Molecular Crystal Structure Research Articles

Theoretical Study on the Vapochromic Ni(II)-Quinonoid Complex: One-Dimensional Stacking Structure-Based Color Switching.

Vapochromic crystals of Ni(II)-quinonoid complexes were theoretically investigated using density functional theory (DFT) calculations. Kato et al. previously reported that the purple crystals of a four-coordinate Ni(II)-quinonoid complex (1P) exhibited vapochromic characteristics upon exposure to methanol gas, resulting in orange crystals of the six-coordinate methanol-bound complex (1O) [Angew. Chem., Int. Ed.2017, 56, 2345-2349]. However, the authors did not characterize the crystal structure of 1P. In the present study, we computationally predicted the crystal structure of 1P by performing a crystal structure search with classical force-field computations followed by optimization using DFT calculations. The simulated powder X-ray diffraction pattern of the DFT-optimized structure agreed with experimental observations, indicating that our predicted crystal structure is reliable. Investigation of the optimized crystal structure of 1P revealed that its color change arose from changes in its 1D-band structure, which consists of Ni 3d orbitals and quinonoid π-orbitals. Intermolecular interactions were weakened upon the binding of methanol to the Ni(II) center in 1O. Consequently, the intermolecular 3d-π interaction in 1P lowered the band gap and induced the red-shifting of the monomeric four-coordinate Ni(II)-quinonoid complex. Meanwhile, the obtained absorption spectrum of 1O closely corresponded to that of the monomeric six-coordinate Ni(II)-quinonoid complex. Our study provides a new strategy for accurately predicting molecular crystal structures and reveals a new insight into vapochromism based on band structure color switching.

Artificial Water Channels—Progress Innovations and Prospects

Artificial Water Channels—Progress Innovations and Prospects

X-ray crystal structure analysis of N'-acetyl-N'-phenyl-2-naphthohydrazide

N'-Acetyl-N'-phenyl-2-naphthohydrazide, a biologically relevant organic molecule, was synthesized following a reported method and characterized based on its single X-ray crystallographic studies. The present manuscript deals with its detailed molecular interactions and X-ray crystal structure. Its space group is P-1 with the following unit cell parameters: a = 8.9164(7), b = 9.7058(9), c = 17.7384(12) Å, α = 88.308(7)°, β = 89.744(6)°, γ = 86.744(7)° and Z = 2. Crystal structure was solved by direct method and refined by full matrix least squares procedure to a final R value of 0.0580 and to a GOOF value of 1.066. The X-ray diffraction analyses showed that the asymmetric unit contains two crystallographically independent molecules. The crystal structure is stabilized by elaborate network of N-H···O and C-H···O hydrogen bonds along with C-H···π and π···π interactions to form supramolecular structures.

Synthesis, crystal structure and vibrational properties studies of (S)-N-(1-phenylethyl)-6-(4-(trifluoromethoxy)phenyl)imidazo[1,2-a]pyridine-2-carboxamide

Imidazo[1,2-a]pyridine derivatives, exhibiting good biological activity, are widely present in drug molecules. The title compound (S)-N-(1-phenylethyl)-6-(4-(trifluoromethoxy)phenyl)imidazo[1,2-a]pyridine-2-carboxamide was designed and synthesized, and the structure was characterized by spectroscopic techniques. The single crystal structure of the target molecule was confirmed by X-ray diffraction, and the optimized molecular crystal structures were determined on the basis of density functional theory (DFT) calculations using B3LYP/6–311+G(2d, p) functional, and compared with the X-ray diffraction data. The molecular structure optimized by DFT was consistent with the crystal structure determined by X-ray single crystal diffraction. The geometrical parameters, molecular electrostatic potential (MEP), and frontier molecular orbital (FMO) analysis of the titled compound are also presented. Vibrational and antitumor analyses of MCF-7 and A375 were also performed in this research.

Study on the water‐tree ageing characteristics of polyethylene/organic montmorillonite and crosslinked polyethylene/organic montmorillonite nanocomposites

AbstractThe dispersion state of nanoparticles affects the properties of composites, and the crosslinking process of polymers affects the dispersion state of nanoparticles. In order to investigate the effects of crosslinking behaviour on the water‐tree ageing characteristics of nanocomposite dielectrics at the molecular level, polyethylene/organic‐montmorillonite (PE/organic montmorillonite (OMMT)) and crosslinked polyethylene/organic‐montmorillonite (XLPE/OMMT) nanocomposites were prepared by the melt blending method, after which the accelerated water‐tree ageing experiments were conducted using a needle electrode. Fourier transform infrared spectroscopy, differential scanning calorimetry, successive self‐nucleation annealing and scanning electron microscope (SEM) tests were conducted to characterise the properties of the samples before and after water‐tree ageing. The results indicate that the initiation probability and the length of water trees in XLPE/OMMT are less than those in PE/OMMT. The carbonyl index in the water‐tree area of the two nanocomposites increases, indicating that the water‐tree ageing is the result of electrochemical degradation. The crystallisability of the water‐tree area degrades, decreasing the crystallinity and the lamellar thickness. The growth of water trees destroys molecular chains and crystal structures, which results in local cracks. There are many holes for the water tree growth in the PE/OMMT specimen. However, the crosslinked meshwork not only restricts the movement of macromolecular chains but also increases the stability of the lamellar barrier effect of OMMT. The combination of the two effects significantly improves the water‐tree resistance of the XLPE/OMMT nanocomposite.

Synthesis, Crystal Structure, and Some Transformations of 9,12-Dichloro-ortho-Carborane

Reaction of ortho-carborane with anhydrous AlCl3 in chloroform results in a mixture of 9-chloro, 9,12-dichloro, and 8,9,12-trichloro derivatives with 9,12-dichloro-ortho-carborane being the main product. Molecular crystal structure of 9,12-dichloro-ortho-carborane was determined by the single crystal X-ray diffraction. The crystal structure of 9,12-Cl2-1,2-C2B10H10 appeared to be nearly isostructural to 9,12-dibromo-ortho-carborane: the crystal packing is built of layers in which molecules are connected via weak hydrogen and halogen bonds. A synthetic scheme for preparation of the hexachloro derivative of cobalt bis(dicarbollide) Cs[8,8′,9,9′,12,12′-Cl6-3,3′-Co(1,2-C2B9H8)2] from 9,12-dichloro-ortho-carborane has been proposed.

Uncovering the Morphological Regulation Mechanism of Low Sensitivity and Highly Energetic Materials in Solvents: Changing Crystal Morphology Induced by Hydrogen Bonding

Low sensitivity and highly energetic materials (LSHEMs) are currently the most promising high-energy materials due to their structural stability. However, many problems exist due to their abundant hydrogen bonding (HB) in the structure, such as low solubility and difficulty controlling the crystallization process. In this paper, aiming at regulating the crystal morphology of LSHEMs, 4,4′,5,5′-tetranitro-1H,1′H-[2,2′-biimidazole]-1,1′-diamine is used as a model substance to explore the mechanism of controlling the crystal morphology in solvents. The molecular structure, crystal structure, and HB sites on crystal faces were investigated by molecular electrostatic potential surface, Hirshfeld surface, and HB analyses, and it was found that the HB density [δ(HB)] of faces is of the order (011) > (11–1) > (110) > (100) in crystal or solution, determining the tendency of interaction with polar solvents. Then, using molecular dynamics simulation and the modified attachment energy model, we found that the attachment energy of crystal faces and the predicted crystal morphologies in different solvents were determined by HB sites on faces and strongly correlated with the solvent polarity. The experimental morphologies were consistent with the trend predicted including the aspect ratio trend, which confirmed our theoretical speculation. This work provides an effective method of choosing solvents for morphology customization of LSHEMs, which will help guide the morphology control and realize the industry application of LSHEMs.

Ultrawideband and High-Resolution Terahertz Spectroscopy: Structural Identification of Glucose

We report on the development of an ultrawideband and high-resolution THz spectroscopic system, which operates over a frequency range of 2–13.5 THz. This work goes beyond conventional THz spectroscopic measurements and demonstrates the capacity to differentiate D- and L-glucoses, which have the same molecular conformation and crystal structure. Furthermore, this system facilitates the structural identification of glucose microcrystals, which exists in α- and β-forms, revealing that L-glucose microcrystals are formed of a mixture of α- and β-D-glucose with approximately equal weight.

Behaviour of occupied and void space in molecular crystal structures at high pressure

Behaviour of occupied and void space in molecular crystal structures at high pressure

Minimal Basis Set Hartree-Fock Corrected with Atom-Centered Potentials for Molecular Crystal Modeling and Crystal Structure Prediction.

Crystal structure prediction (CSP), determining the experimentally observable structure of a molecular crystal from the molecular diagram, is an important challenge with technologically relevant applications in materials manufacturing and drug design. For the purpose of screening the randomly generated candidate crystal structures, CSP protocols require energy ranking methods that are fast and can accurately capture the small energy differences between molecular crystals. In addition, a good ranking method should also produce accurate equilibrium geometries, both intramolecular and intermolecular. In this article, we explore the combination of minimal-basis-set Hartree-Fock (HF) with atom-centered potentials (ACPs) as a method for modeling the structure and energetics of molecular crystals. The ACPs are developed for the H, C, N, and O atoms and fitted to a set of reference data at the B86bPBE-XDM level in order to mitigate basis-set incompleteness and missing correlation. In particular, ACPs are developed in combination with two methods: HF-D3/MINIs and HF-3c. The application of ACPs greatly improves the performance of HF-D3/MINIs for lattice energies, crystal energy differences, energy-volume and energy-strain relations, and crystal geometries. In the case of HF-3c, the improvement in the crystal energy differences is much smaller than in HF-D3/MINIs, but lattice energies and particularly crystal geometries are considerably better when ACPs are used. The resulting methods may be useful for CSP but also for quick calculation of molecular crystal lattice energies and geometries.

Electron Diffraction of 3D Molecular Crystals.

Electron crystallography has a storied history which rivals that of its more established X-ray-enabled counterpart. Recent advances in data collection and analysis have sparked a renaissance in the field, opening a new chapter for this venerable technique. Burgeoning interest in electron crystallography has spawned innovative methods described by various interchangeable labels (3D ED, MicroED, cRED, etc.). This Review covers concepts and findings relevant to the practicing crystallographer, with an emphasis on experiments aimed at using electron diffraction to elucidate the atomic structure of three-dimensional molecular crystals.

Structural transformation of methyl urotropine perchlorate under high pressure.

Based on the first-principles calculations of density functional theory (DFT), the crystal structure, molecular structure, electronic properties, and optical absorption properties of methyl urotropine perchlorate under hydrostatic compression in the range of 0 ~ 100 GPa were calculated. The results show that the crystal structure of methyl urotropine perchlorate undergoes two structural transformations under hydrostatic compression. The H1A-H1B bond breaks at 25 GPa, generating two new covalent bonds N3-H1A and O1-H1B. The covalent bonds of O2A-C1 and Cl1-H3A are formed at 85 GPa. The compression ratio of lattice constants (a, b, c) and unit cell volume change abruptly at 25 GPa and 85 GPa, respectively. The conclusion that new bonds are formed under high pressure is further demonstrated by analyzing the partial density of states (PDOS) of N3, H1A, O1, H1B, O2A, C1, Cl1, and H3A atoms. The absorption spectrum showed that the absorption peak of methyl urotropine perchlorate gradually enhanced with the increase of pressure and the highest absorption peak shifted to high frequency.

Global analysis of the energy landscapes of molecular crystal structures by applying the threshold algorithm

Polymorphism in molecular crystals has important consequences for the control of materials properties and our understanding of crystallization. Computational methods, including crystal structure prediction, have provided important insight into polymorphism, but have usually been limited to assessing the relative energies of structures. We describe the implementation of the Monte Carlo threshold algorithm as a method to provide an estimate of the energy barriers separating crystal structures. By sampling the local energy minima accessible from multiple starting structures, the simulations yield a global picture of the crystal energy landscapes and provide valuable information on the depth of the energy minima associated with crystal structures. We present results from applying the threshold algorithm to four polymorphic organic molecular crystals, examine the influence of applying space group symmetry constraints during the simulations, and discuss the relationship between the structure of the energy landscape and the intermolecular interactions present in the crystals.

Synthesis, crystal structure, and DFT study of 1-cyclopropyl-3-(3-((1-(2-methoxyphenyl)-5-oxo-[1, 2, 4]triazolo[4,3-a]quinazolin-4(5H)-yl)methyl)phenylurea

A new triazoline-quinazolinone compound, 1-cyclopropyl-3-(3-((1-(2- methoxyphenyl)-5-oxo-[1, 2, 4]triazolo[4,3-a]quinazoline-4(5H)-yl)methyl)phenylurea, was attained by nine steps and selected the method of inverse synthetic analysis. Meanwhile, the structure of the title compound was not only certified by MS, 1H NMR, FT-IR, and 13C NMR spectroscopy, but the compound’s single crystal was measured by X-ray diffraction. The optimized molecular crystal structure was ulteriorly determined using density functional theory (DFT), and it was compared with the value of X-ray diffraction. Furthermore, through more deeply studies by means of the molecular electrostatic potential and frontier molecular orbitals (FMOs) of compound 1, more physicochemical properties were investigated.

Structural Phase Transitions in Anthracene Crystals.

Anthracene (C14 H10 ) and its derivatives, π-conjugated molecules in acenes, have been widely researched in terms of their reactions, physical properties, and self-assembly (or crystal engineering). These molecules can be functionalized to tune reactivities, optoelectronic properties, and self-assembling abilities. Structural changes in the molecular assemblies, solid states, and crystals have recently been discovered. Therefore, a systematic discussion of anthracene's molecular structure, packing, and optical properties based on its intermolecular structure and phase transitions is important for future chemical and structural design. In the present review, we discuss anthracene's molecular design, dimer packing, and crystal structure, focusing on the structural phase transitions of its crystals. We also provide examples of the phase transitions of anthracene crystals. Changes to edge-to-face of CH-π interaction and face-to-face packing of π-π interaction affect the thermodynamic stabilities of various crystal structures. These structures can inform the prediction of structural and physical properties.

A Hybrid Machine Learning Approach for Structure Stability Prediction in Molecular Co-crystal Screenings

Co-crystals are a highly interesting material class as varying their components and stoichiometry in principle allows tuning supramolecular assemblies toward desired physical properties. The in silico prediction of co-crystal structures represents a daunting task, however, as they span a vast search space and usually feature large unit cells. This requires theoretical models that are accurate and fast to evaluate, a combination that can in principle be accomplished by modern machine-learned (ML) potentials trained on first-principles data. Crucially, these ML potentials need to account for the description of long-range interactions, which are essential for the stability and structure of molecular crystals. In this contribution, we present a strategy for developing Δ-ML potentials for co-crystals, which use a physical baseline model to describe long-range interactions. The applicability of this approach is demonstrated for co-crystals of variable composition consisting of an active pharmaceutical ingredient and various co-formers. We find that the Δ-ML approach offers a strong and consistent improvement over the density functional tight binding baseline. Importantly, this even holds true when extrapolating beyond the scope of the training set, for instance in molecular dynamics simulations under ambient conditions.

Microwave Irradiated Solid Phase and Catalyst-free Hantzsch 1,4-dihydropyridine Synthesis: Spectral Characterization, Fluorescence Study, and Molecular Crystal Structure

Background: Solvent- and catalyst-free synthesis of 1,4-dihydropyridines (1,4-DHPs) under microwave radiation is directly dealt with the concept of green chemistry. They are the class of pharmacological agents and drugs used as Ca2+ channel blockers, and they behave as photoelectronic functional materials to exhibit fluorescence activity because of the electrondonating and withdrawing groups present in them. Objective: An efficient and rapid microwave-assisted synthesis of 4-(3-bromo-4-hydroxy-5- methoxyphenyl)-3,5-dicarbmethoxy-2,6-dimethyl-1,4-dihydropyridine (4) has been achieved under solvent- and catalyst-free conditions using three components 3-bromo-4-hydroxy-5-methoxy benzaldehyde, 3-oxobutanoic acid methyl ester, and ammonium carbonate in 25 minutes, which was then subjected to spectroscopic characterization, single-crystal X-ray, and fluorescence study. Methods: The characterization methods were 1H and 13C NMR, FT-IR, LC-MS, and elemental analysis. The single crystal structure was developed using a mixture of Methanol: Tetrahydrofuran and was determined by the single-crystal X-ray diffraction method. The fluorescence study was accomplished in a spectrofluorometer by taking cresyl violet as a reference with two organic solvents, methanol and chloroform. Results: The crystal structure is monoclinic, space group P21/n with a = 11.0557(3) Å, b = 7.3544(2) Å, c = 22.4852(7) Å and β = 104.107(2)°. The used single-crystal size is 0.200 × 0.200 × 0.200 mm3. The NH⋅⋅⋅⋅O type intermolecular hydrogen bond is observed between N(1) and O(2) atoms. The absorption and fluorescence spectra were found to depend on the chemical nature of the substituents available on C(4), C(2), and C(3) atoms of the 1,4-DHP ring and solvent properties. Conclusion: The X-ray study shows flattened boat conformation of the 1,4-DHP ring and the presence of intermolecular hydrogen bonding, a major cause of the Ca2+ channel antagonist. More fluorescence has been shown in methanol than chloroform, and the fluorescence nature of the compound (4) may find potential application in the field of biology and chemical sensor.

Reliable crystal structure predictions from first principles

An inexpensive and reliable method for molecular crystal structure predictions (CSPs) has been developed. The new CSP protocol starts from a two-dimensional graph of crystal’s monomer(s) and utilizes no experimental information. Using results of quantum mechanical calculations for molecular dimers, an accurate two-body, rigid-monomer ab initio-based force field (aiFF) for the crystal is developed. Since CSPs with aiFFs are essentially as expensive as with empirical FFs, tens of thousands of plausible polymorphs generated by the crystal packing procedures can be optimized. Here we show the robustness of this protocol which found the experimental crystal within the 20 most stable predicted polymorphs for each of the 15 investigated molecules. The ranking was further refined by performing periodic density-functional theory (DFT) plus dispersion correction (pDFT+D) calculations for these 20 top-ranked polymorphs, resulting in the experimental crystal ranked as number one for all the systems studied (and the second polymorph, if known, ranked in the top few). Alternatively, the polymorphs generated can be used to improve aiFFs, which also leads to rank one predictions. The proposed CSP protocol should result in aiFFs replacing empirical FFs in CSP research.

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