Practical conversion from torsion space to Cartesian space for in silico protein synthesis

Many applications require a method for translating a large list of bond angles and bond lengths to precise atomic Cartesian coordinates. This simple but computationally consuming task occurs ubiquitously in modeling proteins, DNA, and other polymers as well as in many other fields such as robotics. To find an optimal method, algorithms can be compared by a number of operations, speed, intrinsic numerical stability, and parallelization. We discuss five established methods for growing a protein backbone by serial chain extension from bond angles and bond lengths. We introduce the Natural Extension Reference Frame (NeRF) method developed for Rosetta's chain extension subroutine, as well as an improved implementation. In comparison to traditional two-step rotations, vector algebra, or Quaternion product algorithms, the NeRF algorithm is superior for this application: it requires 47% fewer floating point operations, demonstrates the best intrinsic numerical stability, and offers prospects for parallel processor acceleration. The NeRF formalism factors the mathematical operations of chain extension into two independent terms with orthogonal subsets of the dependent variables; the apparent irreducibility of these factors hint that the minimal operation set may have been identified. Benchmarks are made on Intel Pentium and Motorola PowerPC CPUs.     

Parallelized Natural Extension Reference Frame: Parallelized Conversion from Internal to Cartesian Coordinates

The conversion of polymer parameterization from internal coordinates (bond lengths, angles, and torsions) to Cartesian coordinates is a fundamental task in molecular modeling, often performed using the natural extension reference frame (NeRF) algorithm. NeRF can be parallelized to process multiple polymers simultaneously, but is not parallelizable along the length of a single polymer. A mathematically equivalent algorithm, pNeRF, has been derived that is parallelizable along a polymer's length. Empirical analysis demonstrates an order-of-magnitude speed up using modern GPUs and CPUs. In machine learning-based workflows, in which partial derivatives are backpropagated through NeRF equations and neural network primitives, switching to pNeRF can reduce the fractional computational cost of coordinate conversion from over two-thirds to around 10%. An optimized TensorFlow-based implementation of pNeRF is available on GitHub at https://github.com/aqlaboratory/pnerf © 2018 Wiley Periodicals, Inc.     

Sterically-encumbered ionenes as hydroxide ion-conducting polymer membranes

Hydrogen/oxygen-based electrochemical energy conversion cells that operate under highly alkaline conditions deploy inexpensive electrocatalysts compared to their acidic counterparts. Solid polymer electrolyte (SPE) cells offer a reduced system footprint, and an additional reduction in capital cost. Alkaline membrane, SPE systems are attractive because they offer a synergistic combination of the two cost savings. Durable, hydroxide-conducting SPEs operating in highly caustic media are lacking because organic molecules and polymers, particularly their cationic derivatives, are inherently unstable to caustic conditions. This review focuses on an emerging class of alkaline SPE's, Ionenes: polymers that incorporate cations directly into the polymer backbone. The purpose of this opinion piece is to highlight the fact that fixed cationic charges may be incorporated into the polymeric backbone to provide membranes with high conductivity, mechanical strength, and stability, and to dispel the widely-held view that distancing a cationic group from the polymer backbone is a necessary requirement.     

Effect of ligand backbone substituents of nickel α‐diimine complexes on livingness/controllability of olefin polymerization: Competition between monomer isomerization and propagation

Four α‐diimine nickel complexes [(Ar? N?C(R)? C(R)?N? Ar)NiBr₂; R?H, CH₃, cyclohexane‐1,2‐diyl, naphthalene‐1,8‐diyl, Ar?2,6‐i‐Pr₂‐C₆H₃‐) were investigated in propene and hex‐1‐ene polymerization to identify the limits of backbone substituent R size needed to provide living/controlled α‐olefins polymerization by the sufficient suppression of β–H elimination transfer. Propagation kinetics measurements, molar mass on monomer conversion dependencies and reinitiation tests were used to evaluate the livingness of hex‐1‐ene polymerization. Interestingly, living/controlled hex‐1‐ene polymerization was observed in the case of all diimine derivatives including the one bearing only hydrogen atom in backbone positions. Unexpectedly, in the case of catalysts bearing H and CH₃ backbone substituents, we observed the unusual isomerization of hex‐1‐ene into internal hexenes in parallel with its polymerization. Nevertheless, by subtracting the amount of monomer consumed in isomerization side reaction, polymerization still keeps the features of living/controlled process. © 2016 Wiley Periodicals, Inc. J. Polym. Sci., Part A: Polym. Chem. 2016 , 54, 3193–3202     

On the structure and the chain conformation of side-chain liquid crystal polymers

Abstract

Backbone anisotropy and the structure of the mesophases of a series of side-chain liquid crystal polymers have been studied in the bulk by neutron scattering. The backbone conformation is obtained by small-angle neutron scattering on mixtures of hydrogenous polymers with deuteriated backbones. The components of the radius of gyration parallel, R _⊥ and perpendicular, R ∥ to the magnetic field are determined as a function of temperature for both the nematic phase and the smectic phase. It is shown that the polymer backbone is deformed in both phases. When the polymer exhibits only a nematic phase, it adopts a prolate conformation, where the average backbone direction is more or less parallel to the aligned mesogenic groups. Upon transition from the smectic phase to a nematic phase, the backbone in the nematic phase assumes a slightly oblate shape. This tendency towards oblate shape is due to the smectic fluctuations which are always present in such nematic phases. The exentricity of the oblate backbone conformation in the smectic phase is always larger than in the nematic phase. This is attributed to a periodic distribution of the backbone between the mesophase layers. Then, the backbone anisotropy depends not only on the smectic structure (S_A1, S_Ad), but also on the temperature dependence of the density of aligned mesogenic groups in the layers. On the other hand, it is shown that the isotopic mixtures are no longer ideal when polymers deuteriated in the mesogenic moieties are mixed with the corresponding hydrogenous polymers.     

Bicyclo-DNA: a Hoogsteen-selective pairing system

Background: The natural nucleic acids (DNA and RNA) can adopt a variety of structures besides the antiparallel double helix described by Watson and Crick, depending on base sequence and solvent conditions. Specifically base-paired DNA structures with regular backbone units include left-handed and parallel duplexes and triple and quadruple helical arrangements. Given the base-pairing pattern of the natural bases, preferences for how single strands associate are determined by the structure and flexibility of the sugar-phosphate backbone. We set out to determine the role of the backbone in complex formation by designing DNA analogs with well defined modifications in backbone structure.Results: We recently developed a DNA analog (bicyclo-DNA) in which one (γ) of the six torsion angles (a-ζ) describing the DNA-backbone conformation is fixed in an orientation that deviates from that observed in B-DNA duplexes by about +100°, a shift from the synclinal to the antiperiplanar range. Upon duplex formation between homopurine and homopyrimidine sequences, this analog preferentially selects the Hoogsteen and reversed Hoogsteen mode, forming A-T and G-C⁺ base pairs. Base-pair formation is highly selective, but degeneracy is observed with respect to strand orientation in the duplex.Conclusions: The flexibility and orientation of the DNA backbone can influence the preferences of the natural bases for base-pairing modes, and can alter the relative stability of duplexes and triplexes.     

Synthesis and characterization of anionic graft copolymers containing poly(ethylene oxide) grafts

Anionic graft copolymers were synthesized through grafting of poly(ethylene glycol) monomethyl ether (MPEG) onto terpolymers containing succicinic anhydride groups. The backbone polymers were prepared through radical terpolymerization of maleic anhydride, styrene, and one of the following monomers: methyl methacrylate, ethylhexyl methacrylate, and diethyl fumarate. MPEG of different molecular weights were grafted onto the backbone through reactions with the cyclic anhydride groups. In this reaction one carboxylic acid group is formed together with each ester bond. The molecular weights of MPEG were found to influence the rate of the grafting reaction and the final degree of conversion. The graft copolymers were characterized by IR, GPC, and ¹H-NMR. Thermal properties were examined by DSC. Graft copolymers containing 50% w/w of MPEG 2000 grafts were found to be almost completely amorphous, presumably because of crosslinking, and hydrogen bonding between carboxylic acid groups in the backbone and the ether oxygens in MPEG grafts. © 1995 John Wiley & Sons, Inc.     

Determination of the modes of action and synergies of xylanases by analysis of xylooligosaccharide profiles over time using fluorescence‐assisted carbohydrate electrophoresis

The structure of xylan, which has a 1,4‐linked β‐xylose backbone with various substituents, is much more heterogeneous and complex than that of cellulose. Because of this, complete degradation of xylan needs a large number of enzymes that includes GH10, GH11, and GH3 family xylanases together with auxiliary enzymes. Fluorescence‐assisted carbohydrate electrophoresis (FACE) is able to accurately differentiate unsubstituted and substituted xylooligosaccharides (XOS) in the heterogeneous products generated by different xylanases and allows changes in concentrations of specific XOS to be analyzed quantitatively. Based on a quantitative analysis of XOS profiles over time using FACE, we have demonstrated that GH10 and GH11 family xylanases immediately degrade xylan into sizeable XOS, which are converted into smaller XOS in a much lower speed. The shortest substituted XOS produced by hydrolysis of the substituted xylan backbone by GH10 and GH11 family xylanases were MeGlcA²Xyl₃ and MeGlcA²Xyl₄, respectively. The unsubstituted xylan backbone was degraded into xylose, xylobiose, and xylotriose by both GH10 and GH11 family xylanases; the product profiles are not family‐specific but, instead, depend on different subsite binding affinities in the active sites of individual enzymes. Synergystic action between xylanases and β‐xylosidase degraded MeGlcA²Xyl₄ into xylose and MeGlcA²Xyl₃ but further degradation of MeGlcA²Xyl₃ required additional enzymes. Synergy between xylanases and β‐xylosidase was also found to significantly accelerate the conversion of XOS into xylose.     

Synthesis of degradable molecular brushes via a combination of ring-opening polymerization and click chemistry

Acid-degradable molecular brushes with polycarbonate backbone and densely grafted side chains (∼1.9 SCs per backbone repeating unit) were synthesized for the first time using the grafting-onto method. Extremely efficient copper-catalyzed azide-alkyne cycloaddition click reactions between the polycarbonate backbone containing two pendant azido groups per backbone unit and alkynyl-terminated poly (methyl acrylate) (ay-PMA₇₂, average degree of polymerization DP = 72) SCs were demonstrated to finish in 10 min with a quantitative conversion of the azido groups. Similar grafting efficiencies were also achieved when using alkynyl-terminated polystyrene (ay-PS), poly(ethylene oxide) (ay-PEO), and poly (t-butyl acrylate)-b-polystyrene (ay-PtBA-b-PS) to successfully prepare molecular brushes with high grafting density (>1.8 SCs per backbone repeating unit). Under acidic condition, the polycarbonate backbones were completely degradable and the final degraded product of the molecular brushes was a linear polymer chain with molecular weight two times of the SCs. When a mixture of hydrophobic ay-PS and hydrophilic ay-PEO chains was used, amphiphilic heterobrushes PC-g-(PS-co-PEO) were synthesized, which could self-assemble into micelles or vesicles in selective solvents, depending on the ratio of the two SCs in the brush. © 2014 Wiley Periodicals, Inc. J. Polym. Sci., Part A: Polym. Chem. 2015 , 53, 239–248     

Synthesis of fluorinated polythienothiophene-co-benzodithiophenes and effect of fluorination on the photovoltaic properties

Herein, we describe the synthesis of fluorinated polythienothiophene-co-benzodithiophenes (PTBFs) and the characterization of their physical properties, especially their performance in solar cells. Fluorination of the polymer backbone lowered both the HOMO and LUMO energy levels and simultaneously widened the energy bandgap of the polymer (0.1-0.2 eV). Incorporation of fluorine into the various positions of the polymer backbone significantly affected the solar cells' power conversion efficiency from 2.3% to 7.2%. Detailed studies revealed that the polymer containing mono-fluorinated thienothiophene gave the best solar cell performance. Perfluorination of the polymer backbone led to poor compatibility with PC(71)BM molecules, thus poor solar energy conversion efficiency. This is possibly due to the enhanced self-organization properties of the polymer chains and the fluorophobicity effect. Furthermore, it was found that perfluorination of the polymer backbone resulted in poor photochemical stability against singlet oxygen attack. Theoretical studies indicated that the internal polarization caused enhancement of the negative charge density on thienothiophene rings, which rendered them vulnerable to [2+4] cycloaddition reaction with singlet oxygen.     

4,9‐Dihydro‐s‐indaceno[1,2‐b:5,6‐b′]dithiophene‐4,9‐dione functionalized copolymers for organic photovoltaic devices

The synthesis of conjugated polymers 1 – 5 functionalized with 4,9‐dihydro‐s‐indaceno[1,2‐b:5,6‐b′]dithiophene‐4,9‐dione in the backbone is reported and their use in the construction of organic solar cells is demonstrated. Increasing the molar ratio of 2,7‐dibromo‐3,8‐dihexyl‐4,9‐dihydro‐s‐indaceno[1,2‐b:5,6‐b′]dithiophene‐4,9‐dione, relative to 4,4′‐dihexyl‐5,5′‐dibromo‐2,2′‐bithiophene, in the copolymer synthesis significantly lowers the solubility of these polymers. The incorporation of highly conjugated 3,8‐dihexyl‐4,9‐dihydro‐s‐indaceno[1,2‐b:5,6‐b′]dithiophene‐4,9‐dione unit into the polymer backbone has been confirmed by UV–vis absorption. The observation of decreasing quantum yield for the emission in the order of 1 , 2 , 3 is consistent with copolymers with different comonomer content. The power conversion efficiencies of solar cells using blends of these polymers with PCBM ([6,6]‐phenyl C₆₁‐butyric acid methyl ester) were determined to be 0.11% for polymer 1 , 0.33% for 2 , and 0.26% for 3 , respectively. Under identical white light illumination, the power conversion efficiency of the device based on polymer 2 /PCBM as the active layer was three times higher compared to that of device based on polymer 1 /PCBM. Owing to the limited solubility and poor film‐forming ability of polymer 3 , the power conversion efficiency of solar cell based on 3 /PCBM blend is lower than that of 2 /PCBM blend, but is still larger than that of 1 /PCBM blend. © 2008 Wiley Periodicals, Inc. J Polym Sci Part A: Polym Chem 46: 2680–2688, 2008     

A series of bis(phosphinic)diamido yttrium complexes as initiators for lactide polymerization

A series of new bis(phosphinic)diamido yttrium complexes have been synthesized and fully characterized. The complexes adopt dimeric structures, both in solution and in the solid state, where one phosphinic group bonds to one yttrium center and the other bonds to two yttrium centers. The complexes have all been tested as initiators for the ring-opening polymerization of lactide; they are all highly active. The rate of polymerization is controlled by the diamine backbone substituent with the rate depending on the backbone flexibility. The order of decreasing rates were 2,2-dimethyl-1,3-propylene > trans-1,2-cyclohexylene > 1,2-ethylene > 1,2-phenylene. The polymerization kinetics showed, in most cases, an initiation period, during which the percentage conversion and the rate of polymerization were much lower than during propagation. This was attributed to relatively slow initiation by the bulky amido group. The initiator structure was probed using (31)P{ (1)H} NMR spectroscopy, which showed that the dimeric structure was maintained throughout the polymerization. The initiators give rise to controlled ring-opening polymerization as shown by the linear relationship between the percentage conversion and the number-average molecular weight.     

点击化学法快速合成氨基酸功能化的环糊精聚轮烷

通过叠氮-炔环加成点击反应制备了各种氨基酸功能化的生物相容性β-环糊精封端的α-环糊精聚轮烷.利用FTIR和氢核磁共振谱对产物的结构进行了表征.结果证明对于空间位阻较小的分子,点击反应能够在很短的时间(几分钟)内达到近100%的转化率.点击化学为功能化聚轮烷的制备提供了快速有效的新途径.     

FTIR Microscopy for Kinetic Measurements in High‐Throughput Photopolymerization: Experimental Design and Application

Libraries with varying composition and exposure time were developed to enable high‐throughput analysis of conversion using FTIR spectroscopy. This technique was demonstrated by measuring viscosity and backbone chain structure effects using four monomers: DPGDA, TEGDA, bisphenol‐A‐glycidyl diacrylate and ethoxylated bisphenol‐A diacrylate. DPGDA has equivalent viscosity and double bond concentration with a shorter backbone chain length as compared to TEGDA. The ultimate conversion of TEGDA copolymerizations as compared to equivalent DPGDA copolymerizations is lowered from 15 to 5% due to differences in crosslink space chemistry and glass transition temperatures of the copolymer formulation.

     

Synthesis of well‐defined comb‐like graft (co)polymers by nucleophilic substitution reaction between living polymers and polyhalohydrocarbon

A series of graft (co)polymers were synthesized by nucleophilic substitution reaction between iodinated 1,2‐polybutadiene (PB‐I, backbone) and living polymer lithium (side chains). The coupling reaction between PB‐I and living polymers can finish within minutes at room temperature, and high conversion (up to 92%) could be obtained by effectively avoiding side reaction of dimerization when living polymers were capped with 1,1‐diphenylethylene. By virtue of living anionic polymerization, backbone length, side chain length, and side chain composition, as well as graft density, were well controlled. Tunable molecular weight of graft (co)polymers with narrow molecular weight distribution can be obtained by changing either the lengths of side chain and backbone, or the graft density. Graft copolymers could also be synthesized with side chains of multicomponent polymers, such as block polymer (polystyrene‐b‐polybutadiene) and even mixed polymers (polystyrene and polybutadiene) as hetero chains. Thus, based on living anionic polymerization, this work provides a facile way for modular synthesis of graft (co)polymers via nucleophilic substitution reaction between living polymers and polyhalohydrocarbon (PB‐I). © 2013 Wiley Periodicals, Inc. J Polym Sci Part A: Polym Chem, 2013     

New alternating D–A1–D–A2 copolymer containing two electron‐deficient moieties based on benzothiadiazole and 9‐(2‐Octyldodecyl)‐8H‐pyrrolo[3,4‐b]bisthieno[2,3‐f:3',2'‐h]quinoxaline‐8,10(9H)‐dione for efficient polymer solar cells

A novel D–A₁–D–A₂ copolymer denoted as P1 containing two electron withdrawing units based on benzothiadiazole (BT) and 9‐(2‐octyldodecyl)?8H‐pyrrolo[3,4‐b] bisthieno[2,3‐f:3′,2′‐h]quinoxaline‐8,10(9H)–dione (PTQD) units was synthesized and characterized. The resulting copolymer exhibits a broad‐absorption spectrum, relatively deep lying HOMO energy level (?5.44 eV) and narrow optical bandgap (1.50 eV). Bulk heterojunction (BHJ) polymer solar cells (PSCs) based on P1 as donor and PC₇₁BM as acceptor with optimized donor to acceptor weight ratio of 1:2 and processed with DIO/CB solvent showed good photovoltaic performance with power conversion efficiency of 6.21% which is higher than that of the device processed without solvent additive (4.40%). The absorption and morphology investigations of the active layers indicated that structural and morphological changes were induced by the solvent additive. This higher power conversion efficiency could be mainly attributed to the absorption enhancement and improved charge transported in the active layer induced by the better nanoscale morphology of the active layer. This study demonstrated that a copolymer with two different acceptor moieties in the backbone may be promising candidate as donor copolymer for solution processed BHJ PSCs. © 2015 Wiley Periodicals, Inc. J. Polym. Sci., Part A: Polym. Chem. 2016 , 54, 155–168     

Modeling emulsion polymerization stabilized by polymerizable surfactants

A mathematical model for seeded emulsion polymerization stabilized with polymerizable surfactants (surfmers) was developed. The model accounts for the main features of the process and provides information about surfmer conversion as well as surfmer burying inside the polymer particles. The model was validated by comparing its predictions with the experimental results for the effect of particle size, surface properties of the surfmer, and type of initiator on surfmer conversion. The effect of surfmer reactivity on surfmer incorporation to the polymer backbone is also discussed. © 2001 John Wiley & Sons, Inc. J Polym Sci A: Polym Chem 39: 585–595, 2001     

Statistical mechanical model for diffusion of simple penetrants in polymers. I. Theory

Following Di Benedetto it is proposed that noncrystalline polymer regions possess an approximate semicrystalline order with chain bundles that are locally parallel along distances of several nanometers. Packing with on-average four nearest neighbors is assumed. A spherical molecule may move through such a substrate in two distinct ways: (a) along the axis of a “tube” formed by locally parallel chains or (b) perpendicular to this axis by two polymer chains separating sufficiently to permit passage of the molecule. The first process is relatively fast, generally requires little activation energy, and determines the effective jump length in diffusion. The second is responsible for the activation energy of diffusion, which is taken as the minimum energy necessary to produce a symmetrical chain separation which allows transfer of a molecule. This is calculated as a function of the penetrant diameter d and parameters Γ and β which characterize the interchain cohesion and chain stiffness, respectively. Γ is estimated from the polymer density and cohesive energy density by suitably linearizing a relation given by Di Benedetto for the potential between two polymer chains approximated as infinite strings of Lennard-Jones force centers. β is shown to be approximately obtainable from the polymer chain backbone geometry and bond rotation potentials. An expression for the diffusion coefficient D is developed which contains only one disposable parameter, the effective jump length.     

Synthesis of sansalvamide A peptidomimetics: triazole, oxazole, thiazole, and pseudoproline containing compounds

Peptidomimetic-based macrocycles typically have improved pharmacokinetic properties over those observed with peptide analogs. Described are the syntheses of 13 peptidomimetic derivatives that are based on active Sansalvamide A structures, where these analogs incorporate heterocycles (triazoles, oxazoles, thiazoles, or pseudoprolines) along the macrocyclic backbone. The syntheses of these derivatives employ several approaches that can be applied to convert a macrocyclic peptide into its peptidomimetic counterpart. These approaches include peptide modifications to generate the alkyne and azide for click chemistry, a serine conversion into an oxazole, a Hantzsch reaction to generate the thiazole, and protected threonine to generate the pseudoproline derivatives. Furthermore, we show that two different peptidomimetic moieties, triazoles and thiazoles, can be incorporated into the macrocyclic backbone without reducing cytotoxicity: triazole and thiazole.     

Computational study on nonenzymatic peptide bond cleavage at asparagine and aspartic acid

Nonenzymatic peptide bond cleavage at asparagine (Asn) and glutamine (Gln) residues has been observed during peptide deamidation experiments; cleavage has also been reported at aspartic acid (Asp) and glutamic acid (Glu) residues. Although peptide backbone cleavage at Asn is known to be slower than deamidation, fragmentation products are often observed during peptide deamidation experiments. In this study, mechanisms leading to the cleavage of the carboxyl-side peptide bond of Asn and Asp residues were investigated using computational methods (B3LYP/6-31+G**). Single-point solvent calculations at the B3LYP/6-31++G** level were carried out in water, utilizing the integral equation formalism-polarizable continuum (IEF-PCM) model. Mechanism and energetics of peptide fragmentation at Asn were comparatively analyzed with previous calculations on deamidation of Asn. When deamidation proceeds through direct hydrolysis of the Asn side chain or through cyclic imide formationvia a tautomerization routeit exhibits lower activation barriers than peptide bond cleavage at Asn. The fundamental distinction between the mechanisms leading to deamidationvia a succinimideand backbone cleavage was found to be the difference in nucleophilic entities involved in the cyclization process (backbone versus side-chain amide nitrogen). If deamidation is prevented by protein three-dimensional structure, cleavage may become a competing pathway. Fragmentation of the peptide backbone at Asp was also computationally studied to understand the likelihood of Asn deamidation preceding backbone cleavage. The activation barrier for backbone cleavage at Asp residues is much lower (approximately 10 kcal/mol) than that at Asn. This suggests that peptide bond cleavage at Asn residues is more likely to take place after it has deamidated into Asp.