Configuration Of Side Chain Research Articles

Role of the side chain configuration on the effective recovery of phenolic compounds using polymer inclusion membranes based on tertiary amine

Polymer inclusion membranes (PIMs) exhibit great potential in the separation and recovery of valuable materials from wastewater and secondary resources. In this work, the effect of alkyl chain configuration of the functional carriers on the physicochemical properties and permeability of PIMs was investigated. Three tertiary amine isomers with different alkyl chain configurations were selected as carriers: trioctylamine, triisooctylamine, and tris(2-ethylhexyl)amine. Operating conditions like carrier contents, feed solution pH, phenol concentration, and stripping solution properties were also investigated. The results obtained in this study indicate that tertiary amines with less branched alkyl chains perform better phenol transport efficiency. Furthermore, the transport efficiency decreased rapidly with increasing steric hindrance of the carriers. Trioctylamine-based PIM displayed optimal extraction efficiency of 92.8 % and stripping efficiency of 90.8 % due to its lower steric hindrance, higher hydrophilicity, and larger crystallinity. Phenol extraction and stripping efficiencies remained above 85.7 % and 80.8 % after 8 cycles, demonstrating excellent stability.

Tailored thermoelectric performance of poly(phenylene butadiynylene)s/carbon nanotubes nanocomposites towards wearable thermoelectric generator application

In this study, two conjugated polymers (CPs) featuring poly(phenylene butadiynylene) (PPB) were meticulously synthesized and composited with single-walled carbon nanotubes (SWCNTs) to investigate their thermoelectric properties and fabricate wearable thermoelectric generators (TEGs). These CPs, designated as P1 and P2, were tailored with distinct side chain configurations by incorporating 2-butyloctyloxy and 6-(methyldioctylsilyl)hexyloxy groups, respectively. Notably, P2, characterized by longer side chains with branchpoints farther from the backbone, exhibited planar backbone structure and enhanced solubility, consequently engendering stronger π–π interaction with SWCNTs and facilitating the disperse of SWCNTs through polymer wrapping at bundle surface. Such characteristics therefore contributed to the superior thermoelectric performances of the P2/SWCNTs nanocomposite, yielding a higher power factor (PF) of 216.5 μW m−1 K−2 for the spin-coated film. Furthermore, the corresponding wearable TEGs, which were constructed through spray-coating with 14 legs, resulted in an output power of approximately 49.6 nW under a temperature difference of 25 K, exhibiting successful harvesting of waste heat. Further applications also demonstrated operational efficacy under diverse conditions. These findings not only underscored the significance of side chain engineering in tailoring the thermoelectric properties of CP/SWCNTs nanocomposites but also demonstrated the feasibility of fabricating high-performance wearable thermoelectric devices applicable in versatile contexts.

Mechanical Properties of Polydiacetylene Multilayers Studied by AFM Force Spectroscopy.

The blue-to-red chromatic phase transition of polydiacetylene (PDA) is accompanied by the twist and rearrangement of its side chains, which results in shortening of the conjugation length in the backbone. However, how these morphological changes affect its mechanical properties remains elusive. In this work, force spectroscopy mapping by atomic force microscopy was employed to quantify mechanical parameters of PDA thin films such as breakthrough force and Young's modulus at the monomer, blue, and red phases during the chromatic transition. We found that the breakthrough force increased by 113% and Young's modulus decreased by 21% during the blue-to-red transition, highlighting that the subtle change in the side-chain configuration has a dramatic impact on its mechanical properties.

DiAMoNDBack: Diffusion-Denoising Autoregressive Model for Non-Deterministic Backmapping of Cα Protein Traces.

Coarse-grained molecular models of proteins permit access to length and time scales unattainable by all-atom models and the simulation of processes that occur on long time scales, such as aggregation and folding. The reduced resolution realizes computational accelerations, but an atomistic representation can be vital for a complete understanding of mechanistic details. Backmapping is the process of restoring all-atom resolution to coarse-grained molecular models. In this work, we report DiAMoNDBack (Diffusion-denoising Autoregressive Model for Non-Deterministic Backmapping) as an autoregressive denoising diffusion probability model to restore all-atom details to coarse-grained protein representations retaining only Cα coordinates. The autoregressive generation process proceeds from the protein N-terminus to C-terminus in a residue-by-residue fashion conditioned on the Cα trace and previously backmapped backbone and side-chain atoms within the local neighborhood. The local and autoregressive nature of our model makes it transferable between proteins. The stochastic nature of the denoising diffusion process means that the model generates a realistic ensemble of backbone and side-chain all-atom configurations consistent with the coarse-grained Cα trace. We train DiAMoNDBack over 65k+ structures from the Protein Data Bank (PDB) and validate it in applications to a hold-out PDB test set, intrinsically disordered protein structures from the Protein Ensemble Database (PED), molecular dynamics simulations of fast-folding mini-proteins from DE Shaw Research, and coarse-grained simulation data. We achieve state-of-the-art reconstruction performance in terms of correct bond formation, avoidance of side-chain clashes, and the diversity of the generated side-chain configurational states. We make the DiAMoNDBack model publicly available as a free and open-source Python package.

Stereochemistry of aminoacylated cardiolipins and phosphatidylglycerols from bacteria.

Hydrophilic interaction liquid chromatography (HILIC) connected with electrospray high-resolution tandem mass spectrometry (MS) was used for the analysis of unusual amino acid (AA) substituted phosphatidylglycerols (PG) and cardiolipins (CL) in mesophilic and thermophilic bacteria. Individual peaks from the lipid class separation by HILIC were isolated and hydrolyzed to determine the absolute configuration of the aminoacyl side chain. The configuration of the aminoacyl side chain was assigned by indirect liquid chromatography (LC) enantiomer separation after the hydrolysis of the aminoacylated (aminoacyl) lipids using N-(4-nitrophenoxycarbonyl)-l-phenylalanine 2-methoxyethyl ester as chiral derivatizing agent and reversed phase LC-MS for analysis. When two chromatographic methods were combined, less common AAs, such as d-allo-Ile and d-allo-Thr, were identified. The taxonomic classification of bacteria showed that bacteria of the family Bacillaceae (Bacillus and Geobacillus) produce branched-chain AAs, that is, d-allo-Ile, d-Ile, and d-Leu. These AAs were present only in the genera Bacillus and Geobacillus and not in Alicyclobacillus acidoterrestris (family Alicyclobacillaceae). On the contrary, hydroxy AAs, that is, l- and d-Thr, and l- and d-allo-Thr, were identified as aminoacyl-PG and aminoacyl-CL in A. acidoterrestris and were not present in the genera Bacillus and Geobacillus. Therefore, the complete analysis made it possible to identify the stereochemistry of AAs in aminoacyl PGs and CLs and use this fact for chemotaxonomy.

CSIMH: Design of an Efficient Security-Aware Customized Sidechaining Model via Iterative Meta-Heuristics

Blockchains are a secure alternative for long-length data storage & security deployments. Though blockchains are unbounded, their quality of service (QoS) performance reduces after adding a certain number of blocks. Thus, sidechains have become essential for making the system decentralized, secure, and effective for use thereby improving their scalability & QoS performance. Sidechains reduce data storage and extraction delays. However, all sidechains of a single blockchain are the same in size, capacity, and security. This limits their application to real-world use cases that require dynamic security. To overcome this limitation, the authors propose a meta-heuristic approach to design a system that produces customized sidechains based on the quantity and quality of data stored on the chain. The model uses a machine-learning approach to find the best possible sidechain configuration for different data types. It makes the system fast and scalable and improves storage & memory efficiency. The proposed model is tested on multiple data sets and compared with various state-of-art sidechain deployments. An improvement of 18% in terms of mining speed, 27% in terms of energy efficiency, 10% with regards to throughput, and 8% concerning packet delivery ratio is observed. The model is tested under various attacks and faulty nodes to validate its security performance. A consistent QoS performance is observed for the proposed model under these attack types, thereby validating its resiliency for different attacks. This enhancement in performance makes the proposed model eligible for deployment in high-speed, low-energy, and high-security applications like IoT, mobile ad-hoc networks, and sensor networks.

Structural Organization of Asphaltenes and Resins and Composition of Low Polar Components of Heavy Oils

Comparative characteristics of resins, asphaltenes, and low polar components of heavy oils from the Ashalchinskoye (I) and Nurlatskoye (II) oil fields (Republic of Tatarstan, Russia) are given. These oils differ in the age of host rocks (Permian and Devonian, respectively) and the content of their components and heteroatoms. An X-ray phase analysis and scanning and transmission electron microscopy reveal that, in contrast to smooth surface asphaltenes of oil I, asphaltenes of oil II are characterized by a loose and porous surface and smaller sizes of nanoaggregates. Nanoaggregates form a disorderly tangled structure because of the alkyl side-chain configuration, which makes it difficult to stack aromatic sheets. The crystallites of nanoaggregates of asphaltenes of oil II are smaller than the crystallites of nanoaggregates of asphaltenes of oil I. The application of the method of structural-group analysis based on the use of the measured indicators of the elemental composition, average molecular weights, and the results of 1H NMR spectroscopy made it possible to establish that overall sizes of mean molecules of resins and asphaltenes of heavy oil I are larger due to the increased content of aromatic and naphthenic cycles in the naphthenoaromatic system. A feature of the structure of the resin–asphaltene components of oil II is a greater number of alkyl substituents in the side chains. According to gas chromatography–mass spectrometry (GC–MS) analysis, the low polar components under study are characterized by a similar set of saturated hydrocarbons (n-alkanes, mono-, and polycycloalkanes) but differ in the composition of identified aromatic hydrocarbons and heteroorganic compounds. A feature of the low polar components of oil II is the presence of a wider range of n-alkyl- and phenylalkyl-substituted benzenes and nitrogen- and oxygen-organic compounds in their composition.

Enhanced Organic Electrochemical Transistor Performance of Donor-Acceptor Conjugated Polymers Modified with Hybrid Glycol/Ionic Side Chains by Postpolymerization Modification.

Emergent bioelectronic technologies are underpinned by the organic electrochemical transistor (OECT), which employs an electrolyte medium to modulate the conductivity of its organic semiconductor channel. Here we utilize postpolymerization modification (PPM) on a conjugated polymer backbone to directly introduce glycolated or anionic side chains via fluoride displacement. The resulting polymers demonstrated increased volumetric capacitances, with subdued swelling, compared to their parent polymer in p-type enhancement mode OECTs. This increase in capacitance was attributed to their modified side chain configurations enabling cationic charge compensation for thin film electrochemical oxidation, as deduced from electrochemical quartz crystal microbalance measurements. An overall improvement in OECT performance was recorded for the hybrid glycol/ionic polymer compared to the parent, owing to its low swelling and bimodal crystalline orientation as imaged by grazing-incidence wide-angle X-ray scattering, enabling its high charge mobility at 1.02 cm2·V-1·s-1. Compromised device performance was recorded for the fully glycolated derivative compared to the parent, which was linked to its limited face-on stacking, which hindered OECT charge mobility at 0.26 cm2·V-1·s-1, despite its high capacitance. These results highlight the effectiveness of anionic side chain attachment by PPM as a means of increasing the volumetric capacitance of p-type conjugated polymers for OECTs, while retaining solid-state macromolecular properties that facilitate hole transport.

Towards high-throughput screening (HTS) of polyhydroxyalkanoate (PHA) production via Fourier transform infrared (FTIR) spectroscopy of Halomonas sp. R5-57 and Pseudomonas sp. MR4-99.

High-throughput screening (HTS) methods for characterization of microbial production of polyhydroxyalkanoates (PHA) are currently under investigated, despite the advent of such systems in related fields. In this study, phenotypic microarray by Biolog PM1 screening of Halomonas sp. R5-57 and Pseudomonas sp. MR4-99 identified 49 and 54 carbon substrates to be metabolized by these bacteria, respectively. Growth on 15 (Halomonas sp. R5-57) and 14 (Pseudomonas sp. MR4-99) carbon substrates was subsequently characterized in 96-well plates using medium with low nitrogen concentration. Bacterial cells were then harvested and analyzed for putative PHA production using two different Fourier transform infrared spectroscopy (FTIR) systems. The FTIR spectra obtained from both strains contained carbonyl-ester peaks indicative of PHA production. Strain specific differences in the carbonyl-ester peak wavenumber indicated that the PHA side chain configuration differed between the two strains. Confirmation of short chain length PHA (scl-PHA) accumulation in Halomonas sp. R5-57 and medium chain length PHA (mcl-PHA) in Pseudomonas sp. MR4-99 was done using Gas Chromatography-Flame Ionization Detector (GC-FID) analysis after upscaling to 50 mL cultures supplemented with glycerol and gluconate. The strain specific PHA side chain configurations were also found in FTIR spectra of the 50 mL cultures. This supports the hypothesis that PHA was also produced in the cells cultivated in 96-well plates, and that the HTS approach is suitable for analysis of PHA production in bacteria. However, the carbonyl-ester peaks detected by FTIR are only indicative of PHA production in the small-scale cultures, and appropriate calibration and prediction models based on combining FTIR and GC-FID data needs to be developed and optimized by performing more extensive screenings and multivariate analyses.

Design and synthesis of novel orexin 2 receptor agonists with a 1,3,5‑trioxazatriquinane skeleton

A novel series of 1,3,5‑trioxazatriquinane with multiple effective residues (TriMER) derivatives with amino-methylene side chains was designed and synthesized based on the docking-simulation results between orexin receptors (OXRs) and TriMER-type OXR antagonists. In vitro screening against orexin receptors identified six TriMER derivatives with a cis side-chain configuration, and, among these, 20d and 28d showed full agonist activity against OX2R at a concentration of 10 µM. To determine the absolute stereochemistry of these hit compounds, we also conducted the first asymmetric synthesis of a 1,3,5‑trioxazatriquinane skeleton using a Katsuki–Sharpless asymmetric epoxidation as the key reaction and obtained a set of the individual stereoisomers. After evaluating their activity, (+)-20d (EC50 = 3.87 μM for OX2R) and (+)-28d (EC50 = 1.62 μM for OX2R) were determined as eutomers for OX2R agonist activity. Our results provide a new class of skeleton consisting of an (R)-1,3,5‑trioxazatriquinane core with flexible methylene linkers and hydrophobic substituents at the terminals of the side chains via carbamates/sulfonamides as OX2R agonists.

Design of heuristic model to improve blockchain-based sidechain configuration

Design of heuristic model to improve blockchain-based sidechain configuration

Impact of Side-Chain Hydrophilicity on Packing, Swelling, and Ion Interactions in Oxy-Bithiophene Semiconductors.

Exchanging hydrophobic alkyl-based side chains to hydrophilic glycol-based side chains is a widely adopted method for improving mixed-transport device performance, despite the impact on solid-state packing and polymer-electrolyte interactions being poorly understood. Presented here is a molecular dynamics (MD) force field for modeling alkoxylated and glycolated polythiophenes. The force field is validated against known packing motifs for their monomer crystals. MD simulations, coupled with X-ray diffraction (XRD), show that alkoxylated polythiophenes will pack with a "tilted stack" and straight interdigitating side chains, whilst their glycolated counterpart will pack with a "deflected stack" and an s-bend side-chain configuration. MD simulations reveal water penetration pathways into the alkoxylated and glycolated crystals-through the π-stack and through the lamellar stack respectively. Finally, the two distinct ways triethylene glycol polymers can bind to cations are revealed, showing the formation of a metastable single bound state, or an energetically deep double bound state, both with a strong side-chain length dependence. The minimum energy pathways for the formation of the chelates are identified, showing the physical process through which cations can bind to one or two side chains of a glycolated polythiophene, with consequences for ion transport in bithiophene semiconductors.

Dynamic regulation of Zn(II) sequestration by calgranulin C.

Calgranulin C performs antimicrobial activity in the human immune response by sequestering Zn(II). This biological function is afforded with the aid of two structurally distinct Ca(II)-binding EF hand motifs, wherein one of which bears an unusual amino acid sequence. Here, we utilize solution state NMR relaxation measurements to investigate the mechanism of Ca(II)-modulated enhancement of Zn(II) sequestration by calgranulin C. Using C13 /N15 CPMG dispersion experiments we have measured pH-dependent major and minor state populations exchanging on micro-to-millisecond timescale. This conformational exchange takes place exclusively in the Ca(II)-bound state and can be mapped to residues located in the EF-I loop and the linker between the tandem EF hands. Molecular dynamics (MD) simulations spanning nano-to-microsecond timescale offer insights into the role of pH-dependent electrostatic interactions in EF-hand dynamics. Our results suggest a pH-regulated dynamic equilibrium of conformations that explore a range of "closed" and partially "open" sidechain configurations within the Zn(II) binding site. We propose a novel mechanism by which Ca(II) binding to a non-canonical EF loop regulates its flexibility and tunes the antimicrobial activity of calgranulin C.

High Plasticity of the Amicetin Biosynthetic Pathway in Streptomyces sp. SHP 22-7 Led to the Discovery of Streptcytosine P and Cytosaminomycins F and G and Facilitated the Production of 12F-Plicacetin.

A chemical reinvestigation of the Indonesian strain Streptomyces sp. SHP 22-7 led to the isolation of three new pyrimidine nucleosides, along with six known analogues and zincphyrin. The structures of the new compounds (6, 7, 10) were elucidated by employing spectroscopic techniques (NMR, MS, CD, and IR) as well as enantioselective analyses of methyl branched side chain configurations. Application of the precursor-directed feeding approach led to the production and partial isolation of nine further pyrimidine analogues. The new compounds 6, 7, and 11 and three of the known compounds (2-4) were found to possess antimycobacterial and cytotoxic properties.

The Effects of Side-Chain Configurations of a Retro-Inverso-Type Inhibitor on the Human T-Cell Leukemia Virus (HTLV)-1 Protease.

In this study, the effects of side-chain configurations of D-Ile residues of a retro–inverso (RI)-type inhibitor on the human T-cell leukemia virus type 1 (HTLV-1) protease containing a hydroxyethylamine dipeptide isostere were clarified. Prior to evaluation using the RI-type inhibitor, the effects of side-chain configurations of Ile residues of the substrate peptide on the HTLV-1 protease were examined to estimate the influence of side-chain configurations on enzyme activity. Based on the estimation of the influence of side-chain configurations on protease affinity, the RI-type inhibitors containing a D-allo-Ile residue in the corresponding substrate sequence, instead of a D-Ile residue, were synthesized via 9-fluorenylmethoxycarbonyl-based solid-phase peptide synthesis. Refolded recombinant HTLV-1 protease (1-116, L40I) was used for the simple and short evaluation of the inhibitory activities of the synthesized RI-type inhibitors. The results clearly indicated that mimicking the whole topology, comprising both the main- and side-chain structures of the parent inhibitor, is effective for the design of potent RI-modified protease inhibitors.

Towards enantioselective ultrahigh performance liquid chromatography-mass spectrometry-based metabolomics of branched-chain fatty acids and anteiso-fatty acids under reversed-phase conditions using sub-2-μm amylose- and cellulose-derived chiral stationary phases.

Branched-chain fatty acids (BCFAs) are mostly saturated fatty acids with one or more methyl, seldom ethyl, branches in the alkyl chain. They are derived from branched-chain amino acids, ruminant-derived food, or biosynthetic side products of acetyl-CoA carboxylase. They possess iso- (branching at penultimate carbon) and anteiso-fatty acid structure (branching at antepenultimate carbon) or are branched at any other position of the carbon chain. Except for iso-fatty acids, BCFAs are chiral. They are commonly analyzed by GC-MS, while there is a lack of enantioselective LC-MS methods. In this work, we present a methodology for targeted enantioselective UHPLC-ESI-MS/MS metabolomics of BCFAs. It makes use of precolumn derivatization with 1-naphthylamine and reversed-phase elution conditions. A homologous series of short BCFA analytes with distinct chain lengths (having up to eight carbon atoms), branching type (methyl or ethyl), and position of branching (2, 3, and 4, anteiso and iso) has been systematically studied on six commercially available polysaccharide UHPLC columns. Chiralpak IB-U exhibited the highest and broadest enantioselectivity while IH-U maintained enantioselectivity also for BCFAs with chirality distant from the carboxylic function (i.e., with other branching than in 2-position). The method was used to assign the absolute configuration of a 4-methylhexanoic acid side chain of a natural product from Streptomyces sp. SHP 22-7. The potential of the corresponding UHPLC-ESI-QTOF-MS/MS assay for analyzing stereoselectively BCFAs and other short organic acids by untargeted analysis in human urine was further elucidated in a preliminary proof-of-principle test.

Design of heuristic model to improve block-chain-based sidechain configuration

Design of heuristic model to improve block-chain-based sidechain configuration

Isolation, absolute configurations and bioactivities of pestaphilones A–I: Undescribed methylated side chain containing-azaphilones from Pestalotiopsis oxyanthi

Nine undescribed side chain containing azaphilones, pestaphilones A–I, were isolated from the Anoectochilus roxburghii endophytic fungus Pestalotiopsis oxyanthi. The structures of these isolates were identified by spectroscopic data, electronic circular dichroism (ECD) calculations and comparisons, quantum-chemical 13C NMR calculations with DP4+ probability analysis, Rh2(OCOCF3)4-induced ECD, acetonide formation, selective oxidation reaction and X-ray crystallographic data. Structurally, pestaphilones A–I were the first azaphilones characteristically formed via a methyl group at C-9 in the C7 side chain. More importantly, a selective oxidation reaction was firstly set up to resolve the absolute configuration of flexible side chain containing azaphilones, and an acetonide formation based Rh2(OCOCF3)4-induced ECD experiment was performed to identify the configurations of the oxygenated pyranoquinone core in the azaphilones. In bioassay, pestaphilones A–F displayed potential immunosuppressive activity in concanavalin A (Con A)-induced T lymphocyte proliferation, with IC50 values ranging from (9.36 ± 1.14) μM to (35.21 ± 3.25) μM.

Synthesis and evaluation of enantiomers of hydroxychloroquine against SARS-CoV-2 in vitro

Since the end of 2019, the outbreak of Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) has evolved into a global pandemic. There is an urgent need for effective and low-toxic antiviral drugs to remedy Remdesivir’s limitation. Hydroxychloroquine, a broad spectrum anti-viral drug, showed inhibitory activity against SARS-CoV-2 in some studies. Thus, we adopted a drug repurposing strategy, and further investigated hydroxychloroquine. We obtained different configurations of hydroxychloroquine side chains by using chiral resolution technique, and successfully furnished R-/S-hydroxychloroquine sulfate through chemical synthesis. The R configuration of hydroxychloroquine was found to exhibit higher antiviral activity (EC50 = 3.05 μM) and lower toxicity in vivo. Therefore, R-HCQ is a promising lead compound against SARS-CoV-2. Our research provides new strategy for the subsequent research on small molecule inhibitors against SARS-CoV-2.

Non-Covalent Carrier Hydrophobicity as a Universal Predictor of Intracellular Protein Activity.

Over the past decade, extensive optimization of polymeric cell-penetrating peptide (CPP) mimics (CPPMs) by our group has generated a substantial library of broadly effective carriers which circumvent the need for covalent conjugation often required by CPPs. In this study, design rules learned from CPPM development were applied to reverse-engineer the first library of simple amphiphilic block copolypeptides for non-covalent protein delivery, namely, poly(alanine-block-arginine), poly(phenylalanine-block-arginine), and poly(tryptophan-block-arginine). This new CPP library was screened for enhanced green fluorescent protein and Cre recombinase delivery alongside a library of CPPMs featuring equivalent side-chain configurations. Due to the added hydrophobicity imparted by the polymer backbone as compared to the polypeptide backbone, side-chain functionality was not a universal predictor of carrier performance. Rather, overall carrier hydrophobicity predicted the top performers for both internalization and activity of protein cargoes, regardless of backbone identity. Furthermore, comparison of protein uptake and function revealed carriers which facilitated high gene recombination despite remarkably low Cre internalization, leading us to formalize the concept of intracellular availability (IA) of the delivered cargo. IA, a measure of cargo activity per quantity of cargo internalized, provides valuable insight into the physical relationship between cellular internalization and bioavailability, which can be affected by bottlenecks such as endosomal escape and cargo release. Importantly, carriers with maximal IA existed within a narrow hydrophobicity window, more hydrophilic than those exhibiting maximal cargo uptake. Hydrophobicity may be used as a scaffold-independent predictor of protein uptake, function, and IA, enabling identification of new, effective carriers which would be overlooked by uptake-based screening methods.