Final Molecular Structure Research Articles

A Deep Learning Approach to Investigating Clandestine Laboratories Using a GC-QEPAS Sensor

Illicit drug production in clandestine laboratories involves the use of large quantities of different chemicals that can be obtained for legitimate purposes. The identification of these chemicals, including reagents, catalyzers and solvents, is crucial for forensic investigations. From a legal point of view, a drug precursor is a material that is specific and critical to the production of a finished chemical and that constitutes a significant portion of the final molecular structure of the drug. In this study, a gas chromatography quartz-enhanced photoacoustic spectroscopy (GC-QEPAS) sensor—in conjunction with a deep learning model—was evaluated for its effectiveness in the detection and identification of interesting compounds for the production of amphetamine, methamphetamine, 3,4-methylenedioxymethamphetamine (MDMA), phenylcyclohexyl piperidine (PCP), and cocaine. The GC-QEPAS sensor includes a gas sampler, a fast GC for separation, and a QEPAS detector, which excites molecules exiting the GC column using a quantum cascade laser to provide the infra-red (IR) spectrum. The on-site capability of the GC-QEPAS system offers significant advantages over the current instruments employed in this field, including rapid analysis, which is crucial in field operations. This allows law enforcement to quickly identify specimens of interest on site. The system’s performance was validated by taking into account the limit of detection, repeatability, and within-laboratory reproducibility. The results showed excellent repeatability and reproducibility for both the GC and QEPAS modules. The deep learning model, a multilayer perceptron neural network, was trained using IR spectra and retention times, achieving very high classification accuracy in the testing conditions. This study demonstrated the efficacy of the GC-QEPAS sensor combined with a deep learning model for the reliable identification of drug precursors, providing a robust tool for law enforcement during criminal investigations in clandestine laboratories.

Molecular structure characterization of coal with different coalification degrees: a combined study from FT-IR, Raman, 13C NMR spectroscopy and modelling

While extensive research has been conducted on the evolution of coal's molecular structure during coalification, the heterogeneity and complexity of coal continue to impede the accurate and precise quantitative characterization of its structural evolution mechanism. In this study, the organic matter source, coal quality, carbon skeleton structure, and functional group occurrence of coal at different coalification stages have been determined using maceral identification, vitrinite reflectance, industrial quality, elemental analysis, and spectral analysis. Four molecular models have been created through computer-aided molecular design. The results indicate that the hydrogen atoms in the benzene ring structure reduce as coalification increases. The content of aliphatic compounds gradually decreases, while the length of aliphatic side chains first decreases (Ro,max<1.81%) and then increases (Ro,max>1.81%). Moreover, the chemical structure of coal tends to mature and stabilize, as the degree of coal crystallization increases, and the oxygen-containing groups gradually decrease. Therefore, aromatization increases with the condensation reaction dominating in the late stage of coalification. After intensive attempts to determine the chemical bond mode between aromatic carbon, aliphatic side chain, and oxygen functional group, the final molecular structure models are presented as C188H165O13N3 (F-1), C182H161O9N5 (J-1), C195H153O10N3 (T-1), and C193H129O7N3 (W-1). Furthermore, the mechanism of coalification is discussed based on the variation of the side chains and chemical bonds. According to the adsorption heat of functional groups, the methane adsorption capacity increases as the degree of coalification increases. The inflection point of methane adsorption capacity is at Ro,max>1.80%. This study provides a theoretical framework to understand the molecular structure evolution of coals at varying degrees of metamorphism. Additionally, it proposes a reliable method for characterizing coal molecular structures with high accuracy.

Synthesis, characterization, X-ray crystallographic study and in silico ADME predictions of functionalized nitropyrrole derivatives

A catalyst-free, green protocol has been developed for the preparation of polysubstituted nitropyrrole derivatives by the reaction of malononitrile and phenylglyoxal monohydrates, with nitroketene acetals. The structures of the synthesized nitropyrroles were elucidated by the standard spectroscopic techniques including IR, 1H NMR, 13C NMR and elemental analysis and also the final molecular structure as well as relative stereochemistry of compound 4d was confirmed by single crystal XRD-analysis. The ADME studies of the synthesized compounds were performed and key physiochemical properties were calculated by using SwissADME web tool. The distinguished features of the presented method are mild reaction condition, eco-friendly medium, good yields and without column chromatographic purification. All the synthesized compounds obey well with Lipinski's rule of 5 with zero violation having good pharmacokinetics properties.

Chemically modified Jatropha curcas oil for biolubricant applications

Jatropha curcas oil is one of interesting renewable resources for preparation of biolubricants. However, direct application of this oil as a biolubricant is restricted due to its low oxidative stability. This drawback can be overcome by molecule structural redesign through a chemical modification process at its unsaturated functional groups. Jatropha curcas oil was modified via epoxidation, ring opening and esterification processes. Its conversion to the epoxidized oil was performed by using in situ performic acid as a catalyst, then reaction with oleic acid in the presence of p-toluenesulfonic acid as a catalyst in the ring opening process. The final esterification process with oleic acid was catalyzed by sulfuric acid. Molecular structures of the modified oil were determined by measurements of the oxirane oxygen content and by Fourier-transform infrared (FTIR), proton and carbon nuclear magnetic resonance (1H NMR and 13C NMR) spectroscopy analyses. The results showed that the oxidative stability, viscosity, flash point and pour point of the final product were significantly improved. In specific, the ring opening and esterification processes inducing branching and bending in the final oil molecular structure have resulted in the improved viscosity index of 135, the pour point of -29?C and the increased flash point of 250?C.

Synthesis and characterization of polycarbodiimides by MALDI-TOF MS and NMR spectroscopy: kinetic and mechanism study

Matrix-assisted laser desorption/ionization time of flight mass spectrometry and nuclear magnetic resonance spectrometry techniques have been used to characterize carbodiimide oligomers and to identify the reaction intermediate that demonstrates the original synthetic route. The isomerization of the catalyst during the kinetic mechanism of the reaction has been also studied. The number of different isomerization species of the catalysts and the dose of catalysts added during the reaction are responsible for the final molecular weight and structure of the oligomer (linear and branched structures). The study shows that controlling the correct catalyst isomerization reaction can decrease the reaction time by up to 5 h and control the synthesis of linear or branched oligomer structures.

Thiocyanate cadmium(II) coordination compounds with 2,3,5,6-tetrakis(2-pyridyl)pyrazine – Synthesis, structure and luminescent properties

Three new thiocyanate coordination compounds [Cd(NCS)2(μ-tppz)]n (1), [Cd(NCS)(NO3)(tppz)(H2O)] (2), [Cd2(μ1,3-NCS)2(NO3)2(μ-tppz)]n (3) have been successfully synthesized in the reaction of Cd(NO3)2·4H2O or CdCl2·2.5H2O with a versatile polydentate ligand (2,3,5,6-tetrakis(2-pyridyl)pyrazine – tppz) and NCS− anion. The resulted compounds were structurally characterized by single crystal X-ray diffraction analysis and further characterized by infrared spectra, powder X-ray diffraction and thermal analysis. The studies demonstrated a significant impact of the reaction conditions and cadmium salt on the final molecular structures. The compounds 1 and 3 displays an infinitive one-dimensional chain made up of cadmium(II) ions linked by only through tppz bridges (in 1) or a single thiocyanate bridges μ1,3-NCS− and tppz molecules (in 3). The structure 2 consist of the mononuclear, heptacoordinated molecules [Cd(NCS)(NO3)(tppz)(H2O)] assembled by π⋯π and C–S⋯π type interactions into three dimensional supramolecular network. The photoluminescence behavior of 1–3 was investigated in solid state. In addition, the luminescent properties of the mononuclear coordination compound (2) were examined in acetonitrile solution.

Initial mechanisms for the unimolecular decomposition of electronically excited nitrogen-rich energetic salts with tetrazole rings: (NH4)2BT and TAGzT

Unimolecular decomposition of nitrogen-rich energetic salt molecules bis(ammonium)5,5′-bistetrazolate (NH4)2BT and bis(triaminoguanidinium) 5,5′-azotetrazolate TAGzT, has been explored via 283 nm laser excitation. The N2 molecule, with a cold rotational temperature (&amp;lt;30 K), is observed as an initial decomposition product, subsequent to UV excitation. Initial decomposition mechanisms for the two electronically excited salt molecules are explored at the complete active space self-consistent field (CASSCF) level. Potential energy surface calculations at the CASSCF(12,8)/6-31G(d) ((NH4)2BT) and ONIOM (CASSCF/6-31G(d):UFF) (TAGzT) levels illustrate that conical intersections play an essential role in the decomposition mechanism as they provide non-adiabatic, ultrafast radiationless internal conversion between upper and lower electronic states. The tetrazole ring opens on the S1 excited state surface and, through conical intersections (S1/S0)CI, N2 product is formed on the ground state potential energy surface without rotational excitation. The tetrazole rings open at the N2—N3 ring bond with the lowest energy barrier: the C—N ring bond opening has a higher energy barrier than that for any of the N—N ring bonds: this is consistent with findings for other nitrogen-rich neutral organic energetic materials. TAGzT can produce N2 either by the opening of tetrazole ring or from the N=N group linking its two tetrazole rings. Nonetheless, opening of a tetrazole ring has a much lower energy barrier. Vibrational temperatures of N2 products are hot based on theoretical predictions. Energy barriers for opening of the tetrazole ring for all the nitrogen-rich energetic materials studied thus far, including both neutral organic molecules and salts, are in the range from 0.31 to 2.71 eV. Energy of the final molecular structure of these systems with dissociated N2 product is in the range from −1.86 to 3.11 eV. The main difference between energetic salts and neutral nitrogen-rich energetic material is that energetic salts usually have lower excitation energy.

Identification of a Halogenase Involved in the Biosynthesis of Ochratoxin A in Aspergillus carbonarius.

Aspergillus carbonarius is the main responsible fungus of ochratoxin A (OTA) contamination of grapes and derived products. To date, the biosynthetic mechanism of this mycotoxin has been partially elucidated. Availability of genome sequence of A. carbonarius has allowed the identification of a putative gene cluster involved in OTA biosynthesis. This region hosts the previously characterized AcOTAnrps and AcOTApks genes encoding two key enzymes of the biosynthetic pathway. At about 4,400 nucleotides downstream of these loci, a gene encoding a putative flavin dependent-halogenase came out from the annotation data. Its proximity to OTA biosynthetic genes and its sequence analysis have suggested a role in the biosynthesis of OTA, directed to the introduction of the chlorine atom in the C-5 position of the final molecular structure of this mycotoxin. The deduced protein sequence of the halogenase gene, we designated AcOTAhal, shows a high similarity to a halogenase that is located in the OTA cluster of A. niger The deletion of the halogenase gene completely eliminated the production of ochratoxin A in A. carbonarius and determined a significant increase of ochratoxin B, as confirmed by mass spectrometry analysis. Moreover, its expression profile was similar to the two biosynthetic genes previously identified, AcOTApks and AcOTAnrps, indicating a strong correlation of the AcOTAhal gene with the kinetics of OTA accumulation in A. carbonarius. Therefore, experimental evidence confirmed that the chlorination step which converts OTB in OTA represents the final stage of the biosynthetic pathway, supporting our earlier hypothesis on the order of enzymatic steps of OTA biosynthesis in A. carbonarius Ochratoxin A is a potent mycotoxin classified as a possible carcinogen for humans, and Aspergillus carbonarius is the main agent responsible for OTA accumulation in grapes. We demonstrate here that a flavin-halogenase is implicated in the biosynthesis of OTA in A. carbonarius The encoding gene, AcOTAhal, is contiguous to biosynthetic genes that we have already described (nrps and pks), resulting as part of the biosynthetic cluster. The encoded protein is responsible of the introduction of chlorine atom in the final molecular structure and acts at the last step in the pathway. This study can be considered a continuation of an earlier study wherein we started to clarify the molecular basis of OTA biosynthesis in A. carbonarius, which has not been completely elucidated until now. This research represents an important step forward to a better understanding of the production mechanism, which will contribute to the development of improved control strategies to reduce the risk of OTA contamination in food products.

Structure of Ultralong Polyaniline Nanofibers Using Initiators

Detailed morphological and structural characterization of high-aspect-ratio polyaniline nanofibers obtained using a small amount of p-aminodiphenylamine (dimer) or p-phenylenediamine (diamine monomer) as an initiator into a rapidly mixed reaction is presented. Structural characteristics have been investigated by FT-IR, UV−vis−NIR, solid-state 13C NMR, and 15N NMR, while the morphology was examined using scanning electron microscopy (SEM) and transmission electron microscopy (TEM). Nanofibers obtained with the addition of an initiator appear longer and less entangled than those obtained without any initiators. TEM analysis revealed a distinct morphological difference between the nanofibers synthesized with different additives. The p-aminodiphenylamine-initiated polyaniline possesses an electrical conductivity of 3.0 S cm−1, while the p-phenylenediamine-initiated counterpart has a conductivity of 1.7 S cm−1. FT-IR, 1H−13C cross-polarization (CP), 15N direct polarization (DP), and UV−vis−NIR spectroscopy confirm that a regular polyaniline structure prevails in both nanofibers. Therefore, various initiators only result in a slight difference in the final polymer molecular structure and physical properties, but such minor divergence dictates the subsequent chain assembly and affects the supramolecular morphology significantly.

Molecular Rearrangements Involved in the Capsid Shell Maturation of Bacteriophage T7

Maturation of dsDNA bacteriophages involves assembling the virus prohead from a limited set of structural components followed by rearrangements required for the stability that is necessary for infecting a host under challenging environmental conditions. Here, we determine the mature capsid structure of T7 at 1 nm resolution by cryo-electron microscopy and compare it with the prohead to reveal the molecular basis of T7 shell maturation. The mature capsid presents an expanded and thinner shell, with a drastic rearrangement of the major protein monomers that increases in their interacting surfaces, in turn resulting in a new bonding lattice. The rearrangements include tilting, in-plane rotation, and radial expansion of the subunits, as well as a relative bending of the A- and P-domains of each subunit. The unique features of this shell transformation, which does not employ the accessory proteins, inserted domains, or molecular interactions observed in other phages, suggest a simple capsid assembling strategy that may have appeared early in the evolution of these viruses.

Synthesis, characterization and thermal properties of sodium pyruvate thiosemicarbazone and some of its metal complexes

The Schiff base sodium pyruvate thiosemicarbazone (SPTSC) was synthesized from the condensation of sodium pyruvate and thiosemicarbazide hydrochloride in aqueous medium. This molecule coordinates to a variety of divalent metal ions M2+ (M=Fe, Co, Ni, Cu or Cd) and one type of complexes was obtained with general formulae [M (SPTSC)2]. The modes of bonding and overall geometry of the complexes were determined through physicochemical and spectroscopic methods. These studies revealed octahedral geometry of all prepared complexes. Thermal analyses (TG and DTG) of (SPTSC) and all complexes have been carried out to confirm the final molecular structures of free ligand and its metal complexes and also to study their thermal stability. This study confirms that the complexes have been formed by the coordination of metal ion to the (SPTSC) donor atoms only (there is no coordinate and hydrate solvents). Also the study shows that the prepared complexes have more thermal stability than free ligand (SPTSC) and the thermal stability of (SPTSC) has been enhanced by the coordination to metal ions.

Performance properties in thick film silicate dielectric layers using molecular modeling

Molecular modeling was employed to understand various behaviors found in thick film dielectric layers derived from solution-based sol–gel formulation in order to aid their development. For instance, for formulations used as planarizing layers, it was discovered that during certain process steps ionic components could be introduced which greatly influences the extent of shrinkage by up to 50%, a phenomenon not normally seen in traditional spin-on glasses (SOG). Thermodynamic calculations showed that specific ionic contaminants contribute to the cure state of the material, potentially depolymerizing the material and promoting the formation of structures that are more easily deformed. Volumetric analysis and compaction modeling demonstrated that the high extent of shrinkage is expected, depending upon the final molecular structure of the silicate. Calculation of the relative modulus of the different suspected structures also showed that depolymerized structures contribute to the ease of compaction.

Estimation of reinforcement in compatibilized polypropylene nanocomposites by extensional rheology

AbstractStructural characterization in polymer nanocomposites is usually performed using X‐ray scattering and microscopic techniques, whereas the improvements in processing and mechanical properties are commonly investigated by rotational rheometry and tensile testing. However, all of these techniques are time consuming and require quite expensive scientific equipment. It has been shown that a fast and efficient way of estimating the level of reinforcement in polymer nanocomposites can be performed by melt extensional rheology, because it is possible to correlate the level of melt strength with mechanical properties, which reflect both the 3D network formed by the clay platelets/polymer chains as well as final molecular structure in the filled system. The physical network made of silicate filler and polymer matrix has been evaluated by X‐ray diffraction and transmission electron microscopy. Extensional rheometry and tensile testing have been used to measure efficiency of the compatibilizer amount in a polypropylene‐nanoclay system. © 2008 Wiley Periodicals, Inc. J Appl Polym Sci, 2009

Wear performance of 1900 direct compression molded, 1020 direct compression molded, and 1020 sheet compression molded UHMWPE under knee simulator testing

Ultra-high molecular weight polyethylene (UHMWPE) tibial inserts as used in total knee arthroplasy (TKA) are primarily manufactured in one of two ways: (1) machining the components from already consolidated resin or (2) directly consolidating the UHMWPE resin into the final product dimensions. Because these processes involve the introduction of heat and pressure, microscopic inconsistencies may arise and possibly influence wear behavior. To investigate how the two processes affect wear rate, direct, or net shape, molded and machined Ticona (NJ) GUR 1020 resin were compared in a wear test. Results indicate that there is no statistical difference in wear rates when comparing machined or molded inserts ( P = 0.41). Additional testing was then performed to investigate how resin selection influenced wear rate. GUR 1020 and Bassell (Brussels) 1900 were both direct molded into tibial inserts and subject to wear testing. At the conclusion of the wear test no statistical differences in wear rates were found between the molded GUR 1020 and Bassell 1900 resins ( P = 0.14) or between the machined GUR 1020 and molded Bassell 1900 ( P = 0.31) inserts. From this study, it is apparent that resin type and manufacturing method of tibial inserts do not significantly affect wear behavior. More influential parameters are likely post consolidation methods including crosslinking processes with varied irradiation dosage and thermal treatments, as well as sterilization methods which can substantially alter the final molecular structure and properties of the material.

Technical Reports: A Modular Approach to Beam Line Automation: The NIGMS Facility at the NSLS

The last few years have seen an increase in the demand of automation at synchrotron radiation facilities. The main driving forces behind this quest are the Structural Genomics Centers and related projects [1], with their need for large throughput of samples and an increasing number of relatively unskilled users with ever increasing demands. In order to meet the needs of this diverse community, the structure determination process must be streamlined. A production pipeline for high volume determination of structures requires optimization and automation of current processes in use at synchrotron facilities. The ultimate goal is to arrive at a system that, with little more input than a sample, will provide the researcher with the final molecular structure.

Degradable thiol-acrylate photopolymers: polymerization and degradation behavior of an in situ forming biomaterial

Degradable thiol-acrylate photopolymers are a new class of biomaterials capable of rapidly polymerizing under physiological conditions upon exposure to UV light, with or without added photoinitiators, and to depths exceeding 10 cm. These materials are formed in situ, and the versatility of their chemistry affords a high degree of control over the final material properties. For example, variations in monomer mole fractions directly affect the final network molecular structure, varying the time required to achieve complete mass loss from 25 to 100 days, the molecular weight distributions of the degradation products, and the swelling ratios and compressive moduli throughout degradation. Additionally, varying the mole fraction of multifunctional thiol monomer in the initial reaction mixture controls the concentration of reactive sites in the network available for post-polymerization modification of the polymer.

Structure, vibrational-dynamics and first-principles study of diglyme as a model system for poly(ethyleneoxide)

Probable molecular structures of diglyme in the solid state are deduced from a combination of ab initio calculations and inelastic neutron scattering vibrational spectroscopy. The final molecular structures closely resemble that of lithium diglyme, suggesting that all-trans segments are of minor importance in the solid phase. The molecular structures of pure diglyme closely resemble those of lithium ion coordinated diglyme and suggest that no large conformational changes are necessary for lithium ion complexation. The general strategy for obtaining structural information from vibrational spectra is discussed.

Study of the synthesis of poly(4,4′-diphenylether-1,3,4-oxadiazole) in solutions of poly(phosphoric acid)

Using statistical design of experiments, samples of poly(4,4′-diphenylether-1,3,4-oxadiazole)s, POD–DPE, were synthesized through solution polycondensation of 4,4′-diphenylether dicarboxylic acid, DPE, and hydrazine sulphate, HS, in poly(phosphoric acid), PPA, under different reaction conditions. Final polymer molecular structure (average molecular weights, polymer composition, amount of hydrazide groups) is shown to depend strongly upon the polymerization conditions and that adequate properties for membrane synthesis (high average molecular weight, low amounts of hydrazide groups and low gel contents) can only be obtained if high synthesis temperatures (160°C) are used. Empirical and semi-theoretical models are developed to describe the kinetics of POD–DPE production in PPA solutions, showing that the likely existence of cross-linking reactions may explain both the relatively high values and the large fluctuations of the average molecular weight obtained experimentally.

Structure, organization, and expression of genes coding for envelope components in the archaeon Methanosarcina mazei S-6.

The antigenic mosaics of archaeal species are complex and lead to the distinction of different immunotypes. We began the dissection of the antigenic mosaic of the methanogen Methanosarcina mazei S-6 by gene cloning and sequencing. The analysis of the sequence, organization, and in vitro (heterologous) and in vivo expression of two three-gene clusters that encode proteins localized to the cell envelope and that are recognized by antibodies for surface structures is presented in this report. The amino acid sequences and compositions share characteristics with S-layer proteins and, most notably, have repeats of conserved sequences and secondary structures. Expressed genes produced proteins with a tendency to oligomerize, and one of these proteins was susceptible to breakdown at regular intervals. Altogether, the data reveal a modular system (clusters of homologous genes, proteins of similar sequences with conserved repeats) seemingly suitable for assembling an enormous variety of final molecular structures by rearranging and combining genes, proteins, and repeats, and thus generate the observed wide spectrum of antigenic diversity.

A collagen substrate enhances the sealing capacity of tight junctions of A6 cell monolayers.

A6 cells, a kidney derived epithelial cell line, when cultured either on a collagen-coated substrate or on polycarbonate substrate without collagen form confluent monolayers that are similar in cell density and overall morphology. However, the transepithelial electrical resistance (TER) of monolayers grown on the collagen-coated substrate is ninefold higher than that of monolayers grown without collagen. A comparative freeze-fracture study showed that this large difference in TER is not related to the length or number of tight junction strands but to differences in the specific conductance of individual strands. This conductance was obtained considering the TER, the linear junctional density and the mean number of tight junction strands. We estimated the specific linear conductance of the tight junction strands to be 2.56 x 10(-7) S/cm for cells grown on collagen and 30.3 x 10(-7) S/cm for the cells grown without collagen. We also examined changes in distribution and phosphorylation states of the zonula occludens associated protein, ZO-1, during monolayer formation. Immunocytochemistry reveals that the distribution of ZO-1 follows a similar time course and pattern independent of the presence or absence of collagen. While the amount of ZO-1 expression is identical in cells grown on both substrates, this protein is phosphorylated to a greater extent during the initial stages of confluence in cells cultured on collagen. We suggest that the phosphorylation levels of ZO-1 in A6 cells at the early stages of monolayer formation may determine the final molecular structure and specific conductance of the tight junctions strands.