Bond Angle Deviation Research Articles

Vacancies in amorphous silicon: A tight-binding molecular-dynamics simulation

Vacancies formed in amorphous silicon are studied through the tight-binding molecular-dynamics method. Physical properties, such as the electronic density of states and volume change of a single vacancy at various sites, are obtained. The bond-angle deviation and the average valence charge of the atoms next to a vacancy are analyzed and found to be closely related. Even though vacancies at high density can be annihilated at room temperature, no migration of vacancies is observed in the simulations up to 450 K. Divacancy in amorphous silicon is found to behave similarly to a single vacancy of other types. Whereas there are many similarities between the vacancies in amorphous silicon and those formed in crystalline silicon, significant differences are found in some of their properties.

Effect of hydrogen radical exposure on the interfacial and bulk structure of a-Si:H/a-SiNx:H multilayer films

The a-Si:H/a-SiNx:H multilayer films were prepared by a glow discharge CVD method. Hydrogen radical produced by H2 plasma was alternately exposed to both a-Si:H and a-SiNx:H sublayer surfaces while suspending the deposition of each sublayer. The microstructure of the a-Si:H/a-SiNx:H multilayer films with hydrogen radical exposure and without hydrogen radical exposure was studied by means of small angle XRD, IR and Raman scattering measurements. The results indicate that the induced hydrogen radical may break the distorted or unstable Si–Si bonds on the a-Si:H and a-SiNx:H sublayer surfaces, and that the excessive H atoms at the interfaces of the a-Si:H/a-SiNx:H multilayer films may compensate for the surface silicon dangling bond by forming the Si–H bond. It was found that the microstructure of the multilayer films depends strongly on the hydrogen radical exposure time. The value of the silicon bond angle deviation in the a-Si:H(50A)/a-SiNx:H(50A) multilayer film changes from 10 to 7.9 to 12.1° with increasing hydrogen radical exposure time from 0 to 10 to 60 s, correspondingly. Given the exposure time of 10 s, the multilayer film is of the abruptest interface and smallest deviation of interfacial silicon bond angle.

Atomistic Features of the Amorphous-Crystal Interface in Silicon

We simulate the amorphous–crystal interface in silicon using a combination of interatomic potential molecular-dynamics and tight- binding conjugate-gradient relaxation. The samples we create have high quality crystalline and amorphous portions. We develop some localized measures of order to characterize the interface, including a missing neighbor vector and the bond angle deviation. We find that the measures of order interpolate smoothly from a bulk crystal value to a bulk amorphous value across a 7 A thick interface region. The interface structures exhibit a number of interesting features. The crystal planes near the interface are nearly perfect, with a few dimer defects similar to the Si(100) 2×1 reconstruction. Interfaces produced with one constant temperature simulation method are rough, with several layers of atoms forming chains and (111) facets. A different simulation method produces more planar interfaces with only a few chains.

Density functional study of chlorine–oxygen compounds related to the ClO self‐reaction

Geometrical parameters, vibrational frequencies, relative stabilities, and dissociation energies of the three stable Cl2O2 isomers and the OClO and ClOO radicals were investigated by density functional theory (DFT). The present analysis shows that DFT using hybrid functionals is capable of describing these systems to at least the same degree of accuracy as ab initio methods. The average absolute bond-length deviation of ClClO2, ClOOCl, and ClO2 from experimental results is 0.024/0.027 Å, with a maximum deviation for the dichlorine peroxide O(SINGLE BOND)O bond equal to 0.072/0.063 Å, for the B3PW91 and B3LYP functionals, respectively. The average absolute bond-angle deviation for the hybrid functionals is 0.8°. Harmonic vibrational frequencies calculated with DFT give for all Cl(SINGLE BOND)O compounds good agreement with experiments. The dissociation energies of ClOOCl, OClO, and ClOO were found to be in good agreement with experiments, the average error being less than 1.2 kcal/mol. The two isomers chloryl chloride (ClClO2) and dichlorine peroxide (ClOOCl) were found to be approximately 9 kcal/mol more stable than the chlorine chlorite (ClOClO) isomer. The ClOO isomer is predicted to be 3.0 kcal/mol more stable than OClO, in accordance with the experimental value of 4 kcal/mol. © 1998 John Wiley & Sons, Inc. Int J Quant Chem 66: 203–217, 1998

Density functional study of chlorine-oxygen compounds related to the ClO self-reaction

Geometrical parameters, vibrational frequencies, relative stabilities, and dissociation energies of the three stable Cl2O2 isomers and the OClO and ClOO radicals were investigated by density functional theory (DFT). The present analysis shows that DFT using hybrid functionals is capable of describing these systems to at least the same degree of accuracy as ab initio methods. The average absolute bond-length deviation of ClClO2, ClOOCl, and ClO2 from experimental results is 0.024/0.027 Å, with a maximum deviation for the dichlorine peroxide O(SINGLE BOND)O bond equal to 0.072/0.063 Å, for the B3PW91 and B3LYP functionals, respectively. The average absolute bond-angle deviation for the hybrid functionals is 0.8°. Harmonic vibrational frequencies calculated with DFT give for all Cl(SINGLE BOND)O compounds good agreement with experiments. The dissociation energies of ClOOCl, OClO, and ClOO were found to be in good agreement with experiments, the average error being less than 1.2 kcal/mol. The two isomers chloryl chloride (ClClO2) and dichlorine peroxide (ClOOCl) were found to be approximately 9 kcal/mol more stable than the chlorine chlorite (ClOClO) isomer. The ClOO isomer is predicted to be 3.0 kcal/mol more stable than OClO, in accordance with the experimental value of 4 kcal/mol. © 1998 John Wiley & Sons, Inc. Int J Quant Chem 66: 203–217, 1998

Mechanism of Enolase: The Crystal Structure of Asymmetric Dimer Enolase−2-Phospho-d-glycerate/Enolase−Phosphoenolpyruvate at 2.0 Å Resolution,

Enolase, a glycolytic enzyme that catalyzes the dehydration of 2-phospho-d-glycerate (PGA) to form phosphoenolpyruvate (PEP), is a homodimer in all eukaryotes and many prokaryotes. Here, we report the crystal structure of a complex between yeast enolase and an equilibrium mixture of PGA and PEP. The structure has been refined using 29 854 reflections with an F/sigma(F) of >/=3 to an R of 0.137 with average deviations of bond lengths and bond angles from ideal values of 0.013 A and 3.1 degrees , respectively. In this structure, the dimer constitutes the crystallographic asymmetric unit. The two subunits are similar, and their superposition gives a rms distance between Calpha atoms of 0.91 A. The exceptions to this are the catalytic loop Val153-Phe169 where the atomic positions in the two subunits differ by up to 4 A and the loop Ser250-Gln277, which follows the catalytic loop Val153-Phe169. In the first subunit, the imidazole side chain of His159 is in contact with the phosphate group of the substrate/product molecule; in the other it is separated by water molecules. A series of hydrogen bonds leading to a neighboring enolase dimer can be identified as being responsible for ordering and stabilization of the conformationally different subunits in the crystal lattice. The electron density present in the active site suggests that in the active site with the direct ligand-His159 hydrogen bond PGA is predominantly bound while in the active site where water molecules separate His159 from the ligand the binding of PEP dominates. The structure indicates that the water molecule hydrating carbon-3 of PEP in the PEP --> PGA reaction is activated by the carboxylates of Glu168 and Glu211. The crystals are unique because they have resolved two intermediates on the opposite sides of the transition state.

Crystal structure determination of alkaline haemorrhagin AaH III from snake venom ofAgkistrodon acutus

The haemorrhagin AaH III isolated from the snake venom of Agkistrodon acutus is one of the few alkaline ones in snake venoms. Its crystals belong to space group P2(1)2(1)2(1) with a = 9. 573 4 nm, b = 4. 996 7 nm and c = 4.728 8 nm. Its crystal structure was determined by the molecular replacement method according to the model of metalloproteinase Adamalysin II from eastern rattlesnake venom. The AaH III structure has been refined by PROLSQ. The final R factor was 0.254 and the RMS deviations of bond lengths and angles were 0.001 8 nm and 1.5 degrees . The structure comparison suggested that AaH III has a similar structure to other snake venom zinc-metalloproteinases. They all belong to matrix metalloproteinases super-family.

Weighting macromolecular diffraction data.

The results from refinements with six different weighting schemes in PROFFT, SHELXL93 and X-PLOR show that experimental weights, and especially unit weights, tend to overweight the low-angle data at the expense of the higher resolution data. This suggests that the use of unit weights are inappropriate except during initial cycles of refinements. Two alternative weighting schemes, one-line and two-line empirical weights, are shown to produce a relatively even distribution of the weighted r.m.s. error [r.m.s. Err = ( summation operator wDeltaF(2)/n)(1/2)] as a function of sin theta/lambda and result in linear delta(R) normal probability plots. Free R values and free weighted r.m.s. errors from the refinement of a scorpion toxin structure show that the alternative weighting schemes are superior to unit weights, and the r.m.s. deviations of bond distances and angles from the target values and G factors, as calculated by PROCHECK, confirm the superiority of the empirical weighting scheme. It was also observed that changing the value of WA, the contribution of the X-ray gradient to the total function minimized, produced little variation in R free but was directly proportional to the r.m.s. deviation of the bond distances from the target values.

Observation of Improved Structural Ordering in Low H Content, Hot wire Deposited a-Si:H

ABSTRACTWe present the results of X-ray diffraction measurements on a series of device quality hot wire (HW) deposited a-Si:H films in which we vary only the substrate temperature of the growing film, which decreases the bonded film H content in a systematic fashion. By increasing the substrate temperature to ∼375°C, where we deposit our low H content (CH) HW films which exhibit a reduced Staebler-Wronski effect, the width of the first peak in the X-ray diffraction pattern narrows noticeably. We interpret this narrowing to be the first indication of improved medium range ordering in our low CH, device quality HW a-Si:H. We note in addition that measurements of the bond angle deviation, obtained from Raman measurements of the half width of the Si-Si TO phonon mode on the same samples, do not show this same evidence of improved ordering as the substrate temperature is increased. We discuss these differences in the context of sample annealing experiments designed to effuse H from the region of the sample probed by the surface sensitive Raman technique, while leaving the bulk of the material, which is sampled by the X-ray beam, largely unaffected.

Ethyl {[N-(2-Hydroxyethyl)amino](2-hydroxy-1-naphthyl)methyl}phosphonate

The title molecule, C15H20NO5P, has a zwitterionic structure with strong intermolecular N⋯O and O⋯O hydrogen bonds. The coordination around phosphorus is a distorted tetrahedral, with a maximum bond-angle deviation of 12° from the ideal. The P—C bond length is 1.860 (4) Å and the average P—O value is 1.518 (3) Å.

Pseudorotation in heterocyclic five-membered rings: tetrahydrofuran and pyrrolidine

Using the 6-31G ∗∗ basis set, the HF-SCF and Møller-Plesset second-order (MP2) perturbation calculations have been carried out for tetrahydrofuran (THF) and pyrrolidine (PY) with the symmetries given by pseudorotation. On the whole, the MP2 calculations give better results on the puckered structures and energetics of both molecules, which are consistent with diffraction and spectroscopic results. From the MP2/6-31G ∗∗ calculations, the twist conformation 4T 3 is found to be the most stable one for THF, and the twist 1T 2( ax) and the envelope 1E( ax) forms appear to be energetically identical and most feasible for PY. We investigate the correlation between the puckering amplitudes and the sum of deviations of endocyclic bond angles from the standard value. The better correlation may support that the revised pseudorotation model proposed here is more appropriate to describe the puckering of non-equilateral five-membered rings than earlier models.

Effects of hydrogen on structural relaxation and defect evolution in amorphous silicon

Hydrogenation effects on the structural relaxation and defect evolution in amorphous silicon (a-Si) prepared by ion implantation and evaporation have been investigated using Raman scattering spectroscopy and positron lifetime measurements. Bond angle deviation Δθ in nonhydrogenated a-Si was significantly reduced due to 300 °C annealing in atomic hydrogen atmosphere. This indicates that the reduction in Δθ of hydrogenated amorphous silicon (a-Si:H) is not only due to relaxation during the deposition process of a-Si:H films as proposed by Jackson et al. [Philos. Mag. B 64, 611 (1991)] but also due to posthydrogenation of nonhydrogenated a-Si. It was also found that agglomeration of vacancy-type defects in evaporated a-Si during 450 °C annealing is enhanced after posthydrogenation, while no remarkable enhancement can be seen in a-Si prepared by ion implantation.

Structure of a Kunitz-type chymotrypsin from winged bean seeds at 2.95 A resolution.

Thc crystal structure of an alpha-chymotrypsin inhibitor (P6(1)22; a = 61.4, c = 210.9 A) isolated from winged bean (Psophocarpus. tetragonolobus) seeds has been determined at 2.95 A resolution by the molecular-replacement method using the 2.6 A coordinates of Erythrina trypsin inhibitor (ETI) as the starting model (57% sequence homology). This protease inhibitor, WCI, belongs to the Kunitz (STI) family and is a single polypeptide chain with 183 amino-acid residues having a molecular weight of 20 244 Da. Structure refinement with RESTRAIN and X-PLOR has led to a crystallographic R factor of 19.1% for 3469 observed reflections (I > 2sigma) in the resolution range 8-2.95 A. A total of 56 water molecules have been incorporated in the refined model containing 181 amino-acid residues. In the refined structure the deviations of bond lengths and bond angles from ideal values are 0.015 A and 2.2 degrees, respectively. The inhibitor molecule is spherical and consists of 12 antiparallel beta-strands with connecting loops arranged in a characteristic folding (a six-stranded beta-barrel and a six-stranded lid on one hollow end of the barrel) common to other homologous serine protease inhibitors in the Kunitz (STI) family as well as to some non-homologous proteins like interleukin-lalpha and interleukin-lbeta. In the structure the conformation of the protruding reactive-site loop is stabilized through hydrogen bonds mainly formed by the side chain of Asnl4, which intrudes inside the cavity of the reactive-site loop, with the side-chain and main-chain atoms of some residues in the loop region. A pseudo threefold axis exists parallel to the barrel axis of the structure. Each of the three subdomains comprises of four beta-strands with connecting loops.

Crystal Structure of S-Adenosylmethionine Synthetase

Crystal Structure of S-Adenosylmethionine Synthetase

Role of defects during amorphization and relaxation processes in Si

We have investigated the roles of defects for ion-beam-induced amorphization of crystalline Si (c-Si) and structural relaxation of amorphous Si (a-Si). A possible elementary process of amorphization in ion implanted Si has been described using molecular dynamics simulations, in which a divacancy and di-interstitial pair introduced in the c-Si lattice give rise to a local atomic arrangement including five- and seven-member rings. From Raman spectroscopy and positron lifetime measurements, bond angle deviation Δθ and sizes of vacancy-type defects were estimated for ion-beam-induced a-Si (IBa-Si), electron-beam evaporated a-Si (EBa-Si) and ECR plasma CVD a-Si (ECRa-Si). During 450°C annealing, Δθ decreased appreciably and small vacancies were predominant in IB and EBa-Si, while in ECRa-Si large vacancy clusters were formed and Δθ was approximately constant indicating that relaxation processes are suppressed in ECRa-Si. These results suggest that large vacancy-type defects can stabilize amorphous structures.

Raman study of the network disorder in sputtered and glow discharge a-Si:H films

We have carried out a comprehensive study of the Raman spectra of a-Si:H films produced by the glow discharge (GD) and radio frequency sputtering (RFS) deposition techniques. The results show that the short-range disorder (bond-angle deviation), as measured by the width of the TO band (ΓTO), is larger in RFS than in GD a-Si:H films. The intermediate-range disorder (dihedral angle deviation), as measured by the ratio of the intensity of the TA band to that of the TO band (ITA/ITO), is generally larger in RFS than in GD a-Si:H films. However, while the ITA/ITO values of RFS films remain relatively close to those of GD films when the interior is probed, the near surface of RFS films shows much larger values evidencing the existence of a significant disorder gradient along the growth axis. Together, these results indicate that the network order and homogeneity of RFS amorphous silicon is lower than those of GD for substrate temperatures that produce the hydrogenated material. These structural differences are interpreted in terms of the differences between the two film growth processes and are believed to be the reason for the poorer transport properties of RFS a-Si:H films.

Raman Spectroscopy and Positron Lifetime Studies of Structural Relaxation and Defect Evolution in Amorphous Silicon

Correlations between structural relaxation and defect evolution in amorphous silicon (a-Si) and hydrogenated amorphous silicon (a-Si:H) have been investigated by Raman scattering spectroscopy and positron lifetime measurements. Various a-Si films were prepared by ion implantation, evaporation, and electron-cyclotron resonance plasma-enhanced chemical vapor deposition (ECR CVD). The bond angle deviation, Δθ, of nonhydrogenated a-Si decreased during 450° C isothermal annealing, while Δθ of a-Si:H increased due to dehydrogenation. Ion implanted a-Si contained only small vacancies of which size was the same as that of the divacancy in crystalline Si, which were dissociated and annihilated during annealing. On the other hand, both evaporated a-Si and ECR CVD a-Si:H contained larger vacancies, and nanometer-size vacancy clusters were formed during the annealing processes, more significantly in ECR CVD a-Si:H. Based on these experimental results, we concluded that large vacancies tend to form vacancy clusters or microvoids which suppress structural relaxation in a-Si.

Crystal Structure of Abrin-a at 2.14 Å

The crystal structure of abrin-a, a type II ribosome-inactivating protein from the seeds of Abrus precatorius, has been determined from a novel crystalline form by the molecular replacement method using the coordinates of ricin. The structure has been refined at 2.14 Å to a R-factor of 18.9%. The root-mean-square deviations of bond lengths and angles from the standard values are 0.013 Å and 1.82 °, respectively. The overall protein folding is similar to that of ricin, but there are differences in the secondary structure, mostly of the A-chain. Several parts of the molecular surface differ significantly; some of them are quite near the active site cleft, and probably influence ribosome recognition. The positions of invariant active site residues remain the same, except the positions of invariant active site residues remain the same, except the position of Tyr74. Two water molecules of hydrogen-bonded active site residues have been located in the active site cleft. Both of them may be responsible for hydrolyzing the N-C glycosidic bond. The current abrin-a structure is lactose free; this is probably essential for abrin-a crystallization. The B-chain is a glycoprotein, and the positions of several sugar residues of two sugar chains linked to earlier predicted glycosylation sites were determined. One of the sugar chains is a bridge between two neighbouring molecules, since one of its mannose residues is connected to the galactose binding site of the neighboring molecule. Another sugar chain covers the surface of the B-chain. f2 f2 Present address: Tahir H. Tahirov, Department of Life Science, Faculty of Science, Himeji Institute of Technology, Kanaji 1479-1, Kamigori, Ako-gun, Hyogo 678-12, Japan; on leave from Institute of Inorganic and Physical Chemistry, Academy of Science of Azerbaijan, Azizbekov avenue 29, Baku 370143, Azerbaijan. Abbreviations used: SA, simulated annealing; PC, Patterson correlation; RIPs, ribosome inactivating proteins; PAP, pokeweed antiviral protein; NADPH, nicotinamide adenine dinucleotide phosphate; r.m.s.d., root-mean-square deviation.

Structural Studies on Corn Nitrate Reductase: Refined Structure of the CytochromebReductase Fragment at 2.5 Å, its ADP Complex and an Active-site Mutant and Modeling of the CytochromebDomain

The refined crystal structures of the recombinant cytochromebreductase fragment of corn (Zea mays) nitrate reductase, its ADP complex and the active-site mutant Cys242Ser are reported here. The native structure has been refined at 2.5 Å resolution to a crystallographicR-factor of 18.7% with root-mean-square (r.m.s.) deviations from standard bond lengths and angles of 0.013 Å and 2.0°. The diffraction pattern of the crystals is highly anisotropic and correction of this effect lowered the crystallographicR-factor by 5% during the refinement. The structure of the enzyme co-crystallized with ADP has been solved at 2.7 Å resolution and refined to anR-factor of 18.6% with r.m.s. deviations from standard bond lengths and angles of 0.014 Å and 2.1°. It revealed the binding site of the ADP moiety of the NADH cofactor, which is the electron donor for nitrate reduction. Based on this structure, a model of NADH at the active site of the enzyme was built and the implications for electron transfer from NADH to the flavin cofactor are discussed. The crystal structure of an active-site mutant enzyme, Cys242Ser, has been solved by difference Fourier synthesis and refined to anR-factor of 19.0% to 3.0 Å resolution with standard deviations of bond lengths and angles of 0.017 Å and 2.5°. This structure analysis suggests that the observed decrease in catalytic activity of this mutant might be due to misalignment of the nicotinamide ring in its binding site. A model of the heme-containing domain of nitrate reductase has been built based on the X-ray structure of bovine cytochromeb5and has been docked with the cytochromebreductase fragment of nitrate reductase. The model of the complex contains six salt-bridges at the domain-domain interface and a hydrophobic core. In this model, His48, an invariant residue in the cytochromebreductase family, forms an interaction with the propionic acid group of the D-ring of the heme cofactor. This group is in contact with the C-8 methyl group of the flavin ring. Residues that might influence the redox potential of the flavin cofactor are proposed and their possible role in electron transfer is discussed.

Correlation Between Phototransport and Network Order in a-Si:H

ABSTRACTHydrogenated amorphous silicon (a-Si:H) films prepared by the glow discharge (GD) technique show superior optoelectronic properties over those prepared by rf sputtering (RFS). To find out whether this is associated to structural differences in the amorphous network, we have carried out a comprehensive comparison of the Raman spectra of the two types of films grown at different substrate temperatures. The use of two properly chosen excitation radiations allowed the observation of the Raman spectra from the near surface versus that from the bulk of the films. The results show that the short-range order in the bulk of GD films is close to that of the ideal tetrahedral network, having an rms bond angle deviation (Δθ) of ≈9°. In contrast, the smallest value of Δθfound in the RFS films was ≈15°. There is also a short-range order inhomogeneity in both sets of materials that can be reduced significantly by selecting the appropriate substrate temperature. The intermediate-range disorder is relatively small and uniform in GD films, while large differences exist in this parameter between the surface and bulk of RFS films. In general, the results indicate that the short-range order and the inhomogeneity in intermediate-range order present in the RFS films cannot be improved to equal those of GD materials by annealing at temperatures low enough that no substantial hydrogen effusion occurs. These structural differences are argued to be the reasons for the superior phototransport properties of GD over RFS materials and are interpreted in terms of the differences between the two deposition processes.