Liquid Crystallinity and Supramolecular Organization of Regioisomeric Isatin Derivatives: An Experimental and Theoretical Study

Spatially organized chromophores can be beneficial for advanced applications like for example, organic solar cells, laser technology or non‐linear optic devices as well as supramolecular photochemistry. Of particular interest are non‐static ordered forms of molecular organization as for example, liquid crystals. With this in mind we synthesised four new regioisomeric isatin derivatives by Suzuki–Miyaura coupling of 4‐dodecyloxyphenylboronic acid with all four possible regioisomers of bromoisatin. Liquid crystalline properties are found for 5‐(4‐dodecyloxyphenyl)isatin, while the other regioisomers do not display a mesomorphic behaviour. The synthesis, physicochemical investigations including polarization microscopy, differential scanning calorimetry and X‐ray investigations are discussed and accompanied with density functional theory calculations with respect to the target molecules and their possible H‐bonded aggregates. Two distinct setups of supramolecular assemblies for such isatin derivatives are discussed and a model for the mesophase is proposed.     

An N log N approximation based on the natural organization of biomolecules for speeding up the computation of long range interactions

Presented here is a method, the hierarchical charge partitioning (HCP) approximation, for speeding up computation of pairwise electrostatic interactions in biomolecular systems. The approximation is based on multiple levels of natural partitioning of biomolecular structures into a hierarchical set of its constituent structural components. The charge distribution in each component is systematically approximated by a small number of point charges, which, for the highest level component, are much fewer than the number of atoms in the component. For short distances from the point of interest, the HCP uses the full set of atomic charges available. For long‐distance interactions, the approximate charge distributions with smaller sets of charges are used instead. For a structure consisting of N charges, the computational cost of computing the pairwise interactions via the HCP scales as O(N log N), under assumptions about the structural organization of biomolecular structures generally consistent with reality. A proof‐of‐concept implementation of the HCP shows that for large structures it can lead to speed‐up factors of up to several orders of magnitude relative to the exact pairwise O(N²) all‐atom computation used as a reference. For structures with more than 2000–3000 atoms the relative accuracy of the HCP (relative root‐mean‐square force error per atom), approaches the accuracy of the particle mesh Ewald (PME) method with parameter settings typical for biomolecular simulations. When averaged over a set of 600 representative biomolecular structures, the relative accuracies of the two methods are roughly equal. The HCP is also significantly more accurate than the spherical cutoff method. The HCP has been implemented in the freely available nucleic acids builder (NAB) molecular dynamics (MD) package in Amber tools. A 10 ns simulation of a small protein indicates that the HCP based MD simulation is stable, and that it can be faster than the spherical cutoff method. A critical benefit of the HCP approximation is that it is algorithmically very simple, and unlike the PME, the HCP is straightforward to use with implicit solvent models. © 2009 Wiley Periodicals, Inc. J Comput Chem, 2010     

Interactions of Molecules with cis and trans Double Bonds: A Theoretical Study of cis‐ and trans‐2‐Butene

Noncovalent interactions of cis‐ and trans‐2‐butene, as the smallest model systems of molecules with cis and trans double bonds, were studied to find potential differences in interactions of these molecules. The study was performed using quantum chemical methods including very accurate CCSD(T)/CBS method. We studied parallel and displaced parallel interactions in 2‐butene dimers, in butane dimers, and between 2‐butene and saturated butane. The results show the trend that interactions of 2‐butene with butane are the strongest, followed by interactions in butane dimers, whereas the interaction in 2‐butene dimers are the weakest. The strongest calculated interaction energy is between trans‐2‐butene and butane, with a CCSD(T)/CBS energy of ?2.80 kcal mol^?1. Interactions in cis‐2‐butene dimers are stronger than interactions in trans‐2‐butene dimers. Interestingly, some of the interactions involving 2‐butene are as strong as interactions in a benzene dimer. These insights into interactions of cis‐ and trans‐2‐butene can improve understanding of the properties and processes that involve molecules with cis and trans double bonds, such as fatty acids and polymers.     

Simultaneous Aromatic–Beryllium Bonds and Aromatic–Anion Interactions: Naphthalene and Pyrene as Models of Fullerenes,Carbon Single‐Walled Nanotubes,and Graphene

The possibility of forming stable BeR₂:ArH:Y^? (R=H, F, Cl; ArH=naphthalene, pyrene; Y=Cl, Br) ternary complexes in which the beryllium compounds and anions are located on the opposite sides of an extended aromatic system is explored by means of MP2/aug‐cc‐pVDZ ab initio calculations. Comparison of the electron‐density distribution of these ternary complexes with the corresponding BeR₂:ArH and ArH:Y^? binary complexes reveals the existence of significant cooperativity between the two noncovalent interactions in the triads. The energetic effects of this cooperativity are quantified by evaluation of the three‐body interaction energy Δ³E in the framework of the many‐body interaction‐energy (MBIE) approach. Although an essential component of the interaction energies is electrostatic and is well reflected in the changes in the molecular electrostatic potential of the aromatic system on complexation, strong polarization effects, in particular for the BeR₂:ArH interactions, also play a significant role. The charge transfers associated with these polarization effects are responsible for significant distortion of both the BeR₂ and the aromatic moieties. The former are systematically bent in all the complexes, and the latter are curved to a degree that depends on the nature of the R substituents of the BeR₂ subunit.     

Very Long‐Range Effects: Cooperativity between Anion–π and Hydrogen‐Bonding Interactions

The interplay between two important non‐covalent interactions involving aromatic rings (namely anion–π and hydrogen bonding) is investigated. Very interesting cooperativity effects are present in complexes where anion–π and hydrogen bonding interactions coexist. These effects are found in systems where the distance between the anion and the hydrogen‐bond donor/acceptor molecule is as long as ～11 Å. These effects are studied theoretically using the energetic and geometric features of the complexes, which were computed using ab initio calculations. We use and discuss several criteria to analyze the mutual influence of the non‐covalent interactions studied herein. In addition we use Bader’s theory of atoms‐in‐molecules to characterize the interactions and to analyze the strengthening or weakening of the interactions depending upon the variation of the charge density at the critical points.     

Pyrenoimidazole‐Based Deep‐Blue‐Emitting Materials: Optical,Electrochemical, and Electroluminescent Characteristics

A series of pyrenoimidazoles that contained various functional chromophores, such as anthracene, pyrene, triphenylamine, carbazole, and fluorene, were synthesized and characterized by optical, electrochemical, and theoretical studies. The absorption spectra of the dyes are dominated by electronic transitions that arise from the pyrenoimidazole core and the additional chromophore. All of the dyes exhibited blue‐light photoluminescence with moderate‐to‐high quantum efficiencies. They also displayed high thermal stability and their thermal‐decomposition temperatures fell within the range 462–512 °C; the highest decomposition temperature was recorded for a carbazole‐containing dye. The oxidation propensity of the dyes increased on the introduction of electron‐rich chromophores, such as triphenylamine or carbazole. The application of selected dyes that featured additional chromophores such as pyrene, carbazole, and triphenylamine as blue‐emissive dopants into multilayered organic light‐emitting diodes with a 4,4′‐bis(9H‐carbazol‐9‐yl)biphenyl (CBP) host was investigated. Devices that were based on triphenylamine‐ and carbazole‐containing dyes exhibited deep‐blue emission (CIE 0.157, 0.054 and 0.163, 0.041), whereas a device that was based on a pyrene‐containing dye showed a bright‐blue emission (CIE 0.156, 0.135).     

Interplay between cation-pi, anion-pi and pi-pi interactions.

The interplay between three important noncovalent interactions involving aromatic rings is studied by means of high level ab initio calculations. They demonstrate that very strong synergic effects are present in complexes where either cation–π or anion–π and π‐‐π interactions coexist. These strong synergic effects have been studied using the “atoms in molecules” theory and the physical nature of the interactions investigated by means of the molecular interaction potential with polarization (MIPp).     

Tuning the Protein‐Induced Absorption Shifts of Retinal in Engineered Rhodopsin Mimics

Rational design of light‐capturing properties requires understanding the molecular and electronic structure of chromophores in their native chemical or biological environment. We employ here large‐scale quantum chemical calculations to study the light‐capturing properties of retinal in recently designed human cellular retinol binding protein II (hCRBPII) variants (Wang et al. Science, 2012 , 338, 1340–1343). Our calculations show that these proteins absorb across a large part of the visible spectrum by combined polarization and electrostatic effects. These effects stabilize the ground or excited state energy levels of the retinal by perturbing the Schiff‐base or β‐ionone moieties of the chromophore, which in turn modulates the amount of charge transfer within the molecule. Based on the predicted tuning principles, we design putative in silico mutations that further shift the absorption properties of retinal in hCRBPII towards the ultraviolet and infrared regions of the spectrum.     

Theoretical Study on Cooperativity Effects between Anion–π and Halogen‐Bonding Interactions

This article analyzes the interplay between lone pair–π (lp–π) or anion–π interactions and halogen‐bonding interactions. Interesting cooperativity effects are observed when lp/anion–π and halogen‐bonding interactions coexist in the same complex, and they are found even in systems in which the distance between the anion and halogen‐bond donor molecule is longer than 9 Å. These effects are studied theoretically in terms of energetic and geometric features of the complexes, which are computed by ab initio methods. Bader′s theory of “atoms in molecules” is used to characterize the interactions and to analyze their strengthening or weakening depending upon the variation of charge density at critical points. The physical nature of the interactions and cooperativity effects are studied by means of molecular interaction potential with polarization partition scheme. By taking advantage of all aforementioned computational methods, the present study examines how these interactions mutually influence each other. Additionally, experimental evidence for such interactions is obtained from the Cambridge Structural Database (CSD).     

Ab Initio and DFT Studies on CO2 Interacting with Znq+–Imidazole (q=0, 1, 2) Complexes: Prediction of Charge Transfer through σ‐ or π‐Type Models

Using first‐principles methodologies, the equilibrium structures and the relative stability of CO₂@[Zn^q+Im] (where q=0, 1, 2; Im=imidazole) complexes are studied to understand the nature of the interactions between the CO₂ and Zn^q+–imidazole entities. These complexes are considered as prototype models mimicking the interactions of CO₂ with these subunits of zeolitic imidazolate frameworks or Zn enzymes. These computations are performed using both ab initio calculations and density functional theory. Dispersion effects accounting for long‐range interactions are considered. Solvent (water) effects were also considered using a polarizable continuum model approach. Natural bond orbital, charge, frontier orbital and vibrational analyses clearly reveal the occurrence of charge transfer through covalent and noncovalent interactions. Moreover, it is found that CO₂ can adsorb through more favorable π‐type stacking as well as σ‐type hydrogen‐bonding interactions. The inter‐monomer interaction potentials show a significant anisotropy that might induce CO₂ orientation and site‐selectivity effects in porous materials and in active sites of Zn enzymes. Hence, this study provides valuable information about how CO₂ adsorption takes place at the microscopic level within zeolitic imidazolate frameworks and biomolecules. These findings might help in understanding the role of such complexes in chemistry, biology and material science for further development of new materials and industrial applications.     

13C PHIP NMR spectra and polarization transfer during the homogeneous hydrogenation of alkynes with parahydrogen

Homogeneously catalyzed hydrogenations of unsaturated substrates with parahydrogen not only lead to strong polarization signals in ¹H NMR spectra, but also can give rise to strong heteronuclear polarization, especially if the hydrogenations are carried out in low magnetic fields. As a typical example, the polarization transfer from protons to carbon nuclei during the hydrogenation of alkynes is outlined for several substrates. In systems containing easily accessible triple bonds, e.g. phenylethyne or 3,3‐dimethyl‐1‐butyne, polarization transfer occurs to all carbon nuclei in the molecule. Accordingly, in NMR spectra recorded in situ all ¹³C resonances can be observed with good to excellent signal‐to‐noise ratios using only a single transient. The qualitative influence of symmetry and electronic aspects of the substrate and its hydrogenation product on the efficiency of the transfer of polarization to the ¹³C‐nuclei are discussed. Copyright © 2001 John Wiley & Sons, Ltd.     

The Bright Future of Unconventional σ/π‐Hole Interactions

Non‐covalent interactions play a crucial role in (supramolecular) chemistry and much of biology. Supramolecular forces can indeed determine the structure and function of a host–guest system. Many sensors, for example, rely on reversible bonding with the analyte. Natural machineries also often have a significant non‐covalent component (e.g. protein folding, recognition) and rational interference in such ‘living’ devices can have pharmacological implications. For the rational design/tweaking of supramolecular systems it is helpful to know what supramolecular synthons are available and to understand the forces that make these synthons stick to one another. In this review we focus on σ‐hole and π‐hole interactions. A σ‐ or π‐hole can be seen as positive electrostatic potential on unpopulated σ* or π⁽*⁾ orbitals, which are thus capable of interacting with some electron dense region. A σ‐hole is typically located along the vector of a covalent bond such as X?H or X?Hlg (X=any atom, Hlg=halogen), which are respectively known as hydrogen and halogen bond donors. Only recently it has become clear that σ‐holes can also be found along a covalent bond with chalcogen (X?Ch), pnictogen (X?Pn) and tetrel (X?Tr) atoms. Interactions with these synthons are named chalcogen, pnigtogen and tetrel interactions. A π‐hole is typically located perpendicular to the molecular framework of diatomic π‐systems such as carbonyls, or conjugated π‐systems such as hexafluorobenzene. Anion–π and lone‐pair–π interactions are examples of named π‐hole interactions between conjugated π‐systems and anions or lone‐pair electrons respectively. While the above nomenclature indicates the distinct chemical identity of the supramolecular synthon acting as Lewis acid, it is worth stressing that the underlying physics is very similar. This implies that interactions that are now not so well‐established might turn out to be equally useful as conventional hydrogen and halogen bonds. In summary, we describe the physical nature of σ‐ and π‐hole interactions, present a selection of inquiries that utilise σ‐ and π‐holes, and give an overview of analyses of structural databases (CSD/PDB) that demonstrate how prevalent these interactions already are in solid‐state structures.     

Ab initio simulations of two‐dimensional electronic spectra: The SOS//QM/MM approach

Two‐dimensional electronic spectroscopy (2DES) is a cutting‐edge technique for investigating with high temporal resolution energy transfer, structure, and dynamics in a wide range of systems in physical chemistry, energy sciences, biophysics, and biocatalysis. However, the interpretation of 2DES is challenging and requires computational modeling. This perspective provides a roadmap for the development of computational tools that could be routinely applied to simulate 2DES spectra of multichromophoric systems active in the UV region (2DUV) using state‐of‐the‐art ab initio electronic structure methods within a quatum mechanics/molecular mechanics (QM/MM) scheme and the sum‐over‐states (SOS) approach (here called SOS//QM/MM). Multiconfigurational and multireference perturbative methods, such as the complete active space self‐consistent field and second‐order multireference perturbation theory (CASPT2) techniques, can be applied to reliably calculate the electronic properties of multichromophoric systems. Hybrid QM/MM method and molecular dynamics techniques can be used to assess environmental and conformational effects, respectively, that shape the 2D electronic spectra. DNA and proteins are important biological targets containing UV chromophores. We report ab initio simulation of 2DUV spectra of a cyclic tetrapeptide containing two interacting aromatic side chains, a model system for the study of protein structure and dynamics by means of 2DUV spectroscopy. © 2013 Wiley Periodicals, Inc.     

Quantum chemical calculation of exchange interactions in supramolecularly arranged N,N′‐dioxy‐2,6‐diazaadamantane organic biradical

Quantum mechanical exchange effects in purely organic N,N′‐dioxy‐2,6‐diazaadamantane biradical derivatives with promesogenic substituents have been studied. To determine intermolecular exchange energies, packing conditions of the radical core units in layered liquid crystalline phases are simulated using the Gaussian 09 program. The broken symmetry approach gives J ≈ 7 cm^?1 for intramolecular ferromagnetic exchange interactions between nitroxyl radical centers in one molecule. Both ferromagnetic and antiferromagnetic intermolecular interactions are possible in this kind of systems according to the obtained calculation results. Depending on the mutual positioning and orientation of molecules, the intermolecular antiferromagnetic exchange constant can reach a value of ?50 cm^?1, and the intermolecular ferromagnetic constant a value of 10 cm^?1. The simultaneous presence of intramolecular and intermolecular exchange between spin‐carrying centers in this kind of supramolecularly ordered multispin systems is favorable for the formation of magnetically interacting chains and two‐dimensional networks. © 2016 Wiley Periodicals, Inc.     

Enhanced Light‐Harvesting Capacity by Micellar Assembly of Free Accessory Chromophores and LH1‐like Antennas

Biohybrid light‐harvesting antennas are an emerging platform technology with versatile tailorability for solar‐energy conversion. These systems combine the proven peptide scaffold unit utilized for light harvesting by purple photosynthetic bacteria with attached synthetic chromophores to extend solar coverage beyond that of the natural systems. Herein, synthetic unattached chromophores are employed that partition into the organized milieu (e.g. detergent micelles) that house the LH1‐like biohybrid architectures. The synthetic chromophores include a hydrophobic boron‐dipyrrin dye (A1) and an amphiphilic bacteriochlorin (A2), which transfer energy with reasonable efficiency to the bacteriochlorophyll acceptor array (B875) of the LH1‐like cyclic oligomers. The energy‐transfer efficiencies are markedly increased upon covalent attachment of a bacteriochlorin (B1 or B2) to the peptide scaffold, where the latter likely acts as an energy‐transfer relay site for the (potentially diffusing) free chromophores. The efficiencies are consistent with a Förster (through‐space) mechanism for energy transfer. The overall energy‐transfer efficiency from the free chromophores via the relay to the target site can approach those obtained previously by relay‐assisted energy transfer from chromophores attached at distant sites on the peptides. Thus, the use of free accessory chromophores affords a simple design to enhance the overall light‐harvesting capacity of biohybrid LH1‐like architectures.     

Determination of Fluorescence Polarization and Absorption Anisotropy in Molecular Complexes Having Threefold Rotational Symmetry

Abstract— The current work concerns investigation of the polarization properties of complex molecular ensembles exhibiting threefold (C₃) rotational symmetry, particularly with regard to the interplay between their structure and dynamics of internal energy transfer. We assume that the molecules or chromophores in such complexes possess strongly overlapped spectra both for absorption and fluorescence. Such trimeric structures are widely found in biological preparations, as for example the trimer of C-phycocyanin (C-PC). Higher order aggregates, e.g. hex-amers and three-hexamer rods, are also investigated and compared with the trimer case. The theory addresses both steady-state and 8-pulse excitation and establishes some links between them. Monochromophoric, bichro-mophoric and trichromophoric molecular complexes are individually examined. For steady-state excitation, analytical formulas are reported for the degree of fluorescence polarization and absorption anisotropy. It is shown that the polarization is dependent on the chromophore inclination relative to the symmetry axis, the relative efficiencies of absorption and fluorescence by chromophores of different spectral types, and the rates of energy equilibration. To assess the validity of the theory, it has been applied to C-PC aggregates. Here it was found that different C-PC aggregates provide practically identical polarization response. For S-pulse excitation we give analytical formulas for determination of the fluorescence depolarization, and also the depolarization associated with absorption recovery, both for a monochromophoric trimer and some particular cases of bichromophoric trimer. More complicated systems are analyzed by computer modeling. Thus it transpires that the initial polarization anisotropy r(t = 0) takes the value 0.4 for all considered aggregates; the long-time limit r(t →∞) has about the same value as is associated with steady-state excitation. We also show that with steady-state excitation the degree of fluorescence polarization is practically equal for various C₃ aggregates of C-PC, and that the major factor determining the polarization is the chromophore orientation relative to the symmetry axis.     

Future in biomolecular computation

Summary Large-scale computations for biomolecules are dominated by three levels of theory: rigorous quantum mechanical calculations for molecules with up to about 30 atoms, semi-empirical quantum mechanical calculations for systems with up to several hundred atoms, and force-field molecular dynamics studies of biomacromolecules with 10,000 atoms and more including surrounding solvent molecules. It can be anticipated that increased computational power will allow the treatment of larger systems of ever growing complexity. Due to the scaling of the computational requirements with increasing number of atoms, the force-field approaches will benefit the most from increased computational power. On the other hand, progress in methodologies such as density functional theory will enable us to treat larger systems on a fully quantum mechanical level and a combination of molecular dynamics and quantum mechanics can be envisioned. One of the greatest challenges in biomolecular computation is the protein folding problem. It is unclear at this point, if an approach with current methodologies will lead to a satisfactory answer or if unconventional, new approaches will be necessary. In any event, due to the complexity of biomolecular systems, a hierarchy of approaches will have to be established and used in order to capture the wide ranges of length-scales and time-scales involved in biological processes. In terms of hardware development, speed and power of computers will increase while the price/performance ratio will become more and more favorable. Parallelism can be anticipated to become an integral architectural feature in a range of computers. It is unclear at this point, how fast massively parallel systems will become easy enough to use so that new methodological developments can be pursued on such computers. Current trends show that distributed processing such as the combination of convenient graphics workstations and powerful general-purpose supercomputers will lead to a new style of computing in which the calculations are monitored and manipulated as they proceed. The combination of a numeric approach with artificial-intelligence approaches can be expected to open up entirely new possibilities. Ultimately, the most exciding aspect of the future in biomolecular computing will be the unexpected discoveries.     

Novel π‐Electron Extension System via Chromophores Self‐Polymerization to Enhance the NLO Efficiency

A new strategy for the self‐polymerization of chromophores is investigated to develop a 2,7‐carbazole‐based nonlinear optical (NLO) conjugated polymer with an increasing conjugation length of chromophores. Elongation of the conjugation‐path length in chromophores has established engineering guidelines to enhance optical nonlinearity. Compared with the traditional synthesis of an NLO polymer, the chromophores should be well‐designed at a limited conjugation spacer, and then incorporated into a polymer matrix. In this research, the π‐conjugation spacer of chromophores extended perpendicularly to the dipole of chromophores during the polymerization process. Furthermore, this study marks the first research of integrating the π‐electrons of chromophores and conjugated polymers. These conjugated backbones promote a bulk‐polarization response, leading to large NLO coefficients.