Molecular Crystal Structure Research Articles

Effect of annealing on the molecular ordering and crystal structure of iron phthalocyanine thin films on Si (111) surface

The Effect of annealing on molecular ordering in Iron Phthalocyanine (FePc) thin films deposited on Si (111) substrate surface was investigated using lab source (Cu Kα) based x-ray diffraction, synchrotron based 2-dimensional grazing incidence x-ray diffraction, polarization dependent x-ray absorption spectroscopy and hard x-ray photoelectron spectroscopy. Room temperature deposition of FePc on Si substrate resulted in amorphous thin films with randomly oriented FePc molecules. However, annealing of these amorphous films at 200°C led to crystallization with highly ordered FePc molecules having monoclinic crystal lattice structure. The ordered FePc molecules followed edge-on stacking on Si substrate surface with an azimuthally averaged tilt angle of 75±5° between molecular plane and substrate surface. Also, the b-c plane of the unit cell was lying almost parallel to the substrate surface. The edge-on stacking ordering of FePc molecules in annealed thin films led to higher charge conduction as compared to as-deposited films.

Synthesis, crystal structure and DFT study of 2-(3-bromophenyl)-1-(4-morpholinyl)ethanone

2-(3-Bromophenyl)-1-(4-morpholinyl)ethanone belongs to one of morpholine derivatives. In this paper, 2-(3-bromophenyl)-1-(4-morpholinyl)ethanone was synthesized by a two-step synthesis method. In order to determine the structure of the target compound, FT-IR,1H NMR,13C NMR and MS were used for detection. Meanwhile, X-ray diffraction was used to detect the single crystal and obtain the crystal structure data of the target compound. The molecular crystal structure was compared with that determined by density functional theory. The frontier molecular orbitals and molecular electrostatic potential energy were used to further study the physical properties of the compounds.

Synthesis, structure, photoluminescence and magnetism of a series of cobalt‐lanthanide heterometallic complexes originated from 2,3‐dichlorobenzoate and 1,10‐phenanthroline

AbstractA series of 3d–4f heterometallic complexes, namely [Ln2Co2(2,3‐DCB)10(phen)2] [Ln=Nd (1), Sm (2), Eu (3), Gd (4), Tb (5), Dy (6), Er (7)], were obtained through the self‐assembly reactions of Ln(NO3)3 ⋅ nH2O, Co(NO3)2 ⋅ 6H2O, 2,3‐dichlorobenzoic acid (2,3‐HDCB), NaOH and 1,10‐phenanthroline (phen) under solvothermal conditions. Their crystal structures were determined by single‐crystal X‐ray diffraction. They were also characterized by elemental analysis, FT‐IR, powder X‐ray diffraction (PXRD) and thermogravimetric analysis (TGA) and differential thermoanalysis (DTA). These seven complexes have the same molecular formula but different crystal structures. Complexes 1–3, 4 and 5 as well as 6 and 7 are crystallographically isomorphous, respectively. They all exhibit zero‐dimensional (0D) linear tetranuclear cluster structures. These 0D linear tetranuclear clusters can be further connected into a two‐dimensional (2D) supramolecular network via the extensive intermolecular π–π interactions between 2,3‐DCB and phen. The photoluminescent properties of 3, 5 and 6 and the magnetic properties of 1–2 and 4–7 were investigated. Complex 6 shows a slow magnetic relaxation behavior.

Designing thermal regulation materials: Investigating alkylamine length in polymorphic layered hybrid organic-inorganic perovskites

Layered hybrid organic-inorganic perovskites have gained interest in the scientific community due to their feasibility of being used as phase transition materials to store energy by their polymorphism transitions. These compounds represent excellent candidates for cooling electronic devices, given that approximately 55 % of electronic device failures or damage is attributed to internal overheating. Here, we synthesized (C12H25N)2CuCl4, (C14H29N)2CuCl4, (C16H33N)2CuCl4, (C12H24N)2MnCl4, (C14H29N)2MnCl4 and (C16H33N)2MnCl4 to evaluate their potential as thermal regulators and to investigate the dependence of their properties on the length of the alkylamine used. The compounds were synthesized by a liquid phase reaction method and the thermal cycling effect was evaluated after 0, 50, 100 and 200 cycles, between 298 K and 333 K. The crystal structure, molecular structure, and thermal properties of the compounds were characterized and compared before and after the thermal cycling. The maximum enthalpy was obtained for the (C16H33N)2CuCl4 and (C16H33N)2MnCl4 with 98.1 and 90.5 J·g−1, respectively. Additionally, all the components were thermally stable up to 200 cycles, with no evidence of structural degradation or thermal properties decreases. Therefore, our results show that these layered hybrid organic-inorganic perovskites could work as effective thermal regulators. By carefully selecting the alkylamine length, it may be possible to optimize their performance further.

Synthesis, crystal structure, DFT studies, and Hirshfeld surface analysis of a new Strontium Polyphosphate Form [formula omitted

The α-Sr(PO3)2 was synthesized at 273.15 K and P = 1.01325 bar and characterized by single crystal X-ray diffraction analysis, IR & Raman spectroscopy, and Computational simulation (ELF, HSA & DFT) studies. This compound crystallizes in the centrosymmetric triclinic space group P-1 (Z = 4) with a = 5.7938(3) (Å), b = 7.2039(4) (Å), c = 8.0673(4) (Å), α = 97.800(2)°, β = 104.590 (2)°, γ = 106.647(2)° & V = 304.25(3)Å3. The 3D structure contains Sr(PO3)2 chains, which form wavy layers between which exist layers of (PO3)- ions. In addition, theoretical calculations were performed using the DFT/B3LYP/LanL2DZ basis set for crystal molecular structure, Infrared and Raman spectra, and HOMO-LUMO properties of the title compound. 3D-MEPs and the α-Sr(PO3)2-(HOMO/LUMO) were used to assess the total electron density(Global reactivity) and the reactive centres(Local reactivity). Molecular orbital contributions are evaluated by DOS. A comparative study by the SD is in the range DFT/XRD; 0.06 in % for bond lengths and 0.016 in % for angles. The Intermolecular α-Sr(PO3)2 interactions were quantified by HAS. The ELF identifies (non-binding and binding) regions of space that can be associated with electron pairs for elaborated material. The IR spectrum confirms the existence of the functional groups in the elaborated material. The complete vibrational assignments and analysis of the observed fundamental bands of the molecule were carried out.

Crystal structure, vibrational analysis, electronic properties, static and dynamic NLO response and molecular docking study of oxadiazole/pyridine-based Zn(II) complex

In this study, a complex consisting of oxadiazole and pyridine groups coordinated with zinc(II) chloride was synthesized and characterized by using the experimental (FT-IR, Raman and UV spectroscopic techniques) and computational methods. The molecular coordination of the complex exhibited a different orientation due to the position of the Cl-Zn-Cl bond angle, resulting in a distorted octahedral molecular geometry around the central zinc(II) metal ion. The exact crystal molecular structure was uncovered with the experimental single crystal X-Ray diffraction (SCXRD) analysis. Theoretical modeling on the electronic structure properties was performed with the DFT/B3LYP method at the 6–311G(2d,2p)+LanL2DZ computational level. The computational molecular geometry analysis was used to support the experimental structural geometric parameters. Some significant characteristic vibrational bands such as intra-ligand, metal-ligand and metal-chloride groups were investigated by using the experimental FT-IR and Raman spectral techniques and computational method. The electronic transition features and the nature of metal-ligand/chloride coordination environment were determined via help of the UV–Vis., HOMO, LUMO and NBO analyses. The MEP analysis was investigated for the complex. The NLO profile was investigated by analyzing the polarizabilities and the first- and second-order hyperpolarizabilities (α, β and γ) at the static and dynamic (ω = 532 nm and 1064 nm) states with theoretical approach. Lastly, the molecular docking study was performed to determine the anxiolytic activity of the synthesized complex.

Growth and Characterization of Organic 2-Chloro 5-Nitroaniline Crystal Using the Vertical Bridgman Technique

In this article, we discuss the preparation of organic 2-chloro-5 nitroaniline (2C5NA) crystals and their different kinds of physical, chemical, and mechanical properties. The vertical Bridgman approach was used to effectively produce the bulk organic 2C5NA crystal. To produce a good-quality bulk crystal, the shape, dimensions, and cone angle of the ampoule were optimized. Also, the temperature profile was set for the 2C5NA crystal. The growth atmosphere and the lowering rate were identified to obtain a homogeneous mixture of the compounds and initiate the nucleation process. Single-crystal X-ray diffraction (XRD), powder XRD, proton Fourier transform nuclear magnetic resonance (FT-NMR), and Fourier transform infrared investigations were used to confirm the crystal structure, molecular structure, and presence of functional groups in the formed crystal. The formed crystal has a monoclinic crystal structure with the space group P21/c, according to single-crystal XRD analysis. The thermal stability and kinetic parameters were examined using thermogravimetric analysis and differential thermal curves. From dielectric analysis, the electrical conductivity and dielectric behavior of 2C5NA were investigated with variations in frequency and temperature. The organic 2-chloro-5-nitroaniline crystal demonstrates that the indentation size effect is observed in the Vickers micro-hardness test, which was also carried out.

DFT modeling techniques to understand the potential applicability of novel double perovskite semiconductor Ba2LuNbO6 for sustainable thermoelectrics and optoelectronic perspectives

Searching for novel functional materials represents an important direction in the research and development of renewable energy. Herein, experimentally synthesised Ba2LuNbO6 (BLNO) host double perovskite has been theoretically computed by first principles techniques to understand its several physical properties like electronic-structure, mechanical behaviour, transport along with optical and thermal properties upon the basis of full potential linearized augmented plane wave (FP-LAPW) followed by density functional theory (DFT). First and foremost, the attempt was significant made to relax the molecular crystal structure of BLNO at an experimental lattice constant to evaluate its total ground state and cohesive energy (Ecoh) for descripting its required structural stability. After that, we have overseen its mechanical stability from the computation of second order elastic constants (SOEC's). Later on, the electronic properties of this alloy have been executed within the two potential schemes like Perdew-Burke Generalized gradient approximation (PBE-GGA) and Tran-Blaha modified Becke-Johnson (TB-mBJ) which alternatively certifies the retention of the semiconducting nature respectively. Besides this, the essential use of semi-classical Boltzmann theory within the sophisticated scheme of BoltzTraP has been inducted to explore its transport coefficients. And finally, the optical has been summarised to see the applicability of this particular alloy towards optoelectronic application purposes. Therefore, the overall tendency of this particular alloy can favor their potential multiple applications in sustainable thermoelectrics, optoelectronic features etc.

Structural Insights to the Pathophysiology of Effector Induced Immunostimulation in Salmonella Typhimurium: Biocomputational Methods.

The worldwide impact of the foodborne pathogen Salmonella can never be overstated, nor can be the fatal threat of septicemia in patients infected with its Typhimurium serovar. Behind the hyperimmune response in the case of septicemia lies a critical phenomenon of the bacterial pathogenic signals being sensed by different pattern recognition receptors, such as the Typhimurium effector proteins that are detected by toll-like receptors. To mitigate such a threat, precise structural and functional description of these effectors is necessary. The same has been addressed in this article using accelerated biocomputational techniques, beginning with the identification of the functional niche of the effectors and their influence over other proteins. The molecular crystal structures were retrieved, and rigorous molecular docking experiments were conducted among the TLRs and effector proteins in order to examine the interactions. The interactions were thereby evaluated and screened according to their respective strengths using parameters including binding affinity, dissociation constant, hydropathy variation, etc. SopB effectors were found to be detected by three different TLR proteins and GtgE by two other TLRs, while SifA, SrfJ, and SsaV had only a single interacting TLR partner each. Interestingly, TLR9 presented lower sensitivity towards PAMPs of this bacterium. Normal modal analyses in combination with atomistic molecular dynamics simulations that tend to imitate natural cytosolic environments reveal stable and consistent interactions and realistic conformations among the effector-bound TLR complexes. The findings open up new avenues for the development of targeted therapies against Salmonella, which could significantly reduce the global burden of this foodborne pathogen.

Effect of functional group position in co-formers and solvent on cocrystal polymorphism/stoichiomorphism: a case study

In recent years, there has been an increase in the number of reports on cocrystal polymorphism and stoichiomorphism. However, the research on the factors that influence these phenomena is limited. Herein, picolinamide (PAM), nicotinamide (NAM), and isonicotinamide (INA) were selected as co-formers to form multicomponent solids with 4-chloro-3-sulfamoylbenzoic acid (CSBA). Six new cocrystal forms of CSBA were discovered and their crystal structures were determined. It was found that PAM and NAM can only form one cocrystal with CSBA, while INA can form up to four cocrystals, including both cocrystal polymorphism and stoichiomorphism. Molecular electrostatic potential analysis and crystal structure analysis showed that the functional group position of PAM limited the diversity of cocrystal synthons, while the lattice energy limited the diversity of cocrystal synthons when NAM acted as a co-former. Only INA was not subject to these restrictions when forming cocrystals. Finally, the influence of solvents on cocrystals was illustrated by determining the ternary phase diagrams. The mechanism of two similar solvents, ethyl acetate and acetone, controlling the crystallization of cocrystal polymorphism was analyzed by molecular simulations.

Principles and Applications of CF2X Moieties as Unconventional Halogen Bond Donors in Medicinal Chemistry, Chemical Biology, and Drug Discovery.

As an orthogonal principle to the established (hetero)aryl halides, we herein highlight the usefulness of CF2X (X = Cl, Br, or I) moieties. Using tool compounds bearing CF2X moieties, we study their chemical/metabolic stability and their logP/solubility, as well as the role of XB in their small molecular crystal structures. Employing QM techniques, we analyze the observed interactions, provide insights into the conformational flexibilities and preferences in the potential interaction space. For their application in molecular design, we characterize their XB donor capacities and its interaction strength dependent on geometric parameters. Implementation of CF2X acetamides into our HEFLibs and biophysical evaluation (STD-NMR/ITC), followed by X-ray analysis, reveals a highly interesting binding mode for fragment 23 in JNK3, featuring an XB of CF2Br toward the P-loop, as well as chalcogen bonds. We suggest that underexplored chemical space combined with unconventional binding modes provides excellent opportunities for patentable chemotypes for therapeutic intervention.

Twisting, untwisting, and retwisting of elastic Co-based nanohelices

The reversible transformation of a nanohelix is one of the most exquisite and important phenomena in nature. However, nanomaterials usually fail to twist into helical crystals. Considering the irreversibility of the previously studied twisting forces, the reverse process (untwisting) is more difficult to achieve, let alone the retwisting of the untwisted crystalline nanohelices. Herein, we report a new reciprocal effect between molecular geometry and crystal structure which triggers a twisting-untwisting-retwisting cycle for tri-cobalt salicylate hydroxide hexahydrate. The twisting force stems from competition between the condensation reaction and stacking process, different from the previously reported twisting mechanisms. The resulting distinct nanohelices give rise to unusual structure elasticity, as reflected in the reversible change of crystal lattice parameters and the mutual transformation between the nanowires and nanohelices. This study proposes a fresh concept for designing reversible processes and brings a new perspective in crystallography.

Novel study of perovskite materials and the use of biomaterials to further solar cell application in the built environment: A molecular dynamic study

We started by modeling the molecular dynamics-based perovskite crystal structure using the LAMMPS software in this work. We have then evaluated the impacts of the temperature change on the perovskite layer by modifying the structure of the perovskite to the temperature and observing how the structure of the perovskite responded to the change in temperature. Providing heat to the building outside could establish the melting point and the increase in volume. We applied the ETL dubbed C60 within the solar cell, frequently used to create biostructures, then linked this material to photovoltaic structures to evaluate the efficiency of (perovskite) solar cells and the fill factor. Through perovskite solar cells, this effort aims to provide the building with electricity using only environmentally friendly components.

Molecular beam epitaxy and crystal structure of majority a-plane-oriented and substrate-strained 3 Mn3Sn thin films grown directly on sapphire (0001)

Molecular beam epitaxy and crystal structure of majority a-plane-oriented and substrate-strained 3 Mn3Sn thin films grown directly on sapphire (0001)

Molecular beam epitaxy and crystal structure of majority a-plane-oriented and substrate-strained Mn3Sn thin films grown directly on sapphire (0001)

The Kagome antiferromagnet Mn3Sn has garnered much attention due to the presence of exciting properties such as anomalous Hall and Nernst effects. This paper discusses the synthesis of crystalline Mn3Sn thin films, prepared on Al2O3 (0001) substrates at 453±5°C using molecular beam epitaxy. The growth is monitored in situ using reflection high energy electron diffraction and measured ex situ using x-ray diffraction, Rutherford back-scattering, and cross-sectional scanning transmission electron microscopy. Our analysis shows the in-plane lattice constants of a1,M=4.117±0.027 Å and a2,M=4.943±0.033 Å, which is a very unexpected result when compared to the bulk a-plane Mn3Sn. This indicates a strain in the film and makes it challenging to provide a straightforward explanation. In an effort to explain our results, we discuss two possible orientation relationships between the Mn3Sn films and the sapphire substrates. Samples prepared under these conditions appear to have smooth surfaces locally, but overall the film has a 3D island morphology. First-principles calculations provide atomic models of the Mn3Sn (112¯0) lattice on Al2O3 (0001) high symmetry sites, indicating that the L3-R90° is the most stable configuration. A detailed discussion of the experimental data and theoretical results, as well as strain effects, is provided.

High-pressure single-crystal diffraction at the Australian Synchrotron.

A new high-pressure single-crystal diffraction setup has been designed and implemented at the Australian Synchrotron for collecting molecular and protein crystal structures. The setup incorporates a modified micro-Merrill-Bassett cell and holder designed specifically to fit onto the horizontal air-bearing goniometer, allowing high-pressure diffraction measurements to be collected with little to no modification of the beamline setup compared with ambient data collections. Compression data for the amino acid, L-threonine, and the protein, hen egg-white lysozyme, were collected, showcasing the capabilities of the setup.

Investigating the Effects of NaCl on the Formation of AFs from Gluten in Cooked Wheat Noodles.

To clarify the effect of NaCl concentration (0-2.0%) on the formation of amyloid fibrils (AFs) in cooked wheat noodles, the morphology, surface hydrophobicity, secondary structure, molecular weight distribution, microstructure, and crystal structure of AFs were investigated in this paper. Fluorescence data and Congo red stain images confirmed the presence of AFs and revealed that the 0.4% NaCl concentration promoted the production of AFs. The surface hydrophobicity results showed that the hydrophobicity of AFs increased significantly from 3942.05 to 6117.57 when the salt concentration increased from 0 to 0.4%, indicating that hydrophobic interactions were critical for the formation of AFs. Size exclusion chromatography combined with gel electrophoresis plots showed that the effect of NaCl on the molecular weight of AFs was small and mainly distributed in the range of 5-7.1 KDa (equivalent to 40-56 amino acid residues). X-ray diffraction and AFM images showed that the 0.4% NaCl concentration promoted the formation and longitudinal growth of AFs, while higher NaCl concentrations inhibited the formation and expansion of AFs. This study contributes to the understanding of the mechanism of AF formation in wheat flour processing and provides new insight into wheat gluten aggregation behavior.

Reducing overprediction of molecular crystal structures via threshold clustering

Crystal structure prediction is becoming an increasingly valuable tool for assessing polymorphism of crystalline molecular compounds, yet invariably, it overpredicts the number of polymorphs. One of the causes for this overprediction is in neglecting the coalescence of potential energy minima, separated by relatively small energy barriers, into a single basin at finite temperature. Considering this, we demonstrate a method underpinned by the threshold algorithm for clustering potential energy minima into basins, thereby identifying kinetically stable polymorphs and reducing overprediction.

Synthesis, crystal structure, density functional theory and vibration analysis of 5-(4-fluorophenyl)-1H-pyrazol-3-amine

A pyrazole ring derivative 5-(4-fluorophenyl)-1H pyrazole-3-amine was synthesized. The title compound was characterized by 1H NMR, 13C NMR, MS, FT-IR, and single crystal X-ray diffraction. The optimized molecular crystal structure was determined by B3LYP/6-311 + G(2d, p) functional method and based on density functional theory (DFT) calculation. Hirshfeld surface analysis illustrates the study of non-covalent interactions in the title compound. The molecular electrostatic potential (MEP) and major molecular orbitals (FMOs) of the title compounds were analyzed by computational method. Finally, infrared vibration analysis was performed on the target compound.

Synthesis, crystal structures, Hirshfeld surface analysis, and quantum chemistry calculations of two novel hydrous long-chain dibasic ammonium salts CnH2(n+4)N2O6 (n = 31 and 33)

The synthesis of long-chain single-crystal compounds is a gordian knot. Through the salification reaction of carboxylic acid, long-chain n-alkanoic acid was successfully connected at both ends of 1,3-propylene diamine, and the carbon chain of long-chain n-alkanoic acid was doubled. Hydrous 1, 3-propanediamine ditetradecanoate (abbreviated as 3C14) and 1, 3-propanediamine dipentadecanoate (abbreviated as 3C15) were successfully synthesized. The crystal structures of the two compounds were characterized by X-ray single-crystal diffraction. The molecular structure and crystal structure of the two compounds were analyzed, and their composition, spatial structure, and coordination mode were determined. Hirshfeld surface analysis revealed the intermolecular interaction of the two title compounds. The 3D energy framework enabled the intermolecular interaction to be presented more intuitively and digitally, in which dispersion energy can play a leading role. The energy values of HOMO and LUMO of the two title compounds were calculated, and their energy gaps were 0.2947 eV and 1.6286 eV, respectively. The charge distributions in the compounds were visualized using a molecular electrostatic potential (ESP) surface. ESP maps indicated that the electrophilic sites are localized around the oxygen atom. The crystallographic data and parameters of quantum chemical calculation in this paper will provide data and theoretical support for the development and application of such materials.