Molecular Structural Characterization Research Articles

Molecular Structural Characterization of Supercorenene and Triangle-Shaped Discotic Graphene

Chemical and biological properties of polycyclic aromatic compounds rely intimately upon their structures such as the fundamental molecular topology. In this way, quantitative structure-activity and property relationship (QSAR/QSPR) strategies have been formulated for predicting properties of polycyclic benzenoid hydrocarbons and related graphs from their chemical structures. In this paper, we give the exact analytical expression of three types of polycyclic aromatic compounds where the base molecule of these structure contains hexabenzocorenene (HBC). Furthermore, we research the results by MATLAB and obtain the relationship of the indices which they portray the physcio-chemical properties.

Molecular Methods for Assessing the Morphology, Topology, and Performance of Polyamide Membranes.

The molecular-scale morphology and topology of polyamide composite membranes determine the performance characteristics of these materials. However, molecular-scale simulations are computationally expensive and morphological and topological characterization of molecular structures are not well developed. Molecular dynamics simulation and analysis methods for the polymerization, hydration, and quantification of polyamide membrane structures were developed and compared to elucidate efficient approaches for producing and analyzing the polyamide structure. Polymerization simulations that omitted the reaction-phase solvent did not change the observed hydration, pore-size distribution, or water permeability, while improving the simulation efficiency. Pre-insertion of water into the aggregate pores (radius ≈ 4 Å) of dry domains enabled shorter hydration simulations and improved simulation scaling, without altering pore structure, properties, or performance. Medial axis and Minkowski functional methods were implemented to identify permeation pathways and quantify the polyamide morphology and topology, respectively. Better agreement between simulations and experimentally observed systems was accomplished by increasing the domain size rather than increasing the number of ensemble realizations of smaller systems. The largest domain hydrated was an order of magnitude larger by volume than the largest domain previously reported. This work identifies methods that can enable more efficient and meaningful fundamental modeling of membrane materials.

Retracted] On the Temperature Indices of Molecular Structures of Some Networks

The topological index is a molecular predictor that is commonly supported in the research of QSAR of pharmaceuticals to numerically quantify their molecular features. Theoretical and statistical study of drug‐like compounds improves the drug design and finding work‐flow by rationalizing lead detection, instant decision, and mechanism of action comprehension. Using molecular structure characterization and edge segmentation technique, we computed the general temperature topological indices for OTIS networks.

Molecular characterization of gut microbial structure and diversity associated with colorectal cancer patients in Egypt.

a large number of microbes colonizing the gut are highly diverse and complex in their structure, as this complex structure of gut microbiota acts as an indicator of a diseased state. Recently, there is a need for improved biomarkers for colorectal cancer (CRC) and advanced adenoma. Among the CRC associated organisms, bacteria are the most common causes of serious disease and deaths. To understand the dynamic interaction among bacteria colonizing the gut, different approaches have been implicated. in this study, faecal microbial markers were evaluated for detecting CRC. As most of these organisms are anaerobic, different molecular tools are of great values for rapid detection of these bacteria. Samples from Tumor Hospital were screened for the presence of different pathogens by both usual polymerase chain reaction (PCR) and a real-time assay. in a total of 34 samples, by PCR method, bifidobacterium, fusobacterium and Escherichia coli (E. coli) were mainly identified in almost all samples. However, a clear variation in bacterial composition could be observed in Porphyromonas gingivalis, Prevotella intermedia and Peptostreptococcus magnus, where positive results could be detected only in diseased samples. In addition, E. faecium and E. saphenum were mainly identified in diseased samples. In contrast, providencia could be detected mainly in control samples. In realtime assay, the relative abundance was higher for fusobacterium and bifidobacterium markers in CRC patients compared to control samples. However, such increased in abundance has never been observed in both fusobacterium and bifidobacterium in the same sample. these results demonstrated increased abundance of fusobacterium or bifidobacterium can be considered as a sign for impairment or a diseased condition and the possibility of use of the faecal microbiotain CRC patients as a marker for detecting the disease.

Molecular structure characterization of middle-high rank coal via 13C NMR, XPS and FTIR spectroscopy

Elemental analysis, 13C nuclear magnetic resonance (NMR) spectroscopy, X-ray photoelectron spectroscopy (XPS), Fourier transform infrared spectroscopy (FTIR), combined with Grand Canonical ensemble Monte Carlo (GCMC) simulations and energy minimizations were used to establish the molecular structure model of middle-high coal rank accurately. The three-dimensional molecular structure models of middle-high coal rank (from the No. 6 Mine of Pingdingshan (PDS) Mining Area and the No. 4 Mine of Hebi (HB) Mining Area in Henan Province, Xiegou (XG) Mine, Changping (CP) Mine, and Sihe (SH) Mine in Shanxi Province, China) were optimized and constructed. The results showed that the structural arrangement is more orderly and compact with the increase of coal rank. The established molecular formulae for PDS, HB, XG, CP, and SH are respectively C69H43NO3, C166H93N3O8, C191H125N3O7, C169H105N3O7, and C221H123N3O7.

Degree Based Weighted Entropy Indices of Hyaluronic Acid-Curcumin Conjugates: an Anti-Tumor Drug

The topological index is a molecular predictor that is commonly supported in the research of QSAR of pharmaceuticals to numerically quantify their molecular features. Theoretical and statistical study of drug-like compounds improves the drug design and finding work-flow by rationalizing lead detection, instant decision, and mechanism of action comprehension. Using molecular structure characterization and edge segmentation technique, we have computed degree-based entropy and edge weight-based entropy indices of hyaluronic acid-curcumin conjugate which is used as an anti-cancer drug.

VDB Entropy Measures and Irregularity-Based Indices for the Rectangular Kekulene System

Theoretical chemists are fascinated by polycyclic aromatic hydrocarbons (PAHs) because of their unique electromagnetic and other significant properties, such as superaromaticity. The study of PAHs has been steadily increasing because of their wide-ranging applications in several fields, like steel manufacturing, shale oil extraction, coal gasification, production of coke, tar distillation, and nanosciences. Topological indices (TIs) are numerical quantities that give a mathematical expression for the chemical structures. They are useful and cost-effective tools for predicting the properties of chemical compounds theoretically. Entropic network measures are a type of TIs with a broad array of applications, involving quantitative characterization of molecular structures and the investigation of some specific chemical properties of molecular graphs. Irregularity indices are numerical parameters that quantify the irregularity of a molecular graph and are used to predict some of the chemical properties, including boiling points, resistance, enthalpy of vaporization, entropy, melting points, and toxicity. This study aims to determine analytical expressions for the VDB entropy and irregularity-based indices in the rectangular Kekulene system.

Immunomodulatory and antivirus activities of bioactive polysaccharides and structure-function relationship

Bioactive polysaccharides with immunomodulatory and antivirus effects have been widely investigated. However, due to the complexity of molecular structure and insufficient characterization, the correlation between structure and immunomodulatory/antivirus bioactivities have not been well summarized. This review highlights three most studied polysaccharides (i.e. mannan, pectin and glucan) with promising immunomodulatory activities, and the antivirus effects of sulfated polysaccharides and possible mechanisms are also discussed. The proposed structure-function relationship will help extend the application of bioactive polysaccharides as key ingredients in plant-based food, cosmetics, or therapeutic products.

Molecular structure characterization of coal under the water–rock interaction in acid mine drainage (AMD)

AMD weakens the compressive strength of coal pillar and threatens the safety of coal mine production. In order to study the effect of AMD on coal, this paper uses X-ray diffraction (XRD) and Fourier transform infrared (FTIR) test techniques to detect the molecular structure of coal samples treated with different immersion acidity and immersion time. The results show that with the increase of soaking acidity and soaking time, the layer spacing (d002) from 0.349 to 0.353 and La from 55.719 to 57.420 nm, showing a positive correlation; Lc from 1.85 to 1.66 nm and N from 5.31 to 4.71, showing a negative correlation. It shows that the original microcrystalline structure in the coal sample changes due to the chemical reaction of organic matter, the spacing and average diameter of the microcrystalline layers increase, the average height and the number of carbon layers decrease, and the degree of order gradually decreases. Aromatic hydrogen(farH), aromatic carbon(farc), the relative abundance of aromatic and aliphatic functional groups(I) and A(CH2)/A(CH3) gradually decrease, degree of condensation (DOC) and oxygen-containing structural(‘C’) gradually increase. The research results show the molecular structure characteristics of coal in AMD water–rock interaction, and provide a reference for studying the macroscopic characteristics of coal under the action of AMD.

Parallel NMR Supersequences: Ten Spectra in a Single Measurement.

The principles employed in parallel NMR and MRI are applied to NMR supersequences yielding as many as ten 2D NMR spectra in one measurement. We present a number of examples where two NOAH (NMR by Ordered Acquisition using 1H-detection) supersequences are recorded in parallel, thus dramatically increasing the information content obtained in a single NMR experiment. The two parallel supersequences entangled by time-sharing schemes (IPAP-seHSQC, HSQC-COSY, and HSQC-TOCSY) incorporate also modified (sequential and/or interleaved) conventional pulse schemes (modules), including HMBC, TOCSY, COSY, CLIP-COSY, NOESY, and ROESY. Such parallel supersequences can be tailored for specific applications, for instance, the analysis and characterization of molecular structure of complex organic molecules from a single measurement. In particular, the CASPER software was used to establish the structure of a tetrasaccharide, β-LNnTOMe, with a high degree of confidence from a single measurement involving a parallel NOAH-5 supersequence.

Molecular Level Structural Characterization of Self-Assembled Monolayers of Functionalized Bidentate Aromatic Thiols

Molecular Level Structural Characterization of Self-Assembled Monolayers of Functionalized Bidentate Aromatic Thiols

Highly Selective Mitsunobu Esterification of Cellulose with Hydroxycinnamic Acids

AbstractCellulose esters of hydroxycinnamic acids, namely ferulic‐, p‐coumaric‐, and caffeic acid, are synthesized by Mitsunobu esterification applying triphenylphosphine and diisopropyl azodicarboxylate in N,N‐dimethylacetamide/LiCl. The reaction is found to be highly selective and took place at primary hydroxyl groups at position 6 of cellulose without undesired conversion of double bonds and phenolic hydroxyl groups. Molecular structure characterization is performed by FTIR‐ and NMR spectroscopy. The products are soluble in dimethyl sulfoxide and possessed degree of substitution (DS) values of up to 0.5. DS values are determined by two independent methods, namely 1H NMR spectroscopy of peracetylated derivatives and UV spectroscopy of extracted ferulic acid. The synthesis of cellulose hydroxycinnamates is very important to design lignocellulosic model systems and antioxidative bioinspired materials.

PSXIII-1 Effect of varieties and processing methods on physicochemical, nutritional, molecular structural characteristics of feed chickpeas

Abstract The objectives of this study were to evaluate the effect of varieties and heat processing methods on molecular structural, physicochemical, and nutritional characterization of feed chickpeas; evaluate the effect of heat processing methods, dry heat, wet heat and microwave irradiation processing method on feed chickpeas as an alternative source for protein and energy feed for ruminant livestock. To reveal the molecular structure spectral profile of chickpeas varieties and the molecular structure changes when applied heat processing methods, vibrational molecular spectroscopy was applied. Feed chickpea samples were determined for chemical profile, energy values, carbohydrate fractions. Subsequently, chickpea samples were incubated in the rumen of dairy cows for degradation kinetics analysis of nutrients. The intestinal digestion of feed chickpea samples was determined using three-step in vitro method with pre-incubation at 16h. Later, protein and carbohydrate related molecular spectral features before and after incubation were performed using vibrational ATR-FTIR molecular spectroscopy. The interactive relationship between processing induced molecular spectral profile changes and nutrient metabolism and availability were studied. The available results showed that varieties and heat processing methods significantly impacted molecular structural, physicochemical, and nutritional characterization of feed chickpeas.

Quantum chemical computational studies of 1,3-diammonium propylarsenate: a semi organic crystalline salt

A semi organic crystalline salt − 1,3–diammonium propylarsenate (1-3-DAPAS) has been introduced for experimental and theoretical investigation. Gaussian 09 program has been utilized to quantify the quantum chemical theoretical estimations. DFT/B3LYP-6-311++G(d,p) procedure is accustomed to enhance the structure. Molecular structural and vibrational characterization have been carried out and their experimental and theoretical results were correlated. Natural bonding orbital scrutiny and frontier molecular orbital probe endorsed the charge transfer apart from the presence of strong inter and intra molecular interactions. First order hyperpolarizability is computed to study the microscopic behavior of the synthesized compound (1-3-DAPAS). It is calculated from first order hyperpolarizability that 1-3-DAPAS is 7.3246 times that of urea and may be expected potential candidate for the development of NLO materials.

Molecular structure characterization of extracted cellulose from different apple cultivars by transmission electron microscopy.

Molecular structure characterization of extracted cellulose from different apple cultivars by transmission electron microscopy.

Molecular Structural Characterization of Cycloparaphenylene and its Variants

Conjugated aromatic macrocycles are engaging due to their remarkable photophysical and optoelectronic properties. Specifically, the cyclic radially-oriented π-arrangement of cycloparaphenylenes (CPPs) offers to ascend to photophysical properties dissimilar to small particle or carbon nanomaterial. A couple of sizes of CPPs, CPP derivatives, and related carbon nanorings have been integrated and their entrancing properties have gotten uncovered. Structure-based topological indices of these frameworks empower expectation of chemical properties and the bioactivities of these compounds through quantitative structure-activity and structure-property connections strategies. In this article, we derive the mathematical expression of CPP and its side wall contains pyrene and hexabenzocorenene.

Fluorinated quinone derived organosulfur copolymer cathodes for long-cycling, thermostable and flexible lithium–sulfur batteries

Organosulfur copolymers are promising cathode materials in lithium–sulfur batteries because of adjustable molecular structure, tunable electrochemical properties and excellent processability. However, conventional organosulfur copolymers suffer from poor electronic/ionic conductivity and low sulfur content, which limit rate capability and energy density. Herein, fluorinated quinone-derived organics are copolymerized with sulfur via convenient nucleophilic aromatic substitution (SNAr) reaction. The homogeneous distribution of sulfur over poly(tetrafluorohydroquinone)-sulfur (PTFHQS) at molecular level endows excellent Li+ ion diffusivity and fast redox kinetics. The abundant semi-ionic C–F bonds with polar characteristic have strong interactions with polysulfides, thus diminishing the shuttle effect. In result, flexible PTFHQS cathode with ~ 71 wt% sulfur content exhibits high discharge capacity of 643 mAh gtotal–1 (906 mAh gsulfur–1) at 0.5C, stable Coulombic efficiency (>99%), good rate performance of 307 mAh gtotal–1 (432 mAh gsulfur–1) 2.0C, excellent cycling stability (capacity retention of 87% for 600cycles), and functions normally at elevated working temperature (80 °C). Compared to another copolymer of sulfurized tetrafluoro-p-benzoquinone monomer (TFBQS), molecular structure characterization and electrochemical analysis verifies that pre-polymerized skeleton of PTFHQS is conducive to the homogeneous distribution and efficient utilization of sulfur species. We expect this work will bring inspiration to exploit organosulfur compounds with rational molecular structures and convenient synthesis routes for lithium–sulfur batteries.

NAT2 polymorphisms associated with the development of hepatotoxicity after first-line tuberculosis treatment in Mexican patients: From genotype to molecular structure characterization

Background and aimsTo assess the relevance of the slow acetylator phenotype based on NAT2 genotypes, among patients with pulmonary tuberculosis (PTB) that developed hepatotoxicity after first-line tuberculosis treatment in a Northeastern Mexican population. MethodsNinety one PTB patients were included, 7 of them developed hepatotoxicity. NAT2 SNPs (rs1801279, rs1041983, rs1801280, rs1799929, rs1799930, rs1208, and rs1799931) were genotyped by TaqMan allelic discrimination assay. Statistical analyses were performed using Epi Info statistical software 7.0 and SHEsisPlus for haplotype reconstruction. The NAT2 slow non-synonymous SNP were studied by molecular dynamic analysis (MDA). ResultsThe frequency of the haplotype associated with slow acetylation status for PTB was 58%, and for with hepatotoxicity (PTB-H) represented 42.6%. Three haplotypes, NAT2*5Q, NAT2*5U, NAT2*5Va were exclusively present in seven PTB-H patients, (P = 0.01, P = 0.0006, P = 0.01, respectively). These haplotypes include the combination of two SNPs (I114T + R197Q or I114T + G286E). The effect of the SNPs on protein structure is to disrupt the CoA binding site affecting acetylation activity. ConclusionOur study provides insight into slow acetylation NAT2 haplotypes associated with hepatotoxicity after first-line tuberculosis treatment, for first time, in a Mexican population. The molecular mechanism acts at the CoA binding site.

Persistent spectral hypergraph based machine learning (PSH-ML) for protein-ligand binding affinity prediction.

Molecular descriptors are essential to not only quantitative structure activity/property relationship (QSAR/QSPR) models, but also machine learning based chemical and biological data analysis. In this paper, we propose persistent spectral hypergraph (PSH) based molecular descriptors or fingerprints for the first time. Our PSH-based molecular descriptors are used in the characterization of molecular structures and interactions, and further combined with machine learning models, in particular gradient boosting tree (GBT), for protein-ligand binding affinity prediction. Different from traditional molecular descriptors, which are usually based on molecular graph models, a hypergraph-based topological representation is proposed for protein-ligand interaction characterization. Moreover, a filtration process is introduced to generate a series of nested hypergraphs in different scales. For each of these hypergraphs, its eigen spectrum information can be obtained from the corresponding (Hodge) Laplacain matrix. PSH studies the persistence and variation of the eigen spectrum of the nested hypergraphs during the filtration process. Molecular descriptors or fingerprints can be generated from persistent attributes, which are statistical or combinatorial functions of PSH, and combined with machine learning models, in particular, GBT. We test our PSH-GBT model on three most commonly used datasets, including PDBbind-2007, PDBbind-2013 and PDBbind-2016. Our results, for all these databases, are better than all existing machine learning models with traditional molecular descriptors, as far as we know.

Use of Solid-State NMR Spectroscopy for the Characterization of Molecular Structure and Dynamics in Solid Polymer and Hybrid Electrolytes.

Solid-state NMR spectroscopy is an established experimental technique which is used for the characterization of structural and dynamic properties of materials in their native state. Many types of solid-state NMR experiments have been used to characterize both lithium-based and sodium-based solid polymer and polymer–ceramic hybrid electrolyte materials. This review describes several solid-state NMR experiments that are commonly employed in the analysis of these systems: pulse field gradient NMR, electrophoretic NMR, variable temperature T1 relaxation, T2 relaxation and linewidth analysis, exchange spectroscopy, cross polarization, Rotational Echo Double Resonance, and isotope enrichment. In this review, each technique is introduced with a short description of the pulse sequence, and examples of experiments that have been performed in real solid-state polymer and/or hybrid electrolyte systems are provided. The results and conclusions of these experiments are discussed to inform readers of the strengths and weaknesses of each technique when applied to polymer and hybrid electrolyte systems. It is anticipated that this review may be used to aid in the selection of solid-state NMR experiments for the analysis of these systems.