Structural investigation of mM Ni(II) complex isomers using transmission XAFS: the significance of model development

High‐accuracy transmission XAFS determined using the hybrid technique has been used to refine the geometries of bis(N‐n‐propyl‐salicylaldiminato) nickel(II) (n‐pr Ni) and bis(N‐i‐propyl‐salicylaldiminato) nickel(II) (i‐pr Ni) complexes which have approximately square planar and tetrahedral metal coordination. Multiple‐scattering formalisms embedded in FEFF were used for XAFS modelling of the complexes. Here it is shown that an IFEFFIT‐like package using weighting from experimental uncertainty converges to a well defined XAFS model. Structural refinement of (i‐pr Ni) was found to yield a distorted tetrahedral geometry providing an excellent fit, χ_r² = 2.94. The structure of (n‐pr Ni) is best modelled with a distorted square planar geometry, χ_r² = 3.27. This study demonstrates the insight that can be obtained from the propagation of uncertainty in XAFS analysis and the consequent confidence which can be obtained in hypothesis testing and in analysis of alternate structures ab initio. It also demonstrates the limitations of this (or any other) data set by defining the point at which signal becomes embedded in noise or amplified uncertainty, and hence can justify the use of a particular k‐range for one data set or a different range for another. It is demonstrated that, with careful attention to data collection, including the correction of systematic errors with statistical analysis of uncertainty (the hybrid method), it is possible to obtain reliable structural information from dilute solutions using transmission XAFS data.     

探测二茂铁外价轨道(e,2e)反应中的扭曲波效应

利用第三代高效率电子动量谱仪,分别在600和1500 eV两种不同入射电子能量下获得了二茂铁(ferrocene)分子外价轨道的电离能谱和电子动量谱的相关实验结果.并利用非相对论与标量相对论密度泛函方法计算出了二茂铁的重叠型和交错型两种不同构象的理论动量谱.两种构象的外价轨道一一对应,理论电子动量谱基本一样.对二茂铁的外价轨道,在低动量区观测到了强烈的扭曲波效应,这与这些轨道主要由铁原子的3d轨道构成有关.通过相对论和非相对论计算结果的比较,表明相对论效应对于二茂铁的外轨道动量分布几乎没有影响. 关键词： 二茂铁分子 电子动量谱 相对论效应 扭曲波效应     

Predicting XAFS scattering path cumulants and XAFS spectra for metals (Cu,Ni, Fe,Ti, Au) using molecular dynamics simulations

The ability of molecular dynamics (MD) simulations to support the analysis of X‐ray absorption fine‐structure (XAFS) data for metals is evaluated. The low‐order cumulants (ΔR, σ², C₃) for XAFS scattering paths are calculated for the metals Cu, Ni, Fe, Ti and Au at 300 K using 28 interatomic potentials of the embedded‐atom method type. The MD cumulant predictions were evaluated within a cumulant expansion XAFS fitting model, using global (path‐independent) scaling factors. Direct simulations of the corresponding XAFS spectra, χ(R), are also performed using MD configurational data in combination with the FEFFab initio code. The cumulant scaling parameters compensate for differences between the real and effective scattering path distributions, and for any errors that might exist in the MD predictions and in the experimental data. The fitted value of ΔR is susceptible to experimental errors and inadvertent lattice thermal expansion in the simulation crystallites. The unadjusted predictions of σ² vary in accuracy, but do not show a consistent bias for any metal except Au, for which all potentials overestimate σ². The unadjusted C₃ predictions produced by different potentials display only order‐of‐magnitude consistency. The accuracy of direct simulations of χ(R) for a given metal varies among the different potentials. For each of the metals Cu, Ni, Fe and Ti, one or more of the tested potentials was found to provide a reasonable simulation of χ(R). However, none of the potentials tested for Au was sufficiently accurate for this purpose.     

Application of glancing‐emergent‐angle fluorescence for polarized XAFS studies of single crystals

X‐ray absorption fine‐structure (XAFS) data were obtained for the V K‐edge for a series of anisotropic single crystals of (Cr_xV_1–x)₂O₃. The data and the results were compared for the as‐prepared bulk single crystals (measured in fluorescence in two different orientations) and those ground to powder (measured in transmission). For the bulk single crystals, the glancing‐emergent‐angle (GEA) method was used to minimize fluorescence distortion. The reliability of the GEA technique was tested by comparing the polarization‐weighted single‐crystal XAFS data with the experimental powder data. These data were found to be in excellent agreement throughout the entire energy range. Thus, it was possible to reliably measure individual V–V contributions parallel and perpendicular to the c axis of the single crystals, i.e. those unavailable by powder data XAFS analysis. These experiments demonstrate that GEA is a premiere method for non‐destructive high‐photon‐count in situ studies of local structure in bulk single crystals.     

Normal co-ordinate analysis of 1, 8-dibromooctane

The organic compound 1,8-dibromooctane (1,8-DBO) exists in liquid phase at ambient temperatures and has versatile synthetic applications. In its liquid phase 1,8-DBO has been expected to exist in four most probable conformations, with all its carbon atoms in the same plane, having symmetries C _2h , C _i , C ₂ and C ₁ . In the present study a detailed vibrational analysis in terms of assignment of Fourier transform infrared (FT-IR) and Raman bands of this molecule using normal co-ordinate calculations has been done. A systematic set of symmetry co-ordinates has been constructed for this molecule and normal co-ordinate analysis is carried out using the computer program MOLVIB. The force-field transferred from already studied lower chain bromo-alkanes is subjected to refinement so as to fit the observed infrared and Raman frequencies with those of calculated ones. The potential energy distribution (PED) has also been calculated for each mode of vibration of the molecule for the assumed conformations.     

miXAFS: a program for X‐ray absorption fine‐structure data analysis

A new program called miXAFS for the analysis of X‐ray absorption fine‐structure (XAFS) data is presented. miXAFS can analyze the XAFS functions simultaneously for all measured X‐ray absorption edges of the constituent elements in a sample under the constraints for the structural parameters over the edges. The program provides a surface plot of the R‐factor as a function of two structural parameters, which is useful to validate the optimized structural parameters. The structural parameters can be obtained from the XAFS data in a few steps using the setting file and batch process. The program, which is coded in MATLAB and freely available, runs on Macintosh and Windows operating systems. It has a graphical user interface and loads experimental data and XAFS functions in a variety of ASCII data formats.     

Vibrational analysis of 1-chlorooctane

The organic compound 1-chlorooctane exists in liquid state at ambient temperatures and has numerous synthetic applications. Fourier transform infrared and Raman spectra of this molecule have been recorded in the range of 4000−400 cm⁻¹ and 3500−200 cm⁻¹, respectively. A detailed vibrational analysis in terms of assignment of the observed frequencies of this molecule for its four most probable conformations in liquid phase, having symmetries C _s and C _l , has been done using normal co-ordinate calculations. The force-field transferred from already studied lower chain chloro-alkanes is subjected to refinement so as to fit the observed infrared and Raman frequencies with those of calculated ones. The potential energy distribution has also been calculated for each mode of vibration of the molecule for the most probable conformations present in its liquid phase.     

Physical image versus structure relation. Part 14—an attempt to rationalize some acidic region 13C NMR‐pH titration shifts for tetraaza macrocycles throughout the conformational GIAO DFT computational results: a pendant‐arm cyclam case

The most probable time‐averaged conformations of three polyammonium cations H_n 2 ⁿ⁺ (n = 3–5) formed from the macrocyclic pentamine ligand ( 2 , scorpiand) [derivative of 1,4,8,11‐tetraazacyclotetradecane (cyclam)] were analyzed in order to elucidate an origin of ‘wrong‐way’ amine‐protonation shifts found in some ¹³C NMR pH‐profiles determined for the acidic H₂O/D₂O solution. These NMR trends were reproduced quite well in δ_Cs computed for multicomponent shapes of related cations, which were in turn elucidated by the best fitting experimental data to those predicted by the gauge‐independent atomic orbital (GIAO) B3LYP/6‐31G* method, including the IEF‐PCM approach. A consistent DFT methodology of the treatment of such equilibrated cationic mixtures is proposed. Moreover, a few novel ONIOM2‐GIAO B3LYP/6‐31G*:STO‐3G type supermolecular calculations were performed for a simulated presence of bulk water molecules surrounding H₅ 2 ⁵⁺. Copyright © 2009 John Wiley & Sons, Ltd.     

Express analysis of turbulence parameters

A method utilizing a Hartmann sensor for obtaining estimates of the external scale L ₀ of turbulent fluctuations and the structural constant C _n ² during the variation of the parameters of the wavefront of a light beam that has passed through turbulence is suggested. The method is based on Zernike polynomial decomposition of phase fluctuations at the given aperture and on analysis of this expansion coefficient’s statistics. Application of the method for making an estimate of the turbulence characteristics in a water cell yielded results that are in good agreement with the estimates obtained by other methods.     

Investigation of the substituent specific cross‐interaction effects on 13C NMR of the CN bridging group in substituted benzylidene anilines

The substituent effect on ¹³C NMR of the C?N in benzylidene anilines XPhCH?NPhY was investigated, in which the substituents X and Y are in p‐position or in m‐position of the two aromatic rings. The substituent effects including the inductive effects of X and Y, the conjugative effects of X and Y, and the substituent specific cross‐interaction effect were put into one model to quantify the ¹³C NMR chemical shift δ_C(C?N) of the C?N in XPhCH?NPhY. A penta‐parameter correlation equation with correlation coefficient 0.9975 and standard error 0.17 ppm was obtained for 80 samples of compounds. The result shows that the substituents X and Y have an opposite effect on the δ_C(C?N). The electron‐withdrawing effects of X decrease the δ_C(C?N); while the electron‐donating effects of X increase the δ_C(C?N). In contrast, the electron‐withdrawing effects of Y increase the δ_C(C?N); while the electron‐donating effects of Y decrease the δ_C(C?N). A new substituent specific cross‐interaction effect parameter Δσ² was proposed, which indicates that the most substituent specific cross‐interaction effect exists in the pair of max electron‐withdrawing group (EWG) and max electron‐donating group (EDG) or the pair of max EDG and max EWG. Further to verify the obtained correlation equation, 15 samples of model compounds were prepared and their δ_C(C?N) was measured in this work. The predicted δ_C(C?N) values with the obtained equation are in good agreement with the measured ones for these prepared compounds, which confirmed the reliability of the obtained equation. Copyright © 2010 John Wiley & Sons, Ltd.     

Analysis of oxygen shell splitting in hydrothermally grown single crystal ThO2(200)

Single crystals of ThO₂ have been synthesized using hydrothermal growth and studied using the X‐ray absorption fine structure (XAFS) technique. The extended X‐ray absorption fine structure (EXAFS) has been extracted from the XAFS and analyzed using a novel, computational Latin hypercube sampling method. The methodology not only confirms the expected space group and crystal structure, it also identifies the origin of a previously reported split O shell. Since EXAFS is a local order analysis technique, the O shell splitting is identified as an O atom occupying an interstitial site. This result is significant for examining O^2– transport in a ThO₂ matrix and corroborating research indicating partial Th 5f occupancy that is similar to hyper‐stoichiometric UO_2+x compounds. (© 2015 WILEY‐VCH Verlag GmbH &Co. KGaA, Weinheim)     

Conformational energies of silacyclohexanes C5H10SiHMe,C5H10SiH(CF3) and C5H10SiCl(SiCl3) from variable temperature Raman spectra

From variable temperature vibrational Raman spectra, the axial/equatorial enthalpy differences for the substituted silacyclohexanes C₅H₁₀SiHMe, C₅H₁₀SiH(CF₃) and C₅H₁₀SiCl(SiCl₃) were determined. The pure liquids and solutions in various solvents were investigated. Preferred conformations are equatorial for methylsilacyclohexane and axial for trifluoromethylsilacyclohexane, consistent with earlier results from nuclear magnetic resonance experiments and ab initio calculations. For C₅H₁₀SiCl(SiCl₃) an enthalpy difference close to zero was found, which is supported by high‐level which is supported by high‐level quantum chemical calculations at the second‐order Møller‐Plesset (MP2) and coupled cluster with single, double, and perturbative triple excitations (CCSD(T)) levels, which employed various basis sets. A novel synthesis for C₅H₁₀SiCl(SiCl₃) was developed using ClMg(CH₂)₅MgCl instead of BrMg(CH₂)₅MgBr as a starting material. The procedure avoids the formation of partially brominated products, facilitating the purification of the compound. ¹H, ¹³C and ²⁹Si nuclear magnetic resonance data are reported. Copyright © 2012 John Wiley & Sons, Ltd.     

Experimental and theoretical structure and vibrational analysis of ethyl trifluoroacetate,CF3CO2CH2CH3

The molecular structure and conformational properties of ethyl trifluoroacetate, CF₃CO₂CH₂CH₃, were determined in the gas phase by electron diffraction, and vibrational spectroscopy (IR and Raman). The experimental investigations were supplemented by ab initio (MP2) and DFT quantum chemical calculations at different levels of theory. Experimental and theoretical methods result in two structures with C_s (anti–anti) and C₁ (anti–gauche) symmetries, the former being slightly more stable than the latter. The electron‐diffraction data are best fitted with a mixture of 56% anti–gauche and 44% anti–anti conformers. The conformational preference was also studied using the total energy scheme, and the natural bond orbital scheme. Also, the infrared spectra of CF₃CO₂CH₂CH₃ are reported for the gas, liquid and solid states, as is the Raman spectrum of the liquid. The comparison of experimental averaged IR spectra of C_s and C₁ conformers provides evidence for the predicted conformations in the IR spectra. Harmonic vibrational wavenumbers and scaled force fields have been calculated for both conformers. Copyright © 2009 John Wiley & Sons, Ltd.     

Elastic moduli of single-crystal C60

The matrix of elastic constants of the fcc phase of solid C₆₀ has been determined experimentally from measurements of the the velocity of 5 MHz ultrasound in single-crystal samples with different crystallographic orientations. The following values were obtained for the elastic moduli: C ₁₁=14.9±0.9 GPa, C ₁₂=8.8±1.0 GPa, and C ₄₄=6.6±0.18 GPa. The results are compared with theoretical estimates of the elastic moduli and data obtained in previous measurements of the elastic characteristics of solid C₆₀. Fiz. Tverd. Tela (St. Petersburg) 40, 173–175 (January 1998)     

Formation of polymer complexes of transition metals with fullerene

This paper reports on the results of ab initio unrestricted Hartree-Fock (UHF) calculations of the equilibrium geometry and binding energy for the transition-metal complexes Me(C₅H₅)₂ and Me(C₆H₆)₂ and the energetically stable metallofullerene complexes Me(C₆₀)₂, where Me=Ti, V, Cr, Fe, and Ni. The calculation technique is worked out using the ferrocene molecule. The calculated geometry and binding energy agree satisfactorily with the experimental data.     

Synthesis,molecular structure,IR and Raman spectra as well as DFT chemical calculations for alkylamides of thiocyanoacetic acid

This paper reports on room‐temperature infrared (IR) and Raman studies and vibrational characteristics of amide and thiocyano groups of R‐NH‐CO‐CH₂‐SCN n‐alkylamides of thiocyanoacetic acid (R = C₈H₁₇, C₉H₁₉, C₁₂H₂₅ and C₁₄H₂₉). Their molecular structure has been proposed on the basis of optimization process. The experimental wavenumbers have been compared to those obtained from discrete Fourier transform (DFT) quantum chemical calculations performed with the use of B3LYP/6–31G(d,p) approximation. The role of the hydrogen bonds in the stabilization of the structure has been analyzed. It was found that the hydrogen bonding and strong dynamic interactions between the unit cell components are responsible for the deviation of several theoretical wavenumbers from the experimental ones. Copyright © 2009 John Wiley & Sons, Ltd.     

Raman and infrared,microwave spectra,conformational stability,adjusted r0 structural parameters,and vibrational assignments of cyclopentylamine

Fourier transform microwave spectrum of cyclopentylamine, c–C₅H₉NH₂ has been recorded, and seven transitions have been assigned for the most abundant conformer, and the rotational constants have been determined: A = 4909.46(5), B = 3599.01(4), and C = 2932.94(4). From the determined microwave rotational constants and ab initio MP2(full)/6‐311 + G(d,p) predicted structural values, adjusted r₀ parameters are reported with distances (Å): rC_α–C_β = 1.529(3), rC_β–C_γ = 1.544(3), rC_γ–C_γ = 1.550(3), rC_α–N = 1.470(3), and angles (°) ∠CCN = 108.7(5), ∠C_βC_αC_β = 101.4(5), and τC_βC_αC_β′C_γ′ = 42.0(5). The infrared spectra (4000–220 cm⁻¹) of the gas have been recorded. Additionally, the variable temperature (−60 to −100 °C) Raman spectra of the sample dissolved in liquefied xenon was recorded from (3800–50 cm⁻¹). The four possible conformers have been identified, and their relative stabilities obtained with enthalpy difference relative to t‐Ax of 211 ± 21 cm⁻¹ for t‐Eq ≥ 227 ± 22 cm⁻¹ for g‐Eq ≥ 255 ± 25 cm⁻¹ for g‐Ax. The percentage of the four conformers is estimated to be 53% for the t‐Ax, 11 ± 1% for t‐Eq, 20 ± 2% for g‐Ax and 16 ± 2% for g‐Eq at ambient temperature. The conformational stabilities have been predicted from ab initio calculations by utilizing several different basis sets up to aug‐cc‐pVTZ from both MP2(full) and density functional theory calculations by the B3LYP method. Vibrational assignments have been provided for the observed bands for all four conformers, which are predicted by MP2(full)/6‐31G(d) ab initio calculations to predict harmonic force constants, wavenumbers, infrared intensities, Raman activities, and depolarization ratios for all of the conformers. The results are discussed and compared to the corresponding properties of some related molecules. Copyright © 2014 John Wiley & Sons, Ltd.     

Mössbauer, nuclear inelastic scattering and density functional studies on the second metastable state of Na2[Fe(CN)5NO]·2H2O

The structure of the light-induced metastable state SII of Na₂[Fe(CN)₅NO]·2H₂O was investigated by transmission Mössbauer spectroscopy (TMS) in the temperature range between 85 and 135 K, nuclear inelastic scattering (NIS) at 98 K using synchrotron radiation and density functional theory (DFT) calculations. The DFT and TMS results strongly support the view that the NO group in SII takes a side-on molecular orientation and, further, is dynamically displaced from one eclipsed, via a staggered, to a second eclipsed orientation. The population conditions for generating SII are optimal for measurements by TMS, yet they are modest for accumulating NIS spectra. Optimization of population conditions for NIS measurements is discussed and new NIS experiments on SII are proposed.     

Methanol and deuterated species: Infrared data,valence force field,rotamers, and conformation

New infrared measurements of gaseous and matrix-isolated methanol and 7 deuterated species are presented and analyzed. A revised assignment for the species CH₃OH(D) and CD₃OH(D) is used to determine 15 significant parameters of a valence force field by a converged simultaneous least-squares adjustment to 44 observed fundamentals. The respective frequencies calculated for the rotamers of CH₂DOH(D) and CHD₂OH(D) turn out to be a valid prediction as they are used to assign 78 observed fundamentals of the species with partially deuterated methyl groups. The values of the 15 force constant parameters are refined by including all 122 observed fundamentals. The force field contains significant deviations from local C_3v symmetry of the methyl group. Such an asymmetry, in the CH-stretching diagonal part, produces a difference of about 10 cm^?1 in the zero point energy of symmetric and asymmetric rotamers of the species with partially deuterated methyl groups. Calculations based on equilibrium structures with and without methyl tilt yield better agreement with observed data in the nontilted case. A preliminary calculation of relative intensities reproduces the major effects of isotopic substitution and rotational isomerism. Experimental evidence for the staggered conformation is obtained from a comparison of observed data with calculated results based on staggered and eclipsed models.     

Substituent effect on structure,stability, and aromaticity of novel BnNmC20–(n+m) heterofullerenes

We are focusing our calculations on the structural stabilities and electronic properties of 26 novel B_nN_mC_20–(n+m) heterofullerenes, with n, m = 1 ? 5, at B3LYP/6‐311++G** and B3LYP/AUG‐cc‐pVTZ levels of theory. Vibrational frequency calculations on C₂₀ and its analogues show that except B₂N₂C₁₆ (1) and B₂N₂C₁₆ (2), all other heterofullerenes are true minima. The heats of atomization energies, binding energy, band gaps (ΔE_HOMO‐LUMO), aromaticity, nucleus‐independent chemical shifts, thermodynamic stability, kinetic stability against electronic excitation, binding energy as a stability criterion of different configurations, geometrical parameters, conformational structures, conductivity, charge transfer, and possibility for hydrogen storage of these heterofullerenes strongly depend on their number of heteroatoms, topology, filling patterns, and locations as well as “B‐site and N‐site attachments.” B₅N₅C₁₀ contains 5 alternating boron and nitrogen atoms in the equatorial position. It is predicted to be thermodynamically and kinetically the most stable against electron excites. Thus, it is energetically favorable and its electronic properties as well as stabilities make it perhaps a good candidate for an experimental investigation and testing verification.