Residual Electron Density Research Articles

Charge-density analysis of an iron-sulfur protein at an ultra-high resolution of 0.48 Å.

The fine structures of proteins, such as the positions of hydrogen atoms, distributions of valence electrons and orientations of bound waters, are critical factors for determining the dynamic and chemical properties of proteins. Such information cannot be obtained by conventional protein X-ray analyses at 3.0-1.5 Å resolution, in which amino acids are fitted into atomically unresolved electron-density maps and refinement calculations are performed under strong restraints. Therefore, we usually supplement the information on hydrogen atoms and valence electrons in proteins with pre-existing common knowledge obtained by chemistry in small molecules. However, even now, computational calculation of such information with quantum chemistry also tends to be difficult, especially for polynuclear metalloproteins. Here we report a charge-density analysis of the high-potential iron-sulfur protein from the thermophilic purple bacterium Thermochromatium tepidum using X-ray data at an ultra-high resolution of 0.48 Å. Residual electron densities in the conventional refinement are assigned as valence electrons in the multipolar refinement. Iron 3d and sulfur 3p electron densities of the Fe4S4 cluster are visualized around the atoms. Such information provides the most detailed view of the valence electrons of the metal complex in the protein. The asymmetry of the iron-sulfur cluster and the protein environment suggests the structural basis of charge storing on electron transfer. Our charge-density analysis reveals many fine features around the metal complex for the first time, and will enable further theoretical and experimental studies of metalloproteins.

Effects of N2/O2Additives on the Repeatability of the Dynamics of an Atmospheric-Pressure He Plasma Jet

To better understand the role of residual charges in the repeatability of an atmospheric-pressure He plasma plume, the effects of N2/O2 additives on the minimum pulse repetition frequency $f_{\textrm {min}}$ to sustain the repeatable discharge are investigated for the first time. First, when the percentage of N2 gas in He/N2 mixture increases from 0% to 1.7%, $f_{\textrm {min}}$ increases from 130 to 900 Hz. While when the percentage of O2 gas in He/O2 mixture increases from 0.38% to 1.7%, $f_{\textrm {min}}$ keeps almost constant at 300 Hz. Second, a charge collection system is used to measure the residual charge density. The results show that the residual charge density in the plasma core for He/(1%) O2 mixture is much higher than that for He/(1%) N2 mixture. Furthermore, the simulation results on the time-resolved distribution of residual charge density show that the residual electron density just before the following voltage pulse decreases with the increase in N2 percentage, while the residual O2− ion density is independent on the O2 percentage. Finally, the residual charge density of $10^{9}$ cm $^{-3}$ or higher is needed for the repeatable discharge mode.

Pressure-induced ferroelectric to paraelectric transition in LiTaO3 and (Li,Mg)TaO3

X-ray powder diffraction and Raman scattering of LiTaO3 (LT) and (Li,Mg)TaO3 (LMT) have been measured under pressure up to 46 GPa. Above 30 GPa, the ferroelectric rhombohedral phase (R3c, Z = 6) of LiTaO3 transforms to a paraelectric orthorhombic phase (Pnma with Z = 4) with a large hysteresis. Rietveld profile fitting analysis shows that the Li-O bond is compressed and approaches that of Ta-O with pressure. The cation distribution analysis of the orthorhombic perovskite structure shows that Li and Ta are located in the octahedral 8-fold coordination sites. Difference Fourier |Fobs(hkl)| - |Fcal(hkl)| maps of LiTaO3 and (Li,Mg)TaO3 indicate polarization in the c axis direction and a more distinct electron density distribution around the Ta position for (Li,Mg)TaO3 compared to LiTaO3. The observed effective charges indicate that for (Li,Mg)TaO3 without vacancies Ta5+ becomes less ionized as a function of Mg substitution. Considering both site occupancy and effective charge analysis, Ta5+ is reduced to Ta4.13+. Mg2+ and O2- change to Mg1.643+ and O1.732 -, respectively. The space- and time-averaged structures of the dynamical vibration of atoms can be elucidated from the electron density analysis by difference Fourier and temperature factors T(hkl) in the structure refinement. The refinement of the temperature factor is consistent with the cation distribution assuming full stoichiometry. The residual electron density induced from the excess electron in (Li,Mg)TaO3 indicates more electrons around the Ta site, as confirmed by the effective charge analysis. Raman spectra of LiTaO3 and (Li,Mg)TaO3 show notable changes over the measured pressure range. Raman peaks centered at 250 cm−1 and 350 cm−1 at ambient pressure merge above 8 GPa, which we associate with the diminishing of difference in distances between Li-O and Ta-O bonds with pressure in both materials. Raman spectra show significant changes at 28 GPa and 33 GPa for LT and LMT, respectively, due to the structural transition from R3c to Pnma consistent with the x-ray diffraction results.

Experimental and theoretical charge-density analysis of 1,4-bis(5-hexyl-2-thienyl)butane-1,4-dione: applications of a virtual-atom model.

The experimental and theoretical charge densities of 1,4-bis(5-hexyl-2-thienyl)butane-1,4-dione, a precursor in the synthesis of thiophene-based semiconductors and organic solar cells, are presented. A dummy bond charges spherical atom model is applied besides the multipolar atom model. The results show that the dummy bond charges model is accurate enough to calculate electrostatic-derived properties which are comparable with those obtained by the multipolar atom model. The refinement statistics and the residual electron density values are found to be intermediate between the independent atom and the multipolar formalisms.

Transformation of the structure in a series of mixed K2Ni x Co1–x (SO4)2 · 6H2O single crystals

The structure of crystals of solid solutions K2Ni x Co1–x (SO4)2 · 6H2O has been studied. The substitution of nickel atoms for cobalt atoms in the K2Co(SO4)2 · 6H2O structure leads to a decrease in all interatomic distances (Co,Ni)–O. However, the decrease in one of them with the increase in the Ni concentration is smaller than that in the other two. As a consequence, CoO6 octahedra are more distorted than NiO6. Syntheses of the difference electron density show that the structures of crystals of solid solutions K2Co(SO4)2 · 6H2O contain more uninterpreted peaks of the residual electron density than the K2Ni(SO4)2 · 6H2O structure, indicating a change in the character of the hydrogen bond.

InN nanocolumns grown by molecular beam epitaxy and their luminescence properties

InN nanocolumns (NCs) without vertical diameter variation have been grown on GaN templates by molecular beam epitaxy. Growth temperature is the key parameter to obtain such shaped InN NCs. The density and surface distribution can be controlled by the V/III ratio and initial nucleation process. Intense photoluminescence (PL) is observed for the optimal InN NCs, about two orders of magnitude stronger than the InN epilayers. Superior excitation power and temperature dependence of the PL indicate significantly reduced defect density and residual electron density, non-degenerate property, and possibly suggest that there is a small or negligible level of electron accumulation at the smooth non-polar lateral surfaces.

Compressibility and crystal–fluid interactions in all-silica ferrierite at high pressure

The high-pressure behavior of a synthetic siliceous ferrierite has been studied by in situ single-crystal and powder synchrotron X-ray diffraction with a diamond anvil cell, using four different P-transmitting fluids: the non-penetrating silicone oil and the potentially pore-penetrating methanol:ethanol:H2O = 16:3:1 mixture, ethylene glycol and 2methyl-2propen-1ol. The high-pressure experiment in silicone oil shows a remarkable flexibility of the FER framework. Two displacive phase transitions, following the path Pmnn-to-P121/n1-to-P21/n11 with pressure, were observed. The three polymorphs were found to share a virtually identical bulk compressibility, though showing a different anisotropic pattern. The experiments with potentially penetrating media enhanced the occurrence of a complex scenario, from which the P-induced intrusion of fluid molecules into the FER structural voids can be assumed by the different phase-transition paths and compressibility patterns, by the calculated residual electron density and by the different deformation mechanisms at the atomic scale, observed as a function of the used medium. The starting orthorhombic polymorph was always restored upon decompression in all the experiments. The roles of the different surface area in single crystal and polycrystalline samples, and of the process kinetics on the compressibility and crystal–fluid interactions, are discussed.

Selective activators of protein phosphatase 5 target the auto-inhibitory mechanism.

Protein phosphatase 5 (PP5) is an evolutionary conserved serine/threonine phosphatase. Its dephosphorylation activity modulates a diverse set of cellular factors including protein kinases and the microtubule-associated tau protein involved in neurodegenerative disorders. It is auto-regulated by its heat-shock protein (Hsp90)-interacting tetratricopeptide repeat (TPR) domain and its C-terminal α-helix. In the present study, we report the identification of five specific PP5 activators [PP5 small-molecule activators (P5SAs)] that enhance the phosphatase activity up to 8-fold. The compounds are allosteric modulators accelerating efficiently the turnover rate of PP5, but do barely affect substrate binding or the interaction between PP5 and the chaperone Hsp90. Enzymatic studies imply that the compounds bind to the phosphatase domain of PP5. For the most promising compound crystallographic comparisons of the apo PP5 and the PP5-P5SA-2 complex indicate a relaxation of the auto-inhibited state of PP5. Residual electron density and mutation analyses in PP5 suggest activator binding to a pocket in the phosphatase/TPR domain interface, which may exert regulatory functions. These compounds thus may expose regulatory mechanisms in the PP5 enzyme and serve to develop optimized activators based on these scaffolds.

Cholesterol oxidase: ultrahigh-resolution crystal structure and multipolar atom model-based analysis.

Examination of protein structure at the subatomic level is required to improve the understanding of enzymatic function. For this purpose, X-ray diffraction data have been collected at 100 K from cholesterol oxidase crystals using synchrotron radiation to an optical resolution of 0.94 Å. After refinement using the spherical atom model, nonmodelled bonding peaks were detected in the Fourier residual electron density on some of the individual bonds. Well defined bond density was observed in the peptide plane after averaging maps on the residues with the lowest thermal motion. The multipolar electron density of the protein-cofactor complex was modelled by transfer of the ELMAM2 charge-density database, and the topology of the intermolecular interactions between the protein and the flavin adenine dinucleotide (FAD) cofactor was subsequently investigated. Taking advantage of the high resolution of the structure, the stereochemistry of main-chain bond lengths and of C=O···H-N hydrogen bonds was analyzed with respect to the different secondary-structure elements.

The role of residual charges in the repeatability of the dynamics of atmospheric pressure room temperature plasma plume

To better understand the role of residual electrons in the repeatability of an atmospheric pressure plasma plume, the characteristics of a helium plasma jet from the 1st, 2nd,… until the repeatable discharge pulse are investigated for the first time. It's found that the longest plasma plume is achieved in the 1st discharge pulse. The length of the plasma plume becomes shorter and shorter and reaches a constant value in the 3rd discharge pulse and keeps the same for the following pulses. The dynamics of the 1st discharge pulse show that the plasma bullet appears random in nature. Two photomultiplier tubes are used to distinguish the two potential factors that could result in the stochastic dynamics of the plasma bullet, i.e., stochastic ignition of the plasma and the stochastic propagation velocity. The results show that the stochastic propagation velocity occurs only in the 1st and the 2nd discharge pulses, while the stochastic ignition of the plasma presents until the 100th pulse. The dynamics of the plasma propagation become repeatable after about 100 pulses. Detail analysis shows that the repeatability of plasma bullet is due to the residual electrons density. The residual electron density of 109 cm−3 or higher is needed for repeatable discharges mode.

Simulation of stationary glow patterns in dielectric barrier discharges at atmospheric pressure

Self-organized stationary patterns in dielectric barrier discharges operating in glow regime at atmospheric pressure are investigated by a self-consistent two-dimensional fluid model. The simulation results show that two different modes, namely, the diffuse mode and the static patterned mode, can be formed in different ranges of the driving frequency. The discharge operates in Townsend regime in the diffuse mode, while it operates in a glow regime inside the filaments and in a Townsend regime outside the filaments in the stable pattered mode. The forming process of the stationary filaments can be divided into three stages, namely, destabilizing stage, self-assembling stage, and stable stage. The space charge associated with residual electron density and surface charge is responsible for the formation of these stationary glow patterns.

Theoretical Multipolar Atom Model Transfer in Nitro-Derivatives of N-Methylaniline

The nitroanilines are an example of compounds in which the coexistence of electron-rich and electron-deficient substituents, connected through a conjugated π-electronic system, makes their molecular second-order hyperpolarizability and second-harmonic generation efficiency particularly high. This property makes them extremely interesting from the point of view of charge density distribution analysis. The electron density of three isomeric molecules, i.e., N-methyl-2-nitroaniline, N-methyl-3-nitroaniline, and N-methyl-4-nitroaniline, was calculated theoretically through the multipolar atom model transfer. Two types of refinement models, i.e., multipolar atom model (MAM) and independent atom model (IAM), have been applied for analysis of model improvement concerning the electron-density parameters transfer. It results in a more precise molecular structure in terms of geometry and thermal displacement parameters along with a reduction of statistical refinement factors and residual electron densities. The pro...

Carrier dynamics and related electronic band properties of InN films

In the present article, we focus our discussion on the carrier dynamics of the scattering and recombination processes of InN films and the related band-edge energy structure. Various reports on this matter are summarized and some issues are reexamined. The analysis result based on the apparent band–band transition matrix element is consistent with a reported effective heavy hole mass of 0.59 (±0.06) m0. An Ep value related to the transition matrix element of 10–14 eV is thought to be plausible. The ambiguity of the band-edge structure is evaluated by the uncertainty of electron density. The distortion of the conduction band bottom and the ambiguity of the estimation of the many-body effect are discussed. The enhancement of the anisotropic electron-scattering nature with the decrease in residual electron density reveals that the residual electron source has isotropic potentials: point defects or small complexes. Infrared reflectance spectrum analysis reveals the high electron mobility inside grains in spite of the scattering by edge-type dislocations which cause the anisotropic carrier scattering. The recombination processes at low temperatures are dominated by nonradiative processes related to edge-type dislocations, while the thermally activated nonradiative recombination process is independent of the dislocation density. The activation processes and energies of the recombination related to phonon localization are characterized. InN is a peculiar material that has high carrier mobility and a strong electron–phonon interaction, which possibly induces the high nonradiative carrier recombination rate. The control of phonon localization is thus required.

Variations in peak electron densities in the ionosphere of Mars over a full solar cycle

Peak electron densities in the ionosphere of Mars are strongly influenced by the intensity of ionizing solar flux and hence by the solar cycle. Datasets used in previous studies of this relationship have incompletely sampled the range of solar irradiances encountered over a full solar cycle. Here, thousands of Mars Global Surveyor radio occultation measurements and hundreds of thousands of Mars Express topside radar sounder measurements from 1998 to 2013 are used to test whether the conclusions of previous workers withstand a substantial increase in the number of datapoints and near-continuous sampling across a range of ionizing solar irradiances. Data from narrow ranges in solar zenith angle (70°–80°) and latitude (60°N–80°N) are used in order to isolate, to the extent possible, the influence of irradiance. Ionospheric peak electron density increases smoothly with increasing F10.7, but this increase saturates at F10.7 values above 130 units. However, in contrast to some previous work, there is no change in behavior at an F10.7 value of 100 units. Saturation at high values of F10.7 also occurs in Earth’s ionosphere and the underlying cause is that the appropriateness of F10.7 as a proxy for ionizing solar irradiance diminishes at high solar activity. Similar overall trends are seen when the Lyman alpha emission or the Mg II core-to-wing index are used to replace F10.7 as a proxy for ionizing solar irradiance. Even when solar zenith angle and latitude are restricted, a time series of electron density residuals shows noteworthy trends. These trends might indicate a dependence of peak density on season, but they are not caused by changes in the Mars–Sun distance.

Photochromism change by conformation control in macrocyclic boronic ester cavity

N-salicylideneaniline derivatives are known to show photochromism by UV light, and it depends on the molecular conformation in the crystal. The twisted molecule is photochromic but the planar one is not[1,2]. N-salicylidene-2-aminopyridine (2SAP) always has a planar conformation due to the chemical structure without steric hindrance, therefore 2SAP is known as non-photochromic. However, by confining the molecule in a cavity of the macrocyclic boronic ester 1[3], the conformation and photochromism can be controlled. The inclusion crystal of 1 (homo-parallel form) has a special feature to have a channel type crystal structure in which the macrocyclic ring aligned one-dimensionally to include guest molecules. Interestingly, the crystals can reversibly absorb/desorb guests maintaining the crystal structure, because the channel structure is robust. To exchange the included guests, the crystal of 1(homo-parallel form) was immersed in the melt of 2SAP at 90°C. The obtained inclusion crystal showed photochromism. In the crystal structure, the shape of residual electron density for 2SAP indicated the conformation of 2SAP was twisted due to the confining in the cavity, which is the reason for photochromism. On the other hand, the recrystallization of 1 and 2SAP from THF / hexane solution unexpectedly gave hetero-antiparallel form of 1 because of the dynamic covalent bond formation in the boronic esters (Fig.). As this hetero-antiparallel form has planar cavity in the molecule, the conformation of the included guest molecule, 2SAP, is also planar as always seen. Therefore the inclusion crystal is non-photochromic. Thus, photochromism change of 2SAP was realized by conformational control through confining in the cavity of macrocyclic boronic ester.

Structure and H position of tetragonal hydrogarnet derived from CaGeO3garnet

Hydrogarnets, represented by hydrogrossular, are produced by the replacement of (ZO4)4- in garnets by (H4O4)4- (Z: tetrahedral cation) and the vacancies of tetrahedral cations are created by this replacement. Most of reported hydrogarnets crystallizes with cubic symmetry (space group Ia-3d). To our knowledge, Ca3Mn2[SiO4]2.07[H4O4]0.93 with space group I41/acd (tetragonal) [1] has been only reported as a low-symmetry hydrogarnet. In the cubic hydrogarnets, all O atoms are crystallographically equivalent, whereas in low-symmetric one, they can be located at non-equivalent sites. Therefore, the investigation of low-symmetry hydrogarnes is important to gain knowledge of the site preference of H atoms. Recently, we have successfully synthesized the single crystal of a new low-symmetry hydrogarnet CaGe0.924O3H0.304 (= Ca3(CaGe)[GeO4]2.696[H4O4]0.304) with tetragonal space group I41/a, at 3 GPa and 1273 K under the presence of H2O component. This tetragonal hydrogarnet is produced by the partial replacement of (GeO4)4- in high-pressure CaGeO3 garnet, Ca3(CaGe)[GeO4]3, by (H4O4)4-. In the present study, we report the single crystal X-ray diffraction study of this hydrogarnet at 98 and 298 K. In the structure refinement at 298 K, the occupancy parameters resulted in 0.393(2) for tetrahedral Z2(Ge) site, coordinated only by O6 atoms, and showed no significant deviation from 1.0 for the remaining cation sites. The bond valence sums of each atom except O6 atom agree with the valences of occupied atoms, whereas that of O6 atom are 1.50, deviating largely from oxygen valence. Thus, the substitution of OH groups for O atoms in the present sample occurs only at O6 site, which indicates that O6 is the most preferential site for the OH substitution. The position of H atom will be examined from the residual electron density distributions at a low temperature of 98 K, and the hydrogen bonding in the crystal structure will be discussed.

Anharmonicity and isomorphic phase transition: a multi-temperature X-ray single-crystal and powder diffraction study of 1-(2'-aminophenyl)-2-methyl-4-nitroimidazole.

The harmonic model of atomic nuclear motions is usually enough for multipole modelling of high-resolution X-ray diffraction data; however, in some molecular crystals, such as 1-(2'-aminophenyl)-2-methyl-4-nitro-1H-imidazole [Paul, Kubicki, Jelsch et al. (2011 ▶). Acta Cryst. B67, 365-378], it may not be sufficient for a correct description of the charge-density distribution. Multipole refinement using harmonic atom vibrations does not lead to the best electron density model in this case and the so-called 'shashlik-like' pattern of positive and negative residual electron density peaks is observed in the vicinity of some atoms. This slight disorder, which cannot be modelled by split atoms, was solved using third-order anharmonic nuclear motion (ANM) parameters. Multipole refinement of the experimental high-resolution X-ray diffraction data of 1-(2'-aminophenyl)-2-methyl-4-nitro-1H-imidazole at three different temperatures (10, 35 and 70 K) and a series of powder diffraction experiments (20 ≤ T ≤ 300 K) were performed to relate this anharmonicity observed for several light atoms (N atoms of amino and nitro groups, and O atoms of nitro groups) to an isomorphic phase transition reflected by a change in the b cell parameter around 65 K. The observed disorder may result from the coexistence of domains of two phases over a large temperature range, as shown by low-temperature powder diffraction.

Optical and structural characterization of nitrogen-rich InN: Transition from nearly intrinsic to strongly n-type degenerate with temperature

We report on a detailed study of the structural and optical properties of nonstoichiometric nitrogen-rich InN grown on sapphire substrates, by migration enhanced afterglow deposition. The samples were polycrystalline, with the presence of InN dots. Unusually strong photoluminescence emission was measured at cryogenic temperatures, with the peak energy at ∼0.68 eV. Detailed analysis further shows that the sample has very low residual electron density in the range of ∼1016 cm−3 at temperatures below 20 K.

5-Fluoro-N-(2-methyl-3-oxo-1-thia-4-aza-spiro-[4.5]dec-4-yl)-3-phenyl-1H-indole-2-carboxamide.

In the title compound, C24H24FN3O2S, the 1,3-thia­zolidine ring adopts an envelope conformation with the S atom as the flap, while the cyclo­hexane ring is in a chair conformation. In the crystal, mol­ecules are linked by N—H⋯O and C—H⋯F hydrogen bonds, forming a three-dimensional network. The unit cell contains six voids of 57 Å3, but the residual electron density (highest peak = 0.23 e Å−3 and deepest hole = −0.19 e Å−3) in the difference Fourier map suggests no solvent mol­ecule occupies this void.

Bis(1,3-dimethyl-1H-imidazolium) hexafluorosilicate methanol 0.33-solvate

The title compound, 6C5H9N2 +·3SiF6 2−·CH3OH, (I), was prepared by recrystallization of the crude salt from methanol along with solvent-free 2C5H9N2 +·SiF6 2− (II). Crystals of these solvatomorphs can be separated manually. The solvate (I) crystallizes in a rare hexa­gonal space group P6/mcc. Its asymmetric unit comprises one half of an imidazolium cation bis­ected by the crystallographic m-plane, one-sixth and one-twelfth of two crystallographically independent SiF6 2– dianions (Si atoms are located on the 3.2 and 6/m inversion centres), and one-twelfth of a methanol mol­ecule (C atoms are situated on the 622 inversion centres, other atoms are disordered between general positions). In (I), all F atoms of 3.2-located SiF6 2– dianions participate in the formation of symmetry-equivalent contacts to the H atoms of imidazolium fragments, thus forming rod-type ensembles positioned on the -6 axes. These ‘pillar’ rods are, in turn, F⋯H inter­linked through SiF6 2– dianions disordered around the 6/m centres. The twelvefold disordered methanol mol­ecules are appended to this array by O—H⋯F hydrogen bonds to the 6/m located SiF6 2– dianions. In terms of graph-set notation, the first and second level networks in (I) are N 1 = C 2 2(7)[3R 4 4(14)]D 2 2(4) and N 2 = D 2 2(5) (C—H⋯O hydrogen bonds are not considered). After locating all symmetrically independent atoms in the cation and anions, there remained a strong (> 3 e Å−3) residual electron density peak located at the 622 inversion centre. Treatment of this pre-refined model with the SQUEEZE procedure in PLATON [Spek (2009). Acta Cryst. D65, 148–155] revealed two voids per unit cell, indicative of the presence of the solvent methanol mol­ecule disordered about the 622 inversion centre.