T-shaped Dimer Research Articles

Formation of Highly Emissive Anthracene Excimers for Aggregation-Induced Emission/Self-Assembly Directed (Bio)imaging.

AIEgens have emerged as a promising alternative to molecular rotors in bioimaging applications. However, transferring the concept of aggregation-induced emission (AIE) from solution to living systems remains a challenge. Given the highly heterogeneous nature and the compartmentalization of the cell, different approaches are needed to control the self-assembly within the crowded intricate cellular environment. Herein, we report for the first time the self-assembly mechanism of an anthracene-guanidine derivative (AG) forming the rare and highly emissive T-shaped dimer in breast cancer cell lines as a proof of concept. This process is highly sensitive to the local environment in terms of polarity, viscosity, and/or water quantity that should enable the use of the AG as a fluorescence lifetime imaging biosensor for intracellular imaging of cellular structures and the monitoring of intracellular state parameters. Different populations of the monomer and T-shaped and π-π dimers were observed in the cell membrane, cytoplasm, and nucleoplasm, related to the local viscosity and presence of water. The T-shaped dimer is formed preferentially in the nucleus because of the higher density and viscosity compared to the cytoplasm. The present results should serve as a precursor for the development of new design strategies for molecular systems for a wide range of applications such as cell viscosity, density, or temperature sensing and imaging.

Molecular basis for the role of disulfide-linked αCTs in the activation of insulin-like growth factor 1 receptor and insulin receptor.

The insulin receptor (IR) and insulin-like growth factor 1 receptor (IGF1R) control metabolic homeostasis and cell growth and proliferation. The IR and IGF1R form similar disulfide bonds linked homodimers in the apo-state; however, their ligand binding properties and the structures in the active state differ substantially. It has been proposed that the disulfide-linked C-terminal segment of α-chain (αCTs) of the IR and IGF1R control the cooperativity of ligand binding and regulate the receptor activation. Nevertheless, the molecular basis for the roles of disulfide-linked αCTs in IR and IGF1R activation are still unclear. Here, we report the cryo-EM structures of full-length mouse IGF1R/IGF1 and IR/insulin complexes with modified αCTs that have increased flexibility. Unlike the Γ-shaped asymmetric IGF1R dimer with a single IGF1 bound, the IGF1R with the enhanced flexibility of αCTs can form a T-shaped symmetric dimer with two IGF1s bound. Meanwhile, the IR with non-covalently linked αCTs predominantly adopts an asymmetric conformation with four insulins bound, which is distinct from the T-shaped symmetric IR. Using cell-based experiments, we further showed that both IGF1R and IR with the modified αCTs cannot activate the downstream signaling potently. Collectively, our studies demonstrate that the certain structural rigidity of disulfide-linked αCTs is critical for optimal IR and IGF1R signaling activation.

Various Sorts of Chalcogen Bonds Formed by an Aromatic System.

The chalcogen Y atom in the aromatic ring of thiophene and its derivatives YC4H4 (Y = S, Se, Te) can engage in a number of different interactions with another such unit within the homodimer. Quantum calculations show that the two rings can be oriented perpendicular to one another in a T-shaped dimer in which the Y atom accepts electron density from the π-system of the other unit in a Y···π chalcogen bond (ChB). This geometry best takes advantage of attractions between the electrostatic potentials surrounding the two monomers. There are two other geometries in which the two Y atoms engage in a ChB with one another. However, instead of a simple interaction between a σ-hole on one Y and the lone pair of its neighbor, the interaction is better described as a pair of symmetrically equivalent Y···Y interactions, in which charge is transferred in both directions simultaneously, thereby effectively doubling the strength of the bond. These geometries differ from what might be expected based simply on the juxtaposition of the electrostatic potentials of the two monomers.

The influence of a solvent environment on direct non-covalent interactions between two molecules: A symmetry-adapted perturbation theory study of polarization tuning of π–π interactions by water

High-level quantum chemical computations have provided significant insight into the fundamental physical nature of non-covalent interactions. These studies have focused primarily on gas-phase computations of small van der Waals dimers; however, these interactions frequently take place in complex chemical environments, such as proteins, solutions, or solids. To better understand how the chemical environment affects non-covalent interactions, we have undertaken a quantum chemical study of π–π interactions in an aqueous solution, as exemplified by T-shaped benzene dimers surrounded by 28 or 50 explicit water molecules. We report interaction energies (IEs) using second-order Møller–Plesset perturbation theory, and we apply the intramolecular and functional-group partitioning extensions of symmetry-adapted perturbation theory (ISAPT and F-SAPT, respectively) to analyze how the solvent molecules tune the π–π interactions of the solute. For complexes containing neutral monomers, even 50 explicit waters (constituting a first and partial second solvation shell) change total SAPT IEs between the two solute molecules by only tenths of a kcal mol−1, while significant changes of up to 3 kcal mol−1 of the electrostatic component are seen for the cationic pyridinium–benzene dimer. This difference between charged and neutral solutes is attributed to large non-additive three-body interactions within solvated ion-containing complexes. Overall, except for charged solutes, our quantum computations indicate that nearby solvent molecules cause very little “tuning” of the direct solute–solute interactions. This indicates that differences in binding energies between the gas phase and solution phase are primarily indirect effects of the competition between solute–solute and solute–solvent interactions.

Angle robust reflected plasmonic color palettes with expanded color gamut

By investigating the relationship between the color saturation and the square nanoblock period, the plasmonic color filters based on a two-dimensional metal–insulator–metal square nanoblock array structure with the optimum period are designed to generate highly saturated subtractive colors. Then, the realizable color gamut is broadly extended to 70% of the sRGB color space by introducing the supercell array consisted of centrosymmetric T-shaped dimers and the reflective full-color palette can provide a high angular tolerance of ∼30°. Moreover, the smooth transitions between two different colors can be achieved by mixing two types of supercell arrays with different dimensions. The supercell array structure also exhibits high sensitivities and good color responses when exposed on the ambient environments. Such excellent performances open the avenue for full-color display, colorimetric sensing, and filtering applications.

HAB79: A new molecular dataset for benchmarking DFT and DFTB electronic couplings against high-level ab initio calculations

A new molecular dataset called HAB79 is introduced to provide ab initio reference values for electronic couplings (transfer integrals) and to benchmark density functional theory (DFT) and density functional tight-binding (DFTB) calculations. The HAB79 dataset is composed of 79 planar heterocyclic polyaromatic hydrocarbon molecules frequently encountered in organic (opto)electronics, arranged to 921 structurally diverse dimer configurations. We show that CASSCF/NEVPT2 with a minimal active space provides a robust reference method that can be applied to the relatively large molecules of the dataset. Electronic couplings are largest for cofacial dimers, in particular, sulfur-containing polyaromatic hydrocarbons, with values in excess of 0.5eV, followed by parallel displaced cofacial dimers. V-shaped dimer motifs, often encountered in the herringbone layers of organic crystals, exhibit medium-sized couplings, whereas T-shaped dimers have the lowest couplings. DFT values obtained from the projector operator-based diabatization (POD) method are initially benchmarked against the smaller databases HAB11 (HAB7-) and found to systematically improve when climbing Jacob's ladder, giving mean relative unsigned errors (MRUEs) of 27.7% (26.3%) for the generalized gradient approximation (GGA) functional BLYP, 20.7% (15.8%) for hybrid functional B3LYP, and 5.2% (7.5%) for the long-range corrected hybrid functional omega-B97X. Cost-effective POD in combination with a GGA functional and very efficient DFTB calculations on the dimers of the HAB79 database give a good linear correlation with the CASSCF/NEVPT2 reference data, which, after scaling with a multiplicative constant, gives reasonably small MRUEs of 17.9% and 40.1%, respectively, bearing in mind that couplings in HAB79 vary over 4 orders of magnitude. The ab initio reference data reported here are expected to be useful for benchmarking other DFT or semi-empirical approaches for electronic coupling calculations.

Study on Molecular Dynamics of Singular Nature of Physical Properties near Critical Point in Carbon Dioxide System

Based on the molecular dynamics simulations, this paper analyzed the singular nature of physical properties of the carbon dioxide near the critical point. Detailed analysis of density simulation exhibited that an excellent agreement can be obtained by COMPASS forcefield besides the pseudo-critical region, while the peculiar behavior of density can again be observed. The computational domain is divided into the small sub-domains in which the standard deviation are evaluated as density fluctuation, and it shows maximum near the critical point and higher values at supercritical condition than that at subcritical condition. A new 3-parameter model was put forward to define the CO2 dimer distribution after each molecule in the domain had been supplied with the local coordination frame. The result shows that the T-shaped dimer is with higher probability to be formed than the parallel and crossed configuration, and the conversion of these dimer conformations closely associates with the peculiar properties of the critical point.

Strong Dipole-Quadrupole-Exciton Coupling Realized in a Gold Nanorod Dimer Placed on a Two-Dimensional Material.

Simple systems in which strong coupling of different excitations can be easily realized are highly important, not only for fundamental research but also for practical applications. Here, we proposed a T-shaped gold nanorod (GNR) dimer composed of a long GNR and a short GNR perpendicular to each other and revealed that the dark quadrupole mode of the long GNR can be activated by utilizing the dipole mode excited in the short GNR. It was found that the strong coupling between the dipole and quadrupole modes can be achieved by exciting the T-shaped GNR dimer with a plane wave. Then, we demonstrated the realization of strong dipole–quadrupole–exciton coupling by placing a T-shaped GNR on a tungsten disulfide (WS2) monolayer, which leads to a Rabi splitting as large as ~299 meV. It was confirmed that the simulation results can be well fitted by using a Hamiltonian based on the coupled harmonic oscillator model and the coupling strengths for dipole–quadrupole, dipole–exciton and quadrupole–exciton can be extracted from the fitting results. Our findings open new horizons for realizing strong plasmon–exciton coupling in simple systems and pave the way for constructing novel plasmonic devices for practical applications.

Excitonic and charge transfer interactions in tetracene stacked and T-shaped dimers.

Extended quantum chemical calculations were performed for the tetracene dimer to provide benchmark results, analyze the excimer survival process, and explore the possibility of using long-range-corrected (LC) time-dependent second-order density functional tight-biding (DFTB2) for this system. Ground- and first-excited-state optimized geometries, vertical excitations at relevant minima, and intermonomer displacement potential energy curves (PECs) were calculated for these purposes. Ground-state geometries were optimized with the scaled-opposite-spin (SOS) second-order Møller-Plesset perturbation (MP2) theory and LC-DFT (density functional theory) and LC-DFTB2 levels. Excited-state geometries were optimized with SOS-ADC(2) (algebraic diagrammatic construction to second-order) and the time-dependent approaches for the latter two methods. Vertical excitations and PECs were compared to multireference configuration interaction DFT (DFT/MRCI). All methods predict the lowest-energy S0 conformer to have monomers parallel and rotated relative to each other and the lowest S1 conformer to be of a displaced-stacked type. LC-DFTB2, however, presents some relevant differences regarding other conformers for S0. Despite some state-order inversions, overall good agreement between methods was observed in the spectral shape, state character, and PECs. Nevertheless, DFT/MRCI predicts that the S1 state should acquire a doubly excited-state character relevant to the excimer survival process and, therefore, cannot be completely described by the single reference methods used in this work. PECs also revealed an interesting relation between dissociation energies and the intermonomer charge-transfer interactions for some states.

Unusual binary aggregates of perylene bisimide revealed by their electronic transitions in helium nanodroplets and DFT calculations.

The S1 ← S0 electronic transition of perylene bisimide (PBI) and its binary aggregates were investigated using a combination of helium nanodroplet isolation spectroscopy and computational methods. First, well-resolved vibronic bands of the PBI monomer obtained under the superfluid helium nanodroplet environment were compared to simulated vibronic spectra with anharmonic corrections of the band positions. Second, about ten sets of weaker vibronic bands were observed, which show similar vibronic patterns as that of the PBI monomer and have their band origins red-shifted by about 8 to 218 cm-1. Experimental Poisson curve analyses, performed at the origins of these new sets of bands and the PBI monomer, indicate that the carriers of these weaker red-shifted vibronic bands are binary adducts of PBI. Three types of PBI dimer structures where the electronic transition dipole moments of the two subunits are perpendicular to each other were proposed as possible carriers of these red-shifted vibronic patterns. Extensive vibronic simulations were carried out in a multi-step procedure with TD-DFT, vertical Hessian, and finally adiabatic Hessian approaches. Small red-shifted band origins and very similar vibronic patterns to that of the monomer were predicted for unusual, T-shaped, type I dimer structures and are in close agreement with the experimental data. The combined experimental and theoretical results indicate that the helium nanodroplet environment enables the formation of these unusual T-shaped dimers and stabilizes them.

Direct aryl-aryl coupling of pentacene on Au(110).

Selective C-H bond activation of polycyclic aromatic hydrocarbons is challenging due to the relatively high bond dissociation energy and the existence of multiple equivalent C-H sites. Herein, we report a scanning tunneling microscopy study on the covalent coupling of pentacene molecules on Au(110) surfaces. The missing-row reconstruction of Au(110) surfaces strengthens the molecule-substrate interactions. At elevated temperatures (470-520 K), pentacenes undergo direct aryl-aryl coupling via C-H bond activation. Due to the anisotropic feature of the reconstructed Au(110) surface, pentacenes are preferentially oriented parallel or perpendicular, making the linear and T-shaped dimers the predominant products. Based on density functional theory calculations, the aryl C-H bond activation barrier is reduced to 1.42 eV on Au(110)-(1 × 3) reconstructed surfaces, at which the extra row of gold atoms located in the (1 × 3) reconstructed grooves plays a key role.

Tuning the optical response of a plasmonic T-shaped dimer with nanowire loads for improved SERS and sensing applications

Plasmonic nanostructures have important applications for surface-enhanced Raman chips, optical sensors, perfect absorbers, and so on. In this paper, we theoretically investigate the optical properties of a T-shaped dimer (TD) nanostructure and a TD with nanowire loads (TD/NL) nanostructure. By depositing the NLs around the TD, the optical property of the TD is significantly modified, and the extinction spectrum of composite TD/NL appears the splitting resonance peak and shows the asymmetric characteristic of Fano resonance due to the plasmon hybridization. Besides, a stronger electric field enhancement can be obtained in the composite TD/NL nanostructure, and the calculated results show the field enhancement effect of the dark mode in designed TD/NL nanostructure is three times than that in the TD nanostructure. Furthermore, the Fano resonance in TD/NL nanostructure reveals the narrow spectral linewidth and high quality factor, which is advantageous to optical refractive index sensors, and the corresponding sensing sensitivity is as high as 1083 nm RIU−1.

Parametrizing the Spatial Dependence of 1H NMR Chemical Shifts in π-Stacked Molecular Fragments.

Most recently a renewed interest in several areas has arisen in factors governing the 1H NMR chemical shift (1H CS) of protons in aromatic systems. Therefore, it is important to describe how 1H CS values are affected by π-stacking intermolecular interactions. The parametrization of radial and angular dependences of the 1H CS is proposed, which is based on conventional gauge-independent atomic orbital (GIAO) calculations of explicit molecular fragments. Such a parametrization is exemplified for a benzene dimer with intermonomer vertical and horizontal distances which are in the range of values often found in crystals of organic compounds. Results obtained by the GIAO calculations combined with B3LYP and MP2 methods were compared, and revealed qualitatively the same trends in the 1H CS data. The parametrization was found to be quantitatively correct for the T-shaped benzene dimers, and its limitations were discussed. Parametrized 1H CS surfaces should become useful for providing additional restraints in the search of site-specific information through an analysis of structurally induced 1H CS changes.

A Cyclic Periodic Wave Function Approach for the Study of Infinitely Periodic Solid-State Systems. I. Application to the C-H···π(C≡C) Hydrogen Bonding Systems.

The cyclic periodic wave function (CPWF) approach is applied at the AM1 and PM3 semiempirical levels of approximation to infinitely periodic solid-state systems stabilized by weak CH–pi (C–H···π) interactions between repeat units. The reliability of the AM1 and PM3 methods for modeling C–H···π bonding is first demonstrated using two representative dimer systems: the T-shaped ethyne dimer and the T-shaped propyne dimer. The CPWF method is then applied to two different crystal systems that are stabilized by C–H···π interactions: (1) pent-4-ynoic acid solid and (2) a series of three infinite crystal systems—tetrakis(4-ethynylphenyl)methane solid, tetraethynylmethane solid, and tetrabutadiynylmethane solid. A comparison of our results with available data demonstrates that the use of the CPWF approach at the AM1 and PM3 levels of approximation provides a convenient and reliable method for the study of infinitely periodic systems containing very weak C–H···π bonding.

Substituents’ influence on the C–H···π interaction in the T-shaped benzene dimer

We have investigated the CH···π interaction in the T-shaped benzene dimer in the presence of various neutral and cationic substituents, using the CCSD(T)/CBS and B97D/aug-cc-pVTZ method. The results reveal that the strength of the CH···π interaction can be enhanced up to 3.57 kcal/mol for multiple fluorine substitutions. The interaction energy of the dimer can be further increased by choosing electron-withdrawing substitutions, such as nitro and cyano groups. Further, the CH···π interaction energy can be tuned from ~ 5 to ~ 10 kcal/mol by the choice of cationic substituents. The energy decomposition results reveal that, on an average, the dispersion energy is two times larger than the electrostatic energy. However, the total binding energy follows the trend observed in the electrostatic energy component.

Noncovalent Interactions in the Catechol Dimer.

Noncovalent interactions play a significant role in a wide variety of biological processes and bio-inspired species. It is, therefore, important to have at hand suitable computational methods for their investigation. In this paper, we report on the contribution of dispersion and hydrogen bonds in both stacked and T-shaped catechol dimers, with the aim of delineating the respective role of these classes of interactions in determining the most stable structure. By using second-order Møller–Plesset (MP2) calculations with a small basis set, specifically optimized for these species, we have explored a number of significant sections of the interaction potential energy surface and found the most stable structures for the dimer, in good agreement with the highly accurate, but computationally more expensive coupled cluster single and double excitation and the perturbative triples (CCSD(T))/CBS) method.

Possible Formation of Metastable PAH Dimers upon Pickup by Helium Droplets.

Using path-integral molecular dynamics simulations and two quantum-mechanical-based force fields, we have investigated the conformational stability of dimers of a polycyclic aromatic hydrocarbon, perylene (C20H12), produced under typical experimental conditions of successive pick-up under helium nanodroplet environment. The most stable configurations are found to be of the stacked form with different relative orientations of the main molecular axes, perpendicular or T-shaped dimers being energetically much disfavored; however, in the presence of helium our simulations suggest that the time for rearrangement and π-stacking may be rather long and exceed hundreds of picoseconds. In addition, highly metastable dimers that are stacked but with a helium monolayer sandwiched between the two molecules are also found as likely products upon successive pickup. This stabilization occurs owing to the stronger localization of the helium atoms facing the aromatic rings, which is further enhanced in the dimer. The implications of the present results are discussed in the perspective of possible identification by spectroscopic methods.

CH/π-stabilization controls the architecture of the PPh3 propeller in transition-metal complexes. CH/π- and Cl/π-interactions determine its orientation within the molecule

The architecture of the triphenylphosphine propeller in Cr-PPh3 complexes and in the compounds trans-[MCl2(PPh3)2], M=Ni, Pd, and Pt, is analyzed on the basis of a CSD search. The three phenyl rings interact with each other by formation of weak CH/π bonds comparable to the archetypal T-shaped benzene dimer. ortho-CH bonds from inside the propeller bind to ipso- and ortho-carbon atoms of adjacent phenyl rings. In the broad energy minimum A/B there is a discontinuity in the transition from A to B. Binding switches from inside to outside ortho-carbon atoms. ortho-CH bonds from outside the propeller establish similar weak bonds with unsaturated ligands (and the metal atom) which control the arrangement of the PPh3 propeller within the molecule. In the trans-[MCl2(PPh3)2] complexes it is the Cl/π interaction which determines the orientation of the PPh3 propeller in the molecule.

Stability and Anharmonic N-H Stretching Frequencies of 1-Methylthymine Dimers: Hydrogen Bonding versus π-Stacking.

Stability of three hydrogen-bonded and six stacked 1-methylthymine (1 mT) dimers was studied with the DFT-D3 method at various temperatures. It was demonstrated that the stacked dimers are slightly less stable than the hydrogen-bonded counterparts. Existence of T-shaped dimers is addressed. Anharmonic couplings that involve N-H stretching modes of the nine species are studied. Surprisingly, we find that N-H stretching modes of the two 1 mT molecules are significantly coupled in four stacked dimers. The presented results shed light on existence of strong mode couplings between the two N-H stretching modes in stacked aromatic species. Our calculations support the proposal ( J. Phys. Chem. A 2011 , 115 , 9429 - 9439 ) that presence of several dimers is responsible for appearance of wide and structured bands in 1 mT homodimers' jet-cooled spectra above 2900 cm(-1).

A permanently porous single molecule H-bonded organic framework for selective CO2 capture.

Permanent porosity has been realized in a hydrogen bonded framework formed by a single tripodal tricarboxylic acid molecule. The presence of three phenyl rings linked to a flexible sp(3) nitrogen centre renders a near-propeller shape to the molecule generating an unusual 'non-planar' 3-D framework formed by highly directional planar -COOHHOOC- hydrogen bonds, propagating in all three directions. The material shows exceptional hydrolytic, acidic and thermal stability and has a surface area of 1025 m(2) g(-1). Importantly, it shows preferential adsorption of CO2 over N2 with very high selectivities (350 : 1@1 bar, 303 K). DFT modeling shows the presence of stable T-shaped CO2CO2 dimers within the channels suggesting favorable co-operativity between them.