Values Of Bond Distances Research Articles

Strategy to Probe the Local Atomic Structure of Luminescent Rare Earth Complexes by X-ray Absorption Near-Edge Spectroscopy Simulation Using a Machine Learning-Based PyFitIt Approach

Rare earth(III) β-diketonates are highly remarkable luminophores in the visible spectral region among the rare earth compounds, owing to the efficient contribution from the 4f-4f intraconfigurational transitions. To get detailed structural insight into the RE3+ sites (RE = Eu, Gd, and Sm), X-ray absorption near-edge spectroscopy (XANES) can be very potent in probing the local chemical environment around the RE3+ ion. In this work, a PyFitIt machine learning approach was employed as a new strategy to simulate the Eu, Gd, and Sm L3-edge XANES and thereby determine the local atomic structure of the luminescence RE3+ β-diketonate complexes, [Eu(tta)3(H2O)2], [C4mim][Eu(dbm)4], [Gd(tta)3(H2O)2], and [Sm(dbm)3(phen)] (tta, 3-thenoyltrifluoroacetonate; dbm, dibenzoylmethane; phen, phenanthroline; and C4mim, 1-butyl-3-methylimidazolium bromide). Continuous Cauchy wavelet transform validated the PyFitIt calculated XANES by visualizing very efficiently the coordination geometries, composed of O and O/N backscatterers around the RE3+ (RE = Eu and Gd) and Sm3+ ions, respectively, as a pinkish-red color map in the two-dimensional images of the corresponding complexes. Extended X-ray absorption fine structure fit in Artemis also corroborated the three-dimensional structures generated by PyFitIt XANES simulation for all the compounds. Though, relatively slightly higher bond distance values for the Sm3+ complex are due to the higher atomic radius of the Sm3+ ion when compared to the Eu3+ and Gd3+ complexes. Meanwhile, higher Debye-Waller factor (σ2) values for the [C4mim][Eu(dbm)4] when compared to the [Eu(tta)3(H2O)2] indicated the structure disorder, owing to the distortion in the local geometry. It is noteworthy that the optical properties, described mainly by the Ωλ (λ = 2 and 4) 4f-4f intensity parameters, are very sensitive to the local coordination environment around the Eu3+ ion. Thus, a close agreement between the experimental and theoretically calculated Ωλ parameter values confirmed that the PyFitIt calculated square antiprismatic structures are precisely similar to the real structures of the Eu3+ complexes.

Fluorine Effects for Tunable C–C and C–S Bond Cleavage in Fluoro-Julia–Kocienski Intermediates

Classical Julia–Kocienski fluoroolefination represents an indispensable platform for the construction of monofluoroalkenes. Nevertheless, its complex multistep mechanistic manifold along with the u...

In-situ reductive degradation of chlorinated DNAPLs in contaminated groundwater using polyethyleneimine-modified zero-valent iron nanoparticles

Zero-valent iron nanoparticles (ZVIN) have found applications in many strategies for on-site soil and groundwater decontamination. A number of studies have reported the prospective utilization of ZVIN in the reduction of chlorinated organic compounds such as dense non-aqueous phase liquids (DNAPLs) in groundwater. Due to their bioaccumulation and carcinogenesis, DNAPLs in groundwater are a human health hazard and pose environmental risks. Therefore, decontamination of these contaminants is necessary. This study presents the in-situ remediation of trichloroethylene (TCE), perchloroethene (PCE), and 1,2-dichloroethene (1,2–DCE) DNAPLs through the direct injection of polyethylenimine (PEI)-coated ZVIN (PEI–ZVIN composite materials) to facilitate the reduction of contaminants in low-permeability media. A field test was conducted at the premises of a petrochemical company, situated in the Miaoli County of Northern Taiwan that discharged significant amounts of DNAPLs. After in-situ injection and one-day of reaction with groundwater contaminants, ZVIN was further characterized to examine its efficacy in the reduction of pollutants. After the direct injection of PEI–ZVIN, a notable reduction in the concentration of DNAPLs was recorded with conversion from toxic to non-toxic substances. Use of resistivity image profiling (RIP) technique suggested similar conductivity data for the PEI-coated ZVIN suspension and groundwater samples. X-ray absorption near edge structure (XANES) and X-ray absorption fine structure (EXAFS) studies depicted that the oxidation of ZVIN and PEI–ZVIN was occurring after the reductive reaction with contaminated groundwater. The reacted samples had bond distance values of 1.98, 2.00, 1.96, and 1.94 Å. Combining floating surface-coated ZVIN and RIP technique seems promising and environmentally attractive.

Degradation of TCE, PCE, and 1,2–DCE DNAPLs in contaminated groundwater using polyethylenimine-modified zero-valent iron nanoparticles

Remediation of dense non-aqueous phase liquid (DNAPL), which consists primarily of chlorinated solvents, is considered a top priority in the field of groundwater decontamination. Downward migration of DNAPL can lead to formation of impermeable strata due to low solubility and high density. Remediation is therefore one of the most complex technical challenges faced by environmental engineers. In the present work, remediation of trichloroethylene (TCE), perchloroethene (PCE), and 1,2-dichloroethene (1,2-DCE) DNAPL-contaminated groundwater was studied by a reductive reaction with polyethylenimine (PEI) surface-modified zero-valent iron nanoparticles (PEI–nZVI). Compared with fresh nZVI, PEI–nZVI exhibited smaller spherical particles of 20–80 nm and a greater surface area of 53.4 m2/g. Furthermore, slow desorption of the PEI indicated its potential application as a protective shell layer for efficient delivery of active nZVI to the water/DNAPL interface. Laboratory batch remediation results indicate that both nZVI and PEI–nZVI can remove 99% of TCE, PCE, and 1,2-DCE. The rate of reaction for fresh nZVI was higher in the early stage. Comparatively, PEI–nZVI had a higher removal rate and efficiency after 2 h. The kinetic studies also revealed that the removal rate for 1,2-DCE was greater than that for TCE and PCE. Additionally, X-ray absorption near edge structure (XANES) and extended X-ray absorption fine structure (EXAFS) spectroscopy studies indicated that the nZVI and PEI–nZVI have two central Fe atoms coordinated by primarily FeO and FeFe with bond distances of 1.87 Å and 3.05 Å, respectively. Furthermore, after the reductive reaction, nZVI and PEI–nZVI were oxidized to Fe3O4, and bond distance values for the reacted samples were 1.94 Å and 1.96 Å, respectively.

Molecular conformational structures of 2-fluorobenzoyl chloride, 2-chlorobenzoyl chloride, and 2-bromobenzoyl chloride by gas electron diffraction and normal coordinate analysis aided by quantum chemical calculations

The gas phase molecular structures and conformational compositions of 2-fluorobenzoyl chloride, 2-chlorobenzoyl chloride, and 2-bromobenzoyl chloride have been investigated using gas electron diffraction data obtained from experiments performed in the laboratories of the University of Oslo and Oregon State University. The refinements on the experimental data have been aided by normal coordinate calculations as well as extensive ab initio molecular orbital and density functional theory calculations up to the levels of MP4(SDQ) and B3LYP with larger basis sets up to the level of 6-311 + G(2d,p) for the computed molecular geometries, electronic energies, vibrational zero-point energies and entropy corrections, gas mixture conformational compositions, and MP2(fc) quantum mechanical force fields. The three title molecules each exist in the gas phase as two stable non-planar conformers anti and gauche with respect to the halogen atom positions with anti the lower energy conformer in each case. Among the three title molecules there have been found considerable experimental and theoretical support for several trends in molecular or conformational behavior with increasing ortho halogen atomic size: An increasing although disputable trend in the C=O bond distance values; an increasing trend in the average phenyl ring C–C bond distance values; an increasing trend in the contribution of the gauche conformer to the gaseous mixture lowering the standard free energy difference values (ΔG o) correspondingly; and an increasing deviation from full planarity (C s symmetry) in both the anti and the gauche conformers of the title molecules with increasing ortho halogen atomic size. Only in the anti conformer of 2-fluorobenzoyl chloride does the experimental data refinements suggest close to full planarity for these 2-halobenzoyl chloride molecules.

The most stable tautomer of 3-amino-1,2,4-triazin-5-one and its structural geometry

With the purpose of finding predominant tautomer among five possible isomers of 3-amino-1,2,4-triazin-5-one and to refine some unreasonable structural parameters previously reported from X-ray diffraction measurements, a series of ab initio calculations were carried out. In agreement with previous results, our calculations show that 3-amino-1,2,4-triazin-5(2H)-one tautomer is the most stable one. Concerning the predominant tautomer, comparisons were made between structural parameters calculated and those obtained by X-ray crystallographic analysis. The structural geometry of the main skeleton of the molecule calculated by the B3LYP/6-311++G** density functional method are generally in good agreement with the experimental values, and those predicted by Pauling's method. Bond distance values calculated are in excellent agreement with the conventionally accepted bond lengths in similar molecules. All bond distances, bond angles, dihedral angles, dipole moments and rotational constants are presented.

Chemical reasonableness in Rietveld analysis; organics

We know a lot about normal values of bond distances, bond angles, torsion angles, and other molecular parameters. This knowledge can be incorporated into the structure solution process and into Rietveld refinement through the use of restraints and rigid bodies. An important measure of the quality of the refined model is the chemical reasonableness of molecular geometry. Refinement of the structures of calcium tartrate tetrahydrate and guaifenesin is used to illustrate the importance of chemical reasonableness in determining the quality of a Rietveld refinement.

The performance of the new 6‐31G## basis set: Molecular structures and vibrational frequencies of transition metal carbonyls

The performance of the newly proposed 6-31G(##) basis set for calculating the equilibrium structure and vibrational frequencies of transition metal carbonyl complexes has been studied at the HF and DFT levels of theory. The 6-31G(##) basis set has been constructed by augmentation of the 6-31G basis set by diffuse and polarization functions, which are generated from the corresponding 6-31G basis AOs response functions obtained in the frame of propagator approach. The predicted values of bond distances and vibrational frequencies for the title compounds are in good agreement with the experimental data. The relative energies and HOMO-LUMO gaps were also estimated for the series of MCO complexes.

Molecular structure in non-Born–Oppenheimer quantum mechanics

We present the first fully non-Born–Oppenheimer (BO) calculations of the wave function of a molecule with more than two atoms: H 3 + and its isotopomers. We also calculate expectation values of the internuclear distances (i.e., the molecular geometry). Since the operators representing the internuclear distances do not commute with the internal non-BO Hamiltonian, the only information that can be acquired from the wave function are the average values of bond distances and for each subset of identical nuclei in the system only one unique interparticle distance can be determined.

Quantum chemical study of the lanthanide bond length contraction on Ln3+-doped Cs2NaYCl6 crystals (Ln=Ce to Lu)

The lanthanide–chlorine bond length, Re, and the frequency of the symmetric stretching mode, ν̄a1g, of the (LnCl6)3− octahedral defect clusters embedded in Cs2NaYCl6 have been calculated for all 14 Ce3+ to Lu3+ impurities in their ground 4fn electronic state using wave-function-based ab initio methods of solid state quantum chemistry which include relativistic effects and electron correlation within the (LnCl6)3− defect clusters and quantum mechanical interactions between the (LnCl6)3− electronic group and the Cs2NaYCl6 embedding host ions. The bond distance values obtained provide useful data to improve the Judd–Morrison model of the 4f→5d energy separation by explicitly including the local distortions the Ln3+ ions produce in the Cs2NaYCl6 host. The values of the structural parameters Re and ν̄a1g, and their variation across the series have also been studied using simpler models of the embedding host (in vacuo and Madelung embeddings), which has revealed that host effects, particularly those associated with quantum mechanical interactions, strengthen the Ln–Cl bond (decreasing the bond distances and increasing the frequencies of the symmetric bond stretch) and are smaller towards the right end of the series. Electron correlation within the (LnCl6)3− clusters also reduces the bond distance values, but this reduction increases going right from Ce to Lu; its effects on the frequencies of the symmetric stretching mode are negligible. The comparison of the theoretical results with the few available experiments is very satisfactory.

Evolution of local electronic and atomic structure of Co-doped LiMn2O4 cathode material for lithium rechargeable batteries

In situ X-ray absorption spectroscopy (XAS) techniques are performed to investigate the evolution of the local electronic and atomic structure of a spinel cathode material LiCo 0.2 Mn 1.8 O 4 in the 4 V range. Changes in the oxidation state, bond distance, and local disorder of Mn and Co absorbers in the Co-doped LiMn 2 O 4 are measured as a function of potentials. The X-ray absorption near edge spectra shows that charging (Li deintercalation) leads to the oxidation of manganese to Mn 4+ . On the other hand, Co atoms are also oxidized but the edge energy shift is small, which suggests that Co is also electroactive in LiCo 0.2 Mn 1.8 O 4 in the 4 V range. The change in the Debye–Waller factor of the Co–O shell is smaller than that of Mn–O shell. Furthermore, from Debye–Waller factor and bond distance values, it appears that the Co environment fluctuates markedly during discharging.

Synthesis, characterization and X-ray structures of the new dinucleating ligand 2,8-dimethyl-1,4,5,6,7,10,11,12-octahydroimidazo[4,5-h] imidazo[4,5-c][1,6]diazecine-5,11-diethanoic acid and its Cu(II) complex; an alternating chain of Cu(II) ions, coupled both intramolecularly and intermolecularly

The design and synthesis of a new, rigid dinucleating ligand 2,8-dimethyl-1,4,5,6,7,10,11,12-octahydroimidazo[4,5-h] imidazo[4,5-c][1,6]diazecine-5,11-diethanoic acid (H2glymeim) is reported together with its molecular and crystal structure. The rigid ligand structure is confirmed by the structure and magnetic properties of its bis Cu(II) complex, [Cu2(C16H22N6O6)(H2O)4](ClO4)2(H2O)2, (Cu2glymeim). Crystals of free glymeim are composed of units of C16H22N6O4 and eight water molecules linked by a two dimensional network of hydrogen bonds. Six of them contribute to a one-dimensional network that links the organic molecules. The 1,6-diazecine ring shows a chair conformation, with expected angles and bond distance values. A stretched conformation of the glycine residue is observed in the free ligand. When this residue is coordinated, it produces significant stress over the diazecine ring caused by the closure of the glycine residue around the metal ion. The copper complex has a dinuclear structure with a square pyramidal environment around both metal ions. The apical position in the two pyramids point to opposite directions in the molecule and they are related by an inversion center. The pyramidal bases of both copper atoms are in the same plane. The intramolecular metal–metal distance in the complex is 7.445(3) Å. However, the shortest distance is of intermolecular nature, with a value of 5.378(2) Å. The crystal structure of the complex consists of a chain of dinuclear units, with an alternating chain arrangement. Low temperature magnetic susceptibility and EPR are in agreement with an antiferromagnetic dinuclear behavior in solution and like a linear chain uniformly spaced, with J=−8.54 cm−1 and α=1. The magnetic behavior of this compound can be explained as the result of an intramolecular magnetic exchange (long distance), and a superexchange path through the hydrogen bond network between adjacent dinuclear molecules.

Ferrocene compounds. XXVII. Synthesis and structure of 2-(ferrocenylmethyl)propane-1, 3-diol

The title compound was obtained by reduction of diethyl (ferrocenylmethyl)malonate with lithium aluminium hydride in diethyl ether. The structure of this novel ferrocene derivative was assigned by means of elemental analysis, IR, [1H]NMR, and [13C]NMR spectroscopy. The structure was also confirmed by a single crystal X-ray study. The compound crystallizes in monoclinic P21/a space group with unit cell dimensions: a = 9.7360(6), b = 27.040(5), c = 14.767(3) A, β = 103.835(6)°, V = 3774.8(11) A3, Z = 12. The asymmetric unit contains three crystallographically independent molecules. In the ferrocenyl moieties, the Fe–C bond distance values are in the range 2.006(5)—2.051(3) A and C–C distances in the range 1.366(7)–1.425(4) A. The cyclopentadienyl rings in each of the molecules are mutually twisted by about 13° from the eclipsed conformation. The hydroxyl groups are involved in the intermolecular O–H...O hydrogen bond formation with O-O distances in the range 2.686(3)–2.801(4) A forming infinite two-dimensional network in a [0 0 1] plane. The crystal structure is additionally stabilized by C–H-O weak intermolecular hydrogen bonds.

Ab initio theoretical study of interactions in borazane molecule

Some structural and energetical properties of the borazane molecule have been calculated by the Mo/ller–Plesset perturbation theory accurate to the second, third, and fourth orders (MP2, MP3, MP4), the coupled cluster [CCSD(T)] approach, and the symmetry-adapted perturbation theory (SAPT). The geometry has been fully optimized at the MP2 level. The theoretical values for bond distances, bond angles, rotational barrier, dipole moment, vibrational frequencies, and the nuclear quadrupole coupling constants agree well with the experimental data. The dissociation energy, the BN bond distance, and the vibrational frequencies obtained indicate that borazane is to a considerable extent a floppy system, which has to be classified as a strong van der Waals complex rather than a molecule similar (isoelectronic) to ethane. The best estimate for the complex formation enthalpy corrected for the basis set superposition error is equal to 25.7±2 kcal/mol. As revealed by the SAPT analysis the main binding contributions are the induction and electrostatic effects. The dipole moment of the complex increases very strongly [from 1.53 to 5.30 D at the CCSD(T) level] upon the interaction due mainly to the umbrella structural polarization of the BH3 molecule and to the polarization of the electron cloud.

Bis(methylthio)ethylenedithiotetrathiafulvalene

The title compound {alternative nomenclature: 2-[4,5-bis(methylthio)-1,3-dithiol-2-ylidene]-5,6-dihydro-1,3-dithiolo[4,5-b][1,4]dithiine}, C10H10S8, is a molecular crystal with typical values for bond distances and angles. The molecules form columns along the c axis. The inter­molecular S⋯S distances indicate the presence of van der Waals interactions between the columns.

New parameters for the refinement of nucleic acid-containing structures.

Structures at atomic resolution (up to 1.0 A) which contain bases, sugars or the phosphodiester linkage, were selected from the Nucleic Acid Database or the Cambridge Structural Database to build a nucleic acid dictionary from X-ray refined structures. The dictionary consists of the average values for bond distances, bond angles and dihedral angles. The variance of the sample is used to provide information about the expected r.m.s. deviations of the refined parameters. A dictionary was constructed for refinement trials in X-PLOR. The dictionary includes RNA and DNA in C2'-endo and C3'-endo sugar pucker conformations, as well as values for the backbone dihedrals. Tests were performed on the dictionary using three structures: a B-DNA, a Z-DNA and a protein-DNA complex. During the course of refinement, all three structures showed significant improvements as measured by r.m.s. deviations and R factors when compared to the previous DNA dictionary.

Heterocyclic compounds studies. Dynamic 13C NMR investigation and crystal structure of 3‐hydroxy‐1,5‐benzoxathiepine

Abstract1‐5‐benzoxathiepine compounds are a novel class of heterocyclic rings that present interesting properties as central nervous system depressants. With the aim to contribute to the elucidation of the structure‐activity relationship of this class of compounds we report a structural study of the 3‐hydroxy‐1,5‐benzoxathiepine both in solution and in the solid state. Studies by dynamic 13C‐nmr in solution show that three conformations are possible for the oxathiepin ring. A unique chair conformation characterizes the atoms in the oxathiepine ring of the crystallized molecule. The crystal structure was solved by direct methods. Values of bond distances and angles are within the expected range.

Redetermination of the crystal and molecular structure of pteridine

The crystal structure of pteridine has been redetermined from three-dimensional X-ray diffraction data and refined to a final weighted R of 0·053 for 416 independent reflections measured on a diffractometer. A satistical test with the new data indicated that the previously reported molecular orientation (T. A. Hamor and J. M. Robertson, J. Chem. Soc., 1956, 3586) can be rejected at the 0·995 level. The new molecular orientation, also confirmed by least-squares refinement of atomic occupancy factors, has led to significant shifts in observed bond distances and angles, e.g. C(4)–N(3) is increased from 1·28 to 1·35 A, and C(2)–N(3)–C(4) decreased from 123 to 116°. The present molecular geometry is more consistent with expected values for bond distances and angles, and with the results of an MO calculation.

Structure determination of Ls-threonine by neutron diffraction

The structure of the aminoacid, Ls-threonine [NH 3 + CH(CHOHCH3)COO−], space groupP212121,a=13.630(5),b=7.753(1),c=5.162(2) A,z=4, has been determined from neutron diffraction data using direct methods. The intensities of 1148 neutron Bragg reflections were measured from a single crystal. The structural parameters were refined by the method of least squares using anisotropic temperature factors. The finalR(F 2) is 0.068. The structure was also refined from the x-ray data of Shoemakeret al (1950J. Am. Chem. Soc. 72 2328); there is good agreement between the two sets of heavy atom parameters. The parameters of hydrogen atoms are of course more precisely determined in our neutron study. The molecular conformation and the hydrogen bonding scheme are discussed. Weighted average values of bond distances and angles from 14 aminoacid structures with ionized carboxylic groups studied by neutron diffraction at Brookheven and Trombay are also presented.

X-Ray structure of diphenylcyclopropenethione

The structure of diphenylcyclopropenethione has been determined from three-dimensional X-ray diffraction data and average values of bond distances and angles from the two crystallographically independent molecules have been computed.