Arsenate incorporation in gypsum probed by neutron, X-ray scattering and density functional theory modeling

The ability of gypsum, a common sulfate mineral, to host arsenic atoms in its crystalline structure, is demonstrated through experimental structural studies of the solid solutions formed upon synthetic coprecipitation of gypsum (CaSO4 x 2 H2O) and arsenic. Neutron and X-ray diffraction methods show an enlargement of the gypsum unit cell proportional to the concentration of arsenic in the solids and to the pH solution value. The substitution of sulfate ions (SO4(2-)) by arsenate ions is shown to be more likely under alkaline conditions, where the HAsO4(2-) species predominates. A theoretical Density Functional Theory model of the arsenic-doped gypsum structure reproduces the experimental volume expansion. Extended X-ray Absorption Fine Structure (EXAFS) measurements of the local structure around the arsenic atom in the coprecipitated solids confirm solid state substitution and allow some refinement of the local structure, corroborating the theoretical structure found in the simulations. The charge redistribution within the structure upon substitutions of either the protonated or the unprotonated arsenate species studied by means of Mulliken Population Analyses demonstrates an increase in the covalency in the interaction between Ca(2+) and AsO4(3-), whereas the interaction between Ca(2+) and HAsO4(2-) remains predominantly ionic.     

Molecular structure and conformational composition of 1,3-dihydroxyacetone studied by combined analysis of gas-phase electron diffraction data, rotational constants, and results of theoretical calculations. Ideal gas thermodynamic properties of 1,3-dihydroxyacetone

The molecular structure of 1,3-dihydroxyacetone (DHA) has been studied by gas-phase electron diffraction (GED), combined analysis of GED and microwave (MW) data, ab initio, and density functional theory calculations. The equilibrium re structure of DHA was determined by a joint analysis of the GED data and rotational constants taken from the literature. The anharmonic vibrational corrections to the internuclear distances (re-ra) and to the rotational constants (B(i)e-B(i)0) needed for the estimation of the re structure were calculated from the B3LYP/cc-pVTZ cubic force field. It was found that the experimental data are well reproduced by assuming that DHA consists of a mixture of three conformers. The most stable conformer of C2v symmetry has two hydrogen bonds, whereas the next two lowest energy conformers (Cs and C1 symmetry) have one hydrogen bond and their abundance is about 30% in total. A combined analysis of GED and MW data led to the following equilibrium structural parameters (re) of the most abundant conformer of DHA (the uncertainties in parentheses are 3 times the standard deviations): r(C=O)=1.215(2) A, r(C-C)=1.516(2) A, r(C-O)=1.393(2) A, r(C-H)=1.096(4) A, r(O-H)=0.967(4) A, angleC-C=O=119.9(2) degrees, angleC-C-O=111.0(2) degrees, angleC-C-H=108.2(7) degrees, angleC-O-H=106.5(7) degrees. These structural parameters reproduce the experimental B(i)0 values within 0.05 MHz. The experimental structural parameters are in good agreement with those obtained from theoretical calculations. Ideal gas thermodynamic functions (S degrees (T), C degrees p(T), and H degrees (T)-H degrees (0)) of DHA were calculated on the basis of experimental and theoretical molecular parameters obtained in this work. The enthalpy of formation of DHA, -523+/-4 kJ/mol, was calculated by the atomization procedure using the G3X method.     

The ab initio gradient revolution in structural chemistry: The importance of local molecular geometries and the efficacy of joint quantum mechanical and experimental procedures

The use of ab initio gradient calculations to determine structural information is reviewed. The significance of local geometries is discussed. Many calculated structural trends in local geometries are often unobservable by direct quantitative experimental techniques, presenting a challenge to develop more powerful experimental methods. The applications of calculated structural data in interpreting experimental results in microwave spectroscopy and electron diffraction are discussed.     

Neutron diffraction and theoretical DFT studies of two dimensional molecular-based magnet K2[Mn(H2O)2]3[Mo(CN)7]2.6H2O

Exchange mechanisms and magnetic structure in the two-dimensional cyano-bridged molecule-based magnet K2[Mn(H2O)2]3[Mo(CN)7]2.6H2O have been investigated by a combination of neutron diffraction studies on both single crystal and powder samples and theoretical DFT calculations. The experimental spin density has been deduced from a new refinement of previously obtained polarized neutron diffraction (PND) data which was collected in the ordered magnetic state at 4 K under a saturation field of 3 T performed in the C2/c space group, determined by an accurate re-evaluation of the X-ray structure. Positive spin populations were observed on the two manganese sites, and negative spin populations were observed on the molybdenum site, which provides evidence of antiferromagnetic Mo3+-Mn2+ exchange interactions through the cyano bridge. The experimental data have been compared to the results of DFT calculations. Moreover, theoretical studies reveal the predominance of the spin polarization mechanism in the Mo-C-N-Mn sequence, with the antiferromagnetic nature of the interaction being due to the overlap between the magnetic orbitals relative to manganese and molybdenum in the cyano bridging region. The magnetic structure of K2[Mn(H2O)2]3[Mo(CN)7]2.6H2O has been solved at low temperature in zero field by powder neutron diffraction measurements. The structure was found to be ferrimagnetic where the manganese and molybdenum spins are aligned along the axis in opposite directions.     

More user-friendly phosphines? Molecular structure of methylphosphine and its adduct with borane, studied by gas-phase electron diffraction and quantum chemical calculations

The molecular structures of methylphosphine (CH(3)PH(2)) and methylphosphine-borane (CH(3)PH(2).BH(3)) have been determined from gas-phase electron diffraction data and rotational constants, employing the SARACEN method. The experimental geometric parameters generally showed a good agreement with those obtained using ab initio calculations and previous microwave spectroscopy studies. In order to assess the accuracy of the calculated structures a range of ab initio methods were used, including the CCSD(T) method, with correlation-consistent basis sets. The structural environment around the phosphorus atom was found to change significantly upon complexation with borane, with the P-C bond length shortening and the bond angles widening.     

The structure and interaction energies of the weak complexes of CHClF2 and CHF3 with HCCH: a test of density functional theory methods

The structure and interaction energies of the weak non-covalent complexes of CHClF(2) and CHF(3) with HCCH have been predicted using a number of density functional based approaches, and compared with both high resolution spectroscopic data recently reported by Sexton et al. [Phys. Chem. Chem. Phys., 2010, 12, 14263-14270], and with high level benchmark calculations reported herein. We find that this is another case where the M05 and M06 families of functionals, as well as the DFT-D approach, are competitive with the more costly wavefunction based methods. We highlight the problem of deriving unique intermolecular structural parameters from the experimental microwave data.     

Ab initio studies of structural features not easily amenable to experiment : Part 13. Structural consequences of methyl hyperconjugation in some CH3C(=X)Y systems

The molecular structures of several conformations of acetaldehyde, acetic acid and isobutene were completely refined by standard single determinant ab initio procedures on the 4–21G level. Calculated and experimental parameters are in close agreement in all the cases in which the experimental values can be considered as reliably established. In some examples, however, some essential structural features that should be found in CH₃C(=X)Y systems have not yet been resolved by any experimental technique. The structural consequences for methyl hyperconjugation in the various systems are discussed. The study demonstrates that high quality ab initio geometries can provide information which is complementary to experimental results. The calculations are particularly useful in discussing discrepancies between microwave and electron diffraction structures and in interpreting microwave substitution structure uncertainties which are often difficult to determine accurately.     

Vibrational spectra and normal coordinate analysis of a weak ligand complex, Co(p-DMABA)2Cl2 x 2H2O.

The complex Co(p-DMABA)2Cl2 x 2H2O (p-dimethylaminobenzaldehyde, p-DMABA) was prepared from the solid-state reaction of a weak ligand p-DMABA and CoCl2 x 6H2O at lower heating temperature (60 degrees C). It is very difficult to obtain the title complex using solution reaction method, less than isolating single crystals. In order to determine the crystal structure of the title compound, we have to rely on the X-ray powder diffraction data. That is, the crystal structure can be solved directly from powder data, which crucial step is to constitute the structure model. Indirect spectroscopic methods, such as infrared and Raman spectroscopes, and further vibrational assignments made with the aid of normal coordinate calculations by using a modified Urey-Bradley force field, were analyzed to proposed molecular structure. One hundred and fifty-seven internal coordinates were established and 129 theoretical vibrational frequencies were calculated. An appropriate set of internal coordinates and force constants in the course of calculation were introduced, so that the calculated vibration frequencies are good agreement with the observed values. The average difference and the maximum deviation between theoretic and experimental frequencies are 2.44 and 8.0 cm(-1), respectively. Thus the normal coordinate analysis is a powerful tool to the molecular structure. Other structural and spectral properties are also discussed in this paper. The purpose of the present paper is to obtain a good structural model. This model was used as starting model for crystal structure determination from powder X-ray diffraction (XRD) data.     

Spatiotemporal Kinetics in Solution Studied by Time‐Resolved X‐Ray Liquidography (Solution Scattering)

Information about temporally varying molecular structure during chemical processes is crucial for understanding the mechanism and function of a chemical reaction. Using ultrashort optical pulses to trigger a reaction in solution and using time‐resolved X‐ray diffraction (scattering) to interrogate the structural changes in the molecules, time‐resolved X‐ray liquidography (TRXL) is a direct tool for probing structural dynamics for chemical reactions in solution. TRXL can provide direct structural information that is difficult to extract from ultrafast optical spectroscopy, such as the time dependence of bond lengths and angles of all molecular species including short‐lived intermediates over a wide range of times, from picoseconds to milliseconds. TRXL elegantly complements ultrafast optical spectroscopy because the diffraction signals are sensitive to all chemical species simultaneously and the diffraction signal from each chemical species can be quantitatively calculated from its three‐dimensional atomic coordinates and compared with experimental TRXL data. Since X‐rays scatter from all the atoms in the solution sample, solutes as well as the solvent, the analysis of TRXL data can provide the temporal behavior of the solvent as well as the structural progression of all the solute molecules in all the reaction pathways, thus providing a global picture of the reactions and accurate branching ratios between multiple reaction pathways. The arrangement of the solvent around the solute molecule can also be extracted. This review summarizes recent developments in TRXL, including technical innovations in synchrotron beamlines and theoretical analysis of TRXL data, as well as several examples from simple molecules to an organometallic complex, nanoparticles, and proteins in solution. Future potential applications of TRXL in femtosecond studies and biologically relevant molecules are also briefly mentioned.     

Spectroscopic investigation of heterogeneous Ziegler-Natta catalysts: Ti and Mg chloride tetrahydrofuranates, their interaction compound, and the role of the activator

X-ray powder diffraction (XRPD), Infrared, Raman, and UV/Vis spectroscopy have been used to investigate the structural, vibrational, and optical properties of Ti and Mg chloride tetrahydrofuranates as precursors of heterogeneous Ziegler-Natta catalysts for polyethylene production; as well as their interaction compound (pro-catalyst) and the final catalyst obtained after interaction with the AlR(3) activator. Although the structure of the precursors and of the pro-catalyst were well known, that of the catalyst (obtained by reaction of the pro-catalyst with AlR(3)) was not easily obtainable from XRPD data. IR and Raman spectroscopy provided important information on tetrahydrofuran (thf) coordination and on the ν(M-Cl) region; whereas UV/Vis spectroscopy gave the direct proof on both the formal oxidation state and the coordination environment of the active Ti sites. Those presented herein are among the first direct experimental data on the structure of the active Ti sites in Ziegler-Natta catalysts, and can be used to validate the many computational studies that have been increasing exponentially in the last few decades.     

Analyzing solution-phase time-resolved x-ray diffraction data by isolated-solute models

Extracting transient structural information of a solute from time-resolved x-ray diffraction (TRXD) data is not trivial because the signal from a solution contains not only the solute-only term as in the gas phase, but also solvent-related terms. To obtain structural insights, the diffraction signal in q space is often Fourier sine transformed (FT) into r space, and molecular dynamics (MD) simulation-aided signal decomposition into the solute, cage, and solvent terms has so far been indispensable for a clear-cut assignment of structural features. Here we present a convenient method of comparative structural analysis without involving MD simulations by incorporating only isolated-species models for the solute. FT is applied to both the experimental data and candidate isolated-solute models, and comparison of the correlation factors between the experimental FT and the model FTs can distinguish the best candidate among isolated-solute models for the reaction intermediates. The low q region whose influence by solvent-related terms is relatively high can be further excluded, and this mode of truncated Fourier transform (TFT) improves the correlation factors and facilitates the comparison. TFT analysis has been applied to TRXD data on the photodissociation of C(2)H(4)I(2) in two different solvents (methanol and cyclohexane), HgI(2) in methanol, and I(3) (-) in methanol excited at 267 nm. The results are consistent with previous conclusions for C(2)H(4)I(2) in methanol and HgI(2) in methanol, and the new TRXD data reveal that the C(2)H(4)I transient radical has a bridged structure in cyclohexane and I(3) (-) in methanol decomposes into I+I(2) (-) upon irradiation at 267 nm. This TFT method should greatly simplify the analysis because it bypasses MD simulations.     

1H NMR analysis of O‐methyl‐inositol isomers: a joint experimental and theoretical study

Density functional theory (DFT) calculations of ¹H NMR chemical shifts for l ‐quebrachitol isomers were performed using the B3LYP functional employing the 6‐31G(d,p) and 6‐311 + G(2d,p) basis sets. The effect of the solvent on the B3LYP‐calculated NMR spectrum was accounted for using the polarizable continuum model. Comparison is made with experimental ¹H NMR spectroscopic data, which shed light on the average uncertainty present in DFT calculations of chemical shifts and showed that the best match between experimental and theoretical B3LYP ¹H NMR profiles is a good strategy to assign the molecular structure present in the sample handled in the experimental measurements. Among four plausible O‐methyl‐inositol isomers, the l ‐quebrachitol 2a structure was unambiguously assigned based only on the comparative analysis of experimental and theoretical ¹H NMR chemical shift data. The B3LYP infrared (IR) spectrum was also calculated for the four isomers and compared with the experimental data, with analysis of the theoretical IR profiles corroborating assignment of the 2a structure. Therefore, it is confirmed in this study that a combined experimental/DFT spectroscopic investigation is a powerful tool in structural/conformational analysis studies. Copyright © 2012 John Wiley & Sons, Ltd.     

Effects of Fluorine Substitution on the Shape of Neurotransmitters: the Rotational Spectrum of 2‐(2‐Fluorophenyl)Ethanamine

The effects of fluorination on the conformational landscape of adrenergic neurotransmitters is exemplified trough the conformation analysis of 2‐(2‐F‐phenyl)ethanamine (2FPEA) carried out by microwave spectroscopy and quantum chemical calculations. Five different conformers of the nine possible stable ones for 2FPEA are observed by molecular‐beam Fourier‐transform microwave spectroscopy. Their unambiguous identification is possible by comparing the experimental rotational constants and the quadrupole coupling constants with those obtained by quantum chemical calculations carried out at the MP2/6‐311++G(d,p) level of theory. The relative abundances of the conformers in the jet are estimated from the relative intensities in the observed spectra. A qualitative agreement between experimental and theoretical energies was found, and the remaining deviations are explained by population transfer taking place during the adiabatic expansion. The energy landscape, which also takes the interconversion barriers between the conformers into consideration, is thus characterized completely by the strong interplay of quantum chemical methods and precise experimental data. Significant changes in energy and structure of the 2FPEA conformers are found compared to those obtained for the prototype molecule 2‐phenylethanamine (PEA).     

Testing the limits of sensitivity in a solid-state structural investigation by combined X-ray powder diffraction, solid-state NMR, and molecular modelling

A solid state structural investigation of ethoxzolamide is performed on microcrystalline powder by using a multi-technique approach that combines X-ray powder diffraction (XRPD) data analysis based on direct space methods with information from (13)C((15)N) solid-state Nuclear Magnetic Resonance (SS-NMR) and molecular modeling. Quantum chemical computations of the crystal were employed for geometry optimization and chemical shift calculations based on the Gauge Including Projector Augmented-Wave (GIPAW) method, whereas a systematic search in the conformational space was performed on the isolated molecule using a molecular mechanics (MM) approach. The applied methodology proved useful for: (i) removing ambiguities in the XRPD crystal structure determination process and further refining the derived structure solutions, and (ii) getting important insights into the relationship between the complex network of non-covalent interactions and the induced supra-molecular architectures/crystal packing patterns. It was found that ethoxzolamide provides an ideal case study for testing the accuracy with which this methodology allows to distinguish between various structural features emerging from the analysis of the powder diffraction data.     

Chemical bonds without "chemical bonding"? A combined experimental and theoretical charge density study on an iron trimethylenemethane complex

High-resolution X-ray diffraction data, in conjunction with DFT(B3LYP) quantum calculations, have been used in a QTAIM analysis of the charge density in the trimethylenemethane (TMM) complex Fe(eta(4)-C[CH(2)](3))(CO)(3). The agreement between the theoretical and experimental topological properties is excellent. Only one bond path is observed between the TMM ligand and the Fe atom, from the central C(alpha) atom. However, much evidence, including from the delocalization indices and the source function, suggests that there is a strong chemical interaction between the Fe and C(beta) atoms, despite the formal lack of chemical bonding according to QTAIM.     

Investigating magnetostructural correlations in the pseudooctahedral trans-[Ni(II){(OPPh2)(EPPh2)N}2(sol)2] complexes (E = S, Se; sol = DMF, THF) by magnetometry, HFEPR, and ab initio quantum chemistry

In this work, magnetometry and high-frequency and -field electron paramagnetic resonance spectroscopy (HFEPR) have been employed in order to determine the spin Hamiltonian (SH) parameters of the non-Kramers, S = 1, pseudooctahedral trans-[Ni(II){(OPPh(2))(EPPh(2))N}(2)(sol)(2)] (E = S, Se; sol = DMF, THF) complexes. X-ray crystallographic studies on these compounds revealed a highly anisotropic NiO(4)E(2) coordination environment, as well as subtle structural differences, owing to the nature of the Ni(II)-coordinated solvent molecule or ligand E atoms. The effects of these structural characteristics on the magnetic properties of the complexes were investigated. The accurately HFEPR-determined SH zero-field-splitting (zfs) D and E parameters, along with the structural data, provided the basis for a systematic density functional theory (DFT) and multiconfigurational ab initio computational analysis, aimed at further elucidating the electronic structure of the complexes. DFT methods yielded only qualitatively useful data. However, already entry level ab initio methods yielded good results for the investigated magnetic properties, provided that the property calculations are taken beyond a second-order treatment of the spin-orbit coupling (SOC) interaction. This was achieved by quasi-degenerate perturbation theory, in conjunction with state-averaged complete active space self-consistent-field calculations. The accuracy in the calculated D parameters improves upon recovering dynamic correlation with multiconfigurational ab initio methods, such as the second-order N-electron valence perturbation theory NEVPT2, the difference dedicated configuration interaction, and the spectroscopy-oriented configuration interaction. The calculations showed that the magnitude of D (～3-7 cm(-1)) in these complexes is mainly dominated by multiple SOC contributions, the origin of which was analyzed in detail. In addition, the observed largely rhombic regime (E/D = 0.16-0.33) is attributed to the highly distorted metal coordination sphere. Of special importance is the insight by this work on the zfs effects of Se coordination to Ni(II). Overall, a combined experimental and theoretical methodology is provided, as a means to probe the electronic structure of octahedral Ni(II) complexes.     

An efficient method for computing excess free energy of liquid

We present a new theoretical method for efficient calculation of free energy of liquid. This interaction entropy method allows one to compute entropy and free energy of liquid from standard single step MD (molecular dynamics) simulation directly in liquid state without the need to perform MD simulations at many intermediate states as required in thermodynamic integration or free energy perturbation methods. In this new approach, one only needs to evaluate the interaction energy of a single (fixed) liquid molecule with the rest of liquid molecules as a function of time from a standard MD simulation of liquid and the fluctuation of distribution of this interaction energy is then used to calculate the interaction entropy of the liquid. Explicit theoretical derivation of this interaction entropy approach is provided and numerical calculations for the benchmark liquid water system were carried out using three different water models. Numerical analysis of the result was performed and comparison of the computational result with experimental data and other theoretical results were provided. Excellent agreement of calculated free energies with the experimental data using TIP4P model is obtained for liquid water.     

2DIR spectroscopy of human amylin fibrils reflects stable β-sheet structure

The aggregation of human amylin to form amyloid contributes to islet β-cell dysfunction in type 2 diabetes. Studies of amyloid formation have been hindered by the low structural resolution or relatively modest time resolution of standard methods. Two-dimensional infrared (2DIR) spectroscopy, with its sensitivity to protein secondary structures and its intrinsic fast time resolution, is capable of capturing structural changes during the aggregation process. Moreover, isotope labeling enables the measurement of residue-specific information. The diagonal line widths of 2DIR spectra contain information about dynamics and structural heterogeneity of the system. We illustrate the power of a combined atomistic molecular dynamics simulation and theoretical and experimental 2DIR approach by analyzing the variation in diagonal line widths of individual amide I modes in a series of labeled samples of amylin amyloid fibrils. The theoretical and experimental 2DIR line widths suggest a "W" pattern, as a function of residue number. We show that large line widths result from substantial structural disorder and that this pattern is indicative of the stable secondary structure of the two β-sheet regions. This work provides a protocol for bridging MD simulation and 2DIR experiments for future aggregation studies.     

Low-Molecular Pyrazine-Based DNA Binders: Physicochemical and Antimicrobial Properties

Pyrazine and its derivatives are a large group of compounds that exhibit broad biological activity, the changes of which can be easily detected by a substituent effect or a change in the functional group. The present studies combined theoretical research with the density functional theory (DFT) approach (B3LYP/6-311+G**) and experimental (potentiometric and spectrophotometric) analysis for a thorough understanding of the structure of chlorohydrazinopyrazine, its physicochemical and cytotoxic properties, and the site and nature of interaction with DNA. The obtained results indicated that 2-chloro-3-hydrazinopyrazine (2Cl3HP) displayed the highest affinity to DNA. Cytotoxicity studies revealed that the compound did not exhibit toxicity toward human dermal keratinocytes, which supported the potential application of 2Cl3HP in clinical use. The study also attempted to establish the possible equilibria occurring in the aqueous solution and, using both theoretical and experimental methods, clearly showed the hydrophilic nature of the compound. The experimental and theoretical results of the study confirmed the quality of the compound, as well as the appropriateness of the selected set of methods for similar research.