Direct atomic scale observation of linkage isomerization of As4S4 clusters during the photoinduced transition of realgar to pararealgar

The reaction mechanism underlying the photoinduced linkage isomerization of discrete arsenic-sulfur clusters in the realgar form of tetraarsenic tetrasulfide (alpha-As4S4) to its pararealgar form was studied on a natural specimen of the mineral with a combination of in situ single-crystal X-ray photodiffraction and Fourier transform infrared spectroscopy. The photodiffraction technique provided direct atomic resolution evidence of formation of intermediate As4S5 phase in which half of the realgar molecule is retained in its envelope-type conformation, while the other half is transformed by effective switching of positions of one sulfur and one arsenic atom. The initiation and propagation stages of the process are studied under light and dark conditions, during and after photoexcitation with polychromatic visible light. In the "light" reaction stage, the interatomic and cell parameters averaged over the crystal volume and photoexcitation time remain almost unchanged. The residual electron density features are indicative for formation of a small amount of As4S5 clusters, which at this stage do not affect the overall crystalline order. In the "dark" reaction stage, a set of self-sustainable autocatalytic reactions results in strong and nearly isotropic expansion of the unit cell. The structure in the dark stage represents direct evidence of formation of pararealgar which was obtained in yield of about 5% in the single crystal of realgar. The cell expansion is due to increased mole ratio of clusters of pararealgar relative to realgar and to increased intercluster separation. Due to lattice incompatibility, a higher content of the product results in progressive decrease of crystal quality. Creation of small amount of arsenolite (As2O3) which appears as byproduct in the light stage and remains unreacted in the product mixture was confirmed by far-IR spectroscopy.     

Acid–base complexes of polymers

The physical interactions of polymers with neighboring molecules are determined by only two kinds of interactions: London dispersion forces and Lewis acid–base interactions. These two kinds of attractive energies (together with certain steric restrictions) determine solubility, solvent retention, plasticizer action, wettability, adsorption, adhesion, reinforcement, crystallinity, and mechanical properties. The London dispersion force interaction energies of polymers have been quantified by the dispersion force contribution to cohesive energy density (δ²_d) and the dispersion force contribution to surface energy (δ^d). The Lewis acid–base interactions, often referred to as “polar” interactions, can be best quantified by Drago's C_A and E_A constants for acid sites and C_B and E_B constants for basic sites. In this article infrared spectral shifts are featured as a method of determining enthalpies of acid–base interaction, and the C and E constants for polymers, plasticizers, and solvents. Examples are given where acid–base complexation of polymers with solvents dominate solubility and swelling phenomena. Enthalpies of acid–base complexation in polymer blends are determined from spectral shifts.     

Model chemistry calculations of thiophene dimer interactions: origin of pi-stacking

The intermolecular interaction energies of thiophene dimers have been calculated by using an aromatic intermolecular interaction (AIMI) model (a model chemistry for the evaluation of intermolecular interactions between aromatic molecules). The CCSD(T) interaction energy at the basis set limit has been estimated from the MP2 interaction energy near the basis set limit and the CCSD(T) correction term obtained by using a medium-size basis set. The calculated interaction energies of the parallel and perpendicular thiophene dimers are -1.71 and -3.12 kcal/mol, respectively. The substantial attractive interaction in the thiophene dimer, even where the molecules are well separated, shows that the major source of attraction is not short-range interactions such as charge transfer but rather long-range interactions such as electrostatic and dispersion. The inclusion of electron correlation increases the attraction significantly. The dispersion interaction is found to be the major source of attraction in the thiophene dimer. The calculated total interaction energy of the thiophene dimer is highly orientation dependent. Although electrostatic interaction is substantially weaker than dispersion interaction, it is highly orientation dependent, and therefore electrostatic interaction play an important role in the orientation dependence of the total interaction energy. The large attractive interaction in the perpendicular dimer is the cause of the preference for the herringbone structure in the crystals of nonsubstituted oligothiophenes (alpha-terthienyls), and the steric repulsion between the beta-substituents is the cause of the pi-stacked structure in the crystals of some beta-substituted oligothiophenes.     

Origin of attraction and directionality of the pi/pi interaction: model chemistry calculations of benzene dimer interaction.

A model chemistry for the evaluation of intermolecular interaction between aromatic molecules (AIMI Model) has been developed. The CCSD(T) interaction energy at the basis set limit has been estimated from the MP2 interaction energy near the basis set limit and the CCSD(T) correction term obtained by using a medium size basis set. The calculated interaction energies of the parallel, T-shaped,and slipped-parallel benzene dimers are -1.48, -2.46, and -2.48 kcal/mol, respectively. The substantial attractive interaction in benzene dimer, even where the molecules are well separated, shows that the major source of attraction is not short-range interactions such as charge-transfer but long-range interactions such as electrostatic and dispersion. The inclusion of electron correlation increases attraction significantly. The dispersion interaction is found to be the major source of attraction in the benzene dimer. The orientation dependence of the dimer interaction is mainly controlled by long-range interactions. Although electrostatic interaction is considerably weaker than dispersion interaction, it is highly orientation dependent. Dispersion and electrostatic interactions are both important for the directionality of the benzene dimer interaction.     

Rotational Signatures of Dispersive Stacking in the Formation of Aromatic Dimers

The aggregation of aromatic species is dictated by inter‐ and intramolecular forces. Not only is characterizing these forces in aromatic growth important for understanding grain formation in the interstellar medium, but it is also imperative to comprehend biological functions. We report a combined rotational spectroscopic and quantum‐chemical study on three homo‐dimers, comprising of diphenyl ether, dibenzofuran, and fluorene, to analyze the influence of structural flexibility and the presence of heteroatoms on dimer formation. The structural information obtained shows clear similarities between the dimers, despite their qualitatively different molecular interactions. All dimers are dominated by dispersion interactions, but the dibenzofuran dimer is also influenced by repulsion between the free electron pairs of the oxygen atoms and the π‐clouds. This study lays the groundwork for understanding the first steps of molecular aggregation in systems with aromatic residues.     

Understanding the Fundamental Role of π/π, σ/σ, and σ/π Dispersion Interactions in Shaping Carbon‐Based Materials

Noncovalent interactions involving aromatic rings, such as π‐stacking and CH/π interactions, are central to many areas of modern chemistry. However, recent studies proved that aromaticity is not required for stacking interactions, since similar interaction energies were computed for several aromatic and aliphatic dimers. Herein, the nature and origin of π/π, σ/σ, and σ/π dispersion interactions has been investigated by using dispersion‐corrected density functional theory, energy decomposition analysis, and the recently developed noncovalent interaction (NCI) method. Our analysis shows that π/π and σ/σ stacking interactions are equally important for the benzene and cyclohexane dimers, explaining why both compounds have similar boiling points. Also, similar dispersion forces are found in the benzene???methane and cyclohexane???methane complexes. However, for systems larger than naphthalene, there are enhanced stacking interactions in the aromatic dimers adopting a parallel‐displaced configuration compared to the analogous saturated systems. Although dispersion plays a decisive role in stabilizing all the complexes, the origin of the π/π, σ/σ, and σ/π interactions is different. The NCI method reveals that the dispersion interactions between the hydrogen atoms are responsible for the surprisingly strong aliphatic interactions. Moreover, whereas σ/σ and σ/π interactions are local, the π/π stacking are inherently delocalized, which give rise to a non‐additive effect. These new types of dispersion interactions between saturated groups can be exploited in the rational design of novel carbon materials.     

TATB二聚体分子间作用力及其气相几何构型研究

采用对称性匹配微扰理论(SAPT)定量地求得TATB分子间的静电、交换排斥、诱导和色散等分子间作用能项, 从理论上揭示了TATB分子间作用本质; 在此基础上, 阐明了密度泛函在研究TATB二聚体时的适合性问题. 结果表明: (1)在有分子间氢键的TATB二聚体中, 库仑力足以与交换排斥力相抗衡, 起主导作用. (2)含分子间氢键的气相TATB二聚体的合理几何构型为平面型结构, 此结构的产生与色散力无关, 因此不管泛函是否含有近程色散作用, 均应预测到这种强极性的平面型结构. (3)在无分子间氢键的TATB二聚体中, 库仑力难以与交换排斥力相抗衡, 色散作用起到了关键作用; (4)在这种情况下, 未含有近程色散作用的密度泛函不可能给出合理构型. 恰好相反, 含有近程色散作用的密度泛函PBE0却能正确地预测到具有“平行重叠”结构且呈微弱极性的TATB二聚体, 色散力是导致这种构型产生的根本原因. “平行重叠”TATB二聚体是典型的色散体系, 其色散力占绝对主导地位并极有可能起源于两个TATB分子上π电子的相互作用. (5)对于所有TATB二聚体, 色散力或很显著或起主导作用. 由于密度泛函或未含有近程色散, 或只能部分地把近程色散表达出来, 这样使得当前所有密度泛函不可能精确求得这些二聚体的作用能.     

Fluoroaromatic-fluoroaromatic interactions between inhibitors bound in the crystal lattice of human carbonic anhydrase II

Intermolecular interactions of eleven different fluoroaromatic inhibitors are probed within the scaffolding of the crystal lattice of Phe-131-->Val carbonic anhydrase II. The degree and pattern of fluorine substitution on the inhibitor benzyl ring modulate its size, shape, and electronic character. In turn, these properties affect the geometry of intermolecular interactions between the fluoroaromatic rings of two different inhibitor molecules bound in the crystal lattice, as determined by X-ray crystallography. Depending on the degree and pattern of fluorine substitution, we observe a face-to-face (aromatic-aromatic) interaction, an atom-to-face (carbonyl-aromatic) interaction, or no interaction at all. These interaction geometries are analyzed with regard to van der Waals, electrostatic, and possible charge-transfer effects. For the aromatic-aromatic interactions investigated in this study, with aromatic ring quadrupoles specifically "tuned" by the degree and pattern of fluorination, the structural results suggest that London forces and charge-transfer complexation dominate over weakly polar electrostatic interactions in the association of aromatic ring pairs.     

Quantum mechanics based force field for carbon (QMFF-Cx) validated to reproduce the mechanical and thermodynamics properties of graphite

As assemblies of graphene sheets, carbon nanotubes, and fullerenes become components of new nanotechnologies, it is important to be able to predict the structures and properties of these systems. A problem has been that the level of quantum mechanics practical for such systems (density functional theory at the PBE level) cannot describe the London dispersion forces responsible for interaction of the graphene planes (thus graphite falls apart into graphene sheets). To provide a basis for describing these London interactions, we derive the quantum mechanics based force field for carbon (QMFF-Cx) by fitting to results from density functional theory calculations at the M06-2X level, which demonstrates accuracies for a broad class of molecules at short and medium range intermolecular distances. We carried out calculations on the dehydrogenated coronene (C24) dimer, emphasizing two geometries: parallel-displaced X (close to the observed structure in graphite crystal) and PD-Y (the lowest energy transition state for sliding graphene sheets with respect to each other). A third, eclipsed geometry is calculated to be much higher in energy. The QMFF-Cx force field leads to accurate predictions of available experimental mechanical and thermodynamics data of graphite (lattice vibrations, elastic constants, Poisson ratios, lattice modes, phonon dispersion curves, specific heat, and thermal expansion). This validates the use of M06-2X as a practical method for development of new first principles based generations of QMFF force fields.     

Dispersing carbon nanotubes using surfactants

We review the recent advances in dispersing single-wall carbon nanotubes (SWNTs) using amphiphilic surfactants in aqueous solutions. Three aspects are discussed. (1) On the organization of surfactant molecules with SWNTs, new insights at the microscopic level arise from electron microscopy and detailed computer simulation studies. (2) Quantitative measurements, such as molecular interactions between functional groups and SWNTs, the coverage of surfactant on SWNTs in solution, the charge state of the SWNT/surfactant complex, and the degree of dispersion are critical for better understanding dispersion mechanisms and for the further development of dispersion strategies. (3) The thermodynamic driving forces and the role of metastability in the structure of surfactant dispersed SWNT suspensions are analyzed. An outlook on practical and fundamental issues is also presented.     

High-level ab initio computations of structures and interaction energies of naphthalene dimers: origin of attraction and its directionality

The intermolecular interaction energies of naphthalene dimers have been calculated by using an aromatic intermolecular interaction model (a model chemistry for the evaluation of intermolecular interactions between aromatic molecules). The CCSD(T) (coupled cluster calculations with single and double substitutions with noniterative triple excitations) interaction energy at the basis set limit has been estimated from the second-order M?ller-Plesset perturbation interaction energy near saturation and the CCSD(T) correction term obtained using a medium-size basis set. The estimated interaction energies of the set of geometries explored in this work show that two structures emerge as being the lowest energy, and may effectively be considered as isoenergetic on the basis of the errors inherent in out extrapolation procedure. These structures are the slipped-parallel (Ci) structure (-5.73 kcal/mol) and the cross (D2d) structure (-5.28 kcal/mol). The T-shaped (C2v) and sandwich (D2h) dimers are substantially less stable (-4.34 and -3.78 kcal/mol, respectively). The dispersion interaction is found to be the major source of attraction in the naphthalene dimer. The electrostatic interaction is substantially smaller than the dispersion interaction. The large dispersion interaction is the cause of the large binding energies of the cross and slipped-parallel dimers.     

Theoretical study on mesogenic core structures of nematic liquid crystalline compounds

The structures and intermolecular interaction energies of 10 dimers, included in the mesogenic core structures of typical liquid crystalline (LC) compounds, are obtained at the MP2/6-31G(d) level of theory. It is proved that the dispersion energy significantly contributes to the total interaction energy of these dimers. Even when bulky substituents are introduced into the core part, the interaction energy is still large. It is also revealed that when a long intermolecular distance is provided by a high steric repulsion originating from the linkage of two phenyl groups, the dispersion energy is significantly small. However, in this range of intermolecular distances, the electrostatic energy caused by a strong quadrupole-quadrupole attractive interaction plays a dominant role, and as a result, a rather stable dimer is formed. In all 10 dimers, the dispersion, electrostatic, and exchange-repulsion energies strongly depend on the geometrical orientation of the molecules. The calculated interaction energies of these dimers are also compared with the corresponding experimentally measured viscosities. The results suggest an explicit linear relationship between the interaction energies and viscosities.     

Enhanced Aerogen–π Interaction by a Cation–π Force

The interaction between a noble gas atom and an aromatic π‐electron system, which mainly originates from the London dispersion force, is very weak and has not attracted enough attention yet. Herein, we reported a type of notably enhanced aerogen–π interaction between cation–π systems and noble gas atoms. The binding strength of a divalent cation–π system with a xenon atom is comparable to a moderate hydrogen bond (up to ca. 7 kcal mol^?1), whereas krypton and argon atoms produce slightly weaker interactions. Energy‐decomposition analysis reveals that the induction interaction is responsible for the stabilization of divalent cation–π?Xe species besides the dispersion interaction. Our results might be helpful to increase the understanding of some unsolved mysteries of aerogens.     

Quasi-relativistic density functional study of aurophilic interactions

Fifteen molecules containing the Au(I) species have been calculated by ab initio HF and MP2 methods and by five different density functional approaches. The aurophilic Au(d10)-Au(d10) bonding mechanism has been investigated. Both, one-electron interactions (i.e., electrostatic, polarization, charge transfer, and orbital interference) and two-electron effects (i.e., correlation, dispersion) contribute significantly to the so-called 'secondary' or metallophilic bonds representing the Au-Au interaction. Second, the applicability of density functional approaches to this type of bonding has been tested. It is well-known that present day density functionals are not yet designed to simulate the long-range London dispersion forces between nonoverlapping systems, whereas they approximately reproduce the short range dynamical electron correlations of strongly overlapping chemically bonded nondegenerate species. It is found here empirically for the investigated groups of gold(I) cluster compounds that simple local density functionals (LDF) of the Slater (or Slater plus Vosko) type yield rather reasonable estimates for the equilibrium distances, and (on the average) also for the aurophilic interaction energies, though with rather large standard deviations. Still LDF are useful for survey investigations of Au cluster compounds. Common gradient corrected DF are not recommended here, nor are the large core pseudopotentials for Au.     

X-ray diffraction and theoretical studies for the quantitative assessment of intermolecular arene-perfluoroarene stacking interactions

The arene-perfluoroarene stacking interaction was studied by experimental and theoretical methods. A series of compounds with different possibilities for formation of this recognition motif in the solid state were synthesized, and their crystal structures determined by single-crystal X-ray diffraction. The crystal packing of these compounds, as well as the packing of related compounds retrieved from crystallographic databases, were analyzed with quantitative crystal potentials: total lattice energies and the cohesive energies of closest molecular pairs in the crystals were calculated. The arene-perfluoroarene recognition motif emerges as a dominant interaction in the non-hydrogen-bonding compounds studied here, to the point that asymmetric dimers formed over the stacking motif carry over to asymmetric units made of two molecules in the crystal both for pure compounds and for molecular complexes; however, inter-ring distances and angles range from 3.70 to 4.85 A and from 5 to 21 degrees , respectively. Pixel energy partitioning reveals that whenever aromatic rings stack, the largest cohesive energy contribution comes from dispersion, which roughly amounts to 20 kJ mol(-1) per phenyl ring, while the coulombic term is minor but significant enough to make a difference between the arene-arene or perfluoroarene-perfluoroarene interactions on the one hand, and arene-perfluoroarene interactions on the other, whereby the latter are favored by about 10 kJ mol(-1) per phenyl ring. No evidence of special interaction which can be attributed to HF confrontation was recognizable.     

Pnicogen-hydride interaction between FH2X (X = P and As) and HM (M = ZnH, BeH, MgH, Li, and Na)

A pnicogen-hydride interaction has been predicted and characterized in FH(2)P-HM and FH(2)As-HM (M = ZnH, BeH, MgH, Li, and Na) complexes at the MP2/aug-cc-pVTZ level. For the complexes analyzed here, P(As) and HM are treated as a Lewis acid and a Lewis base, respectively. This interaction is moderate or strong since, for the strongest interaction of the FH(2)As-HNa complex, the interaction energy amounts to -24.79 kcal/mol, and the binding distance is equal to about 1.7 ?, much less than the sum of the corresponding van der Waals radii. By comparison with some related systems, it is concluded that the pnicogen-hydride interactions are stronger than dihydrogen bonds and lithium-hydride interactions. This interaction has been analyzed with natural bond orbitals, atoms in molecules, electron localization function, and symmetry adapted perturbation theory methods.     

Herringbone Pattern and CH–π Bonding in the Crystal Architecture of Linear Polycyclic Aromatic Hydrocarbons

The herringbone pattern is a pervasive structural motive found in most molecular crystals involving aromatic compounds. A plot of the experimental sublimation enthalpies of members of increasing size of the acene, phenacene and p‐phenyl families versus the number of carbons uncovers a linear relationship between the two magnitudes, suggesting a major role of CH–π bonding. In this work we undertake the task of evaluating the relevance of the edge‐to‐face interaction (or CH–π bond) in the overall reticular energy of the crystal, to quantitatively assess the importance of this structural element. Following a heuristic approach, we considered the series of acenes, phenacenes and p‐phenyls and analyzed the edge‐to‐face interaction between the molecules as they occur in the experimental crystal network. Isolation of the relevant molecular dimers allows to incorporate some of the most sophisticated tools of quantum chemistry and get a reliable picture of the isolated bond. When compared to the experimental sublimation energy, our results are conclusive: this sole interaction is the largest contribution to the lattice energy, and definitively dictates the crystal architecture in all the studied cases. Elusive enough, the edge‐to‐face interaction is mainly dominated by correlation interactions, specifically in the form of dispersion and, to a less extent, of charge‐transfer terms. A suggestive picture of the bond has been obtained by displaying the differences in local electron densities calculated by either correlated or non‐correlated methods.     

Adsorption geometry of 4-picoline chemisorbed on the Cu(110) surface: a study of forces controlling molecular self-assembly

The adsorption of 4-picoline (4-methylpyridine) on the Cu(110) surface has been studied with time-of-flight electron stimulated desorption ion angular distribution (TOF-ESDIAD) and other methods. Using deuterium labeling in the methyl group and hydrogen labeling on the aromatic ring, it has been possible to separately monitor by TOF-ESDIAD the C-D bond directions and the C-H bond directions in the adsorbed molecule. These triangulation measurements have led to a detailed understanding of the conformation of the adsorbed molecule relative to the Cu(110) crystal lattice, allowing one to witness changes in the molecular conformation as adsorbate-adsorbate interactional effects take place for increasing coverages. At low coverages, the molecule adsorbs by the N atom at an atop Cu site with the aromatic ring parallel to the <001> azimuth and with the molecular axis inclined 33 (+/- 5) degrees along the <001> azimuth. As rows of 4-picoline molecules form long range ordered chain structures oriented along the <112> azimuth, the aromatic ring twists 29 degrees about the inclined molecular axis as a result of forces between the adsorbate molecules. The initial tilting of the molecular axis at low coverage is likely due to the interaction of the positive-outward dipole with its image in the substrate. The ring twist may result from dipoleminus signdipole forces between the adsorbate molecules in the rows formed tending to form nested parallel pyridine rings. These studies are the first to apply the TOF-ESDIAD method for the measurement of the direction of chemical bonds at more than one molecular location within an adsorbed molecule and the new method is named electron stimulated desorption-molecular triangulation (ESD-MT). The results obtained give information of importance in understanding the factors which control conformational effects during the molecular self-assembly of complex adsorbed molecules on surfaces.