Experimental Charge Density Study of a Silylone

An experimental and theoretical charge density study confirms the interpretation of (cAAC)₂Si as a silylone to be valid. Two separated VSCCs present in the non‐bonding region of the central silicon are indicative for two lone pairs. In the experiment, both the two crystallographically independent Si? C bond lengths and ellipticities vary notably. It is only the cyclohexyl derivative that shows significant differences in these values, both in the silylones and the germylones. Only by calculating increasing spheres of surrounding point charges we were able to recover the changes in the properties of the charge density distribution caused by weak intermolecular interactions. The nitrogen–carbene‐carbon bond seems to have a significant double‐bond character, indicating a singlet state for the carbene carbon, which is needed for donor acceptor bonding. Thus the sum of bond angles at the nitrogen atoms seems to be a reasonable estimate for singlet versus triplet state of cAACs.     

Crystal Structure of 1,1,4,4-Tetrafluorocyclohexane at 95 K

The crystal structure of 1,1,4,4-tetrafluorocyclohexane has been determined from X-ray diffraction measurements at 95 K. Internal motion of the CF₂-group can be discerned from analysis of the atomic vibration tensors. The pattern of bond lengths suggests that an anomeric-effect type of interaction between antiperiplanar C,C- and C,F-bonds (as well as between C,H- and C,F-bonds) may be operative in this molecule.     

The Relevance of Experimental Charge Density Analysis in Unraveling Noncovalent Interactions in Molecular Crystals

The work carried out by our research group over the last couple of decades in the context of quantitative crystal engineering involves the analysis of intermolecular interactions such as carbon (tetrel) bonding, pnicogen bonding, chalcogen bonding, and halogen bonding using experimental charge density methodology is reviewed. The focus is to extract electron density distribution in the intermolecular space and to obtain guidelines to evaluate the strength and directionality of such interactions towards the design of molecular crystals with desired properties. Following the early studies on halogen bonding interactions, several “sigma-hole” interaction types with similar electrostatic origins have been explored in recent times for their strength, origin, and structural consequences. These include interactions such as carbon (tetrel) bonding, pnicogen bonding, chalcogen bonding, and halogen bonding. Experimental X-ray charge density analysis has proved to be a powerful tool in unraveling the strength and electronic origin of such interactions, providing insights beyond the theoretical estimates from gas-phase molecular dimer calculations. In this mini-review, we outline some selected contributions from the X-ray charge density studies to the field of non-covalent interactions (NCIs) involving elements of the groups 14–17 of the periodic table. Quantitative insights into the nature of these interactions obtained from the experimental electron density distribution and subsequent topological analysis by the quantum theory of atoms in molecules (QTAIM) have been discussed. A few notable examples of weak interactions have been presented in terms of their experimental charge density features. These examples reveal not only the strength and beauty of X-ray charge density multipole modeling as an advanced structural chemistry tool but also its utility in providing experimental benchmarks for the theoretical studies of weak interactions in crystals.     

Experimental Charge Density Evidence for Pnicogen Bonding in a Crystal of Ammonium Chloride

Chemical binding in crystalline ammonium chloride, a simple inorganic salt with an unexpectedly complex bonding pattern, was studied by using a topological analysis of electron density function derived from high‐resolution X‐ray diffraction. Supported by periodic quantum chemical calculations, it provided experimental evidence for weak σ‐hole bonds (1.5 kcal mol^?1) that involve ammonium cations in a crystal. Our results show this type of supramolecular interaction to be more numerous than has been found to date by using gas‐phase calculations or statistical analysis of CSD.     

Quantifying weak hydrogen bonding in uracil and 4-cyano-4'-ethynylbiphenyl: a combined computational and experimental investigation of NMR chemical shifts in the solid state

Weak hydrogen bonding in uracil and 4-cyano-4'-ethynylbiphenyl, for which single-crystal diffraction structures reveal close CH...O=C and C[triple bond]CH...N[triple bond]C distances, is investigated in a study that combines the experimental determination of 1H, 13C, and 15N chemical shifts by magic-angle spinning (MAS) solid-state NMR with first-principles calculations using plane-wave basis sets. An optimized synthetic route, including the isolation and characterization of intermediates, to 4-cyano-4'-ethynylbiphenyl at natural abundance and with 13C[triple bond]13CH and 15N[triple bond]C labeling is described. The difference in chemical shifts calculated, on the one hand, for the full crystal structure and, on the other hand, for an isolated molecule depends on both intermolecular hydrogen bonding interactions and aromatic ring current effects. In this study, the two effects are separated computationally by, first, determining the difference in chemical shift between that calculated for a plane (uracil) or an isolated chain (4-cyano-4'-ethynylbiphenyl) and that calculated for an isolated molecule and by, second, calculating intraplane or intrachain nucleus-independent chemical shifts that quantify the ring current effects caused by neighboring molecules. For uracil, isolated molecule to plane changes in the 1H chemical shift of 2.0 and 2.2 ppm are determined for the CH protons involved in CH...O weak hydrogen bonding; this compares to changes of 5.1 and 5.4 ppm for the NH protons involved in conventional NH...O hydrogen bonding. A comparison of CH bond lengths for geometrically relaxed uracil molecules in the crystal structure and for geometrically relaxed isolated molecules reveals differences of no more than 0.002 A, which corresponds to changes in the calculated 1H chemical shifts of at most 0.1 ppm. For the C[triple bond]CH...N[triple bond]C weak hydrogen bonds in 4-cyano-4'-ethynylbiphenyl, the calculated molecule to chain changes are of similar magnitude but opposite sign for the donor 13C and acceptor 15N nuclei. In uracil and 4-cyano-4'-ethynylbiphenyl, the CH hydrogen-bonding donors are sp2 and sp hybridized, respectively; a comparison of the calculated changes in 1H chemical shift with those for the sp3 hybridized CH donors in maltose (Yates et al. J. Am. Chem. Soc. 2005, 127, 10216) reveals no marked dependence on hybridization for weak hydrogen-bonding strength.     

Density and temperature effect on hydrogen-bonded clusters in water - MD simulation study

Molecular dynamics NVE simulations have been performed for five thermodynamic states of water including ambient, sub-and supercritical conditions. Clustering of molecules via hydrogen bonding interaction has been studied with respect to the increasing temperature and decreasing density to examine the relationship between the extent of hydrogen bonding and macroscopic properties. Calculations confirmed decrease of the average number of H-bonds per molecule and of cluster-size with increasing temperature and decreasing density. In the sub-and supercritical region studied, linear correlations between several physical quantities (density, viscosity, static dielectric constant) and the total engagement of molecules in clusters of size k > 4, P _k>4, have been found. In that region there was a linear relationship between P _k>4 and the average number of H-bonds per water molecule. The structural heterogeneity resulting from hydrogen bonding interactions in low-density supercritical water has been also discussed.      

Theoretical study on two types of weak interactions between methylenecyclopropane and XY (X,Y = H,F, Cl,and Br)

We present theoretical evidence that the two types of interactions exist in the complexes formed between methylenecyclopropane (MECP) and XY (X, Y = H, F, Cl, and Br). Two seats of XY interacted with MECP are located: (a) is via the pseudo‐π bonding electron pair associated with a C? C bond of the cyclopropane ring and (b) is via the typical‐π bonding of electron pair of the C?C bond of MECP. These two types of weak interactions are compared based on the calculated geometries, interaction energies, frequency changes, and topological properties of electron density. The integration of electron density over the interatomic surface is found to be a good measure for the strength of weak interaction. Furthermore, the total electron density and separated σ and π electron densities are also computed and discussed in this article. The separated electron density shows σ electron density determined the strength and π electron density influenced the direction of the hydrogen/halogen bond. © 2010 Wiley Periodicals, Inc. Int J Quantum Chem, 2011     

Synchrotron X-ray Electron Density Analysis of Chemical Bonding in the Graphitic Carbon Nitride Precursor Melamine

Melamine is a precursor and building block for graphitic carbon nitride (g-CN) materials, a group of layered materials showing great promise for catalytic applications. The synthetic pathway to g-CN includes a polycondensation reaction of melamine by evaporation of ammonia. Melamine molecules in the crystal organize into wave-like planes with an interlayer distance of 3.3 Å similar to that of g-CN. Here we present an extensive investigation of the experimental electron density of melamine obtained from modelling of synchrotron radiation X-ray single-crystal diffraction data measured at 25 K with special focus on the molecular geometry and intermolecular interactions. Both intra- and interlayer structures are dominated by hydrogen bonding and π-interactions. Theoretical gas-phase optimizations of the experimental molecular geometry show that bond lengths and angles for atoms in the same chemical environment (C−N bonds in the ring, amine groups) differ significantly more for the experimental geometry than for the gas-phase-optimized geometries, indicating that intermolecular interactions in the crystal affects the molecular geometry. In the experimental crystal geometry, one amine group has significantly more sp³-like character than the others, hinting at a possible formation mechanism of g-CN. Topological analysis and energy frameworks show that the nitrogen atom in this amine group participates in weak intralayer hydrogen bonding. We hypothesize that melamine condenses to g-CN within the layers and that the unique amine group plays a key role in the condensation process.     

The Effect of Deoxyfluorination on Intermolecular Interactions in the Crystal Structures of 1,6-Anhydro-2,3-epimino-hexopyranoses

The effect of substitution on intermolecular interactions was investigated in a series of 1,6-anhydro-2,3-epimino-hexopyranoses. The study focused on the qualitative evaluation of intermolecular interactions using DFT calculations and the comparison of molecular arrangements in the crystal lattice. Altogether, ten crystal structures were compared, including two structures of C4-deoxygenated, four C4-deoxyfluorinated and four parent epimino pyranoses. It was found that the substitution of the original hydroxy group by hydrogen or fluorine leads to a weakening of the intermolecular interaction by approximately 4 kcal/mol. The strength of the intermolecular interactions was found to be in the following descending order: hydrogen bonding of hydroxy groups, hydrogen bonding of the amino group, interactions with fluorine and weak electrostatic interactions. The intermolecular interactions that involved fluorine atom were rather weak; however, they were often supported by other weak interactions. The fluorine atom was not able to substitute the role of the hydroxy group in molecular packing and the fluorine atoms interacted only weakly with the hydrogen atoms located at electropositive regions of the carbohydrate molecules. However, the fluorine interaction was not restricted to a single molecule but was spread over at least three other molecules. This feature is a base for similar molecule arrangements in the structures of related compounds, as we found for the C4-F_ax and C4-F_eq epimines presented here.     

Density Functional Studies of Diatomic LaO to LuO

Bond distances, vibrational frequencies, electron affinities, ionization potentials, dissociation energies and dipole moments of the title molecules in neutral, positively and negatively charged ions were studied by use of density functional method. Ground electronic state was assigned for each molecule. The bonding patterns were analyzed and compared with both the available data and across the series. It was found that besides ionic component, covalent bonds are formed between the metal s, d and f orbitals and oxygen p orbitals. Contrary to the well known lanthanide contraction, the bond distance is not regular from LaO to LuO for both neutral and charged molecules. An obvious population at 5d orbital was observed through the lanthanide series. 4f electrons also participate the chemical bonding for CeO to NdO and TbO to TmO. For EuO, GdO, YbO and LuO, 4f electrons tend to be localized. The spin multiplicity is regular for neutral and charged molecules. The spin multiplicity of the charged molecules can be obtained by −1 (or +1 for TbO⁺, DyO⁺, YbO⁻ and YbO⁺) compared with the corresponding neutral molecules.     

Energy density distribution in bridged cobalt complexes

In the theory of atoms in molecules (AIM), the charge density is usually a suitable tool for bonding analyses. However, problems arise in some cases. So, no direct Co-Co bond is found in Co2(CO)8. It is shown that the energy density gives deeper insight into the bonding properties. This is demonstrated for Co2(CO)8, Co4(CO)12, and Co2(CO)6(InMe)2. The strategy is not restricted to transition metal compounds; it should be useful to identify any weak bonding or antibonding interactions.     

Extended weak bonding interactions in DNA: pi-stacking (base-base), base-backbone, and backbone-backbone interactions

We report on several weak interactions in nucleic acids, which, collectively, can make a nonnegligible contribution to the structure and stability of these molecules. Fragments of DNA were obtained from previously determined accurate experimental geometries and their electron density distributions calculated using density functional theory (DFT). The electron densities were analyzed topologically according to the quantum theory of atoms in molecules (AIM). A web of closed-shell bonding interactions is shown to connect neighboring base pairs in base-pair duplexes and in dinuleotide steps. This bonding underlies the well-known pi-stacking interaction between adjacent nucleic acid bases and is characterized topologically for the first time. Two less widely appreciated modes of weak closed-shell interactions in nucleic acids are also described: (i) interactions between atoms in the bases and atoms belonging to the backbone (base-backbone) and (ii) interactions among atoms within the backbone itself (backbone-backbone). These interactions include hydrogen bonding, dihydrogen bonding, hydrogen-hydrogen bonding, and several other weak closed-shell X-Y interactions (X, Y = O, N, C). While each individual interaction is very weak and typically accompanied by perhaps 0.5-3 kcal/mol, the sum total of these interactions is postulated to play a role in stabilizing the structure of nucleic acids. The Watson-and-Crick hydrogen bonding is also characterized in detail at the experimental geometries as a prelude to the discussion of the modes of interactions listed in the title.     

Electron Density Studies in Materials Research

Rational material design requires a deep understanding about the relationship between the structure and properties of materials, which are both intimately related to their chemical bonding. Through the experimentally observable electron density, chemical bonding can be understood from experimental and theoretical points of view on an equal footing, and advances in accurate X-ray diffraction measurements and computational techniques over the past decades have provided access to electron density distributions in increasingly complex functional materials. In this Review, selected electron density studies from the literature on a wide range of materials classes are presented, including studies of thermoelectric materials, high pressure electrides, coordination polymers and non-linear optical materials. These studies demonstrate how detailed analysis of chemical bonding based on the electron density provides important understanding of materials beyond arguments based on structure and simple chemical concepts. In cases such as understanding the conducting properties of Zintl semiconductors or the effect of mutual electrical polarization in host–guest systems, it is clearly imperative to go beyond structure and examine the chemical bonding in detail. In the Review, the complementarity between theory and experiment is underlined, which allows for mutual validation of new chemical bonding concepts, and indeed experiment and theory may challenge each other based on the different strengths and weaknesses of each method.     

Theoretical exploration of the cooperative effect in NMF-NMF-amino acid residue hydrogen bonding system

This paper presents a theoretical study of the cooperative effect in sixteen linearly-arranged trimer systems consisting of N-methylformamide dimer and an extra amino acid residue. These trimer systems, NMF-NMF-AAR, in short, have been systematically investigated by full optimization at B3LYP/cc-pVTZ level and subsequent electronic energy calculations at PBE1PBE/cc-pVTZ, HF/cc-pVTZ and MP2/cc-pVTZ, respectively. Obvious spatial transformation due to energetic factors has been found in almost all the trimers. Systematic analysis in weak interaction energy components has shown that: (1) in these trimer systems, the bonding structure and the cooperative effect combine to determine the stability of both HB1 and HB2. For HB2, the structure of the constituent amino acid residue also plays a crucial role by interfering with the neighboring moieties; (2) the large contribution of the cooperative effect to the overall hydrogen bonding energy has claimed the importance of cooperativity in our systems; (3) the non-hydrogen bonding weak interaction components are found to be non-negligible in these trimer systems; (4) moreover, the cooperative effect between these non-hydrogen bonding components is always found to be positive. The good performances of PBE1PBE and PM6 have been established by comparisons between these methods.     

Bonding Energies and Structural Study of Alkylaluminium

Neutral aluminium alkyls are well known to act as ethylene oligomerization and polymerization catalysts and cocatalysts.On the basis of the full optimization of alkylaluminium compounds with Gaussian 98 program package at the B3LYP/6-31G** level,the selected structures and bonding energies were investigated extensively.The geometries and bonding energies of AlR3(R = H,CH3,C2H5,C3H7,C4H9) and Al(C2H5)2R'(R' = C2H5,C3H7,C4H9,C5H11,C6H13) were investigated extensively,and we found that,along with the prolongation of carbon chains the terminal C-C bond is shortened gradually until to a constant value of about 0.1532 nm in C4H9;and the bonding energy almost remains constant.The dative bonding of C2H4 to Al(C2H5)3,whose bonding energy is only 15.30 kJ/mol,is very weak.     

Density functional theory and topological analysis on the hydrogen bonding interactions in cysteine‐thymine complexes

Hydrogen bonding interactions between amino acids and nucleic acid bases constitute the most important interactions responsible for the specificity of protein binding. In this study, complexes formed by hydrogen bonding interactions between cysteine and thymine have been studied by density functional theory. The relevant geometries, energies, and IR characteristics of hydrogen bonds (H‐bonds) have been systematically investigated. The quantum theory of atoms in molecule and natural bond orbital analysis have also been applied to understand the nature of the hydrogen bonding interactions in complexes. More than 10 kinds of H‐bonds including intra‐ and intermolecular H‐bonds have been found in complexes. Most of intermolecular H‐bonds involve O (or N) atom as H‐acceptor, whereas the H‐bonds involving C or S atom usually are weaker than other ones. Both the strength of H‐bonds and the structural deformation are responsible for the stability of complexes. Because of the serious deformation, the complex involving the strongest H‐bond is not the most stable structures. Relationships between H‐bond length (ΔR_X‐H), frequency shifts (Δv), and the electron density (ρ_b) and its Laplace (?²ρ_b) at bond critical points have also been investigated. © 2010 Wiley Periodicals, Inc. Int J Quantum Chem, 2011     

Adsorption mechanism in reversed-phase liquid chromatography. Effect of the surface coverage of a monomeric C18-silica stationary phase

The effect of the bonding density of the octadecyl chains onto the same silica on the adsorption and retention properties of low molecular weight compounds (phenol, caffeine, and sodium 2-naphthalene sulfonate) was investigated. The same mobile phase (methanol:water, 20:80, v/v) and temperature (T = 298 K) were applied and two duplicate columns (A and B) from each batch of packing material (neat silica, simply endcapped or C1 phase, 0.42, 1.01, 2.03, and 3.15 micromol/m2 of C18 alkyl chains) were tested. Adsorption data of the three compounds were acquired by frontal analysis (FA) and the adsorption energy distributions (AEDs) were calculated using the expectation-maximization method. Results confirmed earlier findings in linear chromatography of a retention maximum at an intermediate bonding density. From a general point of view, the saturation capacity of the adsorbent tends to decrease with increasing bonding density, due to the vanishing space intercalated between the C18 bonded chains and to the decrease of the specific surface area of the stationary phase. The equilibrium constants are maximum for an intermediary bonding density (approximately 2 micromol/m2). An enthalpy-entropy compensation was found for the thermodynamic parameters of the isotherm data. Weak equilibrium constants (small deltaH) and high saturation capacities (large deltaS) were observed at low bonding densities, higher equilibrium constants and lower saturation capacities at high bonding densities, the combinations leading to similar apparent retention in RPLC. The use of a low surface coverage column is recommended for preparative purposes.     

Density functional study of the conformational space of 4C1 D-glucuronic acid

The conformational space of (4)C(1) alpha- and beta-d-glucuronic acid was scanned by HF/3-21G(p) calculations followed by optimization of the 15 most stable structures for each, using the B3LYP density functional theory method in conjunction with a diffuse polarized valence triple-zeta basis set. We found a general preference of the alpha anomers in the isolated molecules in agreement with the large endo-anomeric hyperconjugation effects in these structures. From the other intramolecular interactions (exo-anomeric hyperconjugation, hydrogen-bonding, dipole-dipole, and steric interactions), the effect of the hydrogen bonding is the most pronounced and plays a major role in determining the stability order within the alpha and beta series. The most stable conformer of both alpha and beta (4)C(1) d-glucuronic acid is the structure with the maximum number (5) of intramolecular hydrogen bonds. Introduction of solvent (water) effects by the SCI-PCM model resulted in two characteristic changes of the energetic properties: the gas-phase stability order changed considerably, and the energy range of the 15 most stable conformers decreased from 30 to 15 kJ/mol. The geometrical parameters reflect well the superimposed effects of hyperconjugation and hydrogen-bonding interactions. Most characteristics are the variations of the C-O bond distances (within a range of 0.04 A) upon the combined intramolecular effects.