Determination Of Bond Lengths Research Articles

Determination of bond length and some crystal structures of compounds containing the dioxygenyl cation [O2]+

Determination of bond length and some crystal structures of compounds containing the dioxygenyl cation [O₂]⁺

High-energy molecular-frame photoelectron angular distributions: a molecular bond-length ruler.

We present a study on molecular-frame photoelectron angular distributions (MFPADs) of small molecules using circularly polarized synchrotron light. We find that the main forward-scattering peaks of the MFPADs are slightly tilted with respect to the molecular axis. This tilt angle is directly connected to the molecular bond length by a simple, universal formula. We apply the derived formula to several examples of MFPADs of C 1s and O 1s photoelectrons of CO, which have been measured experimentally or obtained by means of ab initio modeling. In addition, we discuss the influence of the back-scattering contribution that is superimposed over the analyzed forward-scattering peak in the case of homo-nuclear diatomic molecules such as N2.

A universal solution of the bond behaviour between CFRP-steel double strap joints considering steel yielding

Steel structures strengthened with CFRP (carbon fiber-reinforced polymer) composite may encounter extreme load such as earthquake or impact which may cause steel yielding and plasticity. But very limited investigations exist on the effect of steel yielding on the bond behaviour between CFRP and steel. This paper presents a comprehensive study on the effect of steel yielding on the bond behaviour of CFRP-steel double strap joints. Firstly, a stress-based analytical model is established for the analysis of the ultimate load and failure initiation position of the double strap joints. This is a universal model which is able to analyse elastic joint as well as plastic joint with steel yielding. Then a series of tensile tests with double strap joints is carried out and the experimental results are used to validate the proposed analytical model. Finally, a parametric analysis is performed using the analytical model and an additional numerical method in which the debonding between steel and CFRP strips is simulated by a cohesive approach. The parametric analysis considers both geometrical and material variables. It can be concluded that the steel yielding has a significant effect on the bond behaviour of CFRP-steel double strap joints, including ultimate load, stress and strain distributions of CFRP, steel and adhesive, and debonding initiation position of the joint. Based on the experimental and analytical results, criteria are proposed for the determination of effective bond length and yielding bond length, debonding initiation position and ultimate load of CFRP-steel joints.

Equilibrium Structure in the Presence of Methyl Internal Rotation: Microwave Spectroscopy and Quantum Chemistry Study of the Two Conformers of 2-Acetylfuran.

For 2-acetylfuran, quantum chemistry predicted and proton magnetic resonance study reported two conformers, anti and syn, differing in the position of the carbonyl group with respect to the O1-C2 bond of the furan ring. The microwave spectrum of the title molecule was recorded in the frequency range from 2 to 26.5 GHz using a molecular jet Fourier transform microwave spectrometer, confirming the presence of both conformers. Spectroscopic parameters such as the rotational and centrifugal distortion constants could be determined with high precision. The spectra of all 13C- and 18O-isotopologues of the energetically more favorable anti-conformer could be assigned, allowing the experimental determination of bond lengths and bond angles from the heavy atom substitution rs and the semi-experimental equilibrium reSE structures. Splittings arising from the internal rotation of the acetyl methyl group could be resolved for both conformers as well as for all assigned isotopologues, from which the barrier to methyl internal rotation was determined. The torsional barrier is largely invariant at around 319 cm-1 in the parent species of anti-2-acetylfuran and its isotopologues, showing that though isotopic substitution greatly influences the rotational properties of the molecule and causes a different microwave spectrum, its effect on the methyl torsion is negligible. On the other hand, conformational effects play a decisive role, as the torsional barrier of 239.780(13) cm-1 found for syn-2-acetylfuran differs significantly from the value for anti-2-acetylfuran. The results are compared and discussed with other methyl-substituted furan derivatives and acetyl group containing ketones for a better understanding of different effects influencing molecular geometry parameters and methyl internal rotations.

Bond-length mapping without two-dimensional scanning by means of photoemission electron microscopy-extended X-ray absorption fine structure measurement

We develop a bond-length mapping technique without two-dimensional scanning by combining photoelectron emission microscopy with extended X-ray absorption fine structure (EXAFS) analysis. Several tens of thousands of EXAFS data are simultaneously acquired, which corresponds to a data acquisition time less than 1 second per spectrum. We apply this technique to an Fe/BaTiO3 thin film, and two-dimensional distribution of the Fe–Fe bond length at the Fe surface is observed. From the Fe K-edge EXAFS analysis, we find that the Fe–Fe bond length is ∼2.52 Å over the whole area with a Gaussian distribution of ∼0.01 Å, which implies that this technique realizes a bond-length mapping with precise bond-length determination.

Improved bond length determination technique for C3 and other linear molecules with a large amplitude bending vibration

A variety of standard techniques exist for estimating molecular bond lengths from spectroscopic data of the vibrational ground state. In typical order of increasing accuracy these different estimates are known as r0, rs, and rm. However, for the C3 molecule each of these spectroscopically determined values is very different from that obtained in a recent high-quality ab initio calculation. We ascribe this difference to the large-amplitude ν2 bending vibration of C3. By recognizing that vibrational averaging means that the molecule is effectively bent, even in the ground vibrational state, we develop a simple new method for estimating the bond length. This involves approximating the rotational parameter along the axis that becomes the molecular axis at linearity as A0=ν22. This value is then used in the evaluation of rm, rather than assuming the molecule is linear. We test this approximation for A0 and also show that the C–C bond length we obtain is in better agreement, by an order of magnitude, with the ab initio value than any of the standard linear approaches.

Bond Length Alternation Observed Experimentally: The Case of 1H-Indazole.

Bond length alternation is a chemical phenomenon in benzene rings fused to other rings, which has been mainly predicted theoretically. Its physical origin is still not clear and has generated discussion. Here, by using a strategy that combines microwave spectroscopy, custom-made synthesis and high-level ab initio calculations, we demonstrate that this phenomenon is clearly observed in the prototype indazole molecule isolated in the gas phase. The 1H-indazole conformer was detected by rotational spectroscopy, and its 17 isotopologues resulting from single and double heavy atom substitution (13 C and 15 N) were also unambiguously observed. Several experimental structures were determined and, in particular, the most useful semi-experimental equilibrium structure (re SE ), allowed determination of the heavy atom bond lengths to milli-Ångstrom precision. The experimentally determined bond length alternation is estimated to correspond to 60:40 contributions from the two resonant forms of 1H-indazole.

Determination of element-deuterium bond lengths in Zintl phase deuterides by 2H-NMR.

The Zintl phase deuterides CaSiD4/3, SrSiD5/3, BaSiD2, SrGeD4/3, BaGeD5/3 and BaSnD4/3 were investigated by nuclear magnetic resonance (NMR) spectroscopy and density functional theory (DFT) calculations to reliably determine element-deuterium bond lengths. These compounds show deuterium bound to the polyanion and deuteride ions in tetrahedral cationic voids. With 2H-NMR experiments we characterised the individual signals of the two distinct crystal sites. Quadrupolar coupling constants (CQ) of the anion-binding site were determined as 58 to 78 kHz (Si compounds), 51 to 61 kHz (Ge compounds) and 38 kHz (Sn compound). These values agree well with the quadrupole couplings derived from DFT using optimized structural models. We further calculated the general element-deuterium distance dependency of CQ using DFT methods that allow an accurate determination of bond lengths via the 2H quadrupole interaction. The thus determined bond lengths are evaluated as d(Si-D) = 1.53-1.59 Å, d(Ge-D) = 1.61-1.65 Å and d(Sn-D) = 1.86 Å. Chemical shifts of the anion-binding site range from 0.3 to 1.3 ppm. The isotropic chemical shifts of the tetrahedral sites are 5.1 ppm (CaSiD4/3), 7.0 to 10.0 ppm (Sr compounds) and 10.7 to 11.6 ppm (Ba compounds).

Quantitative assessment of intermolecular interactions by atomic force microscopy imaging using copper oxide tips.

Atomic force microscopy is an impressive tool with which to directly resolve the bonding structure of organic compounds1-5. The methodology usually involves chemical passivation of the probe-tip termination by attaching single molecules or atoms such as CO or Xe (refs 1,6-9). However, these probe particles are only weakly connected to the metallic apex, which results in considerable dynamic deflection. This probe particle deflection leads to pronounced image distortions, systematic overestimation of bond lengths, and in some cases even spurious bond-like contrast features, thus inhibiting reliable data interpretation8-12. Recently, an alternative approach to tip passivation has been used in which slightly indenting a tip into oxidized copper substrates and subsequent contrast analysis allows for the verification of an oxygen-terminated Cu tip13-15. Here we show that, due to the covalently bound configuration of the terminal oxygen atom, this copper oxide tip (CuOx tip) has a high structural stability, allowing not only a quantitative determination of individual bond lengths and access to bond order effects, but also reliable intermolecular bond characterization. In particular, by removing the previous limitations of flexible probe particles, we are able to provide conclusive experimental evidence for an unusual intermolecular N-Au-N three-centre bond. Furthermore, we demonstrate that CuOx tips allow the characterization of the strength and configuration of individual hydrogen bonds within a molecular assembly.

Coordination compounds containing bis-di-thiol-ene-chelated molybdenum(IV) and oxalate: comparison of terminal with bridging oxalate.

Two coordination compounds containing tetra-n-butyl-ammonium cations and bis-tfd-chelated molybdenum(IV) [tfd2- = S2C2(CF3)22-] and oxalate (ox2-, C2O42-) in complex anions are reported, namely bis-(tetra-n-butyl-ammonium) bis-(1,1,1,4,4,4-hexa-fluoro-but-2-ene-2,3-di-thiol-ato)oxalatomolybdate(IV)-chloro-form-oxalic acid (1/1/1), (C16H36N)2[Mo(C4F6S2)2(C2O4)]·CHCl3·C2H2O4 or (N n Bu4)2[Mo(tfd)2(ox)]·CHCl3·C2H2O4, and bis-(tetra-n-butyl-ammonium) μ-oxalato-bis-[bis-(1,1,1,4,4,4-hexa-fluoro-but-2-ene-2,3-di-thiol-ato)molybdate(IV)], (C16H36N)2[Mo2(C4F6S2)4(C2O4)] or (N n Bu4)2[(tfd)2Mo(μ-ox)Mo(tfd)2]. They contain a terminal oxalate ligand in the first compound and a bridging oxalate ligand in the second compound. Anion 12- is [Mo(tfd)2(ox)]2- and anion 22-, formally generated by adding a Mo(tfd)2 fragment onto 12-, is [(tfd)2Mo(μ-ox)Mo(tfd)2]2-. The crystalline material containing 12- is (N n Bu4)2-1·CHCl3·oxH2, while the material containing 22- is (N n Bu4)2-2. Anion 22- lies across an inversion centre. The complex anions afford a rare opportunity to compare terminal oxalate with bridging oxalate, coordinated to the same metal fragment, here (tfd)2MoIV. C-O bond-length alternation is observed for the terminal oxalate ligand in 12-: the difference between the C-O bond length involving the metal-coordinating O atom and the C-O bond length involving the uncoordinating O atom is 0.044 (12) Å. This bond-length alternation is significant but is smaller than the bond-length alternation observed for oxalic acid in the co-crystallized oxalic acid in (N n Bu4)2-1·CHCl3·oxH2, where a difference (for C=O versus C-OH) of 0.117 (14) Å was observed. In the bridging oxalate ligand in 22-, the C-O bond lengths are equalized, within the error margin of one bond-length determination (0.006 Å). It is concluded that oxalic acid contains a localized π-system in its carb-oxy-lic acid groups, that the bridging oxalate ligand in 22- contains a delocalized π-system and that the terminal oxalate ligand in 12- contains an only partially localized π-system. In (N n Bu4)2-1·CHCl3·oxH2, the F atoms of two of the -CF3 groups in 12- are disordered over two sets of sites, as are the N and eight of the C atoms of one of the N n Bu4 cations. In (N n Bu4)2-2, the whole of the unique N n Bu4+ cation is disordered over two sets of sites. Also, in (N n Bu4)2-2, a region of disordered electron density was treated with the SQUEEZE routine in PLATON [Spek (2015 ▸). Acta Cryst. C71, 9-18].

Nuclear quadrupole coupling in SiH2I2 due to the presence of two iodine nuclei

The rotational spectrum of diiodosilane was measured with a jet-pulsed, cavity Fourier transform microwave (FTMW) spectrometer over the frequency range 8.8–15GHz and assigned for the first time. The complete nuclear quadrupole coupling (NQC) tensors for both iodine nuclei were obtained for the 28Si, 29Si, and 30Si isotopologues of diiodosilane. In addition to the nuclear quadrupole coupling constants (NQCCs), rotational constants, centrifugal distortion constants, and nuclear spin-rotation constants were determined for each silicon isotopologue. Subtle, yet unmistakable, changes in the NQCCs of iodine upon isotopic substitution were observed and will be discussed. A r0 structure of diiodosilane was also fit via isotopic substitution, which led to the determination of bond lengths and angles: r0(SiI)=2.4236(19)Å, r0(SiH)=1.475(21)Å, ∠(ISiI)=111.27(13)°, and ∠(ISiH)=105.9(19)°. These molecular parameters will be compared to the results of a previous gas electron diffraction study.

Study of XAFS of some Fe compounds and determination of first shell radial distance

X-ray absorption fine structure (XAFS) of some Fe compounds have been studied using the latest XAFS analysis software Demeter with Strawberry Perl. The processed XAFS data of the Fe compounds have been taken from available model compound library. The XAFS data have been processed to plot the µ(E) verses E spectra. These spectra have been converted into K-space, R-space and q-space. R-space spectra have been used to obtain first shell radial distance in Fe compounds. Structural parameters like first shell radial distance is useful in determination of bond length in Fe compounds. Hence the study play important role in biological applications.

Determination of bond lengths from extended X-ray absorption fine structure in cobalt(III)-oxo cubane-like clusters

The extended X-ray absorption fine structure (EXAFS) at the K-edge of cobalt has been studied in two cobalt complexes having Co(III)-oxo cubane-like clusters of the type Co4O4(O2CR)4L4 where R is CH3 and L is pyridine (py) in one of the complex and ammonia (NH3) in the other complex. The spectra have been recorded at BL-9 scanning EXAFS beamline at the 2.5-GeV INDUS-2 Synchrotron, RRCAT, Indore, India. The positions of EXAFS maxima and minima have been reported. Using this data, the bond length has been determined by simple bond determination methods, viz., Levy's, Lytle's and Lytle, Sayers and Stern's (LSS) methods. The normalized EXAFS spectra have been Fourier transformed and the value of the bond length has also been determined from the position of the first peak in the Fourier transform. This distance is the phase-uncorrected bond length. LSS method also gives such bond length. The results obtained from Fourier transform and LSS methods have been found to be comparable to each other. For the pyridine complex, the value obtained from Levy's method has been found to be in agreement with the available crystallographic value.

Studies of EXAFSSpectra using Copper (II) Schiff Base complexes and Determination of Bond lengths Using Synchrotron Radiation

X-ray absorption fine structure (XAFS) at the K-edge of copper has been studied in some copper (II) complexes with substituted anilines like (2Cl, 4Br, 2NO2, 4NO2 and pure aniline) with o-PDA (orthophenylenediamine) as ligand. The X-ray absorption measurements have been performed at the recently developed BL-8 dispersive EXAFS beam line at 2.5 GeV Indus-2 Synchrotron Source at RRCAT, Indore, India. The data obtained has been processed using EXAFS data analysis program Athena.The graphical method gives the useful information about bond length and also the environment of the absorbing atom. The theoretical bond lengths of the complexes were calculated by using interactive fitting of EXAFS using fast Fourier inverse transformation (IFEFFIT) method. This method is also called as Fourier transform method. The Lytle, Sayers and Stern method and Levy's method have been used for determination of bond lengths experimentally of the studied complexes. The results of both methods have been compared with theoretical IFEFFIT method.

NEXAFS Chemical State and Bond Lengths of p-Aminobenzoic Acid in Solution and Solid State

Solid-state and solution pH-dependent NEXAFS studies allow direct observation of the electronic state of para-aminobenzoic acid (PABA) as a function of its chemical environment, revealing the chemical state and bonding of the chemical species. Variations in the ionization potential (IP) and 1s→π* resonances unequivocally identify the chemical species (neutral, cationic, or anionic) present and the varying local environment. Shifts in σ* shape resonances relative to the IP in the NEXAFS spectra vary with C-N bond length, and the important effect of minor alterations in bond length is confirmed with nitrogen FEFF calculations, leading to the possibility of bond length determination in solution.

XAFS spectroscopy by an X-ray tube based spectrometer using a novel type of HOPG mosaic crystal and optimized image processing

This paper presents a XAFS laboratory spectrometer with optimized image treatment suitable for determination of bond lengths and chemical species.

Effective data collection and refinement of pertubated structures

Approaches to determining the influence of individual measurements on the precision of crystallographic least squares parameters have been known for a long while.[1] Situations in which the precision of a single parameter (or linear combination of parameters) is critical can include: determination of novel bond lengths; refinement of site occupancies in mixed metal or mixed oxidation state systems; determination of the fraction of excited state molecules in a time-resolved pump-probe experiment. Such calculations are easily applicable to point-detector instruments, where individual influential reflections could be remeasured one-by-one. However, on a modern area detector instrument many reflections are measured on one frame and therefore some consideration of the appropriate strategy of reciprocal space scans is permitted to allow a more efficient use of the instrument. The highly influential partial data collection is then feed into an appropriate refinement model. Occupancies in mixed-metal or mixed-oxidation state systems and fractions and positions of excited state molecules during a time-resolved pump-probe experiment can be determined using direct refinement of the perturbation of the structure from the ground state. Re-factoring to modern Fortran of the Crystals software is in progress to allow the implementation of new algorithms such as a difference refinement.[2] We present an analysis of diffractometer strategy selection to prioritize scans which give the best improvement in specific least-squares parameters and a novel algorithm for the refinement of the partial data using crystals.

Sample Corrugation Affects the Apparent Bond Lengths in Atomic Force Microscopy

Frequency modulation atomic force microscopy (AFM) allows the chemical structure of planar molecules to be determined with atomic resolution. Typically, these measurements are carried out in constant-height mode using carbon monoxide (CO) terminated tips. Such tips exhibit considerable flexibility, i.e., the CO molecule can bend laterally due to the tip-sample interaction. Using epitaxial graphene as a model system, we demonstrate experimentally that the apparent atomic positions measured by AFM depend on the sample corrugation. Using molecular mechanics simulations, we explain these observations by the interplay of the CO bending and the nonlinear background signal arising from the neighboring atoms. These effects depend nontrivially on the tip-sample distance and limit the achievable accuracy on the bond length determination based on AFM experiments.

Comparative analysis of the performance of commonly available density functionals in the determination of geometrical parameters for copper complexes

In this study, a set of 50 transition-metal complexes of Cu(I) and Cu(II), were used in the evaluation of 18 density functionals in geometry determination. In addition, 14 different basis sets were considered, including four commonly used Pople's all-electron basis sets; four basis sets including popular types of effective-core potentials: Los Alamos, Steven-Basch-Krauss, and Stuttgart-Dresden; and six triple-ζ basis sets. The results illustrate the performance of different methodological alternatives for the treatment of geometrical properties in relevant copper complexes, pointing out Double-Hybrid (DH) and Long-range Correction (LC) Generalized Gradient Approximation (GGA) methods as better descriptors of the geometry of the evaluated systems. These however, are associated with a computational cost several times higher than some of the other methods employed, such as the M06 functional, which has also demonstrated a comparable performance. Regarding the basis sets, 6-31+G(d) and 6-31+G(d,p) were the best performing approaches. In addition, the results show that the use of effective-core potentials has a limited impact, in terms of the accuracy in the determination of metal-ligand bond-lengths and angles in our dataset of copper complexes. Hence, these could become a good alternative for the geometrical description of these systems, particularly CEP-121G and SDD basis sets, if one is considering larger copper complexes where the computational cost could be an issue.

Using Pauling's Expanded Bond Order Concept in Determination of Bond Lengths in Polycyclic Aromatic Compounds Having Numerous Fixed Single and Double Bonds

An amended Pauling bond order equation based on the number of Kekulé ( K ) and Dewar (DS) resonance structures is prs = ( K [G – (ers )] + 0.03DS[G – (ers )])/( K [G] + 0.03DS[G]) which reliably predicts the bond order of conjugated hydrocarbons.