Implementation of pi-pi interactions in molecular dynamics simulation

No explicit pi-pi interaction term has been incorporated in the conventional molecular dynamics (MD) simulation programs in spite of its significant role in the folding of biomolecules and the clustering of organic chemicals. In this article, we propose a technique to emphasize the effect of pi-pi interactions using a function of energy and implement it into an MD simulation program. Several trial calculations show that the pi-pi incorporated program gives improved results consistent with experimental data on atom geometry and has no unfavorable interference with the conventional computational framework. This indicates an importance of the explicit consideration of pi-pi interactions in MD simulation.     

Construction of the multidecker anthracene-silver(I) system by intramolecular pi-pi interactions

As a continuation of the study on the construction of the multidecker aromatic compounds with pi-pi interactions, the anthracene derivatives 9,10-dimethylanthracene (dman), 9,10-diphenylanthracene (dpan), and 7,12-dimethylbenz[a]anthracene (dmban) have been studied toward complexation with the silver(I) ion. The crystal structures of [Ag(dman)(0.5)(p-xylene)(ClO(4))], [Ag(2)(dpan)(0.5)(C(6)H(6))(0.5)(CF(3)SO(3))(2)], and [Ag(2)(dmban)(2)(ClO(4))(2)](p-xylene), together with the metal-free ligand dpan, have been determined by single-crystal X-ray diffraction. These pi-electron-rich aromatic compounds are found to have great promise as an approach to the effective self-assembly of high nuclearity in a multilayer fashion.     

A trinuclear Pt(II) compound with short Pt-Pt-Pt contacts. An analysis of the influence of pi-pi stacking interactions on the strength and length of the Pt-Pt bond

In this work we report the first example of a trinuclear Pt(II) complex with Pt-Pt-Pt bonds that are not facilitated by direct intervention of bridging ligands but are partially held by the attractive pi-pi stacking interaction between the phenyl units of the 4,4'-dimethyl-2,2'-bipyridyl ligands. The effect of the pi-pi stacking interactions on the strength and length of the Pt-Pt bond has been discussed using reduced models of the interacting moieties in which the aromatic rings have been removed. The nature of the Pt-Pt bonds has been studied through energy decomposition and atoms-in-molecules analyses. The results indicate that the relatively strong (about 40 kcal mol(-1)) Pt-Pt metallic bond has similar covalent and ionic contributions.     

Luminescence on-off switching via reversible interconversion between inter- and intramolecular aurophilic interactions

Reversible interconversion between inter- and intramolecular AuAu interactions induces luminescence on/off switching in solid state. For the gold(I) photoluminescence system, intermolecular aurophilic interaction is a more significant factor than intramolecular aurophilic interaction.     

Impact of methanol and acetonitrile on separations based on pi-pi interactions with a reversed-phase phenyl column

Studies were performed to investigate the roles of methanol and acetonitrile on the retention mechanism of an active pharmaceutical ingredient (API) and related compounds with a reversed phase phenyl column. Different retention orders were observed depending upon whether acetonitrile or methanol was used as the organic modifier. We propose that acetonitrile impedes the selective pi-pi interactions between the analyte molecules and the phenyl groups in the stationary phase. Further study with 1-naphthoic acid and 1-naphthol as test compounds in the HPLC separation provides additional support for the influence of acetonitrile on pi-pi interactions between analyte molecules and a phenyl stationary phase. This study suggests that methanol be used as the preferred organic modifier with phenyl columns to achieve selectivity based upon pi-pi interactions.     

The effect of multiple substituents on sandwich and T-shaped pi-pi interactions

Sandwich and T-shaped configurations of substituted benzene dimers were studied by second-order perturbation theory to determine how substituents tune pi-pi interactions. Remarkably, multiple substituents have an additive effect on the binding energy of sandwich dimers, except in some cases when substituents are aligned on top of each other. The energetics of substituted T-shaped configurations are more complex, but nevertheless a simple model that accounts for electrostatic and dispersion interactions (and direct contacts between substituents on one ring and hydrogen atoms on the other), provides a good match to the quantum mechanical results. These results provide insight into the manner by which substituents csan be utilized in supramolecular design.     

Anion-pi and pi-pi cooperative interactions regulating the self-assembly of nitrate-triazine-triazine complexes

We theoretically investigate the cooperative enhancement of the interactions between anions and electron-deficient aromatics by pi-pi stacking, focusing on the recent crystallographic observation of anion-pi-pi interactions in a synthesized coordination compound based on 1,3,5-triazine moieties. Using a combination of state-of-the-art dispersion-corrected density functional and quantum Monte Carlo calculations, we rationalize the unusual structural features observed in this nitrate-triazine-triazine complex. We show that the triazine rings are staggered and bent and slip with respect to each other with the nitrate bound off-center in a T-like configuration. Our results indicate that this pi-pi stacking is not simply enforced by the coordination of the triazines within the particular crystal structure but is regulated by cooperative anion-pi and pi-pi interactions. In the nitrate-triazine-triazine complex, this cooperative effect amounts to 6% of the total binding energy. Ways to further increase this energetic enhancement in the design of anion-host architectures are discussed.     

Synthesis, structures, and photoluminescence properties of novel lanthanide tetracyanoplatinates lacking Pt-Pt interactions

The synthesis of a series of lanthanide tetracyanoplatinates all incorporating 2,2′:6′,2″-terpyridine (terpy) have been carried out by reaction of Ln³⁺ nitrate salts with terpy and potassium tetracyanoplatinate. The incorporation of different Ln³⁺ cations results in the isolation of [Ln(DMF)₂(C₁₅H₁₁N₃)(H₂O)₂(NO₃)]Pt(CN)₄ (Ln=La-Nd, Sm-Yb) under otherwise identical reaction conditions. These compounds have been isolated as single crystals and X-ray diffraction has been used to investigate their structural features. All of the reported compounds are isostructural. Crystallographic data for the representative Eu³⁺ compound (EuPt) are (MoKα, λ=0.71073 Å): monoclinic, space group P2₁/c, a=10.1234(4) Å, b=18.7060(7) Å, c=17.1642(5) Å, β=97.249(3)°, V=3224.4(2), Z=4, R(F)=2.78% for 426 parameters with 7724 reflections with I>2σ(I). The structure consists of a zero-dimensional, ionic salt containing complex [Eu(DMF)₂(C₁₅H₁₁N₃)(H₂O)₂(NO₃)]²⁺ cations and anions. The complex cations contain the Eu³⁺ ions in a tri-capped trigonal prismatic coordination environment with one terdentate 2,2′:6′,2″-terpyridine molecule, one bidentate nitrate anion, two O-bound dimethylformamide molecules, and two coordinated water molecules. Photoluminescence data illustrate that EuPt displays intramolecular energy transfer from the coordinated terpy molecule to the Eu³⁺ cation. The uncoordinated tetracyanoplatinate anion also exhibits visible emission.     

From subtle to substantial: role of metal ions on pi-pi interactions

Quantum chemistry calculations reveal that the subtle pi-pi interactions, usually in the range 2-4 kcal/mol, will become substantially significant, from 6 to 17 kcal/mol, in the presence of metal ion. The metal ions have higher affinity toward a pi-pi dimer compared to a single pi-moiety. Considering the widespread occurrence of cation-pi-pi motifs in chemistry and biology, as evident from the database analysis, we propose that the two key noncovalent forces, which govern the macromolecular structure, cation-pi and pi-pi, work in concert.     

Estimates of the ab initio limit for pi-pi interactions: the benzene dimer

State-of-the-art electronic structure methods have been applied to the simplest prototype of aromatic pi-pi interactions, the benzene dimer. By comparison to results with a large aug-cc-pVTZ basis set, we demonstrate that more modest basis sets such as aug-cc-pVDZ are sufficient for geometry optimizations of intermolecular parameters at the second-order M?ller-Plesset perturbation theory (MP2) level. However, basis sets even larger than aug-cc-pVTZ are important for accurate binding energies. The complete basis set MP2 binding energies, estimated by explicitly correlated MP2-R12/A techniques, are significantly larger in magnitude than previous estimates. When corrected for higher-order correlation effects via coupled cluster with singles, doubles, and perturbative triples [CCSD(T)], the binding energies D(e) (D(0)) for the sandwich, T-shaped, and parallel-displaced configurations are found to be 1.8 (2.0), 2.7 (2.4), and 2.8 (2.7) kcal mol(-1), respectively.     

Beyond the benzene dimer: an investigation of the additivity of pi-pi interactions

The benzene dimer is the simplest prototype of pi-pi interactions and has been used to understand the fundamental physics of these interactions as they are observed in more complex systems. In biological systems, however, aromatic rings are rarely found in isolated pairs; thus, it is important to understand whether aromatic pairs remain a good model of pi-pi interactions in clusters. In this study, ab initio methods are used to compute the binding energies of several benzene trimers and tetramers, most of them in 1D stacked configurations. The two-body terms change only slightly relative to the dimer, and except for the cyclic trimer, the three- and four-body terms are negligible. This indicates that aromatic clusters do not feature any large nonadditive effects in their binding energies, and polarization effects in benzene clusters do not greatly change the binding that would be anticipated from unperturbed benzene-benzene interactions, at least for the 1D stacked systems considered. Three-body effects are larger for the cyclic trimer, but for all systems considered, the computed binding energies are within 10% of what would be estimated from benzene dimer energies at the same geometries.     

Synthesis of dendritic oligothiophenes and their self-association properties by intermolecular pi-pi interactions

[structure: see text] The addition of oligothiophene into a dendritic structure causes a self-association behavior by intermolecular pi-pi interactions in a solution and in a solid state. Increasing the generation of the dendritic structure gives not only a high association constant but also sufficient field-effect hole mobility, which indicates that the charge-transporting passes are formed by the strong pi-pi interactions.     

Molecular layer-by-layer self-assembly of water-soluble perylene diimides through pi-pi and electrostatic interactions

A layer-by-layer deposition process has been carried out for two oppositely charged water-soluble perylene diimide dyes without the use of intervening polyelectrolyte layers. The strong pi-pi interactions between the perylene moieties help stabilize the layers and simultaneously diminish the fluorescence quantum yield of the array without strongly affecting the absorption or fluorescence spectra. There is an alternation of fluorescence intensity according to which perylene species is on the outer layer, which is interpreted as the effect of facile energy transfer between the perylenes.     

Ion-triggered multistate molecular switching device based on regioselective coordination-controlled ion binding

Molecular devices capable of accessing different controlled conformational states, while optically signaling the occupied state, are attractive tools for nanotechnology since they relate to both areas of molecular mechanical devices and logic gates. We report here a simple molecular system that allows access to four distinct conformational and optical states. It is based on the regioselective complexation of metal ions to a heterocyclic ligand triad, which is dictated by the accessible coordination geometry and electrostatic properties of two distinct binding subunits. Thus, local conformational switching is brought about by tetrahedral coordination (of Cu(I)) or octahedral coordination (of M(2+) ions) to bidentate and tridentate binding subunits, respectively. The shape modifications undergone represent an ion-controlled nanomechanical device. They give controlled access to four different states that display different physico-chemical (e.g. optical) properties and provide a basis for logic gate operations.     

A bond-length-bond-order relationship for intermolecular interactions based on the topological properties of molecular charge distributions

Ab initio SCF MO calculations for the hydrogen-bonded complexes between nitriles and hydrogen fluoride suggest a strong linear relationship between the charge density at the hydrogen-bond critical point and the hydrogen-bond energy. Further investigation of the topological properties of the charge density indicates that the generalization of the bond-length-bond-order relationship of CC bonds due to Bader et al. may be extended to intermolecular hydrogen bonding. Calculations at the 6–31G^** level, including complete geometry optimization, are reported for the

complexes, where R  H, Li, F, Cl, HO, LiO, NC, HCC, CH₃ and CH₃O.     

痂囊腔菌素A分子构型和分子内氢键的理论研究

用半经验量子化学AM1方法对天然苝醌化合物痂囊腔菌素A(EA)的分子构型和分子内氢键进行了研究;从EA可能的64种构型中选择16种进行了计算.结果表明,EA的X射线晶体结构对应的构型是II型左旋(A)a,a型(II-L-A-a,a);小的生成热差值可以使得异构体间的转换容易进行,有利于发生分子内质子传递.尽管采用AM1方法计算得到的EA各种构象的平面性有所差别,但都很接近晶体的平面性.此外,EA分子内氢键键能的平均值为22.9kJ/mol;II型的氢键键能比I型的大,(9,10)位的氢键键能比(3,4)位的大;EA的平面性是由苝醌环上的侧链取代所决定,而与分子内是否存在氢键无关.