Bond-length distributions for ions bonded to oxygen: metalloids and post-transition metals.
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ABSTRACT:
SUBMITTER: Gagne OC
PROVIDER: S-EPMC5798398 | biostudies-other | 2018 Feb
REPOSITORIES: biostudies-other
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Project description:Bond-length distributions have been examined for 55 configurations of alkali-metal ions and 29 configurations of alkaline-earth-metal ions bonded to oxygen, for 4859 coordination polyhedra and 38?594 bond distances (alkali metals), and for 3038 coordination polyhedra and 24?487 bond distances (alkaline-earth metals). Bond lengths generally show a positively skewed Gaussian distribution that originates from the variation in Born repulsion and Coulomb attraction as a function of interatomic distance. The skewness and kurtosis of these distributions generally decrease with increasing coordination number of the central cation, a result of decreasing Born repulsion with increasing coordination number. We confirm the following minimum coordination numbers: ([3])Li(+), ([3])Na(+), ([4])K(+), ([4])Rb(+), ([6])Cs(+), ([3])Be(2+), ([4])Mg(2+), ([6])Ca(2+), ([6])Sr(2+) and ([6])Ba(2+), but note that some reported examples are the result of extensive dynamic and/or positional short-range disorder and are not ordered arrangements. Some distributions of bond lengths are distinctly multi-modal. This is commonly due to the occurrence of large numbers of structure refinements of a particular structure type in which a particular cation is always present, leading to an over-representation of a specific range of bond lengths. Outliers in the distributions of mean bond lengths are often associated with anomalous values of atomic displacement of the constituent cations and/or anions. For a sample of ([6])Na(+), the ratio Ueq(Na)/Ueq(bonded anions) is partially correlated with ?([6])Na(+)-O(2-)? (R(2) = 0.57), suggesting that the mean bond length is correlated with vibrational/displacement characteristics of the constituent ions for a fixed coordination number. Mean bond lengths also show a weak correlation with bond-length distortion from the mean value in general, although some coordination numbers show the widest variation in mean bond length for zero distortion, e.g. Li(+) in [4]- and [6]-coordination, Na(+) in [4]- and [6]-coordination. For alkali-metal and alkaline-earth-metal ions, there is a positive correlation between cation coordination number and the grand mean incident bond-valence sum at the central cation, the values varying from 0.84?v.u. for ([5])K(+) to 1.06?v.u. for ([8])Li(+), and from 1.76?v.u. for ([7])Ba(2+) to 2.10?v.u. for ([12])Sr(2+). Bond-valence arguments suggest coordination numbers higher than [12] for K(+), Rb(+), Cs(+) and Ba(2+).
| S-EPMC4971548 | biostudies-literature
Project description:Bond-length distributions are examined for 63 transition metal ions bonded to O2- in 147 configurations, for 7522 coordination polyhedra and 41?488 bond distances, providing baseline statistical knowledge of bond lengths for transition metals bonded to O2-. A priori bond valences are calculated for 140 crystal structures containing 266 coordination polyhedra for 85 transition metal ion configurations with anomalous bond-length distributions. Two new indices, ?topol and ?cryst, are proposed to quantify bond-length variation arising from bond-topological and crystallographic effects in extended solids. Bond-topological mechanisms of bond-length variation are (1) non-local bond-topological asymmetry and (2) multiple-bond formation; crystallographic mechanisms are (3) electronic effects (with an inherent focus on coupled electronic vibrational degeneracy in this work) and (4) crystal-structure effects. The indices ?topol and ?cryst allow one to determine the primary cause(s) of bond-length variation for individual coordination polyhedra and ion configurations, quantify the distorting power of cations via electronic effects (by subtracting the bond-topological contribution to bond-length variation), set expectation limits regarding the extent to which functional properties linked to bond-length variation may be optimized in a given crystal structure (and inform how optimization may be achieved) and more. These indices further provide an equal footing for comparing bond-length variation and the distorting power of ions across ligand types, including resolution for heteroligand polyhedra. The observation of multiple bonds is found to be primarily driven by the bond-topological requirements of crystal structures in solids. However, sometimes multiple bonds are observed to form as a result of electronic effects (e.g. the pseudo Jahn-Teller effect, PJTE); resolution of the origins of multiple-bond formation follows calculation of the ?topol and ?cryst indices on a structure-by-structure basis. Non-local bond-topological asymmetry is the most common cause of bond-length variation in transition metal oxides and oxysalts, followed closely by the PJTE. Non-local bond-topological asymmetry is further suggested to be the most widespread cause of bond-length variation in the solid state, with no a priori limitations with regard to ion identity. Overall, bond-length variations resulting from the PJTE are slightly larger than those resulting from non-local bond-topological asymmetry, comparable with those resulting from the strong JTE, and less than those induced by ?-bond formation. From a comparison of a priori and observed bond valences for ?150 coordination polyhedra in which the strong JTE or the PJTE is the main reason underlying bond-length variation, the JTE is found not to have a cooperative relation with the bond-topological requirements of crystal structures. The magnitude of bond-length variation caused by the PJTE decreases in the following order for octahedrally coordinated d 0 transition metal oxyanions: Os8+ > Mo6+ > W6+ >> V5+ > Nb5+ > Ti4+ > Ta5+ > Hf4+ > Zr4+ > Re7+ >> Y3+ > Sc3+. Such ranking varies by coordination number; for [4] it is Re7+ > Ti4+ > V5+ > W6+ > Mo6+ > Cr6+ > Os8+ >> Mn7+; for [5] it is Os8+ > Re7+ > Mo6+ > Ti4+ > W6+ > V5+ > Nb5+. It is concluded that non-octahedral coordinations of d 0 ion configurations are likely to occur with bond-length variations that are similar in magnitude to their octahedral counterparts. However, smaller bond-length variations are expected from the PJTE for non-d 0 transition metal oxyanions.
| S-EPMC7340253 | biostudies-literature
Project description:Variations in mean bond length are examined in oxide and oxysalt crystals for 55 cation configurations bonded to O. Stepwise multiple regression analysis shows that mean bond length is correlated to bond-length distortion in 42 ion configurations at the 95% confidence level, with a mean coefficient of determination (? ?) of 0.35. Previously published correlations between mean bond length and mean coordination number of the bonded anions are found not to be of general applicability to inorganic oxide and oxysalt structures. For two of 11 ions tested for the 95% confidence level, mean bond lengths predicted using a fixed radius for O are significantly more accurate as those predicted using an O radius dependent on coordination number, and are statistically identical otherwise. As a result, the currently accepted ionic radii for O in different coordinations are not justified by experimental data. Previously reported correlation between mean bond length and the mean electronegativity of the cations bonded to the oxygen atoms of the coordination polyhedron is shown to be statistically insignificant; similar results are obtained with regard to ionization energy. It is shown that bond lengths calculated for many ion configurations in a single structure-type leads to a high correlation between and observed mean bond lengths, but bond lengths calculated for a single ion configuration in many different structure-types leads to negligible correlation between and observed mean bond lengths. This indicates that structure type has a major effect on mean bond length, the magnitude of which goes beyond that of the other variables analyzed here.
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Project description:Bond-length distributions are examined for three configurations of the H ion, 16 configurations of the group 14–16 non-metal ions and seven configurations of the group 17 ions bonded to oxygen, for 223 coordination polyhedra and 452 bond distances for the H ion, 5957 coordination polyhedra and 22 784 bond distances for the group 14–16 non-metal ions, and 248 coordination polyhedra and 1394 bond distances for the group 17 non-metal ions. H⋯O and O—H + H⋯O distances correlate with O⋯O distance ( = 0.94 and 0.96): H⋯O = 1.273 × O⋯O – 1.717 Å; O—H + H⋯O = 1.068 × O⋯O – 0.170 Å. These equations may be used to locate the hydrogen atom more accurately in a structure refined by X-ray diffraction. For non-metal elements that occur with lone-pair electrons, the most observed state between the +2 oxidation state is that of highest oxidation state for period 3 cations, and lowest oxidation state for period 4 and 5 cations when bonded to O. Observed O——O bond angles indicate that the period 3 non-metal ions P, S, Cl and Cl are lone-pair seteroactive when bonded to O, even though they do not form secondary bonds. There is no strong correlation between the degree of lone-pair stereoactivity and coordination number when including secondary bonds. There is no correlation between lone-pair stereoactivity and bond-valence sum at the central cation. In synthetic compounds, PO polymerizes one or two bridging oxygen atoms, but not by three. Partitioning our PO dataset shows that multi-modality in the distribution of bond lengths is caused by the different bond-valence constraints that arise for O = 0, 1 and 2. For strongly bonded cations, oxyanions, the most probable cause of mean bond length variation is the effect of structure type, stress induced by the inability of a structure to follow its bond lengths. For ions with stereoactive lone-pair electrons, the most probable cause of variation is bond-length distortion.
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Project description:Disulfide bonds are a post-translational modification (PTM) that can be scrambled or shuffled to non-native bonds during recombinant expression, sample handling, or sample purification. Currently, mapping of disulfide bonds is not easy because of various sample requirements and data analysis difficulties. One step towards facilitating this difficult work is developing a better understanding of how disulfide-bonded peptides fragment during collision induced dissociation (CID). Most automated analysis algorithms function based on the assumption that the preponderance of product ions observed during the dissociation of disulfide-bonded peptides result from the cleavage of just one peptide bond, and in this report we tested that assumption by extensively analyzing the product ions generated when several disulfide-bonded peptides are subjected to CID on a quadrupole time of flight (QTOF) instrument. We found that one of the most common types of product ions generated resulted from two peptide bond cleavages, or a double cleavage. We found that for several of the disulfide-bonded peptides analyzed, the number of double cleavage product ions outnumbered those of single cleavages. The influence of charge state and precursor ion size was investigated, to determine if those parameters dictated the amount of double cleavage product ions formed. It was found in this sample set that no strong correlation existed between the charge state or peptide size and the portion of product ions assigned as double cleavages. These data show that these ions could account for many of the product ions detected in CID data of disulfide bonded peptides. We also showed the utility of double cleavage product ions on a peptide with multiple cysteines present. Double cleavage products were able to fully characterize the bonding pattern of each cysteine where typical single b/y cleavage products could not.
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Project description:Accurate gene prediction in eukaryotes is a difficult and subtle problem. Here we point out a useful feature of expected distributions of spliceosomal intron lengths. Since introns are removed from transcripts prior to translation, intron lengths are not expected to respect coding frame, thus the number of genomic introns that are a multiple of three bases ('3n introns') should be similar to the number that are a multiple of three plus one bases (or plus two bases). Skewed predicted intron length distributions thus suggest systematic errors in intron prediction. For instance, a genome-wide excess of 3n introns suggests that many internal exonic sequences have been incorrectly called introns, whereas a deficit of 3n introns suggests that many 3n introns that lack stop codons have been mistaken for exonic sequence. A survey of genomic annotations for 29 diverse eukaryotic species showed that skew in intron length distributions is a common problem. We discuss several examples of skews in genome-wide intron length distributions that indicate systematic problems with gene prediction. We suggest that evaluation of length distributions of predicted introns is a fast and simple method for detecting a variety of possible systematic biases in gene prediction or even problems with genome assemblies, and discuss ways in which these insights could be incorporated into genome annotation protocols.
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Project description:An increasing demand for esthetic restorations has resulted in an increased use of all-ceramic restorations, such as zirconium. However, one of the challenges the orthodontist must be willing to face is how to increase bond strength between the brackets and various ceramic restorations.Bond strength can beaffected bybracket type, by the material that bracketsaremade of, and their base surface design or retention mode. : Aim: of this study was to perform a comparative analysis of the shear bond strength (SBS) of metallic and ceramic orthodontic brackets bonded to all-zirconium ceramic surfaces used for prosthetic restorations, and also to evaluate the fracture mode of these two types of orthodontic brackets.Twenty samples/semi-crowns of all-zirconium ceramic, on which orthodontic brackets were bonded, 10 metallic and 10 ceramic polycrystalline brackets, were prepared for this research. SBS has been testedby Universal Testing Machine, with a load applied using a knife edged rod moving at a fixed rate of 1 mm/min, until failure occurred. The force required to debond the brackets was recorded in Newton, then SBS was calculated to MPa. In addition, the samples were analyzed using a digital camera magnifier to determine Adhesive Remnant Index (ARI). Statistical data were processed using t-test, and the level of significance was set at α = 0.05.Higher shear bond strength values were observed in metallic brackets bonded to zirconium crowns compared tothoseof ceramic brackets, with a significant difference. During the test, two of the ceramic brackets were partially or totally damaged.Metallic brackets, compared to ceramic polycrystalline brackets, seemed tocreate stronger adhesion with all-zirconium surfaces due to their better retention mode. Also, ceramic brackets showed higher fragility during debonding.
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