Molecular Crystal Structure Research Articles

New insight into the mechanism by which antifreeze peptides regulate the physiological function of Streptococcus thermophilus subjected to freezing stress

IntroductionAntifreeze peptides regulate the physiological functions of frozen cells and even their apoptosis; however, the mechanisms by which antifreeze peptides regulate these processes remain unclear, although the interactions between cell membranes and ice are well known to be important in this process. ObjectivesOur study aims to investigate how antifreeze peptides regulate cell physiological functions during the freezing process. MethodsWe investigated the cryoprotective effect of rsfAFP on the physiological functions of S. thermophilus under freezing stress by measuring cellular metabolism activity, intracellular enzyme activity, cell membrane characterization, and cell apoptosis. The mechanism by which rsfAFP impacts S. thermophilus physiological functions under freezing stress was investigated using multispectral techniques and cryo-TEM. ResultsWe show that a recombinant antifreeze peptide (rsfAFP) interacts with the extracellular capsular polysaccharides and peptidoglycan of Streptococcus thermophilus and ice to cover the outer layer of the membrane, forming a dense protective layer that regulates the molecular structure of extracellular ice crystals, which results in reduced extracellular membrane damage, depressed apoptosis and increased intracellular metabolic activity. This interaction mechanism was indicated by the fact that S. thermophilus better maintained its permeability barrier, membrane fluidity, membrane structural integrity, and cytoplasmic membrane potential during freezing stress with rsfAFP treatment. ConclusionThese results provide new insights into the mechanism by which rsfAFP regulates frozen cellphysiological functionsand apoptosis under freezing stress.

Molecular docking reveals Chitosan nanoparticle protection mechanism for dentin against Collagen-binding bacteria

The medical application of chitosan (Cs) has been for about half a century, but the molecular mechanism has not been elucidated yet. This study is to explore the antibacterial mechanism of chitosan nanoparticles (Csnp) in dentin at the atomic resolution level. Extracted tooth specimen was prepared in three groups: A. control group; B. Csnp treatment under ultrasonic agitation (UA); C. Csnp treatment without UA. A scanning electron microscope (SEM) was used to observe the Csnp distribution on the dentin surface. The incubations of Enterococcus faecalis (E. faecalis) were performed. Further, we explored the protection mechanism of chitosan polymers to collagen type I, using molecular docking technique and crystal structure superimposition analysis. We revealed that Csnp under UA was evenly distributed on the dental surface and the Csnp-pretreated dentin had great antibacterial activity for E. faecalis. Our work demonstrated that Csnp occupied the grooves of the triple-helical collagen surface, strengthened by crosslinking, and interfered with the bond of collagen adhesin through steric hindrance effect and interrupting hydrophobic interaction. Csnp protects dentin against E. faecalis by interacting and crosslinking with collagen type I and prevents bacterial collagen adhesin binding through steric hindrance effect and interrupting hydrophobic interaction.Graphical abstract

Revisiting pure component wax esters as basis of wax‐based oleogels

AbstractCurrent research on wax‐based oleogels indicates wax esters to be the key component in many natural waxes. This necessitates understanding the properties of pure wax esters to unravel the gelling mechanism in wax‐based oleogels. Therefore, available literature data on pure wax esters is summarized and critically reviewed. The detailed analysis of the pre‐existing data on crystallographic (SAXS) and thermal properties, facilitates the interpretation of subsequently performed experiments: Specific wax esters with different carbon numbers and symmetries were studied as such and in oleogels formed in combination with medium chained triglyceride oil at inclusion levels of 10% (w/w). They were characterized regarding their thermal (differential scanning calorimetry [DSC]) and viscoelastic (oscillatory rheology) behavior. It is found that all observations concerning pure wax esters behave systematically, linking molecular makeup, crystal structure, and behavior. The experimental study of oleogels structured by four different binary mixtures of wax esters revealed that substantial chain length differences induce separate crystallization (CN30 + 36 and CN30 + 42). Mixtures of wax esters with only limited chain length difference (≤ 2 carbon atoms) reconfirmed earlier speculations on mixing behavior and crystal structure. Applying mixtures of wax esters only differing in their position of the ester bond (CN36 [14_22] + CN36 [22_14]) indicated ideal mixing behavior in the solid phase of the gels. Surprisingly, the data revealed that additional thermal events occur at specific mixing ratios, predominantly at 1:1 (w/w). Their supposed relation to compound formation certainly needs further confirmation. Rheological analysis confirmed that sequential crystallization results in highest firmness values for the systems studied.

Behavior of Occupied and Void Space in Molecular Crystal Structures at High Pressure.

We report a Monte Carlo algorithm for calculation of occupied (“network”) and unoccupied (“void”) space in crystal structures. The variation of the volumes of the voids and the network of intermolecular contacts with pressure sensitively reveals discontinuities associated with first- and second-order phase transitions, providing insights into the effect of compression (and, in principle, other external stimuli) at a level between those observed in individual contact distances and the overall unit cell dimensions. The method is shown to be especially useful for the correlation of high-pressure crystallographic and spectroscopic data, illustrated for naphthalene, where a phase transition previously detected by vibrational spectroscopy, and debated in the literature for over 80 years, has been revealed unambiguously in crystallographic data for the first time. Premonitory behavior before a phase transition and crystal collapse at the end of a compression series has also been detected. The network and void volumes for 129 high-pressure studies taken from the Cambridge Structural Database (CSD) were fitted to equation of state to show that networks typically have bulk moduli between 40 and 150 GPa, while those of voids fall into a much smaller range, 2–5 GPa. These figures are shown to reproduce the narrow range of overall bulk moduli of molecular solids (ca. 5–20 GPa). The program, called CellVol, has been written in Python using the CSD Python API and can be run through the command line or through the Cambridge Crystallographic Data Centre’s Mercury interface.

Crystal growth, structural, spectral, optical, DFT analysis and Z-scan analysis of pyridine-1-ium-2-carboxylatehydrogenbromide (PHBr) for optoelectronic and nonlinear optical applications

A single crystal of Pyridine-1-ium-2-carboxylatehydrogenbromide (PHBr) was grown using the Slow Evaporation Solution Technique. Using Single Crystal X-Ray Diffraction analysis, the crystal lattice characteristics and molecular structure of the grown crystal of PHBr were found and it corresponds to the Triclinic crystal system with space group Pī. Intra and intermolecular interactions were visualized using Hirshfeld surface analysis. The theoretical calculation conducted by Density Functional Theory (DFT) and it is well agreed with the experimental results. The Molecular optimized geometry, FT-IR and HOMO-LUMO energy gap were computed using the B3LYP level of theory with a 6-31 + G (d,p) basis set. The FT-IR spectrum studies are given here to look at the modes of vibration of numerous functional groups found in the PHBr crystal. The measurements of UV–visible NIR transmittance show that the crystal has a high transmittance over the whole visible spectrum. The Z-scan approach is used to perform third-order nonlinear optical (NLO) investigations on a PHBr crystal and optical properties such as linear and nonlinear refractive index are computed.

Removal of toxic metals from petroleum produced water by dolomite filtration

We conducted experiments and reactive transport simulations to assess the removal of high concentrations of toxic metals (100 mg/L) commonly found in produced water from high saline waters (45,000–115,000 mg/L) using dolomite filters made of compressed powdered dolomite. The focus was on Ba, Sr, Cd, Pb, and As, as well as on guar gum as a metal complexing additive. We found that salinity has a significant impact on the removal of Sr and Ba but a mild impact on the removal of Cd. An increase of pH due the dissolution of dolomite increases the removal of Cd more significantly than the removal of Ba and Sr. The formation of guar-gum complexes of metals in the aqueous phase attenuates the removal of Sr, Ba, and Cd by dolomite filtration, this attenuation process is more significant for Cd than for Sr and Ba. The affinity sequence for the sorption of toxic metals at salinity levels of PW is Pb > Cd > As>Ba>Sr. Higher removal levels predicted for Sr than for Ba and over predictions of Cd removal using previously proposed surface complexation models for dolomite highlights the necessity of further experimental research to incorporate molecular scale surface crystal structure parameters into surface complexation models.

Carrageenan of Red Algae Eucheuma gelatinae: Extraction, Antioxidant Activity, Rheology Characteristics, and Physicochemistry Characterization.

Carrageenan is an anionic sulfated polysaccharide that accounts for a high content of red seaweed Eucheuma gelatinae. This paper focused on the extraction, optimization, and evaluation of antioxidant activity, rheology characteristics, and physic-chemistry characterization of β-carrageenan from Eucheuma gelatinae. The extraction and the optimization of β-carrageenan were by the maceration-stirred method and the experimental model of Box-Behken. Antioxidant activity was evaluated to be the total antioxidant activity and reducing power activity. The rheology characteristics of carrageenan were measured to be gel strength and viscosity. Physic-chemistry characterization was determined, including the molecular weight, sugar composition, function groups, and crystal structure, through GCP, GC-FID, FTIR, and XRD. The results showed that carrageenan possessed antioxidant activity, had intrinsic viscosity and gel strength, corresponding to 263.02 cps and 487.5 g/cm2, respectively. Antioxidant carrageenan is composed of rhamnose, mannose, glucose, fucose, and xylose, with two molecular weight fractions of 2.635 × 106 and 2.58 × 106 g/mol, respectively. Antioxidant carrageenan did not exist in the crystal. The optimization condition of antioxidant carrageenan extraction was done at 82.35 °C for 115.35 min with a solvent-to-algae ratio of 36.42 (v/w). At the optimization condition, the extraction efficiency of carrageenan was predicted to be 87.56 ± 5.61 (%), the total antioxidant activity and reducing power activity were predicted to 71.95 ± 5.32 (mg ascorbic acid equivalent/g DW) and 89.84 ± 5.84 (mg FeSO4 equivalent/g DW), respectively. Purity carrageenan content got the highest value at 42.68 ± 2.37 (%, DW). Antioxidant carrageenan from Eucheuma gelatinae is of potential use in food and pharmaceuticals.

Complexity of Molecular Nets: Topological Approach and Descriptive Statistics

The molecular net complexity (HmolNet) is an extension of the combinatorial complexity (Hmol) of a crystal structure introduced by Krivovichev. It was calculated for a set of 4152 molecular crystal structures with the composition of CxHyOz characterized by the structural class P21/c, Z = 4 (1). The molecular nets were derived from the molecular Voronoi–Dirichlet Polyhedra (VDPmol). The values of the molecular coordination number (CNmol) and critical coordination number (CNcrit) are discussed in relation with the complexity of the crystal structures. A statistical distribution of the set of molecular crystals based on the values of CNmol, CNcrit, and the complexity parameters is obtained. More than a half of the considered structures has CNmol = 14 and CNmol′ = 9 with the Wyckoff set of edges e5dcba. The average multiplicity of intermolecular contacts statistically significantly decreases from 1.58 to 1.51 upon excluding all contacts except those bearing the molecular net. The normalized value of HmolNet is of the logistic distribution type and is distributed near 0.85HmolNet with a small standard deviation. The contribution of Hmol into HmolNet ranges from 35 to 95% (mean 79%, SD 6%), and the subset of bearing intermolecular contacts accounts for 41 to 100% (mean 62%, SD 11%) of the complexity of the full set of intermolecular contacts.

Bis(2,6-diisopropylphenyl) tellurone: a well-defined monomeric diorganotellurone without cocrystallized solvents and without stabilizing intramolecular contacts.

Only two crystal structures of diorganotellurones have been reported to date, both of which contain cocrystallized solvents and one of which is stabilized by intramolecular Te-N secondary bonding interactions. This work describes the crystal structure of bis(2,6-diisopropylphenyl) tellurone, (C12H17)2TeO2 or C24H34O2Te, the first well-defined diorganotellurone without cocrystallized solvents and without stabilizing intramolecular contacts. The molecule has crystallographic twofold symmetry, with half the molecule as the asymmetric unit. The molecular structure is compared to previously reported tellurones and those computed at the density functional theory DFT/B3PW91 level. The molecules form two-dimensional layers as a result of a weak intermolecular hydrogen-bonding network. The layers are then stacked in an antiparallel manner to form the crystal packing structure. The Hirshfeld surface analysis was employed to visualize and quantify the intermolecular contacts in the molecular crystal structure, and the contribution of O...H and H...H interactions was found to be the dominating factor.

Development and assessment of an improved powder-diffraction-based method for molecular crystal structure similarity

The improved variable-cell powder difference (VC-PWDF) method provides a valuable addition to the toolbox of quantitative methods for crystal structure comparison.

SDPD-SX: combining a single crystal X-ray diffraction setup with advanced powder data structure determination for use in early stage drug discovery

A method for routine molecular crystal structure determination on very small (typically <0.1 mg) amounts of crystalline material using powder X-ray diffraction data from a laboratory-based single-crystal diffractometer is reported.

Coarse-grained modelling to predict the packing of porous organic cages.

How molecules pack has vital ramifications for their applications as functional molecular materials. Small changes in a molecule's functionality can lead to large, non-intuitive, changes in their global solid-state packing, resulting in difficulty in targeted design. Predicting the crystal structure of organic molecules from only their molecular structure is a well-known problem plaguing crystal engineering. Although relevant to the properties of many organic molecules, the packing behaviour of modular porous materials, such as porous organic cages (POCs), greatly impacts the properties of the material. We present a novel way of predicting the solid-state phase behaviour of POCs by using a simplistic model containing the dominant degrees of freedom driving crystalline phase formation. We employ coarse-grained simulations to systematically study how chemical functionality of pseudo-octahedral cages can be used to manipulate the solid-state phase formation of POCs. Our results support those of experimentally reported structures, showing that for cages which pack via their windows forming a porous network, only one phase is formed, whereas when cages pack via their windows and arenes, the phase behaviour is more complex. While presenting a lower computational cost route for predicting molecular crystal packing, coarse-grained models also allow for the development of design rules which we start to formulate through our results.

An efficient treatment of ring conformations during molecular crystal structure determination from powder diffraction data

An effective and efficient method for dealing with ring systems during global optimisation-based crystal structure determination from powder diffraction data.

IR spectra of paracetamol

Paracetamol is a very popular medication used to treat pain and fever. IR spectra of paracetamol have been measured for powder crystals. Ab initio calculations of its equilibrium geometry and vibrational spectra were carried out for spectrum interpretation. Differences between the experimental IR spectra of crystalline samples have been analyzed. Variations of molecular structure from the isolated state to molecular crystal were estimated based on the difference between the optimized molecular parameters of free molecules and the experimental bond lengths and angles evaluated for the crystal forms of the title compounds. The role of hydrogen bonds in the structure of molecular crystals of paracetamol is investigated.
 Bangladesh J. Sci. Ind. Res.56(4), 255-262, 2021

Ethylene glycol diglycidyl ether applied to crosslinking dyeing of cotton fabric with madder dye

AbstractCotton fabric dyed with natural madder dye exhibits poor dyeing properties. Although mordant improves the dyeing property of cotton fabric, it changes the madder dye colour tonality (the hue angle). In this study, ethylene glycol diglycidyl ether (EGDE) was used as a crosslinking agent to dye cotton fabrics with natural madder dye and improve the surface colour depth (K/S) and colour fastness. The molecular structure, crystal structure and surface morphology of crosslinked dyed cotton were analysed using Fourier Transform–infrared spectroscopy, X‐ray diffractometry and scanning electron microscopy, respectively. The results showed that crosslinked dyed cotton fabric had two different ether bonds, and that crosslinked dyeing mainly occurred in the amorphous area. Compared with direct dyed cotton fabric, the hue angle (h°) of crosslinked dyed cotton fabric did not undergo an obvious change, K/S increased by 5, and the rubbing fastness, washing fastness and light fastness increased by 2‐3 levels, indicating that the dyeing property of cotton fabric with natural madder dye could be improved by using EGDE as a crosslinking agent. Compared with raw cotton fabric, the bending length of crosslinked dyed cotton fabric was reduced by 2.28 cm, the wrinkle recovery angle increased by 80.7° and the ultraviolet protection factor value was more than 40, indicating that crosslinked dyed cotton fabric had great softness, wrinkle resistance and excellent ultraviolet resistance. In addition, the water contact angle of the cotton fabric only changed slightly after crosslinking dyeing, and the crosslinked dyed cotton fabric still had good hydrophilicity. Therefore, EGDE was a viable crosslinking agent for cotton fabric with madder dye.

Effect of Ultrasonic Treatment on the Structure and Physicochemical Properties of Millet Starch

With the same ultrasonic time and temperature, different ultrasonic powers of 0, 25, 50, 100, 150, 200, 250 W on the structure and properties of millet starch were studied. The hydrolysis rate, microstructure, crystal structure, molecular structure, particle size, rheological and gelatinization properties of millet starch were determined. The experimental results indicated that the hydrolysis rate and particle size of millet starch increased after ultrasonic treatment, hydrolysis rate of millet starch under 250 W ultrasonic treatment for 40 min was 1.037%, the average particle size increased from the original 9.96 to 12.10 μm, and it showed greater transparency and stability. Ultrasonic treatment did not change the crystal type and molecular structure, but caused a slight decrease in order. Ultrasound changed the fluidity of millet starch paste, the shear stress and apparent viscosity of millet starch paste decreased with the increase of ultrasonic power. The peak viscosity, trough viscosity, final viscosity, breakdown and setback of millet starch after ultrasound were significantly reduced, and the thermal stability was improved. Ultrasonic technology is widely used in the processing of modified starch. The results of this study could provide a theoretical basis for the modification of millet starch.

Crystal Structures and Solution Chemical Properties of Two Lactate Complexes Mn[(C3H5O3)2(H2O)2]⋅H2O(s) and Cu(C3H5O3)2(s)

Trihydrated manganese lactate Mn[(C3H5O3)2(H2O)2]⋅H2O(s) and anhydrous copper lactate Cu(C3H5O3)2(s) were synthesized. Crystal structures of the two compounds were characterized by X-ray single crystal diffraction technique. The compositions, spatial structures and coordination modes of the two compounds were determined by analysis of their molecular structures and crystal structures. Lattice potential energies of the compounds were calculated by using the crystallographic data. Molar enthalpies of dissolution of these metal complexes in the ultrapure water were measured by an isoperibol solution-reaction calorimeter with an accuracy of ±0.3%. On the basis of Pitzer's electrolyte solution theory, infinite dilution molar enthalpies of dissolution and Pitzer's parameters of the two lactate complexes soluble in water at T = 298.15 K were calculated. The infinite dilution molar enthalpies (ΔsHm∞) of dissolution of the title compounds were combined with lattice potential energies (UPOT) by a designed thermodynamic cycle, and the average molar enthalpy of hydration of the common lactate ion was calculated to be (407.207 ± 0.038) kJ·mol−1. The mechanism of thermal decomposition or dehydration of the trihydrated manganese lactate was explored by TG-DSC technique, and the difference between molar enthalpies (ΔsHm) of dissolution of trihydrated manganese lactate and anhydrous copper lactate at the same concentration was revealed.

Applying Feasibility Investigation of Resin Modifying Agent in Asphalt Pavement Materials

In order to promote the resin modifying agent applied into pavement materials, a type of resin modifying agent was selected as the modifier to prepare modified asphalt. The molecular crystal structure of the modifying material was characterized by using the X-ray diffraction test (XRD). The microstructure and element composition of PA6 was investigated through focused ion beam scanning electron microscopy (FIB-SEM). The thermal property and functional groups of PA6 were studied by thermogravimetric analysis-Fourier infrared spectroscopy (TG-FTIR) test. The physical property and rheological properties of PA modified asphalt were evaluated to confirm the applying feasibility of PA6 in asphalt. The results indicated that PA6 was the semicrystalline polymer and the existence of γ crystal form might improve the toughness of asphalt materials effectively. The thermal decomposition process of PA6 could be divided into three stages roughly: inert weight loss stage, rapid weight loss stage, and stable stage. The amount of PA6 modifier should be appropriately controlled during the application process to ensure the comprehensive effect of PA6 on high-temperature performance and low-temperature performance. The corresponding initial modulus attenuation value of PA modified asphalt was less than 70# asphalt under the same test conditions.

First-Principles Study on the Direct Bandgap Double Perovskite Series Cs2LiInX6(X = F, Cl, and Br).

A molecular crystal structure model of the lead-free halide chalcogenide semiconductor Cs2LiInX6 (X = F, Cl, and Br) was established, and its energy band, density of states, optical properties, and thermodynamic properties were calculated using the first nature principle and the effect of different pressures on the bandgap of Cs2LiInX6 (X = F and Cl, Cs2LiInF6 with a bandgap of 7.359 eV, Cs2LiInCl6 with a bandgap of 5.098 eV, and Cs2LiInBr6 with a bandgap of 3.755 eV). The absorption of light is mainly due to the transition of halide ions from p- to s-orbitals. The p- and In-s orbitals of halide ions play a major role in light harvesting. Cs2LiInCl6 has low sensitivity to relative pressure and is stable at a 0–100 GPa pressure. In the structure of Cs2LiInX6 (X = F, Cl, and Br), changing the halogen atom can effectively improve its optical properties. Cs2LiInCl6 and Cs2LiInF6 are considered as the most promising candidates for UV detectors. Cs2LiInF6 has a large forbidden band width and a high Debye temperature and shows a high photoluminescence quantum yield in the field of phosphors with great potential in the field of phosphors with high photoluminescence quantum yields. This study is a positive reference for the preparation of lead-free chalcogenide-type ultraviolet detectors with excellent performance.

Synthesis of Boronated Amidines by Addition of Amines to Nitrilium Derivative of Cobalt Bis(Dicarbollide).

A series of novel cobalt bis(dicarbollide) based amidines were synthesized by the nucleophilic addition of primary and secondary amines to highly activated B-N+≡C–R triple bond of the propionitrilium derivative [8-EtC≡N-3,3′-Co(1,2-C2B9H10)(1′,2′-C2B9H11)]. The reactions with primary amines result in the formation of mixtures of E and Z isomers of amidines, whereas the reactions with secondary amines lead selectively to the E-isomers. The crystal molecular structures of E-[8-EtC(NMe2)=HN-3,3′-Co(1,2-C2B9H10)(1′,2′-C2B9H11)], E-[8-EtC(NEt2)=HN-3,3′-Co(1,2- C2B9H10)(1′,2′-C2B9H11)] and E-[8-EtC(NC5H10)=HN-3,3′-Co(1,2-C2B9H10)(1′,2′-C2B9H11)] were determined by single crystal X-ray diffraction.