A variable-temperature X-ray diffraction and theoretical study of conformational polymorphism in a complex organic molecule (DTC)

Gionda, Andrea; Macetti, Giovanni; Loconte, Laura; Rizzato, Silvia; Orlando, Ahmed M.; Gatti, Carlo; Presti, Leonardo Lo

doi:10.1039/c8ra08063a

Cited by 8 publications

(7 citation statements)

References 61 publications

(82 reference statements)

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“…The difference is of the order of one standard deviation. At variance with other cases [ 69 , 70 ], it can be concluded that the distribution of atomic charges in the 1-MUR molecule is not affected significantly by the crystal environment.…”

Section: Resultscontrasting

confidence: 62%

Anharmonic Thermal Motion Modelling in the Experimental XRD Charge Density Determination of 1-Methyluracil at T = 23 K

et al. 2021

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The experimental electron density distribution (EDD) of 1-methyluracil (1-MUR) was obtained by single crystal X-ray diffraction (XRD) experiments at 23 K. Four different structural models fitting an extensive set of XRD data to a resolution of (sinθ/λ)max = 1.143 Å−1 are compared. Two of the models include anharmonic temperature factors, whose inclusion is supported by the Hamilton test at a 99.95% level of confidence. Positive Fourier residuals up to 0.5 eÅ–3 in magnitude were found close to the methyl group and in the region of hydrogen bonds. Residual density analysis (RDA) and molecular dynamics simulations in the solid-state demonstrate that these residuals can be likely attributed to unresolved disorder, possibly dynamical and long–range in nature. Atomic volumes and charges, molecular moments up to hexadecapoles, as well as maps of the molecular electrostatic potential were obtained from distributed multipole analysis of the EDD. The derived electrostatic properties neither depend on the details of the multipole model, nor are significantly affected by the explicit inclusion of anharmonicity in the least–squares model. The distribution of atomic charges in 1-MUR is not affected by the crystal environment in a significant way. The quality of experimental findings is discussed in light of in-crystal and gas-phase quantum simulations.

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Section: Resultscontrasting

confidence: 62%

Anharmonic Thermal Motion Modelling in the Experimental XRD Charge Density Determination of 1-Methyluracil at T = 23 K

et al. 2021

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“…RDF or orientation angle comparisons become less indicative. It can never be neglected that the relative motions of rigid groups in floppy molecules (Lo Presti et al, 2014;Gionda et al, 2018) cause apparent fluctuations, and sometimes significant shifts, of the c.o.m. coordinates.…”

Section: Figurementioning

confidence: 99%

Molecular dynamics simulation of organic crystals: introducing the CLP-dyncry environment

Gavezzotti

Presti

2019

J Appl Cryst

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The CLP‐dyncry molecular dynamics (MD) program suite and force field environment is introduced and validated with its ad hoc features for the treatment of organic crystalline matter. The package, stemming from a preliminary implementation on organic liquids (Gavezzotti & Lo Presti, 2019), includes modules for the preliminary generation of molecular force field files from ab initio derived force constants, and for the preparation of crystalline simulation boxes from general crystallographic information, including Cambridge Structural Database CIFs. The intermolecular potential is the atom–atom Coulomb–London–Pauli force field, well tested as calibrated on sublimation enthalpies of organic crystals. These products are then submitted to a main MD module that drives the time integration and produces dynamic information in the form of coordinate and energy trajectories, which are in turn processed by several kinds of crystal‐oriented analytic modules. The whole setup is tested on a variety of bulk crystals of rigid, non‐rigid and hydrogen‐bonded compounds for the reproduction of radial distribution functions and of crystal‐specific collective orientational variables against X‐ray data. In a series of parallel tests, some advantages of a dedicated program as opposed to software more oriented to biomolecular simulation (Gromacs) are highlighted. The different and improved view of crystal packing that results from joining static structural information from X‐ray analysis with dynamic upgrades is also pointed out. The package is available for free distribution with I/O examples and Fortran source codes.

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“…They correspond to weak type I halogen bonds [39] involving atoms Cl1 and Cl12 of neighboring 4,7-dichloroquinoline ligands, which form infinite chains running approximately along the [1 11] direction (Figure S7) and connected to each other through type II Cl2• • • Cl12 contacts (Figure S8). As expected, direct Br• • • Br interactions are missing, as negatively charged Br − ions tend to be as far apart as possible from each other [10,29]. As they are included in the first coordination sphere of Cu atoms, Br − ions are also unavailable to set up Br• • • Cl contacts.…”

Section: Crystal Packingmentioning

confidence: 54%

“…Cl2•••Cl12 contacts (Figure S8). As expected, direct Br•••Br interactions are missing, as negatively charged Brions tend to be as far apart as possible from each other [10,29]. As they are included in the first coordination sphere of Cu atoms, Brions are also unavailable to set up Br•••Cl contacts.…”

mentioning

confidence: 54%

“…The structure of the title compound was optimized in vacuo with Gaussian09 [27], starting from the X-ray geometry. The Minnesota-class meta-GGA M06 DFT functional [28] was exploited to account for long-range dispersion effects [29], in conjunction with the triple zeta valence polarization (TZVP) basis set proposed by Peintinger [30]. A restricted basis was employed, considering both the singlet and triplet spin states of the complex.…”

Section: Quantum Simulations (Gas Phase)mentioning

confidence: 99%

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Unravelling the Chemistry of the [Cu(4,7-Dichloroquinoline)2Br2]2 Dimeric Complex through Structural Analysis: A Borderline Ligand Field Case

et al. 2020

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Large dark prismatic crystals (P 1 ¯ ) consisting of closely packed centrosymmetric [Cu(4,7-dichloroquinoline)2]2Br4 binuclear units are formed when 4,7-dichloroquinoline (DCQ, C9H5NCl2) binds copper(II). Cu2+ adopts a strongly distorted square pyramidal coordination geometry, perturbed by electrostatic interactions with two axial μ–Br ligands acting as highly asymmetric bridges. It is shown that, as electronic states of ligands are higher in energy than the metal ones, antibonding orbitals bear significant ligand-like character and electronic charge is partially transferred from inner-sphere coordinated halogen atoms to copper. Overall, the title compound sits on the Hoffman’s border between main group and transition chemistry, with non-negligible contributions of the ligands to the frontier orbitals. The relative energy placement of metal and ligand states determines an internal redox process, where the metal is slightly reduced at the expense of partial oxidation of the bromide ligands. In fact, the crystal structure is partially disordered due to the substitution of some penta-coordinated Cu(II) centers with tetra-coordinated Cu(I) ions. The geometry of the complex is rationalized in terms of electrostatic-driven distortions from an ideal octahedral prototype. Implications on the reactivity of Cu(II)–quinoline complexes are discussed.

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A variable-temperature X-ray diffraction and theoretical study of conformational polymorphism in a complex organic molecule (DTC)

Abstract: A small conformational change in the asymmetric unit has a significant effect on how non-covalent interactions determine (i) the crystal packing and (ii) the effect of T on the relative balance of electrostatics and dispersion–repulsions.

Cited by 8 publications

References 61 publications

Anharmonic Thermal Motion Modelling in the Experimental XRD Charge Density Determination of 1-Methyluracil at T = 23 K

Anharmonic Thermal Motion Modelling in the Experimental XRD Charge Density Determination of 1-Methyluracil at T = 23 K

Molecular dynamics simulation of organic crystals: introducing the CLP-dyncry environment

Unravelling the Chemistry of the [Cu(4,7-Dichloroquinoline)2Br2]2 Dimeric Complex through Structural Analysis: A Borderline Ligand Field Case

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