Riccardo Destro

Estimated H-atom anisotropic displacement parameters: a comparison between different methods and with neutron diffraction results

Anisotropic displacement parameters (ADPs) are compared for H atoms estimated using three recently described procedures, both among themselves and with neutron diffraction results. The results convincingly demonstrate that all methods are capable of giving excellent results for several benchmark systems and identify systematic discrepancies for several atom types. A revised and extended library of internal H-atom mean-square displacements is presented for use with Madsens SHADE web server [J. Appl. Cryst. (2006), 39, 757-758; http://shade.ki.ku.dk], and the improvement over the original SHADE results is substantial, suggesting that this is now the most readily and widely applicable of the three approximate procedures. Using this new library--SHADE2--it is shown that, in line with expectations, a segmented rigid-body description of the heavy atoms yields only a small improvement in the agreement with neutron results. The SHADE2 library, now incorporated in the SHADE web server, is recommended as a routine procedure for deriving estimates of H-atom ADPs suitable for use in charge-density studies on molecular crystals, and its widespread use should reveal remaining deficiencies and perhaps overcome the inherent bias in the majority of such studies.

Experimental vs. theoretical topological properties of charge density distributions. An application to the l-alanine molecule studied by X-ray diffraction at 23 K

Abstract By using an aspherical-atom formalism, the electrostatic potential and the dipole moment of l -alanine were recently derived from a 23 K X-ray diffraction study. This paper focusses on how the topological properties of the experimentally derived density differ from those obtained by ab initio wavefunctions of differing accuracy. Factors influencing the theoretical densities, such as basis-set quality, inclusion of electron correlation and crystal-field effects, are scrutinized and the theoretical results compared with those derived from optimum least-squares refined experimental densities and from the very crude independent-atom model. The experimental and theoretical charge distributions show the same number and the same type of critical points in the density field. A close agreement was found for bond critical point locations and density values for both covalent intramolecular interactions and intermolecular hydrogen bonds. Discrepancies in the density Laplacian field portraits are discussed and the subtle effects of the crystal field are pointed out.

Total electronic charge density of L-alanine from X-ray diffraction at 23 K

Abstract From an extensive set of single-crystal X-ray diffracted intensities, measured at 23 K and interpreted in terms of pseudoatoms (multipoles), the experimental charge density ϱ and its Laplacian ∇ 2 ϱ have been obtained for the zwitterionic amino acid L-alanine. The results of the topological analysis of the experimental ϱ, as summarized by the properties of its bond critical points, are presented.

Physicochemical Properties of Zwitterionic l- and dl-Alanine Crystals from Their Experimental and Theoretical Charge Densities

The total experimental electron density distributions rho(r) of zwitterionic L- and DL-alanine crystals, as derived from extensive sets of X-ray diffracted intensities collected at 23 and 19 K, are compared to gain an insight into the different physical properties of the two related chiral compounds in the solid state and to explore the extent of the rho(r) transferability. Relevant parameters that characterize the two crystal forms are obtained, showing differences and similarities in terms of (i) geometric descriptors, (ii) topological indexes, (iii) molecular electrostatic potential Phi(r) distributions, (iv) atomic volumes and charges, (v) molecular electric moments, and (vi) electrostatic interaction energies. To assess the relative stability of the racemate with respect to the pure enantiomer, the crystal lattice energies, as obtained through DFT fully periodic calculations, are also discussed and compared with the experimental sublimation enthalpies after correction for the proton-transfer energies. In-crystal group charges, evaluated with the quantum theory of atoms in molecules, are found to be transferable between the racemic and the pure enantiomer, at variance with group volumes. Similarly, molecular first and third moments are not strictly transferable and indicate that for the zwitterionic alanine molecule the molecular charge distribution in the DL-crystal is more polarized in the c direction by about 10%. By contrast, quantitative agreement is observed for second and fourth moments. Significant differences arise from (1) the crystal packing of the dipole vectors, which are aligned in an antiparallel fashion in the L-crystal, to be compared with a parallel alignment in the racemate, due the polar space group Pna21 of the latter, (2) the strongly attractive electrostatic energy of a homochiral pair in the L-crystal, which is opposed to the corresponding heterochiral pair in the DL-crystal form. The difference between these Ees values amounts to 135-150 kJ mol(-1). Despite this, the two crystal forms are predicted as equally thermodynamically favored by the theoretical P-B3LYP estimates of the crystal lattice energies. Finally, the necessity of an upgrading of the dispersion and exchange-repulsion terms currently adopted within the experimental charge density approach to intermolecular interactions is recognized and discussed.

Proton transfer in the solid state: therymodynamic parameters from an X-ray study in the temperature range 20–293 K

Abstract From single-crystal X-ray diffraction data measured at 293, 240, 147 and 20 K, values of δ H = 1.6±0.6 kcal mol −1 and δ S = ±2.2 cal mol − K − are obtained for the tautomeric equilibrium between the p -quinonemethide and the o -quinone forms of citrinin. A correlation between bond lengths and equilibrium composition at different temperatures is presented.

On the role of data quality in experimental charge-density studies

High-resolution X-ray diffraction data were collected at T = 19 K from two similar spherical crystals of the fungal metabolite citrinin, C(13)H(14)O(5). The two data sets were of markedly different quality, one data set (MQ, medium quality) comprising a single octant of the reciprocal lattice and including reflections with obviously peculiar intensity profiles while the second (HQ, high quality) comprised a hemisphere of reflections and showed no flawed profiles. Parallel multipolar refinements were carried out for both. While most of the resulting geometric parameters, including bond lengths and angles, were in close agreement (the standard uncertainties were approximately twice as large for the MQ data, reflecting the smaller number of observations), the agreement is noticeably worse for electronic properties such as electron densities and their Laplacians at the bond and ring critical points. These latter features are especially sensitive to the quality of the low-angle (and strong) intensities, which was not high for the MQ data. By contrast, the magnitudes of the molecular dipole moment from the two experiments are the same within 1 standard uncertainty, with an angle of about 13 degrees between the two vectors. It is concluded that only true high-quality data allow a fully significant and quantitative analysis of the details of the experimental electron density rho(exp), while high-resolution medium-quality data, measured at very low temperature and adequately processed, can still be used for a qualitative analysis, or for the derivation of overall electronic properties.

Experimental and theoretical charge density distribution of the colossal magnetoresistive transition metal sulfide FeCr2S4

The total charge density distribution rho(r) of the colossal magnetoresistive transition metal sulfide FeCr(2)S(4) was evaluated through a multipole formalism from a set of structure factors obtained both experimentally, by means of single crystal high-quality x-ray diffraction data collected at T=23 K, and theoretically, with an extended-basis unrestricted Hartree-Fock periodic calculation on the experimental geometry. A full topological analysis, followed by the calculation of local energy density values and net atomic charges, was performed using the quantum theory of atoms in molecules. The experimental and theoretical results were compared. Good agreement was found for the topological properties of the system, as well as for the atomic net charges and the nature of the chemical bonds. An analysis of the electron density rho(r), its Laplacian nabla(2)[rho(r)], and the total energy density H(r) at the bond critical points was employed to classify all the interactions that resulted as predominantly closed shell (ionic) in nature. The topological indicators of the bonded interactions for Fe are distinct from those for Cr. The Fe-S bond distances were found to be 0.145 A shorter than the ideal values computed on the basis of Shannons crystal radii, much shorter than the Cr-S distances with respect to their ideal Shannon lengths. Concomitantly, rho(r) and |H(r)| at the bond critical points are greater for Fe-S interactions, indicating that the local concentration of charge density in the internuclear region is larger for the tetrahedrally coordinated iron than for the octahedrally coordinated chromium. The isosurface in the real space for nabla(2)[rho(r)]=0 was plotted for both iron and chromium, pointing out the local zones of valence shell charge concentration and relating them to the partial d-orbital occupancy of the two transition metal atoms.

Geometry and molecular parameters of 3,4-bis(dimethylamino)-3-cyclobutene-1,2-dione and its isomer bis(dimethylamino)squaraine. Combined study by IR spectroscopy, XRD and ab initio MO calculations

Absorption FTIR spectra have been recorded for solutions and solid phases of 3,4-bis(dimethylamino)-3-cyclobutene-1,2-dione and its isomer bis(dimethylamino)squaraine. The crystal structures of the two compounds have been established by XRD and compared with those of other bis(dialkylamino) analogues already studied by the same technique. Ab initio calculations for the squaraine led to a 6–31G** geometry substantially similar to the experimental one, indicating that crystal packing only marginally perturbs the equilibrium configuration of the isolated molecule. In contrast, the geometry of the 3-cyclobutene-1,2-dione derivative shows a degree of planarity considerably greater in the crystal than in the free molecule at the MP2/6–31G* minimum-energy nuclear configuration. The squaraine is predicted to be more stable, at all basis set levels here adopted, than its isomer. Differences and similarities between experimental IR frequencies and their ab initio estimates are presented.

Progress in the Understanding of the Key Pharmacophoric Features of the Antimalarial Drug Dihydroartemisinin: An Experimental and Theoretical Charge Density Study

The accurate, experimental charge density distribution, ρ(r), of the potent antimalarial drug dihydroartemisinin (DHA) has been derived for the first time from single-crystal X-ray diffraction data at T=100(2) K. Gas-phase and solid-state DFT simulations have also been performed to provide a firm basis of comparison with experimental results. The quantum theory of atoms in molecules (QTAIM) has been employed to analyse the ρ(r) scalar field, with the aim of classifying and quantifying the key real-space elements responsible for the known pharmacophoric features of DHA. From the conformational perspective, the bicyclo[3.2.2]nonane system fixes the three-dimensional arrangement of the 1,2,4-trioxane bearing the active O-O redox centre. This is the most nucleophilic function in DHA and acts as an important CH⋅⋅⋅O acceptor. On the contrary, the rest of the molecular backbone is almost neutral, in accordance with the lipophilic character of the compound. Another remarkable feature is the C-O bond length alternation along the O-C-O-C polyether chain, due to correlations between pairs of adjacent C-O bonds. These bonding features have been related with possible reactivity routes of the α- and β-DHA epimers, namely 1) the base-catalysed hemiacetal breakdown and 2) the peroxide reduction. As a general conclusion, the base-driven proton transfer has significant non-local effects on the whole polyether chain, whereas DHA reduction is thermodynamically favourable and invariably leads to a significant weakening (or even breaking) of the O-O bond. The influence of the hemiacetal stereochemistry on the electronic properties of the system has also been considered. Such findings are discussed in the context of the known chemical reactivity of this class of important antimalarial drugs.

Effect of Methoxy Substituents on the Structural and Electronic Properties of Fluorinated Cyclobutenes: A Study of Hexafluorocyclobutene and Its Vinyl Methoxy Derivatives by XRD and Periodic DFT Calculations

The effect of the methoxy substituent on the structure, crystal packing, and electrostatic properties of hexafluorocyclobutene (C(4)F(6)) was investigated in the solid-state with DFT-B3LYP calculations. Full geometry optimizations were done for the parent compound and its two vinyl methoxy derivatives C(4)F(5)OCH(3) and C(4)F(4)(OCH(3))(2), starting from the structures obtained by single-crystal X-ray diffraction at low temperature. A full topological analysis, followed by the calculation of several electrostatic properties, was performed on the periodic electron density using the quantum theory of atoms in molecules. Eventually, the cohesive energies of the three crystals were estimated. In the cyclobutene plane, the methoxy substitution yields a significant electronic rearrangement involving the pi-electrons. The solid-state (periodic) results agree with those obtained by gas-phase calculations on C(4)F(6) and its derivatives at a comparable level of theory. It was found that the substitution of one or two vinylic fluorine atoms with the OCH(3) group considerably influences the molecular dipole moment, which undergoes an enhancement in both the solid and the gas phase as large as 200% and 235% for C(4)F(5)OCH(3) and C(4)F(4)(OCH(3))(2), respectively, with respect to that calculated for C(4)F(6). The charge rearrangement due to the substituents provides a significant electrostatic contribution to the lattice energy, and in turn it can be related to the change in the observed crystal packing on going from C(4)F(6) (space group P2(1)/c) to both of its derivatives (space group P1). It is also shown that the dispersion energy significantly contributes to the lattice stability in all three compounds. Since the DFT calculations, in the limit of large separations, entirely miss the dispersion term, this was estimated by applying a recently proposed dampening function to the semiempirical atom-atom C(6) R(-6) potentials in the mainframe of Spackmans energy decomposition scheme for Mulliken multipoles.