurements. While precise values of the critical exponent for the chain length (N¯) dependence of 〈 k₁ 〉 are not yet available, these results are consistent with the N¯^{? 3/2} dependence predicted by Wilemski-Fixman theory. PDMS chains cyclize somewhat more than two times faster than polystyrene chains of the same length in solvents of similar solvating power and viscosity. These results provide strong support for similar predictions made several years ago by Perico and Cuniberti, who used intrinsic viscosity data to parametrize the Rouse-Zimm model for analysis of polymer cyclization dynamics.     

Elastic behavior of adsorbed single compact chains

Elastic behaviors of short single two-dimensional compact chains adsorbed on the attractive surface are investigated in this paper by using the enumeration calculation method. In our model a single compact chain is fixed with one of its end at a position above the impenetrable surface, and then it is pulled away from the attractive surface slowly through elastic force acting. We investigate the chain size and shape of adsorbed compact chains, such as mean-square end-to-end distance per bond 〈R²〉/N mean-square radii of gyration per bond 〈S²〉_x/N and 〈S²〉_y/N, shape factors 〈δ〉, and fraction of adsorbed monomers f_a in order to illuminate how the size and shape of adsorbed compact chains change during the process of tensile elongation. Especially for strong attraction interaction there are some special behaviors in the chain size and shape during this process. If there exits adsorption interaction, single compact chain is first almost pulled down to the adsorption surface and then moves in the direction of force until to leave the adsorption surface. These changes become more obvious with strong adsorption interaction. Our calculation can show this elastic process of adsorbed compact chains visually and simply. On the other hand, some thermodynamics properties are also studied here. We use average energy per bond, average Helmholtz free energy per bond, elastic force f and energy contribution to elastic force f_u to study the elastic behavior of adsorbed single compact chains in the process of tensile elongation. Elastic force f has a long plateau during the tensile elongation for strong adsorption interaction, which agrees well with experimental and theoretical ones. These investigations can provide some insights into the elastic behaviors of adsorbed protein chains.     

Forced translocation of polymer chains through a nanotube: A case of ultrafiltration

Translocation of polymer chains under the application of an external force has been studied through coarse-grained Monte Carlo simulations. The chains are pulled through a nanotube of finite length and diameter and their translocation times measured. The average translocation time, τ follows a scaling relation involving the chain length, N and applied force, F as, τ ∼ N^ν′F^−μ, where ν′ and μ are two different exponents (ν′ = 0.674, and μ = 0.95 ± 0.05). The scaling law is closely similar to the nanopore translocation scaling law reported by Milchev et al. [Ann N Y Acad Sci 2009;1161:95]. Characteristic signatures of the chain escape time have been exhibited by the square of end-to-end distance R², axial radius of gyration R_g−x and other constituent properties. The behavior of the linear polymers under the application of a pulling force has been exploited to gain insights into the ultrafiltration process of unentangled polymers in dilute solution. The generic pulling force-translocation time (F, τ) data obtained through simulation can be matched reasonably well with the hydrodynamic force-critical macroscopic flow time (f_h, Q_c⁻¹) data and also with the hydrodynamic force-reduced critical microscopic flow time (f_h, q_c⁻¹) data obtained in the ultrafiltration experiment on long linear polystyrene chains in cyclohexane, as recently reported by Ge et al. [Macromolecules 2009;42:4400] The simulation technique reported here may be extended to study biomolecular transports occurring in long protein channels, as studied experimentally through current-time or voltage-time traces.     

Pd-catalyzed hydrosilylation polymerization of a dihydrosilane with diyne/triyne mixed systems affording crosslinked silylene-divinylene polymers and their properties

Treatment of a dihydrosilane (methylphenylsilane, 1) with mixtures of a diyne (p- or m-diethynylbenzene, 2a or 2b) and a triyne (1,3,5-triethynylbenzene, 3a or B,B′,B″-triethynyl-N,N′,N″-trimethylborazine, 3b; 1:2:3=100:95:5, 100:90:10, 100:80:20) in the presence of Pd-PCy₃ (Cy=cyclohexyl) catalyst gave new crosslinked silylenedivinylene polycarbosilanes. In TGA the resulting crosslinked polymers tended to show higher Td₅ values and higher char yields than the corresponding linear polymers. On the other hand, UV/vis absorption spectra of the crosslinked polymers obtained in the reactions of 2a or 2b with 3a exhibited increased broad peaks around 390 nm for 2a or 360 nm for 2b. Coincidently, their fluorescence spectra showed significant increase of the emission peaks in 400-550 nm. The crosslinked polymer derived from 2a and 3b, however, showed decrease of the absorption peak around 390 nm and profound depression of fluorescence peaks in 400-550 nm.