DARC “Logic Method” for Molal Volume Prediction

Abstract

Topological methods for molecule volume prediction based on local fragments centered on all carbons of aliphatic alkanes (C6-C11, C12) are proposed and evaluated. The LOGIC method dealing with local to global information construction is based on local environment (FREL_B) partition of information, both structural and physical, and the use of these FRELs to correlate the molal volumes V. Different topological vectorial sets of various depths, dealing with atom and bond FRELs, are used to optimize the contributions V _D of a set of prime FRELs constituting the reference set structured in a hyperstructure linking 70 FREL_B. The accuracy of determining fragment volumic contributions is traced by the decreasing number of hits resulting in the modeling of the C6-C11 populations. The training set of the V values is tested on the 355 alkanes of the C12 population. This extrapolation leads to excellent statistical results of the LOGIC method, which is a “parent structure free” similarity correlation although its application here is “aliphatic alkane” oriented. The set of V _D values is obtained through the combined use of several topological sets and the resolution of FREL intersections to control redundant structural information. In practice its application is simple and strictly additive.     

PAmXD,6/PP-g-MA blends. I. Compatibilization

This work deals with the study of PAmXD,6/PP-g-MA blends [poly(meta-xylylene adipamide)] and (maleic-anhydride-functionalized-polypropylene) blends. Compatibilization occurs during the blending of the components in a Brabender plastograph at 265 ± 5°C and at a mixing rate of 45 rpm. Kinetic data from the literature indicate that the rate of amine/anhydride reaction is much faster than the rate of amide/anhydride reaction. This interpretation is confirmed by the use of model systems constituted of PAmXD,6 and pyromellitic dianhydride or of PP-g-MA and meta-xylylene diamine. Infrared analyzes of extracted nodules of PAmXD,6/PP-g-MA blends also confirm the extent of the imidization and show that the length of the PAmXD,6 blocks is lower than the free PAmXD,6 one. Segregation mechanisms during the compatibilization are discussed to explain this observation. The structure of the copolymers was deduced from those results and from the previous characterizations of PP-g-MA and PAmXD,6. It consists in a block of PP linked with some blocks of PAmXD,6. The average number of PAmXD,6 blocks depends on the average length of the poly(maleic anhydride) functionality carried on by PP-g-MA. © l997 John Wiley & Sons, Inc. J Polym Sci A: Polym Chem 35: 901–915, 1997     

Macromol. Biosci. 5/2009

Cancer‐cell phenotype is not only the result of malignant progression, but also dependent on the microenvironment surrounding them, including influences from the extracellular matrix and its structural properties. We have investigated the influence of the nanofiber matrix of the self‐assembling peptide, RADA16, in comparison with collagen I and Matrigel on the malignant phenotype of the human breast‐cancer cell, MDA‐MB‐231, in 3D cultures, including the morphology, survival, proliferation rate, migration potential and the effect of these matrices on the malignancy of the cancer cells in vivo. Our data indicate that these tumor cells change their morphology in response to the different 3D matrix in vitro cultures and the RADA16 self‐assembling peptide scaffold mimics an extracellular matrix and could effectively reduce the malignant phenotype of the tumor cells in vitro and in vivo.

     

Mechanism of thermal energy charge transfer reactions: + N2. Analysis of isotopic data

The

+ N₂ charge transfer reaction has been studied in an ICR spectrometer using both ¹⁴N₂ and ¹⁵N₂. The N⁺/N₂⁺ branching ratio was measured from the zero collision limit (ca. 1 × 10^?5 torr total pressure) to collisional saturation (ca. 1 × 10^?3 torr total pressure) for He/N₂ ratios of 5, 10, 50 and 100. The data were analyzed by solving exactly the kinetic equations and the associated power absorption equations. A positive pressure dependence in the N⁺/N₂⁺ branching ratio was observed indicating some N⁺ is formed from collisional dissociation of excited

ions. Comparison is made with recently published data from other groups and previously published data from this laboratory.     

Macromol. Biosci. 1/2013

Front Cover: Highly aligned 3D silk scaffolds using directional freezing in a custom designed chamber was demonstrated. The method is versatile and holds potential to produce complex, multicomponent aligned structures for various tissue engineering and biomedical applications, needing immediate cell alignment to mimic native tissue hierarchy and function. Further details can be found in the article by B. B. Mandal, E. S. Gil, B. Panilaitis, and D. L. Kaplan* on page 48 .

     

- and β-cyclodextrin complexes with n-alkyl carboxylic acids and n-alkyl p-hydroxy benzoates. A molecular mechanics study of 1:1 and 1:2 associations

Molecular mechanics (MM) methods were employed to evaluate stabilization upon formation of inclusion compounds between two different guest molecules and - and β-cyclodextrins (CDs) for two different stoichiometries 1:1 and 1:2. The two guest molecules studied were n-alkyl carboxylic acids and n-alkyl p-hydroxy benzoates with variety of chain lengths. The computed stability for the inclusion compounds between -CDs and n-alkyl carboxylic acids reproduced experimental data reported in the literature. The transition between 1:1/1:2 complexes occurred at an alkyl chain length of n_C=9. It was previously demonstrated by diffusion coefficients measures that a stable 1:2 stoichiometry inclusion compound could be formed between n-alkyl p-hydroxy benzoates and -CD for the chain length n_C>4. The computed results reproduced the experimental ones. The combination between OPLS and GB/SA resulted in better agreements with experiments than those obtained with MM2 and MM3.     

Cumulative indices for Spectrochima Acta, Part A and Spectrochimica Acta, Part B

This article is an electronic publication in Spectrochimica Acta Electronica (SAE), a section of Spectrochimica Acta, Part B (SAB). The hardcopy text is accompanied by an electronic archive, stored on the SAE homepage at http://www.elsevier.nl/locate/sabe. The archive contains data, index and program files. The main article discusses the bibliographical purpose of the program and data files. A collective index for Spectrochimica Acta for volumes since it was split into Parts A and B, and continuing through 1991 for SAA and 1997 for SAB, is presented in DBF format, along with rudimentary data entry and access software.     

X-ray powder diffraction studies and thermal behaviour of NaK2B9O15, Na(Na.17K.83)2B9O15, and (Na.80K.20)K2B9O15

The crystal structures of NaK₂B₉O₁₅ (, , , β=94.080(1)°, R_p=0.047, R_wp=0.059, R_B=0.026), Na(Na_.17K_.83)₂B₉O₁₅ (, , , β=94.228(2)°, R_p=0.053, R_wp=0.068, R_B=0.026), and (Na_.80K_.20)K₂B₉O₁₅ (, , , β=94.071(1)°, Z=4, R_p=0.041, R_wp=0.052, R_B=0.023) were refined in the monoclinic space groups P2₁/c(Z=4) using X-ray powder diffraction data and the Rietveld method. These nonaborates are isostructural to K₃B₉O₁₅. Their crystal structure consists of a three-dimensional open framework built up from three crystallographically independent triborate groups. The alkali metal cations are located on three different sites in the voids of the framework. High-temperature X-ray diffraction studies show that NaK₂B₉O₁₅ decomposes at about 700 °C in accordance with the peritectic reaction NaK₂B₉O₁₅↔K₅B₁₉O₃₁+liquid. The thermal expansion of NaK₂B₉O₁₅ and Na(Na_.17K_.83)₂B₉O₁₅ is highly anisotropic. A similarity of the thermal and compositional (Na-K substitution) deformations of NaK₂B₉O₁₅ is revealed: heating of NaK₂B₉O₁₅ by 1 °C leads to the same deformations of the crystal structure as increasing the amount of K atoms in (Na_1−xK_x)₃B₉O₁₅ by 0.04 at% K.     

Reaction‐induced phase separation in epoxy/polysulfone/poly(ether imide) systems. I. Phase diagrams

Epoxy–aromatic diamine formulations are simultaneously modified with two immiscible thermoplastics (TPs), poly(ether imide) (PEI) and polysulfone (PSF). The epoxy monomer is based on diglycidyl ether of bisphenol A and the aromatic diamines (ADs) are either 4,4′‐diaminodiphenylsulfone or 4,4′‐methylenebis(3‐chloro 2,6‐diethylaniline). The influence of the TPs on the epoxy–amine kinetics is investigated. It is found that PSF can act as a catalyst. The presence of the TP provokes an increase of the gel times. Cloud‐point curves (temperature vs. composition) are shown for epoxy/PSF/PEI and epoxy/PSF/PEI/AD initial mixtures. Phase separation conversions are reported for the reactive mixtures with various TP contents and PSF/PEI proportions. On the basis of phase separation and gelation curves, conversion–composition phase diagrams at constant temperature are generated for both systems. These diagrams can be used to design particular cure cycles to generate different morphologies during the phase separation process, which is discussed in the second part of this series. © 2004 Wiley Periodicals, Inc. J Polym Sci Part B: Polym Phys 42: 3953–3963, 2004     

Macromol. Biosci. 3/2009

The effect of Ph‐OH group content on gelation time, mechanical properties, hydrophobicity, and cellular adhesiveness of hydrogels produced from carboxymethylcellulose derivatives is investigated. A higher Ph‐OH group content induces faster gelation and yields more brittle and hydrophobic gels. After 4 h of seeding, a larger number of L929 fibroblasts adhere to the hydrogel of the CMC‐Ph that contains 15.4 Ph‐OH groups per 100 repeat units of uronic acid (97% adhesion rate) than to the gel of CMC‐Ph with only 8.4 Ph‐OH groups (62% adhesion rate). The results demonstrate that controlling the Ph‐OH group content is an effective and useful way to control cellular adhesion and proliferation on the hydrogels, as well as gelation time and mechanical properties of the gels.

     

Polyelectrolyte complexes. II. Specific aspects of the formation of polycation/dye/polyanion complexes

We report on the formation of the polycation/dye/polyanion (PC/D/PA) complexes by the interaction between nonstoichiometric polycation/dye (PC/D) complexes with polyanions. Polycations differed in their content of the (N,N‐dimethyl‐2‐hydroxypropylene ammonium chloride) units in the main chain. Poly(sodium acrylate) (NaPA), poly(sodium 2‐acrylamido‐2‐methylpropane sulfonate) (NaPAMPS) and poly(sodium styrenesulfonate) (NaPSS) were used as polyanions. Crystal Ponceau 6R (CP6R) and Ponceau 4R (P4R) with two or three sulfonic groups were used as anionic dyes. The interaction between nonstoichiometric PC/D complexes and polyanions was followed by UV‐VIS spectroscopy, viscometry, and conductometry measurements. Formation of PC/D/PA complexes takes place mainly by the electrostatic interaction between the polyanion and the free positive charges of the nonstoichiometric PC/D complex. The stoichiometry and the stability of the tricomponent complexes depended on the polycation structure, the structure and molecular weight of polyanion, the dye structure, and the P/D molar ratio. A high amount of the dye was excluded from the complex before the end point when a branched polycation was used. The higher the solubility of the dye the lower the stability of the PC/D/PA complexes. © 1999 John Wiley & Sons, Inc. J Polym Sci A: Polym Chem 37: 409–418, 1999     

H-bonds of imidazole crystals. II. Determination of the magnitudes of the various anharmonic couplings of vs modes

In this article results given in a previous paper (part I), concerning the spectra of NH and ND species recorded with a polarization parallel to the c axis are analyzed, the necessary corrections on the raw data performed, v_s bands and their first moments are then compared with corresponding quantities predicted from a simple theory which describes quantitatively the anharmonic interactions of a single H-bond with a low frequency vibration of the same H-bond and with binary combinations of modes (Fermi resonances). This allows us to determine the magnitudes of the various anharmonic interactions involved. It appears that the low frequency vibration which modulates v_s is a bending mode of the H-bond (NH ↑ … N), a finding somewhat unexpected, as this low frequency vibration is usually thought to be the stretching vibration v_σ of the H-bond

     

超高效液相色谱法测定青娥丸中松脂醇二葡萄糖苷的含量

建立了超高效液相色谱(UPLC)测定青娥丸中主要活性成分松脂醇二葡萄糖苷(pinoresinol diglucoside, PDG)含量的方法。样品经索氏提取后,提取物再用Waters Oasis HLB SPE固相萃取小柱进行前处理以消除杂质对PDG色谱峰的干扰。色谱条件：采用Waters Acquity C18 BEH UPLC柱(100 mm×1.0 mm, 1.7 μm)分离,以乙腈-水(使用磷酸调pH值至4.0)(9:91, v/v)为流动相,流速为0.1 mL/min,检测波长为227 nm,柱温为25 ℃,进样量为0.5 μL。在上述条件下,松脂醇二葡萄糖苷在1.40～506.00 mg/L范围内呈现良好的线性关系,相关系数r=1;低、中、高3个添加水平下的平均回收率分别为100.51%、102.37%、100.10%(n=9)。该方法准确、灵敏、重现性好,可用于青娥丸的质量控制。     

On the compatibility of the IPP/PA6/EPDM blends with and without functionalized IPP I. Thermo-oxidative behaviour

Binary isotactic polypropylene (IPP)/polyamide 6 (PA6) and ternary IPP/PA6/ethylene–propylene diene terpolymer (EPDM) blends in various ratios were obtained in a Haake Rheocord mixer. Processing behaviour was changed in the presence of IPP functionalized with bismaleimide (BMI), maleic anhydride (MA) and acrylic acid (AA) as reactive compatibilizing agents. The thermal and thermo-oxidative behaviour of blends was studied by differential scanning calorimetry and thermogravimetry. The functionalized IPPs modify the crystallinity degree and the decomposition behaviour of both IPP and PA6 as a result of chemical reactions of functional groups with those of the PA6. The changes depend on the IPP/PA6 or IPP/PA6/EPDM ratio, the chemical nature and amount of the functionalized IPP. On the basis of the processing and thermal data one can conclude that the compatibilizing agent effect increases in the following order: IPP-AA 相似文献   

Forensic discrimination of photocopy and printer toners. III. Multivariate statistics applied to scanning electron microscopy and pyrolysis gas chromatography/mass spectrometry

Copy toner samples were analyzed using scanning electron microscopy with X-ray dispersive analysis (SEM–EDX) and pyrolysis gas chromatography/mass spectrometry (Py–GC/MS). Principal component and cluster analysis of SEM data for 166 copy toner samples established 13 statistically different subgroups, with the presence or absence of a ferrite base being a major division. When toners were compared for which both SEM and reflection–absorption infrared spectral data were available, 41% of the samples could be assigned to specific manufacturers. Py–GC/MS on poly(styrene:acrylate)-based toners produced eight peaks relevant to toner differentiation. One third of the toners clustered in a small group that contained five statistically different subgroups. Of the 57 toners for which both Py–GC/MS and SEM data were available, 31 could be differentiated using the combined analytical results. The synergy of the complementary information provided by Py–GC/MS and SEM narrows matching possibilities for forensic investigations involving copied or laser printed documents.This is publication number 03-04 of the Laboratory Division of the Federal Bureau of Investigation. Names of commercial manufacturers are provided for identification only, and inclusion does not imply endorsement by the Federal Bureau of Investigation.     

A MORE EXACT THEORETICAL INTERPRETATION OF RECENT EXPERIMENTAL DATA OBTAINED USING THE SEPARATED SENSITIZER AND SUBSTRATE METHOD TO INVESTIGATE O2(lδg) INTERACTIONS. POSSIBLE IMPORTANCE OF O2(1σg+)

Abstract— Recent experimental data obtained using the separated sensitizer and substrate method to investigate the interaction of O₂(¹δ_g) with various substances has been re-interpreted by means of a more complete theory. Comparison of experimental and recalculated values of the dependence of relative reaction rates on the sensitizer-substrate separation indicate general accord for experiments in which singlet oxygen acceptors in aqueous solution were used. The presumption is therefore that singlet molecular oxygen O₂(¹δ_g) is indeed the active oxidizing agent and that the theory presented and experiment are entirely in agreement.
For experiments in which bacterial targets were used a very distinct disagreement between theory and experiment is evident, the conclusion being that the kill rate does not depend linearly on the O₂(¹δ_g) concentration in the immediate proximity of the bacteria. However, the data is consistent with a quadratic dependence on the ¹δ_g concentration. A possible conclusion therefore is that the cytotoxic species is actually O₂(¹σ⁺_g), formed by an energy pooling reaction involving two O₂(¹δ_g) molecules.     

Synthesis and structural behavior of the P-functional organotin chlorides [Ph2P(CH2)3]2SnCl2, Ph2P(CH2)3SnCl2Me, and Ph2P(CH2)nSnCl3 (n=2, 3)

The P-functional organotin dichloride [Ph₂P(CH₂)₃]₂SnCl₂ (3) is synthesized by reaction of Ph₂P(CH₂)₃MgCl with SnCl₄ independently of the molar ratio of the starting compounds. The corresponding organotin trichlorides Ph₂P(CH₂)_nSnCl₂R (4: n=2, R=Cl; 5: n=3, R=Cl; 6: n=3, R=Me) are formed in a cleavage reaction of Ph₂P(CH₂)_nSnCy₃ (n=2, 3) with SnCl₄ or MeSnCl₃, respectively. The main features of the crystal structures of 3–6 are both intra- and intermolecular PSn coordinations and the existence of intermolecular Sn---ClSn bridges. For further characterization of the title compounds, the adducts 4(Ph₃PO)₂ (7) and 5(Ph₃PO) (8), as well as the P-oxides and P-sulfides of 3–6 (9–15), are synthesized. The results of crystal structure analyses of 7, 11, 12, and 14 are reported. The structures of 9–15 are characterized by intramolecular P=XSn interactions (X=O, S). A first insight into the structural behavior of the compounds 3–15 in solution is discussed on the basis of multinuclear NMR data.