Approximate anisotropic displacement parameters for H atoms in molecular crystals

Roversi, Pietro; Destro, Riccardo

doi:10.1016/j.cplett.2004.01.092

Cited by 59 publications

(61 citation statements)

References 29 publications

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“…Finally, anisotropic U ij values (ADPs) were introduced for the 30 hydrogen atoms based on spectroscopic information and the molecular rigid-body librations derived from the refined ADPs of the carbon and nitrogen atoms. [57] Quadrupoles, with n = 2, could then also be introduced for the hydrogen atoms. a 0 and a 1 values for the hydrogen atoms were initially set to the standard molecular value of 2.48 bohr À1 and then refined (see the Supporting Information for their final values).…”

Section: Methodsmentioning

confidence: 99%

“…A marked polarization of the Laplacian of 1 around the hydrogen atom towards the acceptor atom N1' can be observed. It has been noted [56,57] that such a feature, typical of some hydrogen bonds, can be seen only if multipole models for the hydrogen atoms include quadrupolar electron-density functions (which, in turn, can be adopted only if anisotropic ADPs for these atoms are taken into account). The bond path trajectory along NH···N is almost perfectly linear, with the NÀH bond path only 0.001 longer than the corresponding internuclear distance and the H···N bond path identical to the atom-atom distance.…”

Section: à3mentioning

confidence: 98%

“…[57] As an approximate check of the values obtained, equivalent U values were compared with the previously refined X-ray U iso values: the difference exceeded 2.5 su in only one case, the average j D/s j value being 1.1. These hydrogen-calculated ADPs were included, and kept fixed, in the least-squares refinement, thus allowing the addition of quadrupoles to the multipolar expansion of the hydrogen atoms.…”

Section: -5 10mentioning

confidence: 99%

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Progress in the Understanding of Drug–Receptor Interactions, Part 1: Experimental Charge‐Density Study of an Angiotensin II Receptor Antagonist (C₃₀H₃₀N₆O₃S) atT=17 K

Destro

Soave

Barzaghi

et al. 2005

Chemistry A European J

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An experimental study of the electron-density distribution rho(r) in an angiotensin II receptor antagonist 1 has been made on the basis of single-crystal X-ray diffraction data collected at a low temperature. The crystal structure of 1 consists of infinite ribbons in which molecules are connected by an N-H...N hydrogen bond and several interactions of the C-H...O, C-H...N, and C-H...S type. The molecular conformation, characterized by the syn orientation of a tetrazole and a pyrimidinone ring with respect to a phenyl spacer group, is stabilized by two short SO and SN intramolecular contacts between a substituted thiophene fragment and the other two heterocycles of 1. The electrostatic nature of these interactions is documented. Furthermore, the Laplacian of rho(r) in the plane defined by the sulfur, oxygen, and nitrogen atoms involved in these interactions shows their strongly directional character as the regions of charge concentration on the valence shell of the nitrogen and oxygen atoms directly face the regions of charge depletion on the valence shell of the sulfur atom. All the chemical bonds and the relevant intra- and intermolecular interactions of 1 have been quantitatively described by the topological analysis of rho(r). Simple relationships between the bond path lengths (R(b)) and the values of rho at the bond critical points (rho(bcp)) have been obtained for the 28 C-C bonds, the seven N-C bonds, and the four O-C bonds. For the first two classes of bonds the relationship is in the form of a straight line, whose parameters, for the C-C bonds, agree, within experimental uncertainty, with those previously derived in our laboratory from a 19 K X-ray diffraction study of crystals of a different compound. Maps of the molecular electrostatic potential phi(r) derived from the experimental charge density display features that are important for the drug-receptor recognition of 1.

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Section: Methodsmentioning

confidence: 99%

Section: à3mentioning

confidence: 98%

Section: -5 10mentioning

confidence: 99%

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Progress in the Understanding of Drug–Receptor Interactions, Part 1: Experimental Charge‐Density Study of an Angiotensin II Receptor Antagonist (C₃₀H₃₀N₆O₃S) atT=17 K

Destro

Soave

Barzaghi

et al. 2005

Chemistry A European J

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“…[21] Anisotropic displacement parameters (ADPs) for hydrogen atoms were also included, as obtained from spectroscopic information and molecular rigid-body librations. [22] All refinements were carried out using the VALRAY [23] program.…”

Section: X-ray Diffractionmentioning

confidence: 99%

Progress in the Understanding of Drug–Receptor Interactions, Part 2: Experimental and Theoretical Electrostatic Moments and Interaction Energies of an Angiotensin II Receptor Antagonist (C₃₀H₃₀N₆O₃S)

Soave¹,

Barzaghi²,

Destro³

2007

Chemistry A European J

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A combined experimental and theoretical charge density study of an angiotensin II receptor antagonist (1) is presented focusing on electrostatic properties such as atomic charges, molecular electric moments up to the fourth rank and energies of the intermolecular interactions, to gain an insight into the physical nature of the drug-receptor interaction. Electrostatic properties were derived from both the experimental electron density (multipole refinement of X-ray data collected at T=17 K) and the ab initio wavefunction (single molecule and fully periodic calculations at the DFT level). The relevance of SO and SN intramolecular interactions on the activity of 1 is highlighted by using both the crystal and gas-phase geometries and their electrostatic nature is documented by means of QTAIM atomic charges. The derived electrostatic properties are consistent with a nearly spherical electron density distribution, characterised by an intermingling of electropositive and -negative zones rather than by a unique electrophilic region opposed to a nucleophilic area. This makes the first molecular moment scarcely significant and ill-determined, whereas the second moment is large, significant and highly reliable. A comparison between experimental and theoretical components of the third electric moment shows a few discrepancies, whereas the agreement for the fourth electric moment is excellent. The most favourable intermolecular bond is show to be an NHN hydrogen bond with an energy of about 50 kJ mol(-1). Key pharmacophoric features responsible for attractive electrostatic interactions include CHX hydrogen bonds. It is shown that methyl and methylene groups, known to be essential for the biological activity of the drug, provide a significant energetic contribution to the total binding energy. Dispersive interactions are important at the thiophene and at both the phenyl fragments. The experimental estimates of the electrostatic contribution to the intermolecular interaction energies of six molecular pairs, obtained by a new model proposed by Spackman, predict the correct relative electrostatic energies with no exceptions.

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“…Modeling of thermal motion in crystals has not received the same attention, yet the static densities and thermal motion are equally important: Together they conform the entire model refined against a single set of measured data. There is no doubt that a correct description of the thermal motion is crucial in order to obtain reliable estimates of the static densities [6,7]. We describe some new approaches to model atomic motion in crystals.…”

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confidence: 99%

Combiningab initiolattice dynamics and diffraction measurements in charge-density studies

Madsen¹

2013

Acta Cryst Sect A

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The use of synchrotron radiation and large area detectors have helped with measurement of charge densities so that the quality and quantity of data has become much better within the last decade. These advances call for new and better models to interpret the data. New approaches to model the static charge densities have been proposed, many of which relying on high-level ab-initio calculations, either by direct refinement or by inclusion in libraries describing typical bonding situations [1][2][3][4][5]. Modeling of thermal motion in crystals has not received the same attention, yet the static densities and thermal motion are equally important: Together they conform the entire model refined against a single set of measured data. There is no doubt that a correct description of the thermal motion is crucial in order to obtain reliable estimates of the static densities [6,7]. We describe some new approaches to model atomic motion in crystals. The SHADE (Simple Hydrogen Anisotropic Displacement Estimator, http://shade.ki.ku.dk) approach to estimate H atom motion has proven to be useful for many systems, yet there are special bonding systems that require other approaches. We present an approach based on combining (segmented) rigid body refinement and periodic ab-initio calculations, and compare with previous approaches and neutron diffraction results. We also demonstrate the transfer of mean square displacements from one structure to another. Both approaches are implemented in a new update of the SHADE server [8]. Using information from periodic ab-initio calculations can be used to describe the vibration of not only hydrogen, but also heavier atoms in the crystal. Our recent calculations of Debye-Waller factors for various test systems [9] has prepared the ground for proposing the refinement of normal modes of vibration against diffraction experiments. This last procedure opens the doors for refining data collected at multiple temperatures, as well as for modeling of thermal diffuse scattering.

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Approximate anisotropic displacement parameters for H atoms in molecular crystals

Cited by 59 publications

References 29 publications

Progress in the Understanding of Drug–Receptor Interactions, Part 1: Experimental Charge‐Density Study of an Angiotensin II Receptor Antagonist (C₃₀H₃₀N₆O₃S) atT=17 K

Progress in the Understanding of Drug–Receptor Interactions, Part 1: Experimental Charge‐Density Study of an Angiotensin II Receptor Antagonist (C₃₀H₃₀N₆O₃S) atT=17 K

Progress in the Understanding of Drug–Receptor Interactions, Part 2: Experimental and Theoretical Electrostatic Moments and Interaction Energies of an Angiotensin II Receptor Antagonist (C₃₀H₃₀N₆O₃S)

Combiningab initiolattice dynamics and diffraction measurements in charge-density studies

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Approximate anisotropic displacement parameters for H atoms in molecular crystals

Cited by 59 publications

References 29 publications

Progress in the Understanding of Drug–Receptor Interactions, Part 1: Experimental Charge‐Density Study of an Angiotensin II Receptor Antagonist (C30H30N6O3S) atT=17 K

Progress in the Understanding of Drug–Receptor Interactions, Part 1: Experimental Charge‐Density Study of an Angiotensin II Receptor Antagonist (C30H30N6O3S) atT=17 K

Progress in the Understanding of Drug–Receptor Interactions, Part 2: Experimental and Theoretical Electrostatic Moments and Interaction Energies of an Angiotensin II Receptor Antagonist (C30H30N6O3S)

Combiningab initiolattice dynamics and diffraction measurements in charge-density studies

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Progress in the Understanding of Drug–Receptor Interactions, Part 1: Experimental Charge‐Density Study of an Angiotensin II Receptor Antagonist (C₃₀H₃₀N₆O₃S) atT=17 K

Progress in the Understanding of Drug–Receptor Interactions, Part 1: Experimental Charge‐Density Study of an Angiotensin II Receptor Antagonist (C₃₀H₃₀N₆O₃S) atT=17 K

Progress in the Understanding of Drug–Receptor Interactions, Part 2: Experimental and Theoretical Electrostatic Moments and Interaction Energies of an Angiotensin II Receptor Antagonist (C₃₀H₃₀N₆O₃S)