Molecular Structure Analysis Research Articles

Composition and molecular structure analysis of hydrophilic/hydrophobic extracellular polymeric substances (EPS) with impacts on sludge dewaterability

Extracellular polymeric substances (EPS) have a significant effect on the dewaterability of waste-activated sludge (WAS); however, the role of polarity distribution (hydrophilic/hydrophobic characteristics) of EPS in sludge dewatering remains unclear. In this study, the relationship between the characteristics of EPS hydrophilic/hydrophobic fractions (composition and molecular structure) and sludge physicochemical properties of 8 different sludge samples was investigated, and a structural equation model was constructed to describe the potential mechanisms of key EPS parameters on sludge dewatering. Experimental results showed that the variation in sludge EPS polarity led to significant changes in the surface hydrophilicity/hydrophobicity and structure compactness, which affected the sludge dewaterability. Specifically, the increase in the content of tyrosine-like proteins, especially those related to hydrophobic acid fraction (HPO-A), played a key role in increasing the surface hydrophobicity of sludge and promoting its dewaterability. In contrast, humic acids in hydrophilic EPS (HPI) could interact with hydrophobic proteins to form dense biopolymers (characterized by high nonprotonated nitrogen (Nnonpr) content), resulting in a more stable and compact structure of the EPS matrix (characterized by low random coil content) and deterioration of sludge dewaterability. This study provides a new perspective for the exploration of the relationship between hydrophilic/hydrophobic biopolymers and sludge dewaterability.

Molecular and electronic structure analysis of [Fe(CO)4(SiX)] (X = O, S, Se and Te): a DFT study

Molecular and electronic structure analysis of [Fe(CO)4(SiX)] (X = O, S, Se and Te): a DFT study

Thermostability enhancement and insight of L-asparaginase from Mycobacterium sp. via consensus-guided engineering.

Acrylamide alleviation in food has represented as a critical issue due to its neurotoxic effect on human health. L-Asparaginase (ASNase, EC 3.5.1.1) is considered a potential additive for acrylamide alleviation in food. However, low thermal stability hinders the application of ASNase in thermal food processing. To obtain highly thermal stable ASNase for its industrial application, a consensus-guided approach combined with site-directed saturation mutation (SSM) was firstly reported to engineer the thermostability of Mycobacterium gordonae L-asparaginase (GmASNase). The key residues Gly97, Asn159, and Glu249 were identified for improving thermostability. The combinatorial triple mutant G97T/N159Y/E249Q (TYQ) displayed significantly superior thermostability with half-life values of 61.65 ± 8.69min at 50°C and 5.12 ± 1.66min at 55°C, whereas the wild-type was completely inactive at these conditions. Moreover, its Tm value increased by 8.59°C from parent wild-type. Interestingly, TYQ still maintained excellent catalytic efficiency and specific activity. Further molecular dynamics and structure analysis revealed that the additional hydrogen bonds, increased hydrophobic interactions, and favorable electrostatic potential were essential for TYQ being in a more rigid state for thermostability enhancement. These results suggested that our strategy was an efficient engineering approach for improving fundamental properties of GmASNase and offering GmASNase as a potential agent for efficient acrylamide mitigation in food industry. KEY POINTS: • The thermostability of GmASNase was firstly improved by consensus-guided engineering. • The half-life and Tm value of triple mutant TYQ were significantly increased. • Insight on improved thermostability of TYQ was revealed by MD and structure analysis.

Triazine-Augmented Catalytic Activity of Cyclobutadiene Tricarbonyl Fe(0) Complexes for Thermal Decomposition of Ammonium Perchlorate

The employment of combustion catalysts is an effective way to improve ammonium perchlorate (AP) decomposition performance during the combustion process of composite solid propellants. A classic half-sandwich iron carbonyl complex was proposed as the leading structure for exploring high-performance combustion catalysts, in which functionalized cyclobutadienes (Cb) tune the thermal stability and catalytic activity. The thermolysis of Fe2(CO)9 and substituted alkynes initiated [2 + 2] cyclization of alkyne triple bonds and gave η4-cyclobutadiene iron(0) tricarbonyl complexes, CbR1,R2-Fe-CO (1–6), with decent yields. A molecular structure analysis found that the conjugation of the aromatic substituents aryl, ferrocenyl (Fc), and triazinyl (Tz) finely tuned the coordination bonds around the Fe(0) center. The DSC/TG experiments found a remarkable thermal stability of CbTz,R-Fe-CO (3–6) with characteristic thermolysis temperatures (CTT) as high as 500 °C. The catalytic experiments demonstrated that the CTT of Cb-Fe-CO (2-6) overlapped with AP high-temperature decomposition (HTD). The thermal cross-coupling of HTD of AP and CTT of CbTz,Fc-Fe-CO (6) significantly augmented catalytic AP decomposition, resulting in a maximum energy release as high as 2828 J/g.

FTIR conformity analysis and performance testings of fresh, aged and expired polymeric paints under different storage conditions

Abstract This study aims to correlate the molecular structure consistency of unmixed paints and the performance of 2-pack three-layer protective dried coatings (mixed and cured paints) in various aging conditions (fresh, aged and expired paints) stored under different conditions. All the physical tests (density, solid content, viscosity and sag resistance) of paints fulfil the required specifications. However, these tests cannot tell if the chemical formulation of retained paints (aged and expired) has undergone changes due to storage. The conformity analysis by Fourier-transform infrared (FTIR) spectroscopy coupled with squared derivative algorithm was employed for molecular structure analysis comparison of the fresh and retained paints. FTIR results show high degree of similarity (r), with r ≥ 0.900 for the properly stored retained paints when compared against its fresh paints using high sensitivity compare algorithm. This finding is validated with a paired Student’s t-test and it turns out that the r values of properly stored paints are not statistically different from the fresh paints. Moreover, the performance test (pull off adhesion and salt-spray) of dried coatings indicates good durability when the properly stored retained paints with high degree of structural similarity are applied on the substrate according to end user specifications. This approach offers a practical solution for the paint manufacturer and user to employ a rapid and non-destructive FTIR structural analysis for the confirmation of structural consistency of retained paints before application instead of disposing the polymeric paint without verification.

Topological study on degree based molecular descriptors of fullerene cages

Fullerenes are an allotrope of carbon that create polyhedral cages. Their bond structures match the sole pentagon and hexagonal-faced planar cubic graphs. Several chemical properties of fullerenes can be studied using its graph structure. Any graph that models a particular molecular structure can be given a topological index or molecular descriptor. Based on the molecular descriptor, it is easy to assess mathematical data and conduct further research on a molecule's physicochemical characteristics. It is a beneficial technique to replace time-consuming, expensive, and labour-intensive laboratory experiments. Molecular descriptors play a significant role in molecular structural analysis by investigating quantitative structure-activity relationships (QSARs) and quantitative structure-property relationships (QSPRs). In this study, some novel degree-based topological indices, multiplicative degree-based topological indices, and entropy versions for fullerene cages and have been computed and derived formula for them. Also, we have obtained the numerical computation and graphical representation of degree-based topological indices and entropy values of and . Understanding the topology of precursor fullerenes is undoubtedly aided by the results of our computations.

Identification and low-frequency vibrational analysis of three free anthraquinones via terahertz spectroscopy

In this study, terahertz time-domain spectroscopy (THz-TDS) was used to obtain the terahertz absorption spectra of three free anthraquinones (Chrysophanol, Emodin, Physcion) in the frequency range of 0.2–4.3 THz. The results show that terahertz spectroscopy is an effective detecting such compounds. Meanwhile, the theoretical spectrum using density functional theory calculations agrees well with the experimental spectrum. A modal decoupling method was used to identify each low-frequency vibrational mode and determine the average contribution of different atoms and groups. Modal decoupling provides a better understanding of molecules' mixed vibrational modes and enables quantifying the atoms' vibrational contributions. Results show that the substituent group facilitates the transition between the fundamental vibrational modes; subsequently, the substituent group shifts the vibrational centre of gravity of the three molecules and affects the vibrational contribution of hydrogen bonds. Furthermore, insignificant Emodin absorption is related to the nearly symmetrical structure formed by the substituents. The feasibility of terahertz analysis of differential molecular structures has also been confirmed.

Synthesis: Molecular Structure, Thermal-Calorimetric and Computational Analyses, of Three New Amine Borane Adducts.

Cyclopropylamine borane C3H5NH2BH3 (C3AB), 2-ethyl-1-hexylamine borane CH3(CH2)3CH(C2H5)CH2NH2BH3 (C2C6AB) and didodecylamine borane (C12H25)2NHBH3 ((C12)2AB) are three new amine borane adducts (ABAs). They are synthesized by reaction of the corresponding amines with a borane complex, the reaction being exothermic as shown by Calvet calorimetry. The successful synthesis of each has been demonstrated by FTIR, Raman and NMR. For instance, the 11B NMR spectra show the presence of signals typical of the NBH3 environment, thereby implying the formation of B-N bonds. The occurrence of dihydrogen bonds (DHBs) for each of the ABAs has been highlighted by DSC and FTIR, and supported by DFT calculations (via the Mulliken charges for example). When heated, the three ABAs behave differently: C3AB and C2C6AB decompose from 68 to 100 °C whereas (C12)2AB is relatively stable up to 173 °C. That means that these ABAs are not appropriate as hydrogen carriers, but the 'most' stable (C12)2AB could open perspectives for the synthesis of advanced materials.

アスファルテン分子モデルの変遷

This paper reviews the average molecular models of asphaltene proposed in past years, and introduces recent results of individual molecular structure analyses. The understanding of the asphaltene molecular structure has evolved as analytical techniques advance. In around 2016, modern mass spectrometry ended the controversy over whether island-type or archipelago-type molecules are correct, and clarified the diversity in chemical composition. Atomic force microscopy techniques can now determine individual molecular structures. The historical changes in our understanding of asphaltene are summarized in five stages (Asphaltene 1.0∼5.0).

A High-Specific-Activity L-aspartate-α-Decarboxylase from Bacillus aryabhattai Gel-09 and Site-Directed Mutation to Improve Its Substrate Tolerance.

L-aspartate-α-decarboxylase (ADC) can recognize L-aspartic acid specifically and catalyze the decarboxylation of L-aspartic acid to β-alanine. In this study, a novel L-aspartate-α-decarboxylase (BaADC) with high specific activity from Bacillus aryabhattai Gel-09 was heterologously expressed and characterized. It exhibited optimal enzyme activity at pH 5.5 and 75°C, and its specific activity was 33.9U/mg. To improve the substrate tolerance of BaADC, site-directed mutation was used to construct variants. The optimal variant BaADC_I88M exhibited higher pH stability and thermostability, with 1.2-fold increase in catalytic efficiency. Moreover, through the fed-batch method, the conversion of L-aspartic acid to β-alanine catalyzed by BaADC_I88M reached 98.6% (128.67g/L) at 12h, which was 1.42-fold that of the wild-type enzyme. The mechanism of improved substrate tolerance was interpreted by molecular dynamics simulation and structural analysis, which revealed that the local conformational change in the active pocket could promote correct protonation. These results suggested that BaADC and its variant are potential candidates for use in the industrial production of β-alanine.

Molecular evolution and population genetics of glutamate decarboxylase acid resistance pathway in lactic acid bacteria.

Glutamate decarboxylase (GAD) pathway (GDP) is a major acid resistance mechanism enabling microorganisms' survival in low pH environments. We aimed to study the molecular evolution and population genetics of GDP in Lactic Acid Bacteria (LAB) to understand evolutionary processes shaping adaptation to acidic environments comparing species where the GDP genes are organized in an operon structure (Levilactobacillus brevis) versus lack of an operon structure (Lactiplantibacillus plantarum). Within species molecular population genetic analyses of GDP genes in L. brevis and L. plantarum sampled from diverse fermented food and other environments showed abundant synonymous and non-synonymous nucleotide diversity, mostly driven by low frequency changes, distributed throughout the coding regions for all genes in both species. GAD genes showed higher level of replacement polymorphism compared to transporter genes (gadC and YjeM) for both species, and GAD genes that are outside of an operon structure showed even higher level of replacement polymorphism. Population genetic tests suggest negative selection against replacement changes in all genes. Molecular structure and amino acid characteristics analyses showed that in none of the GDP genes replacement changes alter 3D structure or charge distribution supporting negative selection against non-conservative amino acid changes. Phylogenetic and between species divergence analyses suggested adaptive protein evolution on GDP genes comparing phylogenetically distant species, but conservative evolution comparing closely related species. GDP genes within an operon structure showed slower molecular evolution and higher conservation. All GAD and transporter genes showed high codon usage bias in examined LAB species suggesting high expression and utilization of acid resistance genes. Substantial discordances between species, GAD, and transporter gene tree topologies were observed suggesting molecular evolution of GDP genes do not follow speciation events. Distribution of operon structure on the species tree suggested multiple independent gain or loss of operon structure in LABs. In conclusion, GDP genes in LABs exhibit a dynamic molecular evolutionary history shaped by gene loss, gene transfer, negative and positive selection to maintain its active role in acid resistance mechanism, and enable organisms to thrive in acidic environments.

Designing of asymmetric non-fullerene based acceptor materials by re-modification of π-spacers with PCE > 20 % for organic solar cell

In this study, four new organic molecules with different compounds called the π-linkers, embedded between dithieno[3,2-b:2′,3′-d]pyrrole donor core and dicyanoindanone end-capped acceptor molecules were theoretically designed and analyzed to be proposed as the new asymmetric small molecule acceptors (SMAs) with the highest power conversion efficiency (PCE) in non-fullerene organic solar cells (OSCs). The charge transportability, stability, electronic, and optical properties were calculated based on the molecular structure analysis with the density functional theory (DFT) approach and the results were compared with dithieno[3,2-b:2′,3′-d]pyrrole based asymmetric SMAs named TPIC with dicyanoindanone end-capped groups. As a result of efficient π-π stacking, the energy differences decreased by 17.71 % and the charge transport increased by 49 %. The molecules showed broad absorption spectra ranging from 400 nm to 1200 nm with significant redshifted wavelength towards the near IR region coupled with low excitation energies. The LUMO energy level of the external donor PM7 is aligned with HOMO energy levels of the architecture acceptor molecules via bandgap tuning and the open-circuit voltage (VOC) increased from 1.002 V to 2.44 V for the highest combination PM7:C4. The efficacious charge transport properties, high excitonic generation with low excitation energies, facile separation, and increased VOC via band-gap tunning; all four designed molecules achieved a champion PCE ranging from 20 % to 34 % at short circuit current density 9, 12, and 15 mA cm−2. The molecules exhibited the highest PCE value for any asymmetric non-fullerene small molecule acceptor-based organic solar cells.

Direct Transformation of SiH4 to a Molecular L(H)2Co═Si═Co(H)2L Silicide Complex.

The synthesis of bimetallic molecular silicide complexes is reported, based on the use of multiple Si-H bond activations in SiH4 at the metal centers of 14-electron LCoI fragments (L = Tp″, HB(3,5-diisopropylpyrazolyl)3-; [BP2tBuPz], PhB(CH2PtBu2)2(pyrazolyl)). Upon exposure of (Tp″Co)2(μ-N2) (1) to SiH4, a mixture of (Tp″Co)2(μ-H) (2) and (Tp″Co)2(μ-H)2 (3) was formed and no evidence for Si-H oxidative addition products was observed. In contrast, [BP2tBuPz]-supported Co complexes led to Si-H oxidative additions with the generation of silylene and silicide complexes as products. Notably, the reaction of ([BP2tBuPz]Co)2(μ-N2) (5) with SiH4 gave the dicobalt silicide complex [BP2tBuPz](H)2Co═Si═Co(H)2[BP2tBuPz] (8) in high yield, representing the first direct route to a symmetrical bimetallic silicide. The effect of the [BP2tBuPz] ligand on Co-Si bonding in 7 and 8 was explored by analysis of solid-state molecular structures and density functional theory (DFT) investigations. Upon exposure to CO or DMAP (DMAP = 4-dimethylaminopyridine), 8 converted to the corresponding [BP2tBuPz]Co(L)x adducts (L = CO, x = 2; L = DMAP, x = 1) with concomitant loss of SiH4, despite the lack of significant Si-H interactions in the starting complex. On heating to 60 °C, 8 underwent reaction with MeCl to produce small quantities of MexSiH4-x (x = 1-3), demonstrating functionalization of the μ-silicon atom in a molecular silicide to form organosilanes.

Structural and thermal analyses of metaxalone cocrystals with succinic, adipic and salicylic acids

Metaxalone (MTX) is a skeletal muscle relaxant drug, crystallized with carboxylic acid coformers like succinic acid (SUC), adipic acid (ADP) and salicylic acid (SAL). Their molecular structure, crystal packing and thermal analysis were studied. In the crystallization screening, two polymorphic forms of MTX-SAL were discovered. Form I of MTX-SAL was obtained from ethanol while form II was obtained concomitantly along with form I in ethyl acetate. All four structures form MTX homodimer of R22(8) motif. In MTX-SUC, the N-H⋅⋅⋅O, O-H⋅⋅⋅N and C-H⋅⋅⋅O hydrogen bonds are involved in the crystal packing and generate a three-dimensional hydrogen-bonded network. In MTX-ADP, the coformer bridges the adjacent MTX homodimers and forms an extended chain. In both the polymorphs of MTX-SAL, the MTX molecule forms a homodimer, which is further connected by SAL coformer. Solvent assisted grinding and slurry techniques were employed to obtain phase pure bulk material. The results obtained in different trials were compared using powder X-ray diffraction (PXRD) and the process was optimized for bulk solid form preparation of MTX-SUC, MTX-ADP and MTX-SAL form I. MTX-SUC exhibits a higher melting point than the other two cocrystals. The close packing indices, crystal densities and melting temperatures between both the MTX-SAL cocrystal polymorphs resulted in the concomitant existence of form II with form I.

Elucidation of molecular crystals with one-, two- or three-dimensional geometrical models.

A brief commentary is given on the article by Thomas & Hughes [Acta Cryst. (2023), B79, 3–23], which presents new geometrical models and structural descriptors for the analysis of molecular crystal structures.

Novel asymmetrical azines appending 1,3,4-thiadiazole sulfonamide: synthesis, molecular structure analyses, in silico ADME, and cytotoxic effect.

Toward finding potential and novel anticancer agents, we designed and prepared novel differently substituted unsymmetrical azine-modified thiadiazole sulfonamide derivatives using the "combi-targeting approach". An efficient procedure for synthesizing the designed compounds starts with 5-acetyl-3-N-(4-sulfamoylphenyl)-2-imino-1,3,4-thiadi-azoline 4. The E/Z configuration for compound 5 was investigated based on spectral analysis combined with quantum mechanical calculation applying the DFT-B3LYP method and 6-31G(d) basis set. The computational results found that the E isomer was energetically more favorable than the Z isomer by 2.21 kcal mol-1. Moreover, 1H and 13C chemical shifts for the E and Z isomers in DMSO were predicted using the GIAO-B3LYP/6-31G(d) computations and IEF-PCM solvation model. The computed chemical shifts for both isomers are consistent with those observed experimentally, indicating that they exist in the solution phase. Moreover, the E/Z configuration for the synthesized azines 7a-c, 9, 11, 13, 15a and 15b was also studied theoretically using the DFT-B3LYP/6-31G(d) calculations. In silico prediction for the biological activities was reported regarding the HOMO-LUMO energy gaps and molecular reactivity descriptors besides the ADMT/drug-likeness properties. The cytotoxic effect of the synthesized compounds has been assayed via the determination of their IC50.

Molecular evolution and structural analyses of proteins involved in metabolic pathways of volatile organic compounds in Petunia hybrida (Solanaceae).

The association between plants and their pollinators is essential for increasing the diversity in angiosperms. Morphological and physiological traits, mainly floral scent, can influence the pollination dynamics and select pollinators for each plant species. In this work, we studied two proteins involved in producing volatile organic compounds in plants, conyferyl alcohol acyltransferase (CFAT) and benzoyl-CoA:benzyl alcohol/phenyl ethanol benzoyl transferase (BPBT) genes. We aimed to understand these proteins with respect to evolutionary and structural aspects and functions in Solanaceae using phylogenetic methods and comparative molecular modeling. We used Bayesian inference to describe the proteins' evolutionary history using Petunia x hybrida as a query to search for homologs in the Solanaceae family. Theoretical 3D models were obtained for both proteins using Panicum virgatum as a template. The phylogenetic tree included several different enzymes with diverse biological roles in Solanaceae, displaying the transferase domain. We identified only one sequence of CFAT in the databases, which belongs to Petunia x hybrida, and found several BPBT sequences from the genera Nicotiana, Solanum, and Capsicum. The 3D structures of CFAT and BPBT have two different domains, and we have identified the amino acid residues essential for the enzymatic activity and interaction with substrates.

Growth mechanism of glucose-based hydrochar under the effects of acid and temperature regulation.

Improving the tailorability of hydrochar synthesis is an effective way to enhance its performance and utilization efficiency. In this study, the growth rate, morphology, and molecular structure of hydrochar were controlled by regulating the pH and temperature of the hydrothermal carbonization process. Growth process analysis indicates that hydrochar has three growth periods: induction, rapid, and stable growth periods. It is mainly controlled by 5-hydroxymethylfurfural (HMF), which is formed by converting glucose and its transformation products. The regulation of acid can significantly shorten the induction period of hydrochar, even under low-temperature conditions (<180℃), and increase the growth rate of hydrochar. However, the degree of hydrochar adhesion varies: the lower the temperature, the greater the degree of its adhesion. Molecular structural analysis demonstrates that hydrochar mainly consists of furan structural domains and aromatic clusters, and its surface is rich in oxygen-containing functional groups. The degree at which hydrochar was aromatized was improved by increasing the reaction temperature (160-220℃); whereas the regulation of acid reduced it and increased the content of oxygen-containing functional groups on the hydrochar surface. Based on these results, it is proposed that hydrochar formation has five stages and three growth periods with or without acid regulation.

Molecular Description and Hirshfeld Analysis of the (−)-(S)-1-[2-(Benzenesulfonamido)-3-phenylpropanoyl]-4-[(4-chloro)phenyl]thiosemicarbazide

(−)-(S)-1-[2-(Benzenesulfonamido)-3-phenylpropanoyl]-4-[(4-chloro)phenyl]thiosemicarbazide was synthesized by condensing (+)-(S)-2-(benzenesulfonamido)-3-phenylpropanylhydrazide with 4-chlorophenyl isothiocyanate in methanol and a single crystal data of [C22H21N4O3S2Cl] is supported by a single crystal X-ray diffraction (XRD) analysis. The title compound, C22H21N4O3S2Cl, has a non-planar configuration and crystallized in the monoclinic crystal system with P21 space group with the following parameters: a = 13.174 (2), b = 6.9239 (13), c = 14.516 (3) Å, β= 115.644 (5)˚, V = 1193.7 (4) Å3 and Z = 2. It has been observed that the crystal structure of the obtained compound contains intra- and intermolecular N—H…O and N—H…S hydrogen bonds between benzenesulfonamido and thiosemicarbazide groups. In addition to molecular structure analysis, Hirshfeld surface (HS) analysis was also examined, and fingerprint plots supported the identification of important intermolecular interactions in molecular structure.

Computational molecular structure analysis, electronic properties of sudan dye doped thioureabarium chloride crystals for nlo Applications

Pure thiourea barium chloride (TBC) crystals were grown by slow evaporation from aqueous solution and slow cooling (0.1oC/ day). The growth was carried out for 21 days by keeping the bath at a temperature of 39oC. Optimal molecular structures are explored by DFT / B3LYP method with 6-31G (d, p) based synthesis. Hyper conjugative interactions, charge delocalization and intra molecular hydrogen bonding have been analyzed using natural bond orbital (NBO) analysis. Moreover lower in the HOMO and LUMO energy gap explains the eventual charge transfer interactions taking place within the molecule, which influences the biological activity of the compound and also energy serves as a measure of the excitability of a compound, the smaller the energy gap, the more easily the compound will be excited. Electronic structures were discussed and the displacement of the electron density was determined. Second – order perturbation theory analysis of the intra molecular bonds of Methyl Orange doped TBC were derived.