Bond Angle Deviation Research Articles

Anharmonicity and local lattice distortion in strained Ge-dilute Si1−xGex alloy

We have investigated the anharmonicity and local lattice distortion in strained Ge-dilute Si1−xGex alloy using Ge K-edge extended x-ray absorption fine structure measurement coupled with ab initio molecular dynamics simulation. Pronounced asymmetry is for the first time revealed for the Ge–Si first nearest-neighbor (NN) distribution even at room temperature, in good agreement with theoretical simulations. In comparison with harmonic approximation, the anharmonicity contributes an additional shift of 0.011 Å to the Ge–Si first NN bond distance, which is further found to be crucial to the qualitative change (i.e., contracting or stretching) of the Ge–Si second NN bond distance relative to the corresponding Si–Si bond distance in bulk Si. As the modifications of higher NN shells arise from the competition between the NN bond-distance stretching and the tetrahedral bond-angle deviation, those results indicate that the anharmonicity is critical in the proper determination of the local strain accommodation mode and thus the substrate effect. Farther NN shells exhibit slight asymmetry. Our findings reconcile the long-standing controversy regarding the dominant local strain relaxation mechanism in strained Ge-dilute Si1−xGex alloys.

Parameterization of the DFTB3 method for Br, Ca, Cl, F, I, K, and Na in organic and biological systems.

We present an extension to the recent 3OB parametrization of the Density Functional Tight Binding Model DFTB31,2 for biological and organic systems. Parameters for the halogens F, Cl, Br, and I have been developed for use in covalently bound systems and benchmarked on a test set of 106 molecules (the ‘OrgX’ set), using bonding distances, bonding angles, atomization energies, and vibrational frequencies to assess the performance of the parameters. Additional testing has been done with the X40 set of 40 supramolecular systems containing halogens,3 adding a simple correction for the halogen bonds that are strongly overbound in DFTB3. Furthermore, parameters for Ca, K, and Na as counterions in biological systems have been created. To benchmark geometries as well as ligand binding energies a test set ‘BioMe’ of 210 molecules has been created that cover coordination to various functional groups frequently occurring in biological systems. The new DFTB3/3OB parameter set outperforms DFT calculations with a double-ζ basis set in terms of energies and can reproduce DFT geometries, with some minor deviations in bond distances and angles due to the use of a minimal basis set.

Applying the Structure Correlation Principle to retro Diels Alder Reactions

The early stages of molecular rearrangements are often apparent in the crystal structures of molecules susceptible to that rearrangement. For example, if a particular bond is broken, or if a particular group migrates during the rearrangement, then deviations of bond distances and angles from their `standard values' along the reaction coordinate are often observed. This is the structure correlation principle,1 which holds provided the molecule exists in the ground state, in a geometry, which is similar to the transition state geometry for the reaction. In this geometry the frontier orbitals whose interactions facilitate the reaction, can mix in the ground state. This paper discusses the application of this principle to pericyclic fragmentation reactions related to the retro Diels Alder reaction, using low temperature X-ray structural analysis of a range of model substrates. The substrates can be classified on the basis of this data into three groups: (i) those that undergo a synchronous retro Diels Alder reaction, (2) those that undergo an asynchronous retro Diels Alder reaction, and (3) those that react via a 2-step process. Examples of molecules falling into these three categories are given below.

Comparison of the accuracy of powder and single-crystal X-ray diffraction techniques in determining organic crystal structure

This study demonstrates the accuracy of powder X-ray diffraction (PXRD) in determining the crystal structures of four organic molecules by comparing the structural information obtained from both single-crystal X-ray diffraction (SXRD) and PXRD techniques. Results showed that the PXRD technique had approximately the same precision as the SXRD technique. The majority of the relative deviations from PXRD-derived lattice parameters were within ±0.2 % of the correct values (average of the SXRD data), whereas the relative deviations in bond lengths and angles are within ±1.0 %. All of the relative deviations were subjected to normal statistical distributions (μ = 0) and coincided with the SXRD data. As an auxiliary implement of SXRD, PXRD is clearly an effective and powerful technique in establishing an accurate characterization of organic molecules.

Irradiation effects of 65 MeV Kr-ions on structure and optical band-gap of nc-Si:H films

In this paper, hydrogenated nano-crystalline silicon (nc-Si:H) films with thickness of 1.0μm were irradiated with 65MeV Kr-ions, and the irradiation induced modification on structural and optical properties of the films are investigated. Characterization of the samples with X-ray diffraction shows that the average crystallite size decreases slightly from 10.9 to 9.4nm, and the integrated intensity ratios of (220) to (111) peak and (311) to (111) peak remain nearly constant after irradiation. The Raman spectra results reveal that the crystalline fraction of the films decreases considerably from 65.6% to 10.3% and at same time the bond angle deviation of amorphous phase increases obviously from 7.7° to 11.5° with increasing the ion fluence. Moreover, the UV–Vis transmittance spectra results show that the optical band-gap decreases from 2.14 to 1.55eV after irradiation. The irradiation induced atomic displacements leads to the amorphization of crystalline phase and the reduction in structural order of amorphous phase in the nc-Si:H films. The improvement of light absorption and the broadening of valence and conduction band-tails, which related to the decrease of crystalline fraction and short range order, respectively, are responsible for the reduction of optical band-gap.

Structural properties and growth evolution of diamond-like carbon films with different incident energies: A molecular dynamics study

Structural properties and growth evolution of diamond-like carbon (DLC) films with different incident energies were investigated systematically by the molecular dynamics simulation using a Tersoff interatomic potential for carbon-carbon interaction. The results revealed that the density, sp3 fraction and residual compressive stress as a function of incident energy increased firstly and then decreased; when the incident energy was 70eV/atom, the density could reach to 3.0g/cm3 with the maximal compressive stress of 15.5GPa. Structure analysis indicated that the deviation of both bond angles and lengths from the equilibrium position led to the generation of a large residual stress, while the high compressive stress mainly attributed to the decrease of both bond angles and lengths among carbon atoms. The growth of DLC films underwent a formation process of “Line-Net” structure accompanied with the interaction of many atomic motion mechanisms, and the “Point” stage was only found for DLC films with low incident energy.

On the transient amorphous silicon structures during solid phase crystallization

By analyzing the solid phase crystallization (SPC) of amorphous silicon (a-Si) with the Johnson-Mehl-Avrami-Kolmogorov (JMAK) model, it was found that the crystallization kinetics was non-ideal, with indications of a non-constant nucleation rate. Detailed structural analysis of the a-Si material during SPC revealed an increasing bond angle distortion from the ideal crystalline silicon (c-Si) bond angle of 109.5°. In addition, infrared measurements indicated a change in SiSi bond polarizability, however its role in the SPC behavior is not clear. The increase in tensile stress, bond angle deviation and bond polarizability together with the increase in crystal fraction may suggest that these parameters could be correlated.

A biophysical elucidation for less toxicity of Agglutinin than Abrin-a from the Seeds of Abrus Precatorius in consequence of crystal structure

X-ray crystal structure determination of agglutinin from abrus precatorius in Taiwan is presented. The crystal structure of agglutinin, a type II ribosome-inactivating protein (RIP) from the seeds of Abrus precatorius in Taiwan, has been determined from a novel crystalline form by the molecular replacement method using the coordinates of abrin-a as the template. The structure has space group P41212 with Z = 8, and been refined at 2.6 Å to R-factor of 20.4%. The root-mean-square deviations of bond lengths and angles from the standard values are 0.009 Å and 1.3°. Primary, secondary, tertiary and quaternary structures of agglutinin have been described and compared with those of abrin-a to a certain extent. In subsequent docking research, we found that Asn200 of abrin-a may form a critical hydrogen bond with G4323 of 28SRNA, while corresponding Pro199 of agglutinin is a kink hydrophobic residue bound with the cleft in a more compact complementary relationship. This may explain the lower toxicity of agglutinin than abrin-a, despite of similarity in secondary structure and the activity cleft of two RIPs.

Comparison of the crystal structure and function to wild-type and His25Ala mutant human heme oxygenase-1

Human heme oxygenase-1 (hHO-1) is a rate-limiting enzyme in heme metabolism. It regulates serum bilirubin level. Site-directed mutagenesis studies indicate that the proximal residue histidine 25 (His25) plays a key role in hHO-1 activity. A highly purified hHO-1 His25Ala mutant was generated and crystallized with a new expression system. The crystal structure of the mutant was determined by X-ray diffraction technology and molecular replacement at the resolution of 2.8 A, and the model of hHO-1 His25Ala mutant was refined. The final crystallographic and free R factors were 0.245 and 0.283, respectively. The standard bond length deviation was 0.007 A, and the standard bond angle deviation was 1.3 degrees . The mutation of His25 to Ala led to an empty pocket underneath the ferric ion in the heme, leading to loss of binding iron ligand. Although this did not cause an overall structural change, the enzymatic activity of the mutant hHO-1 was reduced by 90%. By supplementing imidazole, the HO-1 activity was restored approximately 90% to its normal level. These data suggest that Ala25 remains unchanged in the structure compared to His25, but the important catalytic function of hHO-1 is lost. Thus, it appears that His25 is a crucial residue for proper hHO-1 catalysis.

Structural Insights into KChIP4a Modulation of Kv4.3 Inactivation

Dynamic inactivation in Kv4 A-type K(+) current plays a critical role in regulating neuronal excitability by shaping action potential waveform and duration. Multifunctional auxiliary KChIP1-4 subunits, which share a high homology in their C-terminal core regions, exhibit distinctive modulation of inactivation and surface expression of pore-forming Kv4 subunits. However, the structural differences that underlie the functional diversity of Kv channel-interacting proteins (KChIPs) remain undetermined. Here we have described the crystal structure of KChIP4a at 3.0A resolution, which shows distinct N-terminal alpha-helices that differentiate it from other KChIPs. Biochemical experiments showed that competitive binding of the Kv4.3 N-terminal peptide to the hydrophobic groove of the core of KChIP4a causes the release of the KChIP4a N terminus that suppresses the inactivation of Kv4.3 channels. Electrophysiology experiments confirmed that the first N-terminal alpha-helix peptide (residues 1-34) of KChIP4a, either by itself or fused to N-terminal truncated Kv4.3, can confer slow inactivation. We propose that N-terminal binding of Kv4.3 to the core of KChIP4a mobilizes the KChIP4a N terminus, which serves as the slow inactivation gate.

Structural and optical studies on hot wire chemical vapour deposited hydrogenated silicon films at low substrate temperature

Thin films of hydrogenated silicon are deposited by hot wire chemical vapour deposition technique, as an alternative of plasma enhanced chemical vapour deposition technique. By varying the hydrogen and silane flow rate, we deposited the films ranging from pure amorphous to nanocrystallite-embedded amorphous in nature. In this paper we report extensively studied structural and optical properties of these films. It is observed that the rms bond angle deviation decreases with increase in hydrogen flow rate, which is an indication of improved order in the films. We discuss this under the light of breaking of weak Si–Si bonds and subsequent formation of strong Si–Si bonds and coverage of the growing surface by atomic hydrogen.

MOLECULAR DYNAMICS STUDIES OF CRAMBIN AND BPTI IN TERMS OF ABEEM/MM METHOD

Recently, the ABEEM/MM method (atom-bond electronegativity equalization method fused into molecular mechanics) has successfully been applied to study polypeptide conformations. In order to further test the reliability of this method as well as the transferability of the parameters (including ABEEM and force field parameters), molecular dynamics simulation studies on Crambin and BPTI (298 K, in vacuo) have been performed in terms of ABEEM/MM fluctuating charge force field. Some of their structural properties were obtained, and relative to the X-ray structures, the root-mean-square deviations (RMSD) of bond lengths, bond angles and key dihedral angles, and the coordinate RMSDs of atoms were calculated. The ABEEM/MM results are fairly consistent with those from X-ray experiment.

High-resolution structure of unbound human immunodeficiency virus 1 subtype C protease: implications of flap dynamics and drug resistance

The X-ray crystal structure of the unbound state of human immunodeficiency virus 1 (HIV-1) subtype C protease (C PR) has been determined to 1.20 angstroms resolution in the tetragonal space group P4(1)2(1)2, with one monomer per asymmetric unit and unit-cell parameters a = 46.7, c = 100.8 angstroms, allowing full anisotropic least-squares refinement. The refined model has a conventional R factor of 14.1% for all reflections and estimated standard deviations in bond lengths and angles for all main-chain non-H atoms of 0.014 angstroms and 0.030 degrees , respectively. The structure is compared with three unbound subtype B proteases (B PRs) to identify structural changes arising from the naturally occurring polymorphisms and delineate their implications in antiretroviral drug resistance/susceptibility. The unbound C PR exhibits a larger distance between the tips of the flaps, a downward displacement of the 36-41 loop and an increased thermal stability of the 10s loop when compared with the B PR structures. The C PR structure presents the highest resolution of the unbound state of a non-subtype-B PR and adds to the understanding of flap dynamics and drug resistance.

Experimental determination of optimal root-mean-square deviations of macromolecular bond lengths and angles from their restrained ideal values

A number of inconsistencies are apparent in the recent research paper by Jaskolski et al. [(2007), Acta Cryst. D63, 611-620] concerning their recommendations for the values of the magnitude and resolution-dependence of the root-mean-square deviations (RMSDs) of bond lengths and angles from their restrained ideal values in macromolecular refinement, as well as their suggestions for the use of variable standard uncertainties dependent on atomic displacement parameters (ADPs) and occupancies. Whilst many of the comments and suggestions in the paper regarding updates for the ideal geometry values proposed by Engh and Huber are entirely reasonable and supported by the experimental evidence, the recommendations concerning the optimal values of RMSDs appear to be in conflict with previous experimental and theoretical work in this area [Tickle et al. (1998), Acta Cryst. D54, 243-252] and indeed appear to be based on a misunderstanding of the distinction between RMSD and standard uncertainty (SU). In contrast, it is proposed here that the optimal values of all desired weighting parameters, in particular the weighting parameters for the ADP differences and for the diffraction terms, be estimated by the purely objective procedure of maximizing the experiment-based log(free likelihood). In principle, this allows all weighting parameters that are not known accurately a priori to be scaled globally, relative to those that are known accurately, for an optimal refinement. The RMS Z score (RMSZ) is recommended as a more satisfactory statistic than the RMSD to assess the extent to which the geometry deviates from the ideal values and a theoretical rationale for the results obtained is presented in which the optimal RMSZ is identified as the calculated versus true Z-score correlation coefficient, the latter being a monotonic function of the resolution cutoff of the data. Regarding the proposal to use variable standard uncertainties, it is suggested that any departure from the current practice of using fixed weights for geometric restraints based on experimental values of standard uncertainties be subject to the same experiment-based validation.

A reversible Raman spectral change induced by light in hydrogenated nanocrystalline silicon

This paper reports the reversible ordering-change in nanocrystalline silicon. Experimental data measured by micro-Raman scattering support the idea that irradiating light followed in part by an increase in temperature promotes competition between two dissimilar classes of crystallites in nanocrystalline silicon, in which one class is single crystal-like and the other is surface-like. Theoretical approximations based on the Raman shift reduction to 504 cm −1 estimate that the correlation length evaluating the average distance between defects decreases to 2.55 nm and the root mean square bond angle deviation increases to 5.96 ∘.

Structural Compromise of Disallowed Conformations in Peptide and Protein Structures

Using a data set of 454 crystal structures of peptides and 80 crystal structures of non-homologous proteins solved at ultra high resolution of 1.2 A or better we have analyzed the occurrence of disallowed Ramachandran (phi, psi) angles. Out of 1492 and 13508 non-glycyl residues in peptides and proteins respectively 12 and 76 residues in the two datasets adopt clearly disallowed combinations of Ramachandran angles. These examples include a number of conformational points which are far away from any of the allowed regions in the Ramachandran map. According to the Ramachandran map a given (phi, psi) combination is considered disallowed when two non-bonded atoms in a system of two-linked peptide units with ideal geometry are prohibitively proximal in space. However, analysis of the disallowed conformations in peptide and protein structures reveals that none of the observations of disallowed conformations in the crystal structures correspond to a short contact between non-bonded atoms. A further analysis of deviations of bond lengths and angles, from the ideal peptide geometry, at the residue positions of disallowed conformations in the crystal structures suggest that individual bond lengths and angles are all within acceptable limits. Thus, it appears that the rare tolerance of disallowed conformations is possible by gentle and acceptable deviations in a number of bond lengths and angles, from ideal geometry, over a series of bonds resulting in a net gross effect of acceptable non-bonded inter-atomic distances.

Perspectives for a Reversible Light-Induced Change in Hydrogenated Nanocrystalline Silicon

The measurements in this report suggest that the Raman shift taking place in nanocrystalline silicon is based on the orientational disordering activated by the energy of the irradiating light. We estimate the orientational disordering of crystallites in nanocrystalline silicon in terms of a correlation length and the root mean square (rms) bond angle deviation. We propose that Raman shift determines the correlation length and the rms bond angle deviation, and ultimately indicates the degree of structural disordering in nanocrystalline silicon.

Structural Basis for the Conformational Integrity of the Arabidopsis thaliana HY5 Leucine Zipper Homodimer

The leucine zipper (LZ) domain of the HY5 transcription factor from Arabidopsis thaliana has unique primary structural properties, including major occupation by the Leu residues as well as two buried polar residues in the a positions and a localized distribution of charged and polar residues in the first three heptad repeats. In this study, we solved the crystal structure of the HY5 LZ domain and show that the peculiarities in the primary sequence yield unusual structural characteristics. For example, the HY5 LZ domain exhibits a bipartite charge distribution characterized by a highly negative electrostatic surface potential in its N-terminal half and a nearly neutral potential in its C-terminal half. The LZ N-terminal region also contains two consecutive putative trigger sites for dimerization of the coiled coils. In addition, two buried asparagines at a positions 19 and 33 in the HY5 LZ domain display distinct modes of polar interaction. Whereas Asn(19) shows a conformational flip-flop, Asn(33) is engaged in a permanent hydrogen bond network. CD spectropolarimetry and analytical ultracentrifugation experiments performed with versions of the HY5 LZ domain containing mutations in the a positions yielded further evidence that position a amino acid residues are crucial for achieving an oligomeric state and maintaining stability. However, a low correlation between position a amino acid preference, core packing geometry, and rotamer conformations suggests that the oligomeric state of the LZ domain is not governed entirely by known structural properties. Taken together, our results suggest structural factors conferring conformational integrity of the HY5 LZ homodimer that are more complicated than proposed previously.

Local lattice distortion of Ge-dilute Ge-Si alloy: Multiple-scattering EXAFS study

The local structure of a Ge{sub 0.006}Si{sub 0.994} thin film with dilute Ge impurity in a Si host has been studied by fluorescence x-ray absorption fine structure spectroscopy in the temperature region of 10-300 K using the multiple-scattering data analysis method. Contrary to the elongation of 0.029 A ring for the Ge-Si distance in the first shell, the Ge-Si interatomic distance in the second shell shows a contraction of about 0.013 A ring relative to the corresponding Si-Si distance in the Si host. This coincides with the theoretical result calculated using the formula proposed by Mousseau and Thorpe [Phys. Rev. B 46, 15887 (1992)] which includes both the bond-length mismatch and bond-angle deviation. It turns out that the contraction of the second-shell Ge-Si distance is due to the deviation of the Ge-Si-Si bond angle from the ideal tetrahedral angle. From the obtained Ge-Si distances within the first three shells, it is revealed that dilute Ge doped into a Si host can lead to local distortion rather than an average lattice change.

Consequences of N-Acylation on Structure and Membrane Binding Properties of Dermaseptin Derivative K4-S4-(1-13)

Acyl conjugation to antimicrobial peptides is known to enhance antimicrobial properties. Here, we investigated the consequences of aminolauryl (NC(12)) conjugation to the dermaseptin derivative K(4)-S4-(1-13) (P) on binding properties to bilayer models mimicking bacterial plasma membrane, which is often cited as the ultimate site of action. Isothermal titration calorimetry revealed that acylation was responsible for enhancing the binding affinity of NC(12)-P compared with P (K = 13 x 10(5) and 1.5 x 10(5) m(-1), respectively). Surface plasmon resonance measurements confirmed the isothermal titration calorimetry results (K(app) = 12.6 x 10(5) and 1.53 x 10(5) m(-1), respectively) and further indicated that enhanced adhesion affinity (K(adhesion) = 3 x 10(5) and 1 x 10(5) m(-1), respectively) was coupled to enhanced tendency to insert within the bilayer (K(insertion) = 4.5 and 1.5, respectively). To gain insight into the molecular basis for these observations, we investigated the three-dimensional structures in the presence of dodecylphosphocholine using NMR. The ensemble of NMR-calculated structures (backbone root mean square deviation <0.6 A) showed that the acyl moiety was responsible for a significant molecular reorganization, possibly affecting the electrostatic potential distribution in NC(12)-P relative to that of P. The combined data present compelling evidence in support of the hypothesis that N-acylation affects antimicrobial properties by modifying the secondary structure of the peptide in a manner that facilitates contact with the membrane and consequently increases its disruption.