Spatial arrangements, intermolecular interactions, and symmetries in single crystals

Simultaneous control of the magnetic and electric properties of materials is crucial for their application in next-generation memory and sensor devices. Herein, we report a single-crystal Co(II) co...

The stationary states of condensed systems such as crystals are characterized by energy bands. These energy bands are described by a dispersion relation and a density function. Within the Frenkel tight-binding method, the physical quantities that determine the band structure are the intermolecular resonance interactions. The density functions for the first excited singlet states of crystalline benzene and naphthalene are determined experimentally from spectral data involving band ↔ band transitions. The experimental results are not in complete agreement with a transition octopole model for the intermolecular interactions. Mixed molecular crystals provide theoretically and experimentally tractable systems for studying the properties of molecular aggregates. This knowledge is basic to understanding the liquid and biological states and may in the future be of significant technological importance. Spectroscopic observations on isotopic mixed crystals of naphthalene are made to determine the energy of the crystal states that correlate with the 1B2u state of the free naphthalene molecule. The spectral data for the dilute crystals are interpreted in terms of a one-particle Green's function and are consistent with the band structure as observed in band ↔ band transitions. The transition energies of guest levels disagree with a model involving configuration interaction with charge transfer states. New theoretical models are suggested, and the data available for evaluating these models are outlined. Very high resolution spectra at 4.2 °K reveal fine structure in the 1B2u ← 1Ag and 3BIu → 1Ag electromc trans1t10ns of the naphthalene mixed crystals. Some of the structure corresponds to the resonance splitting of pairs of guest molecules in the host lattice. In the Frenkel tight-binding approximation, this structure gives directly the intermolecular excitation transfer matrix elements responsible for the exciton mobilities and the energy band structures. Optical spectra of 13CC5H6-C6H6 mixed crystals show that the shallow impurity 13CC5H6 shifts the 1B2u factor group components by 2 cm-1 and increases the linewidth by 5 cm-1 in going from 6% to 50% 13CC5H6. The effect is explained qualitatively by an extension of the Frenkel exciton theory to the mixed crystal system. Exciton structure in the two lowest ungerade triplet states of crystalline naphthalene is reported. For the lowest state the calculated splitting of 40 cm-1 is in good agreement with the experimental result. The Raman scattering tensor for each vibrational mode is determined by polarized Raman scattering from oriented single crystals. The experimental data when compared with the phosphorescence spectrum of the C10H8 - C10D8 mixed crystal allow unambiguous vibrational assignments to be made and provide a measure of the intermolecular interactions in the crystal. It is found that the crystal effects on the gerade vibrations are small. Frequency shifts are 2-4 cm-1; exciton splittings are less than 1 cm-1; and intensities are described qualitatively by the oriented gas model.

Intermolecular interactions between cholesterol and lipids in cell membranes, which play critical roles in cellular processes such as the formation of nano-domains, depend on the molecular structure of the lipids. The diffusion and the spatial arrangement of cholesterol within the lipid membranes also change with the type of lipids. For example, the flip-flop, an important transport mechanism for cholesterol in the membranes, can be facilitated significantly by the presence of unsaturated lipids. However, how the structure of lipids affects the spatial arrangement and the dynamics of cholesterol remains elusive at a molecular level. In this study, we investigate the effects of lipid-cholesterol interactions on the spatial arrangement and the dynamics of cholesterol. We perform molecular dynamics simulations for the binary component membranes of lipids and cholesterol. We employ seven different kinds of lipids by changing either the degree of a saturation level or the length of lipid tails. We find from our simulations that the rate of cholesterol flip-flop is enhanced as the lipids are either less saturated or shorter, which is consistent with previous studies. Interestingly, when the lipid tails are fully saturated and sufficiently long, the center in between two leaflets becomes metastable for cholesterol to stay at. Because the cholesterol at the membrane center diffuses faster than that within leaflets, regardless of the lipid type, such an emergence of the metastable state (in terms of the cholesterol position) complicates the cholesterol diffusion significantly.

Inter-molecular interactions in ultrahigh molecular weight polyethylene single crystals

In this thesis, several 2,2-disubstituted 1,3- diketones are synthesized. Acetyl acetone is used as the starting material to prepare 3,3-dibenzylpentane-2,4-dione (DB-1), 3-acetyl-3-benzylheptane-2,6-dione (BM-1), 3-allyl-3-benzylpentane-2,4- dione (BA-1), 3,3-diallylpentane- 2,4-dione (DA-1), and 3-allyl-3-benzylpentane- 2,4-dione (AM-1). The crystals of DB-1 and BM-1 can be obtained and their structures were solved by single crystal X-ray diffraction. In his study on the conformation of 2,2-dimethyl-1,3-diketone, John B. Rogan suggested that the conformation D is the most favored one. In our case of BM-1, from two torsion angles defined by carbonyl C, carbonyl O, the carbon atom at 3-position and the carbon atom of the 3-substituent, one can conclude that BM-1 adopts conformation D. Also from the angle between two planes from by carbonyl plane, one can come to the same conclusion. On the other hand, DB-1 does not adopt conformation D. For the purpose of studying the reason of the difference between the conformation in these two compounds, intermolecular and intra-molecular interaction are surveyed. In DB-1, inter- or intra-molecular hydrogen bonds and phenyl interaction is not present. However, there is intermolecular interaction in the crystal structure of BM-1. A tentative conclusion on the possible interaction that results in conformation D is that there is interaction between two carbonyl groups. Therefore, IR spectra of these compounds are studied. The IR absorption peak for a typical carbonyl groups is 1715 cm-1, but in BM-1, the carbonyl group peak is at 1693.19 cm-1, about 20 cm-1 less than that of typical ketone group. Similarly shift of the carbonyl absorption peaks are observed for BA-1, DA-1 and AM-1. In DB-1, two carbonyl absorption peaks are at 1705.73 cm-1 and 1691.27 cm-1. These differences can be accounted for by the p-p interaction between carbonyl group and phenyl ring. In conclusion, most of 2,2-disubstituted 1,3- diketones adopt conformation D. But DB-1 is an exception.

Synthesis, characterization, crystal structure and theoretical simulation of novel ethyl 2-(7-hydroxy-4-methyl-2-oxo-2H-chromen-3-yl)acetate

In Drosophila, phototransduction is mediated by G(q)-activation of phospholipase C and is a well studied model system for understanding the kinetics of signal initiation, propagation and termination controlled by G proteins. The proper intracellular targeting and spatial arrangement of most proteins involved in fly phototransduction require the multi-domain scaffolding protein InaD, composed almost entirely of five PDZ domains, which independently bind various proteins including NorpA, the relevant phospho lipase C-beta isozyme. We have determined the crystal structure of the N-terminal PDZ domain of InaD bound to a peptide corresponding to the C-terminus of NorpA to 1.8 A resolution. The structure highlights an intermolecular disulfide bond necessary for high affinity interaction as determined by both in vitro and in vivo studies. Since other proteins also possess similar, cysteine-containing consensus sequences for binding PDZ domains, this disulfide-mediated 'dock-and-lock' interaction of PDZ domains with their ligands may be a relatively ubiquitous mode of coordinating signaling pathways.

Due to a recent expansion of research into metal complexes with stable NR connected with prospects for the production of a radically new class of magnetic materials [50, 51], a great amount of data has been accumulated, in particular, on CC with anionic NR ligands. But until recently there were no reviews analyzing the structural features of these compounds. The reason for this is, evidently, dissimilarity of both the NR ligands and the CC based on them. The systematic studies on the synthesis, crystal structures, and magnetic properties of CC with 3-imidazoline NR permitted analysis of the crystallochemical structure of compounds. As the present paper is virtually the first publication that overviews structural studies of CC with NR, we did not undertake to give a complete analysis of the “structure-property” relationship. Nevertheless, the structural data obtained for CC with 3-imidazoline NR allow one to make some correlations between the character of exchange interactions and the electronic and spatial structure of CC [6, 7, 31]. It is known that to choose an exchange cluster model, one needs information on the relative arrangement of PMC. But the quantum-chemical calculations of the electronic states of a system require exact data on the stereochemistry of a coordination unit and mutual arrangement of PMC. Besides, it should be noted that the relationship between crystal symmetry (centrosymmetric or acentric space group) and magnetic properties will not become adequate unitl crystal structure and symmetry studies have been carried out in a magnetic field at appropriate temperatures, i.e., under conditions of measurement of magnetic parameters for compounds of a given class. In the near future, this research will certainly be continued, both in the field of synthesis of CC with 3-imidazoline NR and preparation of their single crystals, and in the field of studies on their structure, magnetic and other physical properties, as well as of quantum-chemical calculations.

Lead-free (K0.5Na0.5)NbO3-LiNbO3 (KNN-LN) and (K0.5Na0.5)NbO3-LiTaO3 (KNN-LT) ferroelectric single crystals, with the dimensions of 11 ´ 11 ´ 5 mm3 and 5 ´ 5 ´ 3 mm3, were grown successfully using the top-seeded solution growth (TSSG) method, respectively. The crystal structures were analyzed by means of X-ray diffraction, showing orthorhombic symmetry for KNN-LN single crystals and coexistence of orthorhombic and tetragonal symmetry for KNN-LT single crystals at room temperature. The orthorhombic-tetragonal (TO-T) and tetragonal-cubic (TC) phase transition temperatures are 195 °C and 420 °C for the KNN-LN single crystals, and 130 °C and 280 °C for KNN-LT single crystals, respectively. The remnant polarization (Pr) is 27.8 μC/cm2 with a coercive field (Ec) of 17 kV/cm for KNN-LT single crystals. The two single crystals showed 90° domains with layers in (parallel) straight lines, while KNN-LT single crystals have a larger domain region. The actual stoichiometry deviates easily from the original composition in the process of crystal growth, thus, an appropriate nominal composition and optimized crystal growth method is desired to get high-quality crystals in the future.

Halide-modulated self-assembly of metal-free perovskite single crystals for bio-friendly X-ray detection

How to Become a Protein Crystallographer in a Nanoscience Lab

Validation of general ideas about the origins of conformational differences in proteins is critical in order to arrive at meaningful functional insights. Here, principal component analysis (PCA) and distance difference matrices are used to validate some such ideas about the conformational differences between 291 myoglobin structures from sperm whale, horse and pig. Almost all of the horse and pig structures form compact PCA clusters with only minor coordinate differences and outliers that are easily explained. The 222 whale structures form a few dense clusters with multiple outliers. A few whale outliers with a prominent distortion of the GH loop are very similar to the cluster of horse structures, which all have a similar GH-loop distortion apparently owing to intermolecular crystal lattice hydrogen bonds to the GH loop from residues near the distal histidine His64. The variations of the GH-loop coordinates in the whale structures are likely to be owing to the observed alternative intermolecular crystal lattice bond, with the change to the GH loop distorting bonds correlated with the binding of specific `unusual' ligands. Such an alternative intermolecular bond is not observed in horse myoglobins, obliterating any correlation with the ligands. Intermolecular bonds do not usually cause significant coordinate differences and cannot be validated as their universal cause. Most of the native-like whale myoglobin structure outliers can be correlated with a few specific factors. However, these factors do not always lead to coordinate differences beyond the previously determined uncertainty thresholds. The binding of unusual ligands by myoglobin, leading to crystal-induced distortions, suggests that some of the conformational differences between the apo and holo structures might not be `functionally important' but rather artifacts caused by the binding of `unusual' substrate analogs. The causes of P6 symmetry in myoglobin crystals and the relationship between crystal and solution structures are also discussed.

Several years ago we embarked on a project to calculate optimal crystal-packing and crystal-structure parameters based on potential functions from energy-partitioned ab-initio intermolecular SCF calculations plus calculations of dispersion energy contributions. Our approach, aimed at evaluating the intermolecular interactions, such as in polymer propagation and in molecular crystals, and at analyzing the optimal crystal packing, is based on nonempirical ab-initio calculations for smaller molecular aggregates (monomers, dimers, trimers, etc.), partitioning the total SCF interaction energies into the different components, and then fitting these components individually to functional forms or when necessary recalculating or estimating explicitly for certain interaction components for each different unit cell dimension change. We derived and implemented a complete program, including higher order terms and special features necessary only for calculations on crystals. We also derived and implemented a complete CRYSTAL program which, given the crystal symmetry, allows us to vary and optimize the crystal-structure parameters. We carried out test crystal optimization calculations on N2 and on CO2 both to check out the entire CRYSTAL program package and to explore the extensive programs written for various ab-initio based methods for calculating reliable intermolecular interactions. We investigated such aspects as the comparison of the various intermolecular interaction terms calculated from the potential functions compared with those calculated by ab-initio wave functions. We also investigated for the CRYSTAL program how many surrounding unit cells had to be included for energy convergence. We investigated the crystal CH3NO2. We calculated the intermolecular interactions at more than 50 geometries, partitioned the interaction energies, and fit these to functional forms. The agreement of our calculated unit cell dimensions with experiment was excellent, within 1 to 2.8%. Furthermore, our method fits the partitioned ΔESCF results to atom-class-atom-class potential functions, which enables a general library of such potential functions to be built up for the molecular classes of interest.

The effect mechanism of lattice distortion caused by heterovalent rare‐earth and alkaline‐earth ions co‐doping in the electrical properties of piezo‐ceramics is generally concerning. Herein, the Sm2O3/MgO co‐doped 0.65(Ba0.96Sr0.04TiO3)–0.35(Bi0.50Na0.50TiO3) (BST–BNT: x(Sm, Mg)) (0 ≤ x ≤ 0.25 wt%) ceramics are prepared by Pechini sol–gel method. The reversibility transition from the tetragonal P4/mmm relaxation paraelectric phase to the tetragonal P4mm relaxation ferroelectric phase confirms the doping‐modulated piezoelectric constants’ response to the spatial symmetry. Excessive Sm3+ and Mg2+ in the interstitial lattice inhibit the Jahn–Teller effect of distortion in the crystal spatial symmetry. The restored P4/mmm spatial symmetry of BST–BNT: x(Sm, Mg) (x = 0.15 wt%) ceramics contributes to the large electric‐induced strain, increased Curie temperature, and the stabilized frequency dependence of the Curie temperature (TC [1 MHz] = 167 °C, εr [1 MHz] = 2151.92, d33 = 43 pC N−1, Smax/Emax = 535.22 pm V−1). The samples with large electric‐induced strain and good temperature stability of electrical properties can be applied in the heat dissipation actuators.

EPR of trigonal bipyramidal copper(II) complexes with tripod ligands