Journal articles: 'Bader’s topological analysis'

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Khrustalev, Victor N., Anna O. Savchenko, Anna I. Zhukova, Natalia Yu Chernikova, Michael A. Kurykin, Alexander S. Novikov, and Alexander G. Tskhovrebov. "Attractive fluorine···fluorine interactions between perfluorinated alkyl chains: a case of perfluorinated Cu(II) diiminate Cu[C2F5–C(NH)–CF=C(NH)–CF3]2." Zeitschrift für Kristallographie - Crystalline Materials 236, no. 3-4 (March 26, 2021): 117–22. http://dx.doi.org/10.1515/zkri-2021-2009.

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Abstract A synthesis of the perfluorinated copper diiminate complex Cu[C2F5–C(NH)–CF=C(NH)–CF3]2 (3) and its self-assembly into infinite 1D chains in the crystal via Type II C(sp3)–F···F–C(sp3) contacts between perfluoroethyl substituents is reported. Rare Type II F···F interactions were studied by DFT calculations and topological analysis of the electron density distribution within the formalism of Bader’s theory (QTAIM method). This is the first report which discusses Type II contacts between perfuoroalkyl chains.

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Bulatova, Margarita, Anna A. Melekhova, Alexander S. Novikov, Daniil M. Ivanov, and Nadezhda A. Bokach. "Redox reactive (RNC)CuII species stabilized in the solid state via halogen bond with I2." Zeitschrift für Kristallographie - Crystalline Materials 233, no. 6 (June 27, 2018): 371–77. http://dx.doi.org/10.1515/zkri-2017-2107.

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AbstractThe crystal structure of [Cu2(μ-O)(μ-I)2(CNXyl)4]·I2(2·I2) was determined from single-crystal X-ray diffraction data. The adduct2·I2represents the first example of structurally characterized isocyanide-copper(II) complexes. In the structure of2·I2,2forms independent chains connected through molecular iodine via I···I–I···I halogen bonding. The DFT calculations and topological analysis of the electron density distribution within the formalism of Bader’s theory (QTAIM method) were performed for model complex2·I2and the obtained results allowed the attribution of these contacts to moderate strength (3.8–5.3 kcal/mol) non-covalent contacts exhibiting some covalent character.

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Nenajdenko, Valentine G., Namiq G. Shikhaliyev, Abel M. Maharramov, Gulnar T. Atakishiyeva, Aytan A. Niyazova, Naila A. Mammadova, Alexander S. Novikov, Ivan V. Buslov, Victor N. Khrustalev, and Alexander G. Tskhovrebov. "Structural Organization of Dibromodiazadienes in the Crystal and Identification of Br···O Halogen Bonding Involving the Nitro Group." Molecules 27, no. 16 (August 11, 2022): 5110. http://dx.doi.org/10.3390/molecules27165110.

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Nitro functionalized dibromodiazadiene dyes were prepared and fully characterized including X-ray single crystal analysis. Electron deficient dibromodiazadienes were found to be able to act as donors of halogen bonding (XB), while the nitro group acted as an acceptor of the XB. Depending on the substituents, the Br···O XB competed with other weak interactions, and for some of the dyes, they even outcompeted the XB involving the nitro group. However, the nitro functionalized dibromoalkenes 6a and 10a, which had only the nitro moiety as the most plausible acceptor of the XB, reliably formed 1D chains via Br⋯O XB. Experimental work was supported by the DFT calculations and topological analysis of the electron density distribution within the framework of Bader’s theory (QTAIM method).

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Nenajdenko, Valentine G., Namiq G. Shikhaliyev, Abel M. Maharramov, Khanim N. Bagirova, Gulnar T. Suleymanova, Alexander S. Novikov, Victor N. Khrustalev, and Alexander G. Tskhovrebov. "Halogenated Diazabutadiene Dyes: Synthesis, Structures, Supramolecular Features, and Theoretical Studies." Molecules 25, no. 21 (October 29, 2020): 5013. http://dx.doi.org/10.3390/molecules25215013.

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Novel halogenated aromatic dichlorodiazadienes were prepared via copper-mediated oxidative coupling between the corresponding hydrazones and CCl4. These rare azo-dyes were characterized using 1H and 13C NMR techniques and X-ray diffraction analysis for five halogenated dichlorodiazadienes. Multiple non-covalent halogen···halogen interactions were detected in the solid state and studied by DFT calculations and topological analysis of the electron density distribution within the framework of Bader’s theory (QTAIM method). Theoretical studies demonstrated that non-covalent halogen···halogen interactions play crucial role in self-assembly of highly polarizable dichlorodiazadienes. Thus, halogen bonding can dictate a packing preference in the solid state for this class of dichloro-substituted heterodienes, which could be a convenient tool for a fine tuning of the properties of this novel class of dyes.

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Merli, Marcello, and Luciana Sciascia. "Bader’s topological analysis of the electron density in the pressure-induced phase transitions/amorphization in α-quartz from the catastrophe theory viewpoint." Physics and Chemistry of Minerals 40, no. 6 (March 23, 2013): 455–66. http://dx.doi.org/10.1007/s00269-013-0583-7.

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Parisi, Filippo, Luciana Sciascia, Francesco Princivalle, and Marcello Merli. "The pressure-induced ringwoodite to Mg-perovskite and periclase post-spinel phase transition: a Bader’s topological analysis of the ab initio electron densities." Physics and Chemistry of Minerals 39, no. 2 (November 1, 2011): 103–13. http://dx.doi.org/10.1007/s00269-011-0465-9.

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Kinzhalov, Mikhail A., Svetlana A. Katkova, Elizaveta P. Doronina, Alexander S. Novikov, Ivan I. Eliseev, Vasiliy A. Ilichev, Andrey A. Kukinov, Galina L. Starova, and Nadezhda A. Bokach. "Red photo- and electroluminescent half-lantern cyclometalated dinuclear platinum(II) complex." Zeitschrift für Kristallographie - Crystalline Materials 233, no. 11 (October 25, 2018): 795–802. http://dx.doi.org/10.1515/zkri-2018-2075.

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Abstract New cyclometalated dinuclear platinum(II) complex bearing bridged 4,6-dimethylpyrimidine-2(1H)-thiolate (μ-C6H7N2S-κN,S) ligands, [{Pt(ppy)(μ-C6H7N2S-κN,S)}2] (3) (ppy=(2-phenylpyridinato-C2,N)) was prepared via the reaction of chloro-bridged dimer [{Pt(ppy)Cl}2] with 4,6-dimethylpyrimidine-2(1H)-thione (C6H8N2S) in the presence of t-BuOK. The complex holds dinuclear frameworks with short Pt(II)···Pt(II) distance (2.8877(3) Å), and exhibit red intense luminescence from the triplet metal-metal-to-ligand charge-transfer at 697 nm in CH2Cl2 solution and at 649 nm in solid state at RT. Single crystal XRD analysis reveals the metallophilic interactions Pt···Pt with significant covalent contribution in the structure of 3 which were studied by quasi-relativistic and relativistic DFT calculations (viz., M06/MWB60(Pt) and 6-311+G* (other atoms); M06/DZP-DKH levels of theory) and topological analysis of the electron density distribution within the framework of Bader’s theory (QTAIM method). Estimated strength of the Pt···Pt contact is 8.1–12.2 kcal/mol and it is mostly determined by crystal packing effects and weak attractive interactions between the adjacent metal centers due to overlapping of their dz2 and pz orbitals. An organic light-emitting diode based on this complex showed red electroluminescence with maximal luminance of 115 cd/m2 and current efficiency of 2.45 cd/A at this luminance.

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Kandhakumar, Gopal, Chinnasamy Kalaiarasi, and Poomani Kumaradhas. "Structure and charge density distribution of amine azide based hypergolic propellant molecules: a theoretical study." Canadian Journal of Chemistry 94, no. 2 (February 2016): 126–36. http://dx.doi.org/10.1139/cjc-2015-0416.

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A quantum chemical calculation and charge density analysis of some amine azide based propellants (DMAZ, DMAEH, ADMCPA, AMCBA and ACPA) have been carried out to understand the geometry, bond topological, electrostatic, and energetic properties. The topological properties of electron density of the molecules were determined using Bader’s theory of atoms in molecules from the wave functions obtained from the density functional method (B3LYP) with the 6-311G** basis set. The electron density distribution of these molecules reveals the nature of chemical bonding in the molecules. The azide group attached C−N bonds of all molecules exhibit the electron density of ρbcp(r) ∼1.639 e Å−3 and the Laplacian of electron density ∇2ρbcp(r) is ∼–14.0 e Å−5, in which the corresponding values of the ADMCPA molecule are relatively high, 1.725 e Å–3 and –15.2 e Å−5 respectively, whereas for the methylamine group attached C–N bonds, these values are found to be higher (1.824 e Å–3 and –17.25 e Å−5). The Laplacian of terminal N–N bonds of the azide group is highly negative, indicating that these charges are highly concentrated, whereas the charge concentration of the dimethylamine group attached N–N bond of DMEAH is very much less, confirming that the bond is the weakest bond among the molecules. The energy density has been calculated for each bond of the molecules, which insights the energy density distribution of the molecules. Relatively, the molecules exhibit distinct electrostatic properties that are related to different charge distribution in the molecules. Large negative electrostatic potential regions are found at the vicinity of the amine and azide groups of the molecules. The charge imbalance parameter of the molecules has been determined and shows that the DMAEH molecule is the least sensitive molecule in this series.

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Yazdani-Kachoei, M., and S. Jalali-Asadabadi. "Topological analysis of electron density in half-Heusler ZrXBi (X = Co, Rh) compounds: A density functional theory study accompanied by Bader’s quantum theory of atoms in molecules." Journal of Alloys and Compounds 828 (July 2020): 154287. http://dx.doi.org/10.1016/j.jallcom.2020.154287.

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Mikherdov, Alexander, Alexander Novikov, Mikhail Kinzhalov, and Andrey Zolotarev. "Intra-/Intermolecular Bifurcated Chalcogen Bonding in Crystal Structure of Thiazole/Thiadiazole Derived Binuclear (Diaminocarbene)PdII Complexes." Crystals 8, no. 3 (February 27, 2018): 112. http://dx.doi.org/10.3390/cryst8030112.

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The coupling of cis-[PdCl2(CNXyl)2] (Xyl = 2,6-Me2C6H3) with 4-phenylthiazol-2-amine in molar ratio 2:3 at RT in CH2Cl2 leads to binuclear (diaminocarbene)PdII complex 3c. The complex was characterized by HRESI+-MS, 1H NMR spectroscopy, and its structure was elucidated by single-crystal XRD. Inspection of the XRD data for 3c and for three relevant earlier obtained thiazole/thiadiazole derived binuclear diaminocarbene complexes (3a EYOVIZ; 3b: EYOWAS; 3d: EYOVOF) suggests that the structures of all these species exhibit intra-/intermolecular bifurcated chalcogen bonding (BCB). The obtained data indicate the presence of intramolecular S•••Cl chalcogen bonds in all of the structures, whereas varying of substituent in the 4th and 5th positions of the thiazaheterocyclic fragment leads to changes of the intermolecular chalcogen bonding type, viz. S•••π in 3a,b, S•••S in 3c, and S•••O in 3d. At the same time, the change of heterocyclic system (from 1,3-thiazole to 1,3,4-thiadiazole) does not affect the pattern of non-covalent interactions. Presence of such intermolecular chalcogen bonding leads to the formation of one-dimensional (1D) polymeric chains (for 3a,b), dimeric associates (for 3c), or the fixation of an acetone molecule in the hollow between two diaminocarbene complexes (for 3d) in the solid state. The Hirshfeld surface analysis for the studied X-ray structures estimated the contributions of intermolecular chalcogen bonds in crystal packing of 3a–d: S•••π (3a: 2.4%; 3b: 2.4%), S•••S (3c: less 1%), S•••O (3d: less 1%). The additionally performed DFT calculations, followed by the topological analysis of the electron density distribution within the framework of Bader’s theory (AIM method), confirm the presence of intra-/intermolecular BCB S•••Cl/S•••S in dimer of 3c taken as a model system (solid state geometry). The AIM analysis demonstrates the presence of appropriate bond critical points for these interactions and defines their strength from 0.9 to 2.8 kcal/mol indicating their attractive nature.

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Martell, Jaime M., James B. Tee, and Russell J. Boyd. "Topological properties of the electronic structures of the reactants, transition states, and products of the reactions of the hydroxyl radical with the series C2HnF6−n, n = 1–6." Canadian Journal of Chemistry 74, no. 6 (June 1, 1996): 786–800. http://dx.doi.org/10.1139/v96-087.

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Properties of the bond critical points, including the electron density and its Laplacian, and distances to bonded nuclei, for all species (reactants, transition states, and products) in the reactions of the hydroxyl radical with the series C2HnF6−nn = 1–6 were calculated using Bader's atoms-in-molecules methodology. The electron density and its Laplacian at the bond critical points correlate with bond strength, as measured by bond dissociation energies. The positions of the bond critical points vary with the electronegativity of surrounding atoms. Charge development in the course of the reactions was monitored using Mulliken population analysis at the HF/6-31G(d), HF/6-311G(d,p)//HF/6-31G(d), MP2/6-311G(d,p)//HF/6-31G(d), and HF/6-311G(d,p)//MP2/6-31G(d,p) levels of theory, and natural population analysis and Bader population analysis at the highest common level of theory, MP2/6-311G(d,p)//HF/6-31G(d). In general, there is a buildup of charge in the transition states, concentrated near the reaction centre, which dissipates somewhat as the reaction proceeds to products. The description of charge transfer varies somewhat with the three methods. Key words: topological properties, atomic charges, charge development, reactions of the hydroxyl radical with fluorinated ethanes.

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Terlan, Bürgehan, Lev Akselrud, Alexey I. Baranov, Horst Borrmann, and Yuri Grin. "On the transferability of electron density in binary vanadium borides VB, V3B4 and VB2." Acta Crystallographica Section B Structural Science, Crystal Engineering and Materials 71, no. 6 (December 1, 2015): 777–87. http://dx.doi.org/10.1107/s2052520615018363.

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Binary vanadium borides are suitable model systems for a systematic analysis of the transferability concept in intermetallic compounds due to chemical intergrowth in their crystal structures. In order to underline this structural relationship, topological properties of the electron density in VB, V3B4 and VB2 reconstructed from high-resolution single-crystal X-ray diffraction data as well as derived from quantum chemical calculations, are analysed in terms of Bader's Quantum Theory of Atoms in Molecules [Bader (1990). Atoms in Molecules: A Quantum Theory, 1st ed. Oxford: Clarendon Press]. The compounds VB, V3B4 and VB2 are characterized by a charge transfer from the metal to boron together with two predominant atomic interactions, the shared covalent B—B interactions and the polar covalent B—M interactions. The resembling features of the crystal structures are well reflected by the respective B—B interatomic distances as well as by ρ(r) values at the B—B bond critical points. The latter decrease with an increase in the corresponding interatomic distances. The B—B bonds show transferable electron density properties at bond critical points depending on the respective bond distances.

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Dittrich, Birger. "Is there a future for topological analysis in experimental charge-density research?" Acta Crystallographica Section B Structural Science, Crystal Engineering and Materials 73, no. 3 (June 1, 2017): 325–29. http://dx.doi.org/10.1107/s2052520617006680.

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Topological analysis using Bader and co-worker'sAtoms in Moleculestheory has seen many applications in theoretical chemistry and experimental charge-density research. A brief overview of successful early developments, establishing topological analysis as a research tool for characterizing intramolecular chemical bonding, is provided. A lack of vision in many `descriptive but not predictive' subsequent studies is discussed. Limitations of topology for providing accurate energetic estimates of intermolecular interaction energies are put into perspective. It is recommended that topological analyses of well understood bonding situations are phased out and are only reported for unusual bonding. Descriptive studies of intermolecular interactions should have a clear research focus.

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Palatinus, Lukáš, Siriyara Jagannatha Prathapa, and Sander van Smaalen. "EDMA: a computer program for topological analysis of discrete electron densities." Journal of Applied Crystallography 45, no. 3 (May 16, 2012): 575–80. http://dx.doi.org/10.1107/s0021889812016068.

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EDMAis a computer program for topological analysis of discrete electron densities according to Bader's theory of atoms in molecules. It locates critical points of the electron density and calculates their principal curvatures. Furthermore, it partitions the electron density into atomic basins and integrates the volume and charge of these atomic basins.EDMAcan also assign the type of the chemical element to atomic basins based on their integrated charges. The latter feature can be used for interpretation ofab initioelectron densities obtained in the process of structure solution. A particular feature ofEDMAis that it can handle superspace electron densities of aperiodic crystals in arbitrary dimensions.EDMAfirst generates real-space sections at a selected set of phases of the modulation wave, and subsequently analyzes each section as an ordinary three-dimensional electron density. Applications ofEDMAto model electron densities have shown that the relative accuracy of the positions of the critical points, the electron densities at the critical points and the Laplacian is of the order of 10−4or better.

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Mardaleishvili, I. R., A. V. Vologznina, A. S. Novikov, A. I. Shienok, L. S. Kol’tsova, N. L. Zaichenko, V. A. Nadtochenko, and A. G. Tskhovrebov. "Hydrogen bonding in the crystal of 1,1'-((1E,1'E)-(pyridine-3,4-diylbis(azanylylidene))bis(methanylylidene))-bis(naphthalen-2-ol) acetonitrile solvate: combined experimental and theoretical study." Журнал структурной химии 63, no. 4 (2022): 510–12. http://dx.doi.org/10.26902/jsc_id91711.

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The title compound, 1,1'-((1E,1'E)-(pyridine-3,4-diylbis(azanylylidene))bis(methanylylidene))bis(naphthalen-2-ol) (1), was synthesized and structurally characterized. The compound cocrystallized with one MeCN molecule. Interestingly, one of two salicylaldehyde Schiff base fragments exists in enol form, while the other one — in a ketone form. Moreover, cocrystallized acetonitrile molecule forms hydrogen bonding with three hydrogen atoms of the dye molecule. The nature and energies of intermolecular and intramolecular hydrogen bonds were studied theoretically using DFT calculations and topological analysis of the electron density distribution within the formalism of Bader's theory (QTAIM method).

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Scheins, S., M. Messerschmidt, and P. Luger. "Submolecular partitioning of morphine hydrate based on its experimental charge density at 25 K." Acta Crystallographica Section B Structural Science 61, no. 4 (July 19, 2005): 443–48. http://dx.doi.org/10.1107/s010876810501637x.

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The electron density distribution of morphine hydrate has been determined from high-resolution single-crystal X-ray diffraction measurements at 25 K. A topological analysis was applied and, in order to analyze the submolecular transferability based on an experimental electron density, a partitioning of the molecule into atomic regions was carried out, making use of Bader's zero-flux surfaces to yield atomic volumes and charges. The properties obtained were compared with the theoretical calculations of smaller fragment molecules, from which the complete morphine molecule can be reconstructed, and with theoretical studies of another opiate, Oripavine PEO, reported in the literature.

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Ghiasi, Reza. "A chromium carbene (OC)5Cr=C(OEt)(–C≡C–Ph): Quantum mechanical study of molecular structure, HOMO–LUMO analysis, IR spectroscopy, natural bond orbital analysis." Journal of Theoretical and Computational Chemistry 14, no. 03 (May 2015): 1550022. http://dx.doi.org/10.1142/s0219633615500224.

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In this work, the structural, electronic properties, 13 C and 1 H NMR parameters and first hyperpolarizability of a chromium carbene ( OC )5 Cr = C ( OEt )(– C ≡ C – Ph ) complex were theoretically computed in gas phase and different solvents. Also, the solvent effect on structural parameters, frontier orbital energies, – C ≡ C – and C ≡ O stretching frequencies of complex has been carried out based on polarizable continuum model (PCM). The results indicate that the polarity of solvents has played a significant role on the structures and properties of complex. 1 H and 13 C NMR chemical shifts were calculated by using the gauge-independent atomic orbital (GIAO) method. In analyzing the structural characteristics of this structure, Cr – CO and Cr – C carbene bonds were identified and characterized in detail by topological parameters such as electron density ρ(r) and Laplacian of electron density ∇2ρ(r) from Bader's atom in molecules theory.

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Vank, Judith C., Carlos P. Sosa, Andras Perczel, and Imre G. Csizmadia. "Peptide models XXVII. An exploratory ab initio study on the 21st amino acid side-chain conformations of N-formyl-L-selenocysteinamide (For-L-Sec-NH2) and N-acetyl-L-selenocysteine-N-methylamide (Ac-L-Sec-NHMe) in their γL backbone conformation." Canadian Journal of Chemistry 78, no. 3 (March 1, 2000): 395–408. http://dx.doi.org/10.1139/v00-029.

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Selenocysteine is expected to have 9 × 9 = 81 conformations [3 × 3 = 9 backbone: ψ (g+,a,g-) × ϕ (g+,a,g-) and 3 × 3 = 9 side-chain: χ1 (g+,a,g-) × χ2 (g+,a,g-)]. In the present study, all the torsional modes of the side-chain (χ1: rotation about the Cα-Cβ and χ2: rotation about the Cβ-Se bonds) were investigated in the relaxed γL backbone [(ϕ,ψ); (g-,g+)] conformation. Seven out of the nine expected minima were found at the RHF/3-21G level of theory for N-formyl-L-selenocysteinamide (For-L-Sec-NH2) and N-acetyl-L-selenocysteine-N-methylamide (Ac-L-Sec-NHMe). The stabilization energy exerted by the -CH2-SeH side-chain has been compared with that of -CH2-SH and -CH2-OH. Relative energies of the various conformers were also obtained via single point calculations at the B3LYP/6-31G(d,p) level of theory. Topological analysis of the electron density has been performed by Bader's Atoms in Molecule (AIM) approach using the results. The structures were also optimized at the B3LYP/6-31+G(d,p) level of theory.Key words: selenocysteine side-chain conformations, ab initio MO study, Multidimensional Conformational Analysis (MDCA), Atoms in Molecules (AIM), Bader's electron density analysis.

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Chęcińska, Lilianna, Simon Grabowsky, Magdalena Małecka, Agnieszka J. Rybarczyk-Pirek, Andrzej Jóźwiak, Carsten Paulmann, and Peter Luger. "Experimental and theoretical electron-density study of three isoindole derivatives: topological and Hirshfeld surface analysis of weak intermolecular interactions." Acta Crystallographica Section B Structural Science 67, no. 6 (November 17, 2011): 569–81. http://dx.doi.org/10.1107/s0108768111041747.

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A combined experimental and theoretical study of three isoindole derivatives was made on the basis of a topological analysis of their electron-density distributions. Experimental electron densities were determined from high-resolution X-ray diffraction data sets measured with synchrotron radiation at 100 K, whereas theoretical calculations were performed using DFT methods at the B3LYP\6-311++G(3df,3pd) level of approximation. Both experimental and theoretical models are in good agreement with each other. Since the analysed structures possess a variety of hydrogen-bonding interactions, weak intermolecular contacts of C—H...C(π), C,N(π)...C,N(π) and H...H types were subject to our special interest and are discussed in detail. They were characterized quantitatively and qualitatively by topological properties using Bader's Atoms in Molecules theory and by mapping the electron-density distribution, electrostatic potential and a geometric function on the Hirshfeld surface. This way the forces and directions of intermolecular interactions as present on the molecular surfaces were depicted and described. These interactions not only guide crystal packing, but are likewise important for recognition processes involving (aza)isoindole fragments in a biological environment.

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Ivanov, Yu V., and E. L. Belokoneva. "Multipole refinement and electron density analysis in natural borosilicate datolite using X-ray diffraction data." Acta Crystallographica Section B Structural Science 63, no. 1 (January 15, 2007): 49–55. http://dx.doi.org/10.1107/s0108768106041681.

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The electron density distribution in the layer silicate datolite, Ca[BOH(SiO4)], was analyzed using high-precision single-crystal X-ray diffraction data (Mo Kα, T = 293 K). The Hansen–Coppens multipole model and Bader's topological analysis of the electron density provides a basis for the quantitative characterization of the bonded interaction of datolite. The results are presented both in the form of maps of the electron density distribution and its Laplacian, and in a compact way in terms of the critical points of the electron density. The relative electronegativities are also discussed. It was shown that closed-shell type interactions exist between Ca and O atoms, whereas Si—O and B—O bonds exhibit an intermediate nature with a strong covalent component. An analysis of the topology of the electrostatic potential demonstrates the relevance of considering this physical property to obtain a complete picture of structure-forming factors.

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Kalaiarasi, Chinnasamy, Christy George, Rajesh G. Gonnade, Venkatesha R. Hathwar, and Kumaradhas Poomani. "Experimental and theoretical charge density, intermolecular interactions and electrostatic properties of metronidazole." Acta Crystallographica Section B Structural Science, Crystal Engineering and Materials 75, no. 6 (October 26, 2019): 942–53. http://dx.doi.org/10.1107/s2052520619011272.

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Metronidazole is a radiosensitizer; it crystallizes in the monoclinic system with space group P21/c. The crystal structure of metronidazole has been determined from high-resolution X-ray diffraction measurements at 90 K with a resolution of (sin θ/λ)max = 1.12 Å−1. To understand the charge-density distribution and the electrostatic properties of metronidazole, a multipole model refinement was carried out using the Hansen–Coppens multipole formalism. The topological analysis of the electron density of metronidazole was performed using Bader's quantum theory of atoms in molecules to determine the electron density and the Laplacian of the electron density at the bond critical point of the molecule. The experimental results have been compared with the corresponding periodic theoretical calculation performed at the B3LYP/6-31G** level using CRYSTAL09. The topological analysis reveals that the N—O and C—NO2 exhibit less electron density as well as negative Laplacian of electron density. The molecular packing of crystal is stabilized by weak and strong inter- and intramolecular hydrogen bonding and H...H interactions. The topological analysis of O—H...N, C—H...O and H...H intra- and intermolecular interactions was also carried out. The electrostatic potential of metronidazole, calculated from the experiment, predicts the possible electrophilic and nucleophilic sites of the molecule; notably, the hydroxyl and the nitro groups exhibit large electronegative regions. The results have been compared with the corresponding theoretical results.

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Mestres, Jordi, Miquel Duran, and Juan Bertrán. "Comparative electronic analysis between hydrogen transfers in the CH4/CH3+, CH4/CH3•, and CH4/CH3− systems: on the electronic nature of the hydrogen (H−, H•, and H+) being transferred." Canadian Journal of Chemistry 74, no. 6 (June 1, 1996): 1253–62. http://dx.doi.org/10.1139/v96-141.

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A comparative electronic analysis of the generally termed hydrogen transfers between CH4 and the CH3+, CH3•, and CH3− fragments is presented. These systems are taken as simple models of hydride (H−), hydrogen (H•), and proton (H+) transfers between two carbon fragments (in these simple cases being modelized by two CH3+, CH3•, and CH3− fragments, respectively). The study is mainly focused on analysis of the electronic nature of the type of hydrogen being transferred in each system, and for this reason a topological analysis of charge density distributions was performed. Computation of Bader atomic charges and construction of the charge density, gradient vector field, and Appalachian of the charge density maps reveal the specific features of the electronic nature of the transferring H−, H•, and H+. Moreover, characterization of the bond critical points on the charge density surface permits clarification of the differences in atomic interactions between H−, H•, and H+ and the carbon belonging to each CH3+, CH3•, and CH3− fragment, respectively. A charge density redistribution analysis is also performed to quantify the reorganization of the electron density when going from the reactant complex to the transition state. Finally, effects of inclusion of the correlation energy at the MP2 and CISD levels are also discussed. Key words: electron density, hydrogen transfer, topological density analysis, molecular similarity, Bader density analysis.

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Liu, Yan Zhi, and Huian Tang. "X·F (X=C, N, O and S) Noncovalent Weak Intermolecular Interactions." Advanced Materials Research 881-883 (January 2014): 192–95. http://dx.doi.org/10.4028/www.scientific.net/amr.881-883.192.

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A number of X···F (X=C, N, O and S) noncovalent weak intermolecular interaction systems of CH3-F···XO2 (X=C, N, O and S) has been investigated at B3LYP/6-311++G(d, p) computational level. A topological analysis of the electron density for the X···F (X=C, N, O and S) noncovalent weak bonds was performed using Baders theory of atom-in-molecules (AIM). The interaction content of the F···X in H3CF···CO2 complex would mainly represent more π property than others. The interaction energies data without (ΔE) and with (ΔEcp) BSSE correction showed that the stability of the four complexes of the H3CF···DB2 system increases in the order of H3CF···O3 < H3CF···NO2 < H3CF···CO2 < H3CF···SO2.

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NIRMALA, V., and P. KOLANDAIVEL. "POST HARTREE–FOCK AND DENSITY FUNCTIONAL THEORY STUDIES ON (BN)n=1–10 CLUSTERS." International Journal of Nanoscience 04, no. 03 (June 2005): 377–88. http://dx.doi.org/10.1142/s0219581x0500319x.

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Density functional theory and Møller–Plesset perturbation theory methods have been used to study the ring clusters of ( BN )n=1–10 employing 6-311++G** basis set. The binding energies have been corrected for the basis set superposition error (BSSE). Static polarizability of these ring clusters has been investigated. A simple expression for the size dependence of polarizability has been invoked, so that the same relation can be useful for predicting the polarizability of larger clusters. The topological properties were analyzed employing the Bader's atoms in molecules theory. A good correlation between the structural parameters and the properties of electron density is found. Localization and delocalization indices were also used for the analysis of molecular electronic structure by an electron pair perspective. The contribution of stereo electronic interactions to the molecular properties as a function of ring size is analyzed based on the natural bond orbital (NBO) analysis.

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25

Munshi, Parthapratim, and Tayur N. Guru Row. "Intra- and intermolecular interactions in small bioactive molecules: cooperative features from experimental and theoretical charge-density analysis." Acta Crystallographica Section B Structural Science 62, no. 4 (July 12, 2006): 612–26. http://dx.doi.org/10.1107/s0108768106017393.

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The topological features of the charge densities, ρ(r), of three bioactive molecules, 2-thiouracil [2,3-dihydro-2-thioxopyrimidin-4(1H)-one], cytosine [4-aminopyrimidin-2(1H)-one] monohydrate and salicylic acid (2-hydroxybenzoic acid), have been determined from high-resolution X-ray diffraction data at 90 K. The corresponding results are compared with the periodic theoretical calculations, based on theoretical structure factors, performed using DFT (density-functional theory) at the B3LYP/6-31G** level. The molecules pack in the crystal lattices via weak intermolecular interactions as well as strong hydrogen bonds. All the chemical bonds, including the intra- and intermolecular interactions in all three compounds, have been quantitatively described by topological analysis based on Bader's quantum theory of `Atoms In Molecules'. The roles of interactions such as C—H...O, C—H...S, C—H...π and π...π have been investigated quantitatively in the presence of strong hydrogen bonds such as O—H...O, N—H...O and N—H...S, based on the criteria proposed by Koch and Popelier to characterize hydrogen bonds and van der Waals interactions. The features of weak intermolecular interactions, such as S...S in 2-thiouracil, the hydrogen bonds generated from the water molecule in cytosine monohydrate and the formation of the dimer via strong hydrogen bonds in salicylic acid, are highlighted on a quantum basis. Three-dimensional electrostatic potentials over the molecular surfaces emphasize the preferable binding sites in the structure and the interaction features of the atoms in the molecules, which are crucial for drug–receptor recognition.

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26

Dehestani, Maryam, and Leila Zeidabadinejad. "QTAIM investigation of bis(pyrazol-1-yl)methane derivative and its Zn(II) complexes (ZnLX2, X=Cl, Br or I)." Journal of the Serbian Chemical Society 80, no. 8 (2015): 997–1008. http://dx.doi.org/10.2298/jsc150224027z.

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Topological analyses of the electron density using the quantum theory of atoms in molecules (QTAIM) have been carried out at the B3PW91/6-31g (d) theoretical level, on bis(pyrazol-1-yl)methanes derivatives 9-(4-(di (1H-pyrazol-1-yl)-methyl)phenyl)-9H-carbazole (L) and its zinc(II) complexes: ZnLCl2 (1), ZnLBr2 (2) and ZnLI2 (3). The topological parameters derived from Bader theory were also analyzed; these are characteristics of Zn-bond critical points and also of ring critical points. The calculated structural parameters are the frontier molecular orbital energies highest occupied molecular orbital energy (EHOMO), lowest unoccupied molecular orbital energy (ELUMO), hardness (?), softness (S), the absolute electronegativity (?), the electrophilicity index (?) and the fractions of electrons transferred (?N) from ZnLX2 complexes to L. The numerous correlations and dependencies between energy terms of the Symmetry Adapted Perturbation Theory approach (SAPT), geometrical, topological and energetic parameters were detected and described.

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27

Faroque, Muhammad Umer, Sajida Noureen, Maqsood Ahmed, and Muhammad Nawaz Tahir. "Electrostatic properties of the pyrimethamine–2,4-dihydroxybenzoic acid cocrystal in methanol studied using transferred electron-density parameters." Acta Crystallographica Section C Structural Chemistry 74, no. 1 (January 1, 2018): 100–107. http://dx.doi.org/10.1107/s2053229617017788.

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The crystal structure of the cocrystal salt form of the antimalarial drug pyrimethamine with 2,4-dihydroxybenzoic acid in methanol [systematic name: 2,4-diamino-5-(4-chlorophenyl)-6-ethylpyrimidin-1-ium 2,4-dihydroxybenzoate methanol monosolvate, C12H14ClN4 +·C7H5O4 −·CH3OH] has been studied using X-ray diffraction data collected at room temperature. The crystal structure was refined using the classical Independent Atom Model (IAM) and the Multipolar Atom Model by transferring electron-density parameters from the ELMAM2 database. The Cl atom was refined anharmonically. The results of both refinement methods have been compared. The intermolecular interactions have been characterized on the basis of Hirshfeld surface analysis and topological analysis using Bader's theory of Atoms in Molecules. The results show that the molecular assembly is built primarily on the basis of charge transfer between 2,4-dihydroxybenzoic acid and pyrimethamine, which results in strong intermolecular hydrogen bonds. This fact is further validated by the calculation of the electrostatic potential based on transferred electron-density parameters.

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Held, Jeanette, and Sander van Smaalen. "The active site of hen egg-white lysozyme: flexibility and chemical bonding." Acta Crystallographica Section D Biological Crystallography 70, no. 4 (March 21, 2014): 1136–46. http://dx.doi.org/10.1107/s1399004714001928.

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Chemical bonding at the active site of hen egg-white lysozyme (HEWL) is analyzed on the basis of Bader's quantum theory of atoms in molecules [QTAIM; Bader (1994),Atoms in Molecules: A Quantum Theory.Oxford University Press] applied to electron-density maps derived from a multipole model. The observation is made that the atomic displacement parameters (ADPs) of HEWL at a temperature of 100 K are larger than ADPs in crystals of small biological molecules at 298 K. This feature shows that the ADPs in the cold crystals of HEWL reflect frozen-in disorder rather than thermal vibrations of the atoms. Directly generalizing the results of multipole studies on small-molecule crystals, the important consequence for electron-density analysis of protein crystals is that multipole parameters cannot be independently varied in a meaningful way in structure refinements. Instead, a multipole model for HEWL has been developed by refinement of atomic coordinates and ADPs against the X-ray diffraction data of Wang and coworkers [Wanget al.(2007),Acta Cryst.D63, 1254–1268], while multipole parameters were fixed to the values for transferable multipole parameters from the ELMAM2 database [Domagalaet al.(2012),Acta Cryst.A68, 337–351] . Static and dynamic electron densities based on this multipole model are presented. Analysis of their topological properties according to the QTAIM shows that the covalent bonds possess similar properties to the covalent bonds of small molecules. Hydrogen bonds of intermediate strength are identified for the Glu35 and Asp52 residues, which are considered to be essential parts of the active site of HEWL. Furthermore, a series of weak C—H...O hydrogen bonds are identified by means of the existence of bond critical points (BCPs) in the multipole electron density. It is proposed that these weak interactions might be important for defining the tertiary structure and activity of HEWL. The deprotonated state of Glu35 prevents a distinction between the Phillips and Koshland mechanisms.

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FAZLI, M., A. F. JALBOUT, H. RAISSI, H. GHIASSI, and M. YOOSEFIAN. "ANALYSIS OF THE INTRA-MOLECULAR HYDROGEN BOND STRENGTH IN 3-HYDROXY-PROPENETHIAL (HPT)." Journal of Theoretical and Computational Chemistry 08, no. 04 (August 2009): 713–32. http://dx.doi.org/10.1142/s0219633609004289.

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The molecular structure and intra-molecular hydrogen bond energy of 20 conformers of 3-hydroxy-propenethial were investigated by using the MP2 and B3LYP levels of theory coupled to the 6-311++G** basis set. Also, computations for all the possible conformations of HPT in water and carbon tetrachloride solution were performed. The calculated geometrical parameters and conformational analyses in both gas phase and solution reveal that the closed ring hydrogen bonded structures are more stable than the remainder of the species. Hydrogen bond energies for various hydrogen-bonded conformers were obtained and investigated by means of the Bader theory of atoms in molecules (which is based on topological properties of the electron density).

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Farrugia, Louis J., Paul R. Mallinson, and Brian Stewart. "Experimental charge density in the transition metal complex Mn2(CO)10: a comparative study." Acta Crystallographica Section B Structural Science 59, no. 2 (March 26, 2003): 234–47. http://dx.doi.org/10.1107/s0108768103000892.

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An accurate experimental charge density study at 100 K of Mn2(CO)10 [bis(pentacarbonylmanganese)(Mn—Mn)] has been undertaken. A comparison with previously reported structural determinations reveals no evidence for significant Mn—Mn bond lengthening between 100 and 296 K. The nature of the metal–metal and metal–ligand atom interactions has been studied by topological analysis using the Atoms in Molecules (AIM) approach of Bader [(1990), Atoms in Molecules: a Quantum Theory.Oxford: Clarendon Press]. An analysis of the density ρ(r), the Laplacian of the density ∇2ρ(r b ) and the total energy densities H(r b ) at the bond critical points is used to classify all the chemical bonds as covalent in nature. The results are compared qualitatively and quantitatively with previous charge density studies on this molecule and DFT calculations at the 6-311+G* B3LYP level. The topological properties of the theoretical and experimental densities are in close agreement.

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Bichara, Laura Cecilia, Hernán Enrique Lanús, Evelina Gloria Ferrer, Mónica Beatriz Gramajo, and Silvia Antonia Brandán. "Vibrational Study and Force Field of the Citric Acid Dimer Based on the SQM Methodology." Advances in Physical Chemistry 2011 (June 20, 2011): 1–10. http://dx.doi.org/10.1155/2011/347072.

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We have carried out a structural and vibrational theoretical study for the citric acid dimer. The Density Functional Theory (DFT) method with the B3LYP/6-31G∗ and B3LYP/6-311++ methods have been used to study its structure and vibrational properties. Then, in order to get a good assignment of the IR and Raman spectra in solid phase of dimer, the best fit possible between the calculated and recorded frequencies was carry out and the force fields were scaled using the Scaled Quantum Mechanic Force Field (SQMFF) methodology. An assignment of the observed spectral features is proposed. A band of medium intensity at 1242 together with a group of weak bands, previously not assigned to the monomer, was in this case assigned to the dimer. Furthermore, the analysis of the Natural Bond Orbitals (NBOs) and the topological properties of electronic charge density by employing Bader's Atoms in Molecules theory (AIM) for the dimer were carried out to study the charge transference interactions of the compound.

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32

Foroutan-Nejad, Cina, Gholam Hossein Shafiee, Abdolreza Sadjadi, and Shant Shahbazian. "Ab initio charge density analysis of (B6C)2 and B4C3 species How to describe the bonding pattern?" Canadian Journal of Chemistry 84, no. 5 (May 1, 2006): 771–81. http://dx.doi.org/10.1139/v06-059.

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In this study, a detailed topological charge density analysis based on the quantum theory of atoms in molecules (QTAIM) developed by Bader and co-workers, has been accomplished (using the B3LYP method) on the CB62 anion and three planar isomers of the C3B4 species, which had been first proposed by Exner and Schleyer as examples of molecules containing hexacoordinate carbon atoms. The analysis uncovers the strong (covalent) interactions of boron atoms as well as the "nondirectional" interaction of central carbon atom with those peripheral atoms. On the other hand, instabilities have been found in the topological networks of (B6C)2 and B4C3(para) species. A detailed investigation of these instabilities demonstrates that the topology of charge density has a floppy nature near the equilibrium geometries of the species under study. Thus, these species seems to be best described as complexes of a relatively concrete ring containing boron or carbon atoms and a central carbon atom that is confined in the plane of the molecule, but with nondirectional interactions with the surrounding atoms.Key words: hypervalency, hexacoordinate carbon, quantum theory of atoms in molecules, charge density analysis, ab initio methods.

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Grishina, Maria A., and Vladimir A. Potemkin. "Topological Analysis of Electron Density in Large Biomolecular Systems." Current Drug Discovery Technologies 16, no. 4 (December 11, 2019): 437–48. http://dx.doi.org/10.2174/1570163815666180821165330.

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Background: A great step toward describing the structure of the molecular electron was made in the era of quantum chemical methods. Methods play a very important role in the prediction of molecular properties and in the description of the reactivity of compounds, which cannot be overestimated. There are many works, books, and articles on quantum methods, their applications, and comparisons. At the same time, quantum methods of a high level of theory, which give the most accurate results, are time-consuming, which makes them almost impossible to describe large complex molecular systems, such as macromolecules, enzymes, supramolecular compounds, crystal fragments, and so on. Objective: To propose an approach that allows real-time estimation of electron density in large systems, such as macromolecules, nanosystems, proteins. Methods: AlteQ approach was applied to the tolopogical analysis of electron density for “substrate - cytochrome” complexes. The approach is based on the use of Slater’s type atomic contributions. Parameters of the atomic contributions were found using high resolution X-ray diffraction data for organic and inorganic molecules. Relationships of the parameters with atomic number, ionization potentials and electronegativities were determined. The sufficient quality of the molecular electron structure representation was shown under comparison of AlteQ predicted and observed electron densities. AlteQ algorithm was applied for evaluation of electron structure of “CYP3A4 – substrate” complexes modeled using BiS/MC restricted docking procedure. Topological analysis (similar to Atoms In Molecules (AIM) theory suggested by Richard F.W. Bader) of the AlteQ molecular electron density was carried out for each complex. The determination of (3,-1) bond, (3,+1) ring, (3,+3) cage critical points of electron density in the intermolecular “CYP3A4 – substrate” space was performed. Results: Different characteristics such as electron density, Laplacian eigen values, etc. at the critical points were computed. Relationship of pKM (KM is Michaelis constant) with the maximal value of the second Laplacian eigen value of electron density at the critical points and energy of complex formation computed using MM3 force field was determined. Conclusion: It was shown that significant number of (3,-1) bond critical points are located in the intermolecular space between the enzyme site and groups of substrate atoms eliminating during metabolism processes.

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Munshi, Parthapratim, Tejender S. Thakur, Tayur N. Guru Row, and Gautam R. Desiraju. "Five varieties of hydrogen bond in 1-formyl-3-thiosemicarbazide: an electron density study." Acta Crystallographica Section B Structural Science 62, no. 1 (January 17, 2006): 118–27. http://dx.doi.org/10.1107/s0108768105033689.

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In an attempt to investigate the putative S—H...N hydrogen bond, we have studied the title compound, 1-formyl-3-thiosemicarbazide, which was revealed in a CSD search as a crystal structure which might show such an interaction. However, a redetermination of the structure at room temperature and careful analysis showed that the earlier study [Saxena et al. (1991). Acta Cryst. C47, 2374–2376] on which the CSD search was based was in error and that the possibility of an S—H...N hydrogen bond is negated. The presence of five other varieties of hydrogen bond (N—H...O, N—H...S, N—H...N, C—H...O, C—H...S) in the crystal packing prompted us to redirect our efforts and to undertake a study of the charge-density distribution at 90 K. The topological analysis of these five varieties of hydrogen bond was carried out with Bader's quantum theory of `atoms in molecules' and by applying Koch–Popelier's criteria. The analysis reveals that the hydrogen-bond strength is highest for N—H...O and lowest for C—H...S with N—H...S, N—H...N and C—H...O forming the middle order.

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Parisi, Filippo, Luciana Sciascia, Francesco Princivalle, and Marcello Merli. "Pressure stability field of Mg-perovskite under deep mantle conditions: A topological approach based on Bader's analysis coupled with catastrophe theory." Ceramics International 45, no. 2 (February 2019): 2820–27. http://dx.doi.org/10.1016/j.ceramint.2018.07.294.

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Choi, Sai Cheng, and Russell J. Boyd. "Analysis of intramolecular hydrogen bonding in terms of the topological properties of the charge density. The protonated fluoroacetones." Canadian Journal of Chemistry 64, no. 10 (October 1, 1986): 2042–47. http://dx.doi.org/10.1139/v86-337.

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A new method for the analysis of intramolecular hydrogen bonding is proposed and applied to the equilibrium structures of the protonated fluoroacetones. The method, based on a theory of molecular structure due to Bader, uses the topological properties of the charge density to elucidate the types of interactions within a molecule of interest. The calculations show a strong basis set dependence. In particular, the STO-3G optimized geometries exhibit intramolecular hydrogen bonding between a fluorine substituent and the carbonyl proton, whereas some calculations with geometries optimized at the 4-31G and 6-31G* levels indicate a direct bonding interaction between the fluorine and oxygen atoms. Two types of catastrophe point, namely conflict and bifurcation, are possible in protonated monofluoroacetone. Only the latter was located in the present calculations.

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Wang, Ruimin, Christian W. Lehmann, and Ulli Englert. "Weak interactions in chain polymers [M(μ-X)2 L 2]∞ (M = Zn, Cd; X = Cl, Br; L = substituted pyridine) – an electron density study." Acta Crystallographica Section B Structural Science 65, no. 5 (August 28, 2009): 600–611. http://dx.doi.org/10.1107/s0108768109028626.

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The experimental electron-density distributions in crystals of five chain polymers [M(μ-X)2(py)2] (M = Zn, Cd; X = Cl, Br; py = 3,5-substituted pyridine) have been obtained from high-resolution X-ray diffraction data sets (sin θ/λ > 1.1 Å−1) at 100 K. Topological analyses following Bader's `Atoms in Molecules' approach not only confirmed the existence of (3, −1) critical points for the chemically reasonable and presumably strong covalent and coordinative bonds, but also for four different secondary interactions which are expected to play a role in stabilizing the polymeric structures which are unusual for Zn as the metal center. These weaker contacts comprise intra- and inter-strand C—H...X—M hydrogen bonds on the one hand and C—X...X—C interhalogen contacts on the other hand. According to the experimental electron-density studies, the non-classical hydrogen bonds are associated with higher electron density in the (3, −1) critical points than the halogen bonds and hence are the dominant interactions both with respect to intra- and inter-chain contacts.

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Faroque, Muhammad Umer, Sajida Noureen, Shafaat Hussain Mirza, Muhammad Nawaz Tahir, and Maqsood Ahmed. "Structure and electrostatic properties of the pyrimethamine–3,5-dihydroxybenzoic acid cocrystal in water solvent studied using transferred electron-density parameters." Acta Crystallographica Section C Structural Chemistry 75, no. 1 (January 1, 2019): 46–53. http://dx.doi.org/10.1107/s2053229618017060.

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Pyrimethamine is an antimalarial drug. The cocrystal salt form of pyrimethamine with 3,5-dihydroxybenzoic acid in water solvent has been synthesized, namely 2,4-diamino-5-(4-chlorophenyl)-6-ethylpyrimidin-1-ium 3,5-dihydroxybenzoate hemihydrate, C12H14ClN4 +·C7H5O4 −·0.5H2O. X-ray diffraction data were collected at room temperature. Refinement of the crystal structure was carried out using the classical Independent Atom Model (IAM), while the electrostatic properties were studied by transferring electron-density parameters from an electron-density database. The Cl atom was refined anharmonically. The results of both refinement methods were compared. Topological analyses were carried out using Bader's theory of Atoms in Molecules (AIM). The three-dimensional Hirshfeld surface analysis and the two-dimensional fingerprint maps of individual molecules revealed that the crystal structures are dominated by H...O/O...H and H...H contacts. Other close contacts are also present, including weak C...H/H...C contacts. Charge transfer between the pyrimethamine and 3,5-dihydroxybenzoic acid molecules results in a molecular assembly based on strong intermolecular hydrogen bonds. This is further validated by the calculation of the electrostatic potential based on transferred electron-density parameters. The current work proves the significance of the transferability principle in studying the electron-density-derived properties of molecules in cases where high-resolution diffraction data at low temperature are not available.

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Hasil, Asma, Arshad Mehmood, and Maqsood Ahmed. "Experimental and theoretical charge-density analysis of hippuric acid: insight into its binding with human serum albumin." Acta Crystallographica Section B Structural Science, Crystal Engineering and Materials 75, no. 4 (July 30, 2019): 750–62. http://dx.doi.org/10.1107/s2052520619007911.

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In order to comprehend the binding of an important metabolite, hippuric acid, with human serum albumin and to understand its chemical and electronic nature, an experimental charge-density analysis has been carried out using high-resolution diffraction data collected under cryogenic conditions, and all the results have been compared with theoretical findings using the B3LYP/6-311++g(2d,2p) level of theory. The structure displays very strong classical hydrogen bonds as well as other noncovalent interactions, which have been fully characterized using Hirshfeld surface analysis and Bader's quantum theory of atoms in molecules. Contact analysis on the Hirshfeld surfaces shows that the O...H, C...H and C...N intermolecular interactions are enriched and gives their relative strengths. Topological analysis of the electron density shows the charge concentration/depletion of hippuric acid bonds in the crystal structure. Electrostatic parameters such as atomic charges and dipole moments were calculated. The mapping of atomic basins and the calculation of respective charges show the atomic volumes of each atom as well as their charge contributions in the hippuric acid crystal structure. The dipole-moment calculations show that the molecule is very polar in nature. Calculations of the electrostatic potential show that the chain part of the molecule has a higher concentration of negative charge than the ring, which might be instrumental in its strong binding with the polar residues of site II of human serum albumin.

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Paskaš Mamula, Bojana, Bojana Kuzmanović, Mirjana Medić Ilić, Nenad Ivanović, and Nikola Novaković. "Bonding mechanism of some simple ionic systems: Bader topological analysis of some alkali halides and hydrides revisited." Physica B: Condensed Matter 545 (September 2018): 146–51. http://dx.doi.org/10.1016/j.physb.2018.06.008.

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Scheins, S., B. Dittrich, M. Messerschmidt, C. Paulmann, and P. Luger. "Atomic volumes and charges in a system with a strong hydrogen bond: L-tryptophan formic acid." Acta Crystallographica Section B Structural Science 60, no. 2 (March 18, 2004): 184–90. http://dx.doi.org/10.1107/s0108768104001739.

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A high-resolution X-ray diffraction data set was collected within 48 h at 100 K with synchrotron radiation and area detection. A full topological analysis was applied to the resulting electron-density model. This analysis was followed by a Bader partitioning making use of the zero-flux surfaces of the electron-density gradient vector field. The atomic and bonding properties obtained were compared with the results of previous experimental studies, and with theoretical calculations for the title complex and free tryptophan as reported in the literature. The agreement between experiment and theory is similar to the agreement between different theoretical calculations. There is no charge transfer via the strong hydrogen bond; however, its strength is indicated by the very small atomic volume of the H atom involved.

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Tang, Ting-Hua, Dennis M. Whitfield, Stephen P. Douglas, Jiri J. Krepinsky, and Imre G. Csizmadia. "Differential reactivity of carbohydrate hydroxyls in glycosylations. III. Structure, stability, and reactivity of 2′-deoxycytidine model compound-BF3 complexes." Canadian Journal of Chemistry 72, no. 8 (August 1, 1994): 1803–15. http://dx.doi.org/10.1139/v94-229.

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The possibility of complexation between an acidic promoter like BF3 and the alcoholic aglycone has been studied as a key mechanistic intermediate in glycosylation reactions operating via an electron-deficient anomeric carbon. The BF3 complexes at O3′,O4′,O5′, and N3 of the model compound of 3′-,4-N-diacetyl-2′-deoxyribocytosine (1) have been studied. The last regioisomer of the four BF3 complexes was found to have the weakest hydrogen bond and yet was the most stable isomer energetically. Furthermore, the O5′ nucleophilicity of this isomer was the most pronounced, as evaluated by Bader-type charge density topological analysis at the HF/6-31G**//HF/3-21G level of theory. This indicates that such a complex will make glycosylation at the O5′ oxygen possible.

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Khalilov, Leonard M., Ekaterina S. Mescheryakova, Kamil Sh Bikmukhametov, Natalia N. Makhmudiyarova, Kamil R. Shangaraev, and Arthur R. Tulyabaev. "Twist-chair conformation of the tetraoxepane ring remains unchanged in tetraoxaspirododecane diamines." Acta Crystallographica Section C Structural Chemistry 76, no. 3 (February 18, 2020): 276–86. http://dx.doi.org/10.1107/s2053229620001382.

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A detailed structural analysis has been performed for N,N′-bis(4-chlorophenyl)-7,8,11,12-tetraoxaspiro[5.6]dodecane-9,10-diamine, C20H22Cl2N2O4, (I), N,N′-bis(2-fluorophenyl)-7,8,11,12-tetraoxaspiro[5.6]dodecane-9,10-diamine, C20H22F2N2O4, (II), and N,N′-bis(4-fluorophenyl)-7,8,11,12-tetraoxaspiro[5.6]dodecane-9,10-diamine, C20H22F2N2O4, (III). The seven-membered ring with two peroxide groups adopts a twist-chair conformation in all three compounds. The lengths of the C—N and O—O bonds are slightly shorter than the average statistical values found in the literature for azepanes and 1,2,4,5-tetraoxepanes. The geometry analysis of compounds (I)–(III), the topological analysis of the electron density at the (3, −1) bond critical points within Bader's quantum theory of `Atoms in molecules' (QTAIM) and NBO (natural bond orbital) analysis at the B3LYP/6-31G(d,2p) level of theory showed that there are n O→σ*(C—O), n N→σ*(C—O) and n O→σ*(C—N) stereoelectronic effects. The molecules of compounds (I) and (III) are packed in the crystals as zigzag chains due to strong N—H...O and C—H...O hydrogen-bond interactions, whereas the molecules of compound (II) form chains in the crystals bound by N—H...O, C—H...π and C—H...O contacts. All these data show that halogen atoms and their positions have a minimal effect on the geometric parameters, stereoelectronic effects and crystal packing of compounds (I)–(III), so that the twist-chair conformation of the tetraoxepane ring remains unchanged.

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Bibila Mayaya Bisseyou, Yvon, Nouhza Bouhmaida, Benoit Guillot, Claude Lecomte, Noel Lugan, Noureddine Ghermani, and Christian Jelsch. "Experimental and database-transferred electron-density analysis and evaluation of electrostatic forces in coumarin-102 dye." Acta Crystallographica Section B Structural Science 68, no. 6 (November 16, 2012): 646–60. http://dx.doi.org/10.1107/s0108768112042826.

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The electron-density distribution of a new crystal form of coumarin-102, a laser dye, has been investigated using the Hansen–Coppens multipolar atom model. The charge density was refined versus high-resolution X-ray diffraction data collected at 100 K and was also constructed by transferring the charge density from the Experimental Library of Multipolar Atom Model (ELMAM2). The topology of the refined charge density has been analysed within the Bader `Atoms In Molecules' theory framework. Deformation electron-density peak heights and topological features indicate that the chromen-2-one ring system has a delocalized π-electron cloud in resonance with the N (amino) atom. The molecular electrostatic potential was estimated from both experimental and transferred multipolar models; it reveals an asymmetric character of the charge distribution across the molecule. This polarization effect is due to a substantial charge delocalization within the molecule. The molecular dipole moments derived from the experimental and transferred multipolar models are also compared with the liquid and gas-phase dipole moments. The substantial molecular dipole moment enhancements observed in the crystal environment originate from the crystal field and from intermolecular charge transfer induced and controlled by C—H...O and C—H...N intermolecular hydrogen bonds. The atomic forces were integrated over the atomic basins and compared for the two electron-density models.

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45

Kalinowski, Roman, Birger Dittrich, Christian B. Hübschle, Carsten Paulmann, and Peter Luger. "Experimental charge density of L-alanyl-L-prolyl-L-alanine hydrate: classical multipole and invariom approach, analysis of intra- and intermolecular topological properties." Acta Crystallographica Section B Structural Science 63, no. 5 (September 14, 2007): 753–67. http://dx.doi.org/10.1107/s0108768107030388.

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A high-resolution dataset of the tripeptide L-alanyl-L-prolyl-L-alanine hydrate was measured at 100 K using synchrotron radiation and CCD area detection. Electron densities were obtained from a full multipole refinement of the X-ray experimental data, from an invariom transfer and from a theoretical calculation. Topological and atomic properties were derived via an AIM analysis [Atoms in Molecules; see Bader (1990). Atoms in Molecules: A Quantum Theory, No. 22 in International Series of Monographs on Chemistry, 1st ed. Oxford: Clarendon Press] of these densities and compared with each other, as well as with results from the literature of other oligopeptides and amino acids. By application of the invariom formalism to a dataset of limited resolution, its performance was compared with a conventional spherical refinement, highlighting the possibility of aspherically modelling routine structure-determination experiments. The hydrogen-bonding scheme was subject to a detailed analysis according to the criteria of Koch & Popelier [(1995), J. Phys. Chem. 99, 9747–9754] as well as to the characterization of Espinosa et al. [(1998), Chem. Phys. Lett. 285, 170–173; (1999), Acta Cryst. B55, 563–572; (2002), J. Chem. Phys. 117, 5529–5542] using the results from the refined and invariom multipole densities as well as the spherical-density model, which are critically compared.

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46

Overgaard, Jacob, Mette Schmøkel, Lasse Bjerg, Simone Cenedese, Mads Jørgensen, Yu-Sheng Chen, and Bo Iversen. "Synchrotron charge density studies of chemical bonding in the polymorphs of FeS2." Acta Crystallographica Section A Foundations and Advances 70, a1 (August 5, 2014): C1338. http://dx.doi.org/10.1107/s2053273314086616.

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The experimental charge density (CD) distributions in both polymorphs of the photovoltaic compound iron-disulphide (FeS2; cubic pyrite and orthorhombic marcasite) will be described.[1] The CDs are determined by multipole modelling using synchrotron X-ray diffraction data collected at 10 K on extremely small single crystals (<10 mu) thus minimizing the influence of systematic errors such as absorption, extinction and TDS, and exploiting experiences gained from our recent synchrotron studies of CoSb3.[2] The analysis of the charge density in both polymorphs of FeS2 provides an opportunity to see how the different geometries affect local atomic properties, such as 2-center chemical bonding, atomic charges and d-orbital populations. In particular, the data and the resulting multipole models enable us to link the atomic-centered view that emerges from the multipole analysis with the band structure approach. This is carried out by combination with results from periodic calculations on the compounds in the experimental geometries using WIEN2k, thereby providing unambiguous answers to a number of unsolved issues regarding the nature of the bonding in FeS2. The chemical bonding will be characterized by topological analyses showing that the Fe-S bonds are polar covalent bonds, with only minor charge accumulation but significantly negative energy densities at the bond critical points. Using the IAM as reference, density is found to accumulate in-between the atoms, supporting a partial covalent bonding description. The homopolar covalent S-S interaction is seemingly stronger in pyrite than in marcasite, determined not only from the shorter distance but also from all topological indicators. Integrated atomic (Bader) charges show significantly smaller values than those estimation based on crystal-field theory of Fe2+, S-1. In connection with this, the experimentally derived d-orbital populations on Fe are found to deviate from the commonly assumed full t2g set, empty eg set, and they fit very well with the theoretical individual atomic orbitals projected density of states showing a higher dxy participation in the valence band in marcasite compared with pyrite. Thus, the differences between the two polymorphic compounds are directly reflected in their valence density distributions and d-orbital populations.

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Yoosefian, Mehdi, Elaheh Ayoubi, and Leonard Ionut Atanase. "Palladium-Doped Single-Walled Carbon Nanotubes as a New Adsorbent for Detecting and Trapping Volatile Organic Compounds: A First Principle Study." Nanomaterials 12, no. 15 (July 27, 2022): 2572. http://dx.doi.org/10.3390/nano12152572.

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Volatile organic compounds (VOCs) are in the vapor state in the atmosphere and are considered pollutants. Density functional theory (DFT) calculations with the wb97xd exchange correlation functional and the 6-311+G(d,p) basis set are carried out to explore the potential possibility of palladium-doped single-walled carbon nanotubes (Pd/SWCNT-V), serving as the resource for detecting and/or adsorbing acetonitrile (ACN), styrene (STY), and perchloroethylene (PCE) molecules as VOCs. The suggested adsorbent in this study is discussed with structural parameters, frontier molecular orbital theory, molecular electrical potential surfaces (MEPSs), natural bond orbital (NBO) analyses, and the density of states. Furthermore, following the Bader theory of atoms in molecules (AIM), the topological properties of the electron density contributions for intermolecular interactions are analyzed. The obtained results show efficient VOC loading via a strong chemisorption process with a mean adsorption energy of −0.94, −1.27, and −0.54 eV for ACN, STY, and PCE, respectively. Our results show that the Pd/SWCNT-V can be considered a good candidate for VOC removal from the environment.

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48

Sirohiwal, Abhishek, Venkatesha R. Hathwar, Dhananjay Dey, Roshni Regunathan, and Deepak Chopra. "Characterization of fluorine-centred `F...O' σ-hole interactions in the solid state." Acta Crystallographica Section B Structural Science, Crystal Engineering and Materials 73, no. 2 (March 14, 2017): 140–52. http://dx.doi.org/10.1107/s2052520616017492.

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In the current study, the crystal structure of 1-(3-nitrophenyl)-2,2,2-trifluoroethanone (A1) and (E)-4-((4-fluorophenyl) diazenyl)phenol (A2) has been analyzed for the characterization of the presence of a `unique' and `rare' intermolecular C(sp3/sp2)—F...O contact, which has been observed to play a significant role in the crystal packing. Theoretical charge-density calculations have been performed to study the nature and strength associated with the existence of this intermolecular F...O contact, wherein the F atom is attached to ansp3-hybridized C atom in the case of A1 and to ansp2hybridized carbon in the case of A2. The crystal packing of the former contains two `electronically different' Csp3—F...O contacts which are present across and in between the layers of molecules. In the latter case, it is characterized by the presence of a very `short' (2.708 Å) and `highly directional' (168° at ∠C4—F1...O1 and 174° at ∠C10—O1...F1) Csp2—F...O contact. According to the Cambridge Structural Database (CSD) study, it is a rare example in molecular crystals. Topological features of F...O contacts in the solid state were compared with the gas-phase models. The two-dimensional and three-dimensional static deformation density obtained from theoretical multipole modeling confirm the presence of a charge depleted region on the F atoms. Minimization of the electrostatic repulsion between like charges are observed through subtle arrangements in the electronic environment in two of the short intermolecular F...O contacts. These contacts were investigated using inputs from pair energy decomposition analysis, Bader's quantum theory of atoms in molecules (QTAIM), Hirshfeld surface analysis, delocalization index, reduced density gradient (RDG) plot, electrostatic potential surface and distributed atomic polarizability. The intermolecular energy decomposition (PIXEL) and RDG–NCI (non-covalent interaction) analysis of the F...O contacts establish the interaction to be dispersive in nature. The mutual polarization of an O atom by fluorine andviceversaprovides real physical insights into the role of atomic polarizability in interacting atoms in molecules in crystals.

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Kožíšková, Júlia Adamko, Martin Breza, Marián Valko, Peter Herich, Lukáš Bučinský, and Jozef Kožíšek. "Electronic structure of Schiff-base peroxo{2,2′-[1,2-phenylenebis(nitrilomethanylylidene)]bis(6-methoxyphenolato)}titanium(IV) monohydrate: a possible model structure of the reaction center for the theoretical study of hemoglobin." IUCrJ 8, no. 2 (February 18, 2021): 295–304. http://dx.doi.org/10.1107/s205225252100004x.

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An extensive characterization of [Ti(C22H18N2O6)]·H2O was performed by topological analysis according to Bader's quantum theory of atoms in molecules (QTAIM) from the experimentally (multipole model) and theoretically (DFT) determined electron density. To the best of our knowledge, this study is the first example of an experimental electronic structure of a coordination compound in which a peroxo anion is bonded to a 3d central atom. The titanium coordination polyhedron could be described as a deformed tetrahedral pyramid if the midpoint of the peroxide O—O bond (side-on mode) is considered to be in the quasi-apical position. According to the multipole model (MM) results, the titanium atom has a positive QTAIM charge of 2.05 e− which does not correspond to the formal Ti (IV) oxidation state. On the other hand, the peroxo oxygen atoms O(1) and O(2) have MM QTAIM charges of −0.27 and −0.12, respectively. This asymmetric charge density distribution on the peroxo oxygens is in agreement with the distorted orientation of the O2 moiety with respect to the titanium atom. Despite the fact that the overall MM charge of the O2 moiety is more remote from the formal −2 charge than from neutral O2, the O—O distance remains close to that in the peroxo O2 2− anion. In the case of DFT results, the titanium atom charge is also found to be close to +2, the O2 x− moiety charge is around −1, the optimized O—O distance is shorter by only ca 0.04 Å than the experimental value of 1.5005 (16) Å, and the DFT d-populations on titanium are found to be lower than the experimental MM value. This study is the first experimental electronic structure of a transition metal peroxo complex.

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Breuers, Verena, Christian Lehmann, and Walter Frank. "Charge density study of the first mixed-valent tetraphosphete." Acta Crystallographica Section A Foundations and Advances 70, a1 (August 5, 2014): C1345. http://dx.doi.org/10.1107/s2053273314086549.

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The first λ3,λ5-tetraphosphete contains a 4π-electron four-membered ring as the central structural unit of a dispirocyclic system and can thus be classified as an analogue to diphosphetes and cyclodiphosphazenes. According to its crystal structure the central P4unit exhibits not only P–P bonds which are of equal length (P1–P2 2,139(1) Å, P1–P2A 2,142(1) Å), but also rhombic distortion (P1–P2–P1A 79,4(1)0, P2–P1–P2A 100,6(1)0).[1] Therefore its electronic structure cannot be described as 'Phosphacyclobutadiene' but either as a bis(ylide) or as a system with delocalized double bonds. After various quantum chemical calculations and an extensive examination of its reaction and coordination behavior failed to answer this question, we addressed the problem via a detailed analysis of its charge density distribution. The experimental charge density based on high resolution X-ray diffraction data collected at low temperature is determined by multipole least squares refinement using the program packageXD2006.[2] In a first step, the static deformation density exhibits charge density which is located mainly outside of the P4ring plane at the λ3-phosphorus atoms but simultaneously redistributed into the P–P bond area. In addition to that, a study of its topological properties and an inspection of the Laplacian of the electron density according to Bader's `Quantum Theory of Atoms in Molecules' (QTAIM)[3] further highlight the bonding features. They reveal polar Si–N, Si–C and P–N bonds with a decreasing amount of electrostatic contribution as well as four valence shell charge concentrations (thus sp3hybridization) at each of the phosphorus atoms. Finally supported by theoretical calculations, the results illustrate the unique bonding situation in the P4unit combining a high ylidic character with unusual not exclusively sigma-like P–P bonds.

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Journal articles on the topic 'Bader’s topological analysis'

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