Analysis Of Atomic Structure Research Articles

Short Carboxylic Acid-Carboxylate Hydrogen Bonds Can Have Fully Localized Protons.

Short hydrogen bonds (H-bonds) have been proposed to play key functional roles in several proteins. The location of the proton in short H-bonds is of central importance, as proton delocalization is a defining feature of low-barrier hydrogen bonds (LBHBs). Experimentally determining proton location in H-bonds is challenging. Here, bond length analysis of atomic (1.15-0.98 Å) resolution X-ray crystal structures of the human protein DJ-1 and its bacterial homologue, YajL, was used to determine the protonation states of H-bonded carboxylic acids. DJ-1 contains a buried, dimer-spanning 2.49 Å H-bond between Glu15 and Asp24 that satisfies standard donor-acceptor distance criteria for a LBHB. Bond length analysis indicates that the proton is localized on Asp24, excluding a LBHB at this location. However, similar analysis of the Escherichia coli homologue YajL shows both residues may be protonated at the H-bonded oxygen atoms, potentially consistent with a LBHB. A Protein Data Bank-wide screen identifies candidate carboxylic acid H-bonds in approximately 14% of proteins, which are typically short [⟨dO-O⟩ = 2.542(2) Å]. Chemically similar H-bonds between hydroxylated residues (Ser/Thr/Tyr) and carboxylates show a trend of lengthening O-O distance with increasing H-bond donor pKa. This trend suggests that conventional electronic effects provide an adequate explanation for short, charge-assisted carboxylic acid-carboxylate H-bonds in proteins, without the need to invoke LBHBs in general. This study demonstrates that bond length analysis of atomic resolution X-ray crystal structures provides a useful experimental test of certain candidate LBHBs.

Physical Stabilization of Pharmaceutical Glasses Based on Hydrogen Bond Reorganization under Sub-Tg Temperature

Amorphous solid dispersions (ASDs) play a key role in the pharmaceutical industry through the use of high-energy amorphous state to improve solubility of pharmaceutical agents. Understanding the physical stability of pharmaceutical glasses is of great importance for their successful development. We focused on the anti-HIV agent, ritonavir (RTV), and investigated the influence of annealing at temperatures below the glass transition temperature (sub-Tg) on physical stability, and found that the sub-Tg annealing effectively stabilized RTV glasses. Through the atomic structure analyses using X-ray pair distribution functions and infrared spectroscopy, we ascertained that this fascinating effect of the sub-Tg annealing originated from strengthened hydrogen bonding between molecules and probably from a better local packing associated with the stronger hydrogen bonds. The sub-Tg annealing is effective as a physical stabilization strategy for some pharmaceutical molecules, which have relatively large energy barrier for nucleation.

Analysis of the local atomic structure of quantum dots of the CdS family

The microwave synthesis of quantum dots based on CdS has been performed, the temperature (T 180°C and 150°C) and synthesis duration (10 min and 5 min) have been varied. The analysis of the peak broadening in X-ray diffraction has shown that the average particle size in the synthesized samples is 10.02 nm for the CdST = 180°C sample and 5.22 nm for the CdST = 150°C sample. For both synthesis temperatures particles of sphalerite phase are formed but the sample CdST = 180°C contained some impurity of wurtzite phase too. CdK-XANES spectra in the standard samples and quantum dots have been recorded using a Rigaku R-XAS X-ray absorption laboratory spectrometer. The theoretical analysis of the CdK-XANES spectra of bulk samples of CdS and CdS nanoparticles has been performed. It has been shown that the theoretical difference spectra between bulk CdS and CdS with decreased lattice parameters demonstrate the same tendency as the experimental difference spectra between bulk CdS and the quantum dot samples under study. It has been shown that the theoretical CdK-edge HERFD-XANES spectrum in CdS demonstrates considerably more detailed structure pointed to the need of the analysis of experimental CdK-edge HERFDXANES spectra to pick out more precise information on local atomic structure parameters of small semiconducting quantum dots.

Exploring the atomic structure of 1.8 nm monolayer-protected gold clusters with aberration-corrected STEM

Monolayer-protected (MP) Au clusters present attractive quantum systems with a range of potential applications e.g. in catalysis. Knowledge of the atomic structure is needed to obtain a full understanding of their intriguing physical and chemical properties. Here we employed aberration-corrected scanning transmission electron microscopy (ac-STEM), combined with multislice simulations, to make a round-robin investigation of the atomic structure of chemically synthesised clusters with nominal composition Au144(SCH2CH2Ph)60 provided by two different research groups. The MP Au clusters were “weighed” by the atom counting method, based on their integrated intensities in the high angle annular dark field (HAADF) regime and calibrated exponent of the Z dependence. For atomic structure analysis, we compared experimental images of hundreds of clusters, with atomic resolution, against a variety of structural models. Across the size range 123–151 atoms, only 3% of clusters matched the theoretically predicted Au144(SR)60 structure, while a large proportion of the clusters were amorphous (i.e. did not match any model structure). However, a distinct ring-dot feature, characteristic of local icosahedral symmetry, was observed in about 20% of the clusters.

The pH Dependent Protein Structure Transitions and Related Spin-State Transition of Cytochrome c′ from Alcaligenes xylosoxidans NCIMB 11015

Abstract The unusual magnetic/spectroscopic properties of Cytochrome c′ (Cyt c′) have been discussed, especially concerning the possibility of a quantum mechanically mixed-spin configuration of heme Fe(III). Here, four unique-spin species were identified from the magnetic circular dichroism (MCD) spectra of Cyt c′ from Alcaligenes xylosoxidans (AxCyt c′). The electrospray ionization mass spectrometric (ESI-MS) and circular dichroism (CD) spectroscopic data showed the overall conformation of AxCyt c′ was unchanged, in complete contrast to the drastic changes in the heme MCD spectra over the range of pH 3.5 and 11.8. The pH dependency of ESI-MS, electronic absorption, MCD, and CD spectroscopic properties of AxCyt c′ enabled us to reveal the undiscovered correlation between the protein-folding state and the electronic structure of the active site as a function of pH. The mechanism of alkaline spin-state transition through the rearrangement of the hydrogen-bonding linkage between Helix C and D is also proposed on the basis of atomic resolution crystal structure analyses (A. Takashina, M. Unno, T. Kohzuma, Chem. Lett. 2015, 44, 268).

Local atomic structure analysis of SiC interface with oxide using chemical-state-selective X-ray absorption spectroscopy

A local atomic structure analysis of the interface between chemical vapor-deposited SiO2 and 4H-SiC was achieved via a combination of chemical-state-selective X-ray absorption spectroscopy and the use of a sample with a very thin oxide film. The Si K-edge spectrum, which monitors the SiC-assigned Auger peak, allows the SiC side of the SiO2/SiC interface to be selectively measured through the SiO2 film. We estimate the coordination number of the first nearest neighbor to be reduced by 17% with respect to the SiC bulk. This suggests that C vacancy defects exist at the SiC side of the interface.

Deformation behavior of metallic glasses with shear band like atomic structure: a molecular dynamics study.

Molecular dynamics simulations were employed to investigate the plastic deformation within the shear bands in three different metallic glasses (MGs). To mimic shear bands, MG specimens were first deformed until flow localization occurs, and then the volume of the material within the localized regions was extracted and replicated. Homogeneous deformation that is independent of the size of the specimen was observed in specimens with shear band like structure, even at a temperature that is far below the glass transition temperature. Structural relaxation and rapid cooling were employed to examine the effect of free volume content on the deformation behavior. This was followed by detailed atomic structure analyses, employing the concepts of Voronoi polyhedra and “liquid-like” regions that contain high fraction of sub-atomic size open volumes. Results suggest that the total fraction of atoms in liquid-like regions is a key parameter that controls the plastic deformation in MGs. These are discussed in the context of reported experimental results and possible strategies for synthesizing monolithic amorphous materials that can accommodate large tensile plasticity are suggested.

On the tetragonality of martensites in ferrous shape memory alloy Fe3Pt: A first-principles study

First-principles calculations have been performed to study the effects of point defects on the tetragonality of martensites in ferrous shape memory alloy Fe3Pt. By computing the Bain path, I show that by considering point defects, all the face-centered cubic (fct) and body-centered cubic (bct) phases with c/a values close to the experimental observations are predicted. Atomic structure analysis gives evidence about the proposed “antiferrodistortive transformation” which was previously derived from the softened phonon mode of Fe3Pt. We discuss the dependence of the Bain path on the concentration of defects and show that the observed bct structures are closely related to the particular shape of the L12 Bain path. Magnetism is identified as the origin of the extremely flat Bain path. The role of the enhanced band Jahn-Teller effect in stabilizing the fct phases is discussed.

Effects of alloying on the behavior of B and S at Σ5 (2 1 0) grain boundary in γ-Fe

To get the atomic scale understanding of impurities induced intergranular embrittlement or enhancement and the control of these effects on austenitic stainless steels, behavior of impurities B and S at γ-Fe grain boundary (GB) and effects of alloying elements (Cr, Ni, Mn, Co, Mo) additions on the cohesive properties of the γ-Fe GB doped by impurities are investigated by performing density functional theory (DFT) calculations. The results showed that, as the GB enhancer and embrittler respectively, impurities B and S tend to stay at the interstitial sites of γ-Fe GB, while alloying elements also can segregate at the GB studied. The presence of all the alloying elements considered can inhibit B GB segregation to some extent due to the higher segregation energies and can impair the enhancement effect of B on GB cohesion. However, these elements almost have no impact on GB segregation and embrittlement effect of S, except for Ni, Mn and Mo:Ni and Mo inhibit and improve S GB segregation, respectively; Mn and Mo strongly enhance and reduce S-induced GB embrittlement, respectively. Moreover, the remedial effect of (Cr+Ni), (Cr+Mn) on S-induced GB embrittlement is also discussed. Additional atomic structure and total valence charge density analysis demonstrated and explained our conclusions.

X-ray crystallographic evidence for the simultaneous presence of axial and rhombic sites in cupredoxins: atomic resolution X-ray crystal structure analysis of pseudoazurin and DFT modelling

The simultaneous presence of axial (blue) and rhombic (green) Cu sites in pseudoazurin is described from experiments and computational modelling.

Self-aligned synthesis of a NiPt-alloycore@Ptshellnanocrystal with contrivable heterojunction structure and oxygen reduction activity

A bimetallic NiPt nanocrystal (NC) has been synthesized using the wet chemical reduction method; it was sequentially designed in the presence of carbon nanotubes. NiPt@Pt NC is a nanocrystal with the configuration of a NiPt alloy core and tuneably thick Pt shell. Under optimum conditions (Pt = 20 at%), the oxygen reduction current of NiPt@Pt NC is 1.08-fold at 0.85 V (vs. RHE), as compared to Pt NC, and the onset voltage (VOC) is 0.905 V. The results of the atomic and crystal structure analyses show that such an enhancement is largely due to the impact of the local strain and the electronic dipole at the heterogeneous Pt–Ni interface. Most importantly, we have proposed a robust technique for programming the atomic structural configuration and oxygen reduction activity of NC, which shows comparable performance and ~80% less Pt loading than Pt NC.

19pPSA-40 光電子回折分光法によるRhドープSrTiO_3光触媒の原子構造解析

19pPSA-40 光電子回折分光法によるRhドープSrTiO_3光触媒の原子構造解析

Ab Initio Investigation on Cu/Cr Codoped Amorphous Carbon Nanocomposite Films with Giant Residual Stress Reduction.

Amorphous carbon films (a-C) codoped by two metal elements exhibit the desirable combination of tribological and mechanical properties for widely potential applications, but are also prone to catastrophic failure due to the inevitable residual compressive stress. Thus far, the residual stress reduction mechanism remains unclear due to the insufficient understanding of the structure from the atomic and electronic scale. In this paper, using ab initio calculations, we first designed a novel Cu/Cr codoped a-C film and demonstrated that compared with pure and Cu/Cr monodoped cases, the residual stress in Cu/Cr codoped a-C films could be reduced by 93.6% remarkably. Atomic bond structure analysis revealed that the addition of Cu and Cr impurities in amorphous carbon structure resulted in the critical and significant relaxation of distorted C-C bond lengths. On the other hand, electronic structure calculation indicated a weak bonding interaction between the Cr and C atoms, while the antibonding interaction was observed for the Cu-C bonds, which would play a pivot site for the release of strain energy. Those interactions combined with the structural evolution could account for the drastic residual stress reduction caused by Cu/Cr codoping. Our results provide the theoretical guidance and desirable strategy to design and fabricate a new nanocomposite a-C films with combined properties for renewed applications.

The effect of atomic structure on interface spin-polarization of half-metallic spin valves: Co2MnSi/Ag epitaxial interfaces

Using density functional theory calculations motivated by aberration-corrected electron microscopy, we show how the atomic structure of a fully epitaxial Co2MnSi/Ag interfaces controls the local spin-polarization. The calculations show clear difference in spin-polarization at Fermi level between the two main types: bulk-like terminated Co/Ag and Mn-Si/Ag interfaces. Co/Ag interface spin-polarization switches sign from positive to negative, while in the case of Mn-Si/Ag, it is still positive but reduced. Cross-sectional atomic structure analysis of Co2MnSi/Ag interface, part of a spin-valve device, shows that the interface is determined by an additional layer of either Co or Mn. The presence of an additional Mn layer induces weak inverse spin-polarisation (−7%), while additional Co layer makes the interface region strongly inversely spin-polarized (−73%). In addition, we show that Ag diffusion from the spacer into the Co2MnSi electrode does not have a significant effect on the overall Co2MnSi /Ag performance.

Atomic investigation of alloying Cr, Ti, Y additions in a grain boundary of vanadium

The effect of alloying additions (Cr, Ti and Y) in a vanadium (V) ∑3 (111) grain boundary (GB) is investigated by first-principles calculations. To determine site preference and segregation properties of Cr, Ti and Y in the GB and bulk, we calculate the formation energies and segregation energies for different interstitial and substitutional sites. Cr/Ti/Y atom prefers to segregate to the substitutional sites of the GB from bulk environment, whereas Cr segregation to GB is very weak. Based on the Rice and Wang's model, Cr acts as the GB cohesion, while Ti and Y are strong embrittlers. The analysis of atomic and electronic structures provides a reasonable expansion for the embrittlement behavior. Moreover, the effect of Cr, Ti and Y in the GB on solution of interstitial impurities C, N, O, H, and He are determined. The results show that Cr restrains solution of these impurities in the GB, while Ti tends to form Ti–N complex by absorbing N impurities and Y can absorbs O and He impurities. The present calculations are helpful for understanding the behavior of alloying Cr, Ti, Y additions at the grain boundary of vanadium.

Analysis of the local atomic structure of a surface using EELFS spectroscopy data: Possibilities and the prospects for development

In this paper, the possibility of studying the local atomic structure of a substance surface by means of analysis of extended fine structures of the electron energy-loss spectra (extended energy-loss fine structure (EELFS) spectroscopy) is considered. The possibilities, restrictions, and the prospects for development of this method are considered.

Effect of interstitial impurities on grain boundary cohesive strength in vanadium

We studied the embrittling and strengthening effects of non-metallic (C, N, O, S, Si, and B) and metallic (Fe and Mo) interstitial impurities at a ∑3 (111) [11¯0] grain boundary (GB) in vanadium (V) using first-principles calculations. All impurities incorporated into the GB are exothermic reaction except for Mo along with outward expansion of the GB space. Upon optimization, the small C, N, and O impurities at the GB prefer the same interstitial site, while the S, Si, B, Fe and Mo impurities prefer another interstitial site. According to strengthening energy calculations, C, N, B, and Fe act as the GB cohesion, while O and S are strong embrittlers as well Si and Mo are weak embrittlers. The analysis of atomic and electronic structures indicate that the embrittling and strengthening behavior of the impurities mainly depends on the bonding behavior of the impurity with surrounding vanadium atoms, the impurity species and the atomic size.

Linking Atomic Structure and Local Chemistry at Manganese‐Segregated Antiphase Boundaries in ZrO2–La2/3Sr1/3MnO3 Thin Films

This paper presents direct experimental evidence of Mn segregation at three types of antiphase boundaries in La2/3Sr1/3MnO3 thin films doped with ZrO2. The local atomic structure of these antiphase boundaries is investigated by high‐angle annular dark‐field and annular bright‐field imaging in a scanning transmission electron microscope. Chemical composition and cation valence are determined by electron energy‐loss spectroscopy. The evidence that strain relaxation and ZrMn substitution are driving forces for the formation of the antiphase boundaries is found in this study. Analysis of atomic structure, image contrast, Mn valence state, and Mn occupancy shows that the antiphase boundaries are charge‐neutral with minimized internal electric fields.

Analysis of the local atomic structure of manganese and its oxides by extended energy loss fine structure spectroscopy

A technique for determining parameters of the local atomic structure of a manganese-oxygen system by the extended energy loss fine structure method has been proposed. Experimental extended energy loss fine structure spectra of the clean surface of metallic manganese and its stoichiometric oxides have been measured. Normalized oscillating portions have been separated from the experimental spectra and analyzed by solving the inverse problem using the Tikhonov regularization. The parameters of the local atomic structure of the objects under study, i.e., coordination numbers, bond lengths, and their variance parameters, have been determined.

β-Hydrogen Elimination Mechanism in the Absence of Low-Lying Acceptor Orbitals in EH2(t-C4H9) (E = N-Bi).

The β-hydrogen elimination reactions of group 15 alkyl compounds at the example of EH2(t-C4H9) (element E = N-Bi) were investigated and compared to the group 13 example of GaH2(t-C4H9). With the aid of extensive density functional theory based analysis of atomic and electronic structures at the transition state, we can derive three distinct reaction classes. The gallium compound follows the well-known β-hydride route with participation of an empty p orbital at the metal in a concerted, synchronous fashion, exhibiting a low barrier. For compounds with group 15 elements, we find highly nonsynchronous reactions with high reaction barriers. In the case of nitrogen, a proton-like H atom is transferred via attack of the nitrogen nonbonding electron pair. For the heavier homologues (P-Bi), E-Cα bond breaking occurs first and the H atom does not carry charge at the transition state. The reaction barrier in group 15 homologues is thus determined by the E-Cα bond strength down the group. The results enable a rationale for ligand design for precursors involved in chemical vapor-phase deposition processes because a good ligand needs to stabilize the positive charge at Cα.