Bonds or not bonds? Pancake bonding in 1,2,3,5-dithiadiazolyl and 1,2,3,5-diselenadiazolyl radical dimers and their derivatives

Unusually long bonds or short intermolecular contacts occur in the title compounds reminiscent of pancake bonding. Pancake bonding interactions seem analogous to π-stacking interactions, but they display much shorter contact distances than normally seen in van der Waals (vdW) dimers. The interpretation of these SN and SeN containing structures has been an outstanding challenge for some time. The antibonding (π*) singly occupied molecular orbital (SOMO) of the radical is the source of two-electron multicenter bonding (2e/mc). Preferred conformations thus can be traced back to SOMO-SOMO overlap. We used several computational methods to understand the nature of pancake bonding in the title compounds including four wave function methods (WFT) and a dozen density functional theories (DFT) including empirical dispersion corrections. We used experimental data and high level CCSD(T)/6-311++G(d,p) and MRPT2/6-311++G(d,p) calculations for comparison. The analysis provided the interpretation a wealth of experimental data including conformational preferences of these SN and SeN containing radical dimers leading to a better overall understanding of pancake bonding. Analysis of the various components of the inter-radical interactions showed that SOMO-SOMO bonding interaction and dispersion interaction contribute to the binding energy and neither of these interactions alone is sufficient to bind the dimer. The dimer is predicted to show weak diradical character.     

Pancake Bond Orders of a Series of π‐Stacked Triangulene Radicals

Conjugated radicals are capable of forming π‐stacking “pancake‐bonded” dimers. Members of the family of triangulene hydrocarbons, non‐Kekulé neutral multiradicals, can utilize more than one singly occupied molecular orbital (SOMO) to form multiple pancake‐bonded dimers with formal bond orders of up to five. The resulting dimer binding energies can be quite high and the intermolecular contacts rather small compared to the respective van der Waals values. The preferred configurations are driven by the large stabilization energy of overlapping SOMOs.     

Charge shift bonding concept in radical π-dimers

We show that pancake bonding in radical π-dimers display features of charge shift (CS) bonding. While the CS bonding concept has been developed to interpret the unusual aspects of σ-bonds around centers with a large number of lone pairs, such as F(2) and HOOH, we find a similar role played by the nonbonding or slightly bonding π-electron pairs in π-stacking radical dimers. Arguments and computational evidence indicate that the CS bonding concept developed by Shaik and Hiberty et al. captures essential features of the intermolecular bonding in radical π-dimers in which the overlap of the two radical centered singly occupied molecular orbitals (SOMOs) play a crucial role. By using the tetracyanoethylene anion dimer, [TCNE](2)(2-), as a model, we show that compared to CAS(2,2) calculations, significant binding contributions are recovered in the calculations simply by including selected intrapair excitations of the SOMO-SOMO bonding orbitals and the nonbonding π-orbitals. This observation is the basis for the analogy of chemical bonding between pancake bonded radical π-dimers and other charge shift bonded molecules, such as F(2). By extending the CS bonding concept to a new class of molecules, we find a novel application of the lone pair bond weakening effect (LPBWE) in which the doubly occupied π-orbitals play the role of lone pairs.     

A polarizable dipole–dipole interaction model for evaluation of the interaction energies for NH···OC and CH···OC hydrogen‐bonded complexes

In this article, a polarizable dipole–dipole interaction model is established to estimate the equilibrium hydrogen bond distances and the interaction energies for hydrogen‐bonded complexes containing peptide amides and nucleic acid bases. We regard the chemical bonds N? H, C?O, and C? H as bond dipoles. The magnitude of the bond dipole moment varies according to its environment. We apply this polarizable dipole–dipole interaction model to a series of hydrogen‐bonded complexes containing the N? H···O?C and C? H···O?C hydrogen bonds, such as simple amide‐amide dimers, base‐base dimers, peptide‐base dimers, and β‐sheet models. We find that a simple two‐term function, only containing the permanent dipole–dipole interactions and the van der Waals interactions, can produce the equilibrium hydrogen bond distances compared favorably with those produced by the MP2/6‐31G(d) method, whereas the high‐quality counterpoise‐corrected (CP‐corrected) MP2/aug‐cc‐pVTZ interaction energies for the hydrogen‐bonded complexes can be well‐reproduced by a four‐term function which involves the permanent dipole–dipole interactions, the van der Waals interactions, the polarization contributions, and a corrected term. Based on the calculation results obtained from this polarizable dipole–dipole interaction model, the natures of the hydrogen bonding interactions in these hydrogen‐bonded complexes are further discussed. © 2013 Wiley Periodicals, Inc.     

The effect of chromophore-chromophore interaction on the spectral luminescent properties of oxazine dye dimers

Spectral and luminescent properties were studied for chemical dimers and molecular aggregates of Nile Red oxazine dye in solutions. Chemical bonding of two oxazine dye molecules leads to the formation of a dimer whose spectral behavior is in close agreement with the exciton model constructed for “physical” molecular aggregates. Chemical dimers luminesce, whereas dimers formed because of van der Waals interactions do not.     

Anisotropy of the van der Waals Configuration of Atoms in Complex,Condensed, and Gas-Phase Molecules

Anisotropic van der Waals (vdW) radii of 5b–7bsubgroup elements were determined from structures of gas-phase van der Waals complexes and crystal molecular compounds. The anisotropy of the van der Waals configuration of atoms was shown to decrease when going from isolated molecules to the condensed state. Variations in intermolecular distances, which are usually explained in terms of the formation of hydrogen bonds, are substantially governed by the anisotropic effect.     

Investigation of the distinction between van der Waals interaction and chemical bonding based on the PAEM‐MO diagram

In recent years, the basic problem of understanding chemical bonding, nonbonded, and/or van der Waals interactions has been intensively debated in terms of various theoretical methods. We propose and construct the potential acting on one electron in a molecule‐molecular orbital (PAEM‐MO) diagram, which draws the PAEM inserted the MO energy levels with their major atomic orbital components. PAEM‐MO diagram is able to show clear distinction of chemical bonding from nonbonded and/or vdW interactions. The rule for this is as follows. Along the line connecting two atoms in a molecule or a complex, the existence of chemical bonding between these two atoms needs to satisfy two conditions: (a) a critical point of PAEM exists and (b) PAEM barrier between the two atoms is lower in energy than the occupied major valence‐shell bonding MO which contains in‐phase atomic components (positive overlap) of the two considered atoms. In contrast to the chemical bonding, for a nonbonded interaction or van der Waals interaction between two atoms, both conditions (a) and (b) do not be satisfied at the same time. This is demonstrated and discussed by various typical cases, particularly those related to helium atom and H? H bonding in phenanthrene. There are helium bonds in HHeF and HeBeO molecules, whereas no H? H bonding in phenanthrene. The validity and limitation for this rule is demonstrated through the investigations of the curves of the PAEM barrier top and MO energies versus the internuclear distances for He₂, H₂, and He₂⁺ systems. © 2014 Wiley Periodicals, Inc.     

Lennard-Jones parameters for small diameter carbon nanotubes and water for molecular mechanics simulations from van der Waals density functional calculations

Lennard-Jones (LJ) parameters are derived for classical nonpolarizable force fields for carbon nanotubes (CNTs) and for CNT-water interaction from van der Waals (vdW) enhanced density functional calculations. The new LJ parameters for carbon-carbon interactions are of the same order as those previously used in the literature but differ significantly for CNT-water interactions. This may partially originate from the fact that in addition to pure vdW interactions the polarization and other quantum mechanics effects are embedded into the LJ-potential.     

van der Waals interactions of polycyclic aromatic hydrocarbon dimers

Density functional theory is in principle exact and includes also long-range interactions, such as the van der Waals interactions. These are, however, part of the exchange-correlation energy functional that needs to be approximated, and are absent in the local and semilocal standard implementations. Recently a density functional which includes van der Waals interactions for planar systems has been developed, which we show can be extended to provide a treatment of planar molecules. We use this functional to calculate binding distances and energies for dimers of three of the smallest polycyclic aromatic hydrocarbons (PAHs)--naphthalene, anthracene, and pyrene.     

Revisiting the main group cyclopentadienyl metal complexes in terms of the through-space coupling concept

The structures and properties of metal complexes are traditionally treated in terms of hybridization and electronic ligand effects. What is notoriously neglected, however, is the fact that in such an aggregate the ligands approach so closely to one another — on the order of van der Waals (vdW) distances — that intramolecular packing effects come into play. Actually, non-bonded interactions between any atoms bonded to some central atom are increasingly recognized as an important factor in determining bond distances, bond angles and the like. The class of the main group cyclopentadienyl (Cp) metal complexes appears to be a case study in this respect, because of the large extension of the Cp group and its ring structure on the one hand, and on the other, the minimal d-orbital involvement, dissimilar to the transition-metal analogues. It is shown that the diverse array of structural arrangements, such as linear, ring-slipped, bent, and polymeric chain structures, as well as their reactivities, are brought under the umbrella of one treatment with the aid of the through-space coupling (TSC) concept. This is the molecular orbital representation of vdW repulsive–attractive forces. As a central feature, the individual ligands are at first combined to a united system of TSC orbitals and then allowed to interact with the metal AOs. The energy splitting of the TSC orbitals and the electron density shift from one of them to a vacant metal orbital determine the repulsive and attractive interligand forces and hence fine-tune the geometry of the complex. Along these lines a physical explanation for the interplay between vdW attraction and repulsion becomes available. More specifically we are dealing here with complexes of the type Cp′_nML_m (n=1–3, m=0–3) via united {Cp′_nL_m} molecular orbitals. Bending and slipping of the Cp′ ligands are rooted in vdW attraction and repulsion, respectively, with geometry and hapticity of the Cp′-metal bonding adjusted so as to optimize TSC.     

The bonding in the ozone molecule: From a different perspective

A new qualitative treatment of the bonding in ozone is presented. It is based upon a combination of several simple concepts: the nonparticipation of the pairs of electrons tightly held in the atomic 2s orbitals; simple overlap of the 2p orbitals to form sigma bonds; interaction of three 2p orbitals to yield bonding and nonbonding pi molecular orbitals that are populated by electron pairs; and van der Waals repulsion between the two terminal oxygen atoms forcing these atoms apart to yield the bond angle of 117° as a compromise. Both the assumptions and the resulting bonding picture are in accord with the photoelectron spectroscopic data, the results from sophisticated molecular orbital calculations, and the common physical properties of ozone.     

Importance of van der Waals Interactions in QM/MM Simulations

The importance of accurately treating van der Waals interactions between the quantum mechanical (QM) and molecular mechanical (MM) atoms in hybrid QM/MM simulations has been investigated systematically. First, a set of van der Waals (vdW) parameters was optimized for an approximate density functional method, the self-consistent charge-tight binding density functional (SCC-DFTB) approach, based on small hydrogen-bonding clusters. The sensitivity of condensed phase observables to the SCC-DFTB vdW parameters was then quantitatively investigated by SCC-DFTB/MM simulations of several model systems using the optimized set and two sets of extreme vdW parameters selected from the CHARMM22 forcefield. The model systems include a model FAD molecule in solution and a solvated enediolate, and the properties studied include the radial distribution functions of water molecules around the solute (model FAD and enediolate), the reduction potential of the model FAD and the potential of mean force for an intramolecular proton transfer in the enediolate. Although there are noticeable differences between parameter sets for gas-phase clusters and solvent structures around the solute, thermodynamic quantities in the condensed phase (e.g., reduction potential and potential of mean force) were found to be less sensitive to the numerical values of vdW parameters. The differences between SCC-DFTB/MM results with the three vdW parameter sets for SCC-DFTB atoms were explained in terms of the effects of the parameter set on solvation. The current study has made it clear that efforts in improving the reliability of QM/MM methods for energetical properties in the condensed phase should focus on components other than van der Waals interactions between QM and MM atoms.     

Water monomer interaction with gold nanoclusters from van der Waals density functional theory

We investigate the interaction between water molecules and gold nanoclusters Au(n) through a systematic density functional theory study within both the generalized gradient approximation and the nonlocal van der Waals (vdW) density functional theory. Both planar (n = 6-12) and three-dimensional (3D) clusters (n = 17-20) are studied. We find that applying vdW density functional theory leads to an increase in the Au-Au bond length and a decrease in the cohesive energy for all clusters studied. We classify water adsorption on nanoclusters according to the corner, edge, and surface adsorption geometries. In both corner and edge adsorptions, water molecule approaches the cluster through the O atom. For planar clusters, surface adsorption occurs in a O-up/H-down geometry with water plane oriented nearly perpendicular to the cluster. For 3D clusters, water instead favors a near-flat surface adsorption geometry with the water O atom sitting nearly atop a surface Au atom, in agreement with previous study on bulk surfaces. Including vdW interaction increases the adsorption energy for the weak surface adsorption but reduces the adsorption energy for the strong corner adsorption due to increased water-cluster bond length. By analyzing the adsorption induced charge rearrangement through Bader's charge partitioning and electron density difference and the orbital interaction through the projected density of states, we conclude that the bonding between water and gold nanocluster is determined by an interplay between electrostatic interaction and covalent interaction involving both the water lone-pair and in-plane orbitals and the gold 5d and 6s orbitals. Including vdW interaction does not change qualitatively the physical picture but does change quantitatively the adsorption structure due to the fluxionality of gold nanoclusters.     

Synthesis and photophysical properties of self-assembled metallogels of platinum(II) acetylide complexes with elaborate long-chain pyridine-2,6-dicarboxamides

A series of platinum(II) acetylide complexes with elaborate long-chain pyridine-2,6-dicarboxamides was synthesized. These metal complexes are capable of immobilizing organic solvents to form luminescent metallogels through a combination of intermolecular hydrogen bonding, aromatic π-π, and van der Waals interactions. Fibrillar morphologies were identified by TEM for these metallogels. Unique photophysical properties associated with the sol-to-gel transition have been disclosed with luminescence enhancement at elevated temperatures, which is in sharp contrast to typical thermotropic organogels or metallogels reported in the literature. Such unusual luminescence enhancement is attributed to the increased degree of freedom at higher temperatures that results in the formation of favorable molecular aggregates in the excited state through enhanced aromatic π-π and metallophilic Pt(II)···Pt(II) interactions. Structurally similar Pt-bp3 is not able to gel any common organic solvents. The inability of Pt-bp3 to form gels illustrates the importance of gelation to the macroscopic photophysical properties; Pt-bp3 does not show emission enhancement at elevated temperatures due to its low tendency to form strong aggregates in the ground state.     

Short but Weak: The Z‐DNA Lone‐Pair⋅⋅⋅π Conundrum Challenges Standard Carbon Van der Waals Radii

Current interest in lone‐pair???π (lp???π) interactions is gaining momentum in biochemistry and (supramolecular) chemistry. However, the physicochemical origin of the exceptionally short (ca. 2.8 Å) oxygen‐to‐nucleobase plane distances observed in prototypical Z‐DNA CpG steps remains unclear. High‐level quantum mechanical calculations, including SAPT2+3 interaction energy decompositions, demonstrate that lp???π contacts do not result from n→π* orbital overlaps but from weak dispersion and electrostatic interactions combined with stereochemical effects imposed by the locally strained structural context. They also suggest that the carbon van der Waals (vdW) radii, originally derived for sp³ carbons, should not be used for smaller sp² carbons attached to electron‐withdrawing groups. Using a more adapted carbon vdW radius results in these lp???π contacts being no longer of the sub‐vdW type. These findings challenge the whole lp???π concept that refers to elusive orbital interactions that fail to explain short interatomic contact distances.     

乙酰胆碱酯酶AChE与1,7-二氮杂咔唑抑制剂的作用机理的分子动力学模拟

通过分子对接、分子动力学(MD)模拟以及成键自由能分析方法,从原子水平上模拟研究了3种1,7-二氮杂咔唑衍生物(分别记为M1、M2和M3)与ACh E的结合模式及相互作用机理,分析和讨论了研究体系的静电相互作用和范德华相互作用(vd W)。用MM-PBSA方法计算的3种抑制剂与ACh E之间的结合自由能与抑制剂的实验生物活性数据(IC50值)相对应。分析结果表明,残基S286与抑制剂之间形成的氢键作用有利于抑制剂与ACh E之间的结合。范德华相互作用,尤其是抑制剂与关键残基W279和Y334的作用,对抑制剂与ACh E之间的结合自由能有较大的贡献,在区分抑制剂M1(或M2)和M3的生物活性上发挥着重要的作用。     

Power series expansion of the random phase approximation correlation energy: The role of the third- and higher-order contributions

We derive a power expansion of the correlation energy of weakly bound systems within the random phase approximation (RPA), in terms of the Coulomb interaction operator, and we show that the asymptotic limit of the second- and third-order terms yields the van der Waals (vdW) dispersion energy terms derived by Zaremba-Kohn and Axilrod-Teller within perturbation theory. We then show that the use of the second-order expansion of the RPA correlation energy results in rather inaccurate binding energy curves for weakly bonded systems, and discuss the implications of our findings for the development of approximate vdW density functionals. We also assess the accuracy of different exchange energy functionals used in the derivation of vdW density functionals.