Experimental Charge Density Analysis Research Articles

Halogen...halogen interactions from experimental charge-density analysis

Halogen...halogen interactions from experimental charge-density analysis

Correction to Experimental and Theoretical Charge Density Analysis of Polymorphic Structures: The Case of Coumarin 314 Dye

ADVERTISEMENT RETURN TO ISSUEPREVAdditions and Correc...Additions and CorrectionsORIGINAL ARTICLEThis notice is a correctionCorrection to Experimental and Theoretical Charge Density Analysis of Polymorphic Structures: The Case of Coumarin 314 DyeParthapratim Munshi, Christian Jelsch*, Venkatesha R. Hathwar, and Tayur N. Guru RowCite this: Cryst. Growth Des. 2010, 10, 10, 4670Publication Date (Web):August 24, 2010Publication History Received21 July 2010Published online24 August 2010Published inissue 6 October 2010https://doi.org/10.1021/cg1009658Copyright © 2010 American Chemical SocietyRIGHTS & PERMISSIONSArticle Views451Altmetric-Citations1LEARN ABOUT THESE METRICSArticle Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated. Share Add toView InAdd Full Text with ReferenceAdd Description ExportRISCitationCitation and abstractCitation and referencesMore Options Share onFacebookTwitterWechatLinked InReddit PDF (554 KB) Get e-AlertsSUBJECTS:Aromatic compounds,Chemical structure,Electrical properties,Mathematical methods Get e-Alerts

Experimental Charge Density Analysis of Symmetrically Substituted Ferrocene Derivatives

Experimental charge density analysis of three symmetrically substituted ferrocene derivatives: 1,1'- dimethyl ferrocene (1), decamethyl ferrocene (2), and 1,1'-diacetyl ferrocene (3) was conducted. The electron donating or accepting propensities of the ferrocene substituents were evaluated. The metal ligand interactions in all analyzed compounds were found to be similar in terms of charge density concentrations at Bond Critical Points (BCPs), laplacian values, and deformation density features. The monopole population of iron in all cases tend to be slightly negative, suggesting charge donation from Cp ligands. d orbital populations in all cases adopt values in agreement with theoretical calculations and ligand field theory. The charge distribution over analyzed molecules does not correlate with the formal oxidation potential in the analyzed compounds, as compound 2 in the currently studied structure takes the place suitable for an unsubstituted ferrocene. The non-intuitive low energy of the eclipsed conformation of 1 compound finds some explanation in the existence of a bond critical point between atoms of the two methyl groups in the structure. An asymmetry of the atomic surroundings of the two oxygen atoms in the 3 structure, reflected by the differences in charge rho(r(BCP)) and nabla(2)rho(r(BCP)) values and the shape of deformation density in the regions of oxygen lone electron pairs, is described.

Experimental and Theoretical Charge Density Analysis of Polymorphic Structures: The Case of Coumarin 314 Dye

Experimental charge density distributions in two known conformational polymorphs (orange and yellow) of coumarin 314 dye are analyzed based on multipole modeling of X-ray diffraction data collected at 100 K. The experimental results are compared with the charge densities derived from multipole modeling of theoretical structure factors obtained from periodic quantum calculation with density functional theory (DFT) method and B3LYP/6-31G(d,p) level of theory. The presence of disorder at the carbonyl oxygen atom of ethoxycarbonyl group in the yellow form, which was not identified earlier, is addressed here. The investigationof intermolecular interactions, based on Hirshfeld surface analysis and topological properties via quantum theory of atoms in molecule and total electrostatic interaction energies, revealed significant differences between the polymorphs. The differences of electrostatic nature in these two polymorphic forms were unveiled via construction of three-dimensional deformation electrostatic potential maps plotted over the molecular surfaces. The lattice energies evaluated from ab initio calculations on the two polymorphic forms indicate that the yellow form is likely to be the most favorable thermodynamically. The dipole moments derived from experimental and theoretical charge densities and also from Lorentz tensor approach are compared with the single-molecule dipole moments. In each case, the differences of dipole moments between the polymorphs are identified.

Conjugation in 1,4-diphenylbutadiyne and 1,2-diphenylacetylene: A combined experimental and theoretical study

We have performed a combined experimental and theoretical study of the molecular system of 1,4-diphenylbutadiyne and compared with previously reported 1,2-diphenylacetylene. 1,4-Diphenylbutadiyne exists as a half molecule in the asymmetric unit. Experimental charge density analysis of the molecule showed that the acetylenic linkers have triple bond character close to an ideal triple bond, in clear contrast to the situation 1,2-diphenylacetylene, where the charge density parameters resemble more closely those of a double bond due to extended conjugation. The influence of the reduced conjugation on the transport characteristics has been obtained using the Landauer’s formalism. Thus, 1,4-diphenylbutadiyne is found less conducting than 1,2-diphenylacetylene.

Rh(C7H8)(PPh3)Cl]: an experimental charge-density study

In order to gain a deeper understanding into the bonding situation in rhodium complexes containing rhodium-carbon interactions, the experimental charge-density analysis for [Rh(C(7)H(8))(PPh(3))Cl] (1) is reported. Accurate, high-resolution (sin theta/lambda = 1.08 A(-1)), single-crystal data were obtained at 100 K. The results from the investigation were interesting in relation to the interactions between the rhodium metal centre and the norbornadiene fragment and illustrate the importance of such analyses in studying bonding in organometallic complexes.

Synthesis and Structure of a Hexacoordinate Carbon Compound

In an exploration of six coordination and hypervalence in carbon compounds, steric constraints have been employed to bring four ether O atoms in close proximity to an allenic carbon atom. The dimethylated dication 2 is confirmed to have hexacoordinate carbon by experimental charge density analysis and DFT calculations and is arguably hypervalent.

Experimental electron density studies of non-steroidal synthetic estrogens: Diethylstilbestrol and dienestrol

An experimental charge density analysis has been carried out on two synthetic estrogens, diethylstilbestrol (DES) and dienestrol (DNS), to further investigate the alignment and binding of estrogenic compounds to the estrogen receptor, and to also establish a relationship between the biological function and the electronic properties of steroidal and non-steroidal estrogens by analysis of their electron density distribution. X-ray diffraction data for DES and DNS were obtained using a Rigaku R-Axis Rapid high-power rotating anode diffractometer with a curved image plate detector at 20(1) K. The total electron density was modeled using the Hansen–Coppens multipole model. Relatively strong O···H O hydrogen bonds, weak O···H C hydrogen bonds, and a number of intermolecular H···H interactions were characterized from the topological analyses of the total electron density of DES and DNS. Mapping of the electrostatic potential onto the molecular surface revealed negative regions around all the hydroxyl oxygens, above and below the aromatic rings as expected from previous studies. A proposed alignment and binding of DES and DNS to the estrogen receptor is discussed in terms of the atomic charges and electrostatic potential derived from the electron density distribution.

Strength vs. Accessibility: Unraveling the Patterns of Self‐Recognition in a Conformationally Locked Amino Alcohol

AbstractUnlike the self‐assembly of aminols studied till date, that of the conformationally locked, trans‐amino alcohol under study is unique in having the amino protons serving as mere spectators in the crystal packing. The principal non‐covalent interactions, holding the molecules in the crystal lattice, are O–H···N hydrogen bonds, and the rarely encountered π‐π stacking interactions between the isolated double bonds. Experimental charge density analyses have been carried out on the amino alcohol not only to characterize the non‐covalent interactions existing in the supramolecular assembly in terms of the topological features of electron density at their bond critical points, but also to elucidate the apparent presence of the “spectator” amino hydrogen atoms beyond the criteria of mere geometry. (© Wiley‐VCH Verlag GmbH & Co. KGaA, 69451 Weinheim, Germany, 2008)

Dipole Moment Enhancement in Molecular Crystals from X‐ray Diffraction Data

Although reliable determination of the molecular dipole moment from experimental charge density analyses on molecular crystals is a challenging undertaking, these values are becoming increasingly common experimental results. We collate all known experimental determinations and use this database to identify broad trends in the dipole moment enhancements implied by these measurements as well as outliers for which enhancements are pronounced. Compelling evidence emerges that molecular dipole moments from X-ray diffraction data can provide a wealth of information on the change in the molecular charge distribution that results from crystal formation. Most importantly, these experiments are unrivalled in their potential to provide this information in such detail and deserve to be exploited to a much greater extent. The considerable number of experimental determinations now available has enabled us to pinpoint those studies that merit further attention, either because they point unequivocally to a considerable enhancement in the crystal (of 50 % or more), or because the experimental determinations suggest enhancements of 100 % or more--much larger than independent theoretical estimates. In both cases further detailed experimental and theoretical studies are indicated.

Role of Triple Bond in 1,2-Diphenylacetylene Crystal: A Combined Experimental and Theoretical Study

We have performed a combined experimental and theoretical study of the molecular system of 1,2-diphenylacetylene. The occurrence of two different geometries of the molecule in the crystal structure, one being planar and the other tilted by approximately 6 degrees , has been investigated in relation to the nature of the acetylenic linker. The experimental charge density analysis shows that the acetylenic linker exhibits a noncylindrical density reminiscent of the strong conjugation present in the molecule. The pi-orbitals of the acetylenic linker derived from density functional theory (DFT) calculations are found to sustain a variety of conjugation lengths between the phenyl rings, thereby giving flexibility to the molecule to arrange itself in various packing conformations in the crystal. It is interesting that the energy involved for such distortions is only kBT, allowing several polymorphic forms of the crystal structure as reported in the literature. The distortions entertained by the molecule and the corresponding changes in the charge density distribution and energy are all relevant to molecular electronics.

Pointers toward the Occurrence of C−F···F−C Interaction: Experimental Charge Density Analysis of 1-(4-Fluorophenyl)-3,6,6-trimethyl-2-phenyl-1,5,6,7-tetrahydro-4H-indol-4-one and 1-(4-Fluorophenyl)-6-methoxy-2-phenyl-1,2,3,4-tetrahydroisoquinoline

A charge density study of crystalline 1-(4-fluorophenyl)-3,6,6-trimethyl-2-phenyl-1,5,6,7-tetrahydro-4H-indol-4-one (A) and 1-(4-fluorophenyl)-6-methoxy-2-phenyl-1,2,3,4-tetrahydroisoquinoline (B) has been carried out using high-resolution X-ray diffraction data collected at 113(2) K. Weak intermolecular interactions of the type C-H...O, C-H...pi, and pi...pi hold the molecules together in the crystal lattice along with interactions of the type C-H...F and unusual C-F...F-C examined via charge density analysis. The topological features are evaluated in terms of Bader's theory of atoms in molecules through the first four criteria of Koch and Popelier. The C-F...F-C contact is observed to be across the center of symmetry in B and not in A, and further, this interaction appears to possess a certain correlation with the electron density properties at the critical point which suggests that such an interaction fits into the hierarchy of weak interactions.

Reassessment of Large Dipole Moment Enhancements in Crystals: A Detailed Experimental and Theoretical Charge Density Analysis of 2-Methyl-4-nitroaniline

The molecular dipole moment of MNA in the crystal has been critically reexamined, to test the conclusion from an earlier experimental charge density analysis that it was substantially enhanced due to a combination of strong intermolecular interactions and crystal field effects. X-ray and neutron diffraction data have been carefully measured at 100 K and supplemented with ab initio crystal Hartree-Fock calculations. Considerable care taken in the measurement and reduction of the experimental data excluded most systematic errors, and sources of error and their effects on the experimental electron density have been carefully investigated. The electron density derived from a fit to theoretical structure factors assisted in the determination of the scale and thermal motion model. The dipole moment enhancement for MNA in the crystal is much less than that reported previously and only on the order of 30-40% (approximately 2.5 D). In addition to the dipole moment, experimental deformation electron density maps, bond critical point data, electric field gradients at hydrogen nuclei, and atomic and group charges all agree well with theoretical results and trends. Anisotropic modeling of the motion of hydrogen atoms, integral use of periodic ab initio calculations, and improved data quality are all aspects of this study that represent a considerable advance over previous work.

Charge density based classification of intermolecular interactions in molecular crystals

Evaluation of intermolecular interactions in terms of both experimental and theoretical charge density analyses has produced a unified picture with which to classify strong and weak hydrogen bonds, along with van der Waals interactions, into three regions.

Electrostatic complementarity in an aldose reductase complex from ultra-high-resolution crystallography and first-principles calculations.

The electron density and electrostatic potential in an aldose reductase holoenzyme complex have been studied by density functional theory (DFT) and diffraction methods. Aldose reductase is involved in the reduction of glucose in the polyol pathway by using NADPH as a cofactor. The ultra-high resolution of the diffraction data and the low thermal-displacement parameters of the structure allow accurate atomic positions and an experimental charge density analysis. Based on the x-ray structural data, order-N DFT calculations have been performed on subsets of up to 711 atoms in the active site of the molecule. The charge density refinement of the protein was performed with the program MOPRO by using the transferability principle and our database of charge density parameters built from crystallographic analyses of peptides and amino acids. Electrostatic potentials calculated from the charge density database, the preliminary experimental electron density analysis, DFT computations, and atomic charges taken from the amber software dictionary are compared. The electrostatic complementarity between the cofactor NADP+ and the active site shows up clearly. The anchoring of the inhibitor is due mainly to hydrophobic forces and to only two polar interaction sites within the enzyme cavity. The potentials calculated by x-ray and DFT techniques agree reasonably well. At the present stage of the refinement, the potentials obtained directly from the database are in excellent agreement with the experimental ones. In addition, these results demonstrate the significant contribution of electron lone pairs and of atomic polarization effects to the host and guest mechanism.

Probing the hydrogen bond through experimental charge densities

Experimental charge density analysis has been carried out by using low-temperature X-ray diffraction data on molecular crystals exhibiting a variety of hydrogen bond interactions. The various types of hydrogen-bonded interactions examined include O–H⋯O, N–H⋯O, C–H⋯O, O–H⋯N, N–H⋯N, N–H⋯S and C–H⋯S bonds. Static deformation density maps reveal depletion of electron density in the hydrogen-acceptor (H⋯A) regions. While the total density and the Laplacian at the H⋯A critical points exhibit an exponential dependence on the H⋯A distance, the positive curvature of the density, λ3, closely follows the exponential relation with a considerably better correlation factor. The relation derived based on the data for 218 hydrogen bonds of various types is given by 0.47×103exp(−2.5×dH⋯A).

Nature of the P [sbnd]O bond in diphenylphosphonic acid: experimental charge density and electron localization function analysis

Analysis of the electron density function and the ELF on the basis of the high resolution diffraction X-ray investigation of Ph2P(O)OH at 110 K have revealed that, in the vicinity of the oxygen atom of the P=O group, three lone pairs in an antiperiplanar orientation in respect to OH and Ph substituents are localised.

Experimental Charge Densities of Semiconducting Cage Structures Containing Alkaline Earth Guest Atoms Work at the X10c beamline at NSLS was supported by the Division of Materials Sciences of the US Department of Energy (DE-AC02-98CH10886). B.B.I. and A.E.C.P. gratefully acknowledge support from the Danish and Swedish Research Councils (SNF, TFR, STINT). This work was partially supported by the Office of Naval

That guest atoms donate electrons to framework atoms is a generally accepted concept. Nevertheless, evidence for the presence of neutral guest atoms in thermoelectric clathrate structures is presented in the form of experimental X-ray charge density analysis and X-ray absorption near-edge structure (XANES) data. The picture shows the deformation density (DD) determined by the maximum entropy method for Ba8Ga16Ge30; the DD shows that both the Ba guest atoms are disordered.