Theoretical studies of uracil–(H2O)n (n = 1–7) clusters by ab initio and ABEEMσπ/MM fluctuating charge model

Uracil–(H₂O)_n (n = 1–7) clusters were systemically investigated by ab initio methods and the newly constructed ABEEMσπ/MM fluctuating charge model. Water molecules have been gradually placed in an average plane containing uracil. The geometries of 38 uracil–water complexes were obtained using B3LYP/6-311++G** level optimizations, and the energies were determined at the MP2/6-311++G** level with BSSE corrections. The ABEEMσπ/MM potential model gives reasonable properties of these clusters when comparing with the present ab initio data. For interaction energies, the root mean square deviation is 0.96 kcal/mol, and the linear coefficient reaches 0.997. Furthermore, the ABEEMσπ charges changed when H₂O interacted with the uracil molecule, especially at the sites where the hydrogen bond form. These results show that the ABEEMσπ/MM model is fine giving the overall characteristic hydration properties of uracil–water systems in good agreement with the high-level ab initio calculations.     

An estimation method of binding free energy in terms of ABEEMσπ/MM and continuum electrostatics fused into LIE method

A method is proposed for the estimation of absolute binding free energy of interaction between proteins and ligands. The linear interaction energy method is combined with atom‐bond electronegativity equalization method at σπ level Force field (fused into molecular mechanics) and generalized Born continuum model calculation of electrostatic solvation for the estimation of the absolute free energy of binding. The parameters of this method are calibrated by using a training set of 24 HIV‐1 protease–inhibitor complexes (PDB entry 1AAQ). A correlation coefficient of 0.93 was obtained with a root mean square deviation of 0.70 kcal mol^?1. This approach is further tested on seven inhibitor and protease complexes, and it provides small root mean square deviation between the calculated binding free energy and experimental binding free energy without reparametrization. By comparing the radii of gyration and the hydrogen bond distances between ligand and protein of three training model molecules, the consistent comparison result of binding free energy is obtained. It proves that this method of calculating the binding free energy with appropriate structural analysis can be applied to quickly assess new inhibitors of HIV‐1 proteases. To test whether the parameters of this method can apply to other drug targets, we have validated this method for the drug target cyclooxygenase‐2. © 2010 Wiley Periodicals, Inc. J Comput Chem, 2011     

Alkali Metal-Transition Metal π-Complexes

In this progress report a new principle is described for the synthesis of multimetal π-complexes with hitherto unknown structural features. The nickel(0)-olefin complexes 1,5,9-cyclododecatrienenickel(0) and bis(1,5-cyclooctadiene)nickel(0) react unexpectedly with main-group metals, in particular alkali metals, their hydrides, and organometallic compounds, to give nickelligand species with a surplus charge. These species endeavor to transfer the excess charge onto π-ligands such as olefins or dinitrogen. Multimetal complexes with electron rich transition metal π-ligand units can, in addition, be prepared from metallocenes, alkali metals, and unsaturated compounds. The syntheses, structures, and reactions of this new class of substances will be summarized.     

Insight into Markovnikov regioselectivity rule via molecular face and ABEEM‐σπ theory

Electrophilic additions of HCl to a series of asymmetric alkenes in the gas phase are investigated by the Molecular Face (MF) theory and ABEEM‐σπ model. The interesting features of regioselectivity for these reactions are characterized by the electron density (ED) encoded on the MF of alkenes and charge distribution of alkenes obtained via the ABEEM‐σπ model, respectively. It is then demonstrated that for a series of alkenes, the Hammett constant σ_p (substituent constant) has a good linear correlation with K_ED, where K_ED is character of the ED at the π region in the initial state of alkenes. Comparison between investigations using MF, ABEEM‐σπ, molecular electrostatic potential, and DFT theories, in essence, give similar conclusions for explaining the regioselectivity of the electrophilic additions to alkenes, although from different points of view. © 2010 Wiley Periodicals, Inc. Int J Quantum Chem, 2011     

Facile Fabrication of Solid‐state Electrochemiluminescence Sensor via Non‐covalent π‐π Stacking and Covalent Bonding on Graphite Electrode

Herein, a facile and efficient method was developed for fabrication of solid‐state electrochemiluminescence (ECL) sensor via non‐covalent π‐π stacking and covalent bonding on the graphite electrode (GE) surface. The electrode was firstly modified with 1‐aminopyrene via π‐π stacking between GE surface and the pyrene moiety. Thereafter a stable and efficient solid‐state ECL sensor was fabricated by covalent immobilization of ruthenium(II) onto the GE surface via amidation reaction between the 1‐aminopyrene and bis(2,2′‐bipyridyl)(4‐methyl‐4′‐carboxypropyl‐2,2′‐bipyridyl) ruthenium(II) bishexafluorophosphate. The sensor has been investigated using tripropylamine and tetracycline as representative analytes, and low detection limits of 0.7 nM and 3.5 nM (S/N=3) were reached, respectively.     

σ–π Continuum in Indole–Palladium(II) Complexes

The intrinsic features of (hetero‐arene)–metal interactions have been elusive mainly because the systematic structure analysis of non‐anchored hetero‐arene–metal complexes has been hampered by their labile nature. We report successful isolation and systematic structure analysis of a series of non‐anchored indole–palladium(II) complexes. It was revealed that there is a σ–π continuum for the indole–metal interaction, while it has been thought that the dominant coordination mode of indole to a metal center is the Wheland‐intermediate‐type σ‐mode in light of the seemingly strong electron‐donating ability of indole. Several factors which affect the σ‐ or π‐character of indole–metal interactions are discussed.     

The Influence of Oxygen Atoms on Conformation and π–π Stacking of Ladder‐Type Donor‐Based Polymers and Their Photovoltaic Properties

A novel ladder‐type donor pyran‐bridged indacenodithiophene (IDTP) is developed by introducing two oxygen atoms into indacenodithiophene unit. IDTP possesses a twisted backbone and leads to facially asymmetric arrangement of side chains, resulting in enhanced local π–π stacking of according polymer poly[(5,5,11,11‐tetrakis(4‐octylphenyl)‐5,11‐dihydrothieno[2′,3′:5,6]pyrano[3,4‐g]thieno[3,2‐c]isochromene)‐alt‐4,7‐(5‐fluoro‐2,1,3‐benzothiadiazole)] (PIDTP)‐FBT, which shows extended absorption range. Moreover, oxygen atoms render deeper highest occupied molecular orbital (HOMO) levels of poly[indacenodithiophene‐alt‐4,7‐(5‐fluoro‐2,1,3‐benzothiadiazole)] (PIDTP)‐FBT compared with PIDT‐FBT, therefore bringing a higher open‐circuit voltage (V _oc).     

Construction of Hetero‐Four‐Layered Tripalladium(II) Cyclophanes by Transannular π⋅⋅⋅π Interactions

A synthetic strategy for the generation of new molecular species utilizing a provision of nature is presented. Nano‐dimensional (23(2)×21(1)×16(1) ų) hetero‐four‐layered trimetallacyclophanes were constructed by proof‐of‐concept experiments that utilize a suitable combination of π???π interactions between the central aromatic rings, tailor‐made short/long spacer tridentate donors, and the combined helicity. The behavior of the unprecedented four‐layered metallacyclophane system offers a landmark in the development of new molecular systems.     

Preparation of σ- and π-Benzyl Type Derivatives of Molybdenum

The reaction of -LiM₀(CO)₂Cp with α-chloromethylnaphthalene gives a yellow, crystalline σ-benzyl type derivative of molybdenum (1). Irridation of (1) in n-hexane gives a red π-benzyl type derivative (2). Both complexes (1) and (2) are stable in air.     

Local orbitals for the study of the π→π* excitation in polyenes

Localized orbitals have recently been employed in large ab initio calculations, but their use has generally been restricted to ground‐state problems. In this work, we analyze the molecular orbitals of the excited states, optimized with a recently proposed local procedure. This method produces local orbitals of the CAS–SCF type, which permits its application to the study of excited states. In particular, we focus on the π→π* triplet excited state in polyenes, calculated using a 2/2 CAS space which includes two electrons in one π and one π* orbitals. In small polyenes, these two singly occupied active orbitals are delocalized all along the molecule. The extent of the delocalization is analyzed by studying polyenes of increasing size. Different polyenes have been studied, going from C₁₄H₁₆ to the C₇₀H₇₂ polyene. The relation of the π→π* excitation with the cation and anion systems is also discussed. © 2004 Wiley Periodicals, Inc. Int J Quantum Chem, 2005     

Development of modified force field for cation–amino acid interactions: Ab initio-derived empirical correction terms with comments on cation–π interactions

The modeling of voltage-gated ion-channel proteins is a continuing challenge for force-field calculations because of the diverse range of interactions involved. In particular, current force fields are not parameterized for either ion–amino acid or amino acid–electric field interactions. To address the parameterization of ion–amino acid interactions, we have tested the use of empirical correction terms, derived from ab initio calculations of single amino acids (representing the peptide backbone) interacting with K⁺ ions. Having demonstrated the utility of such an approach, we then extended the application to the amino acid side chains. The calculation of the interaction of K⁺ with serine, cysteine, methionine, lysine, arginine, aspartate, histidine (uncharged), tyrosine, tryptophan, and phenylalanine, both completes the parameterization of the molecular environments contained in the amino acids, and allows specific comment on these ion–functional group interactions. The cation–π interactions were of particular interest, given recent proposals in the literature and the fear that force fields would not be able to treat such interactions. We present a comprehensive comparison of the ab initio (DFT [BLYP], 6-311 G**) and force field (CHARMm22.0) assessments of these interactions. © 1998 John Wiley & Sons, Inc. J Comput Chem 19: 1515–1525, 1998     

Intramolecular π–π Interactions in Flexibly Linked Partially Fluorinated Bisarenes in the Gas Phase

Three compounds with phenyl and pentafluorophenyl rings bridged by (CH₂)₃ and (CH₂)₂SiMe₂ units were synthesized by hydrosilylation and C−C coupling reactions. Their solid‐state structures are dominated by intermolecular π stacking interactions, primarily leading to dimeric or chain‐type aggregates. Analysis of free molecules in the gas phase by electron diffraction revealed the most abundant conformer to be significantly stabilized by intramolecular π–π interactions. For the silicon compounds, structures characterized by σ–π interactions between methyl and pentafluorophenyl groups are second lowest in energy and cannot be excluded completely by the gas electron diffraction experiments. C₆H₅(CH₂)₃C₆F₅, in contrast, is present as a single conformer. The gas‐phase structures served as a reference for the evaluation of a series of (dispersion‐corrected) quantum‐chemical calculations.     

Hole Mobility Modulation in Single‐Crystal Metal Phthalocyanines by Changing the Metal–π/π–π Interactions

Weak intermolecular interactions in organic semiconducting molecular crystals play an important role in determining molecular packing and electronic properties. Single crystals of metal‐free and metal phthalocyanines were synthesized to investigate how the coordination of the central metal atom affects their molecular packing and resultant electronic properties. Single‐crystal field‐effect transistors were made and showed a hole mobility order of ZnPc>MnPc>FePc>CoPc>CuPc>H₂Pc>NiPc. Density functional theory (DFT) and 1D polaron transport theory reach a good agreement in reproducing the experimentally measured trend for hole mobility. Additional detail analysis at the DFT level suggests the metal atom coordination into H₂Pc planes can tune the hole mobility via adjusting the intermolecular distances along the shortest axis with closest parallel π stackings.     

Photophysical properties of σ–π‐conjugated alternating oligothienylene–oligosilylene polymers

UV‐visible absorption and fluorescence properties of three series of σ–π‐conjugated polymers (copolymers of alternative oligothienylene and oligosilylene units) have been studied in dioxane solution. The energies of the absorption maximum, fluorescence maximum, and the 0–0 transition are found to be linearly dependent on the reciprocal of the number of thiophene rings in the repeating unit of the polymer chain, but almost independent of the silicon atom number. The σ–π‐conjugation in the polymers results in red shift in the absorption and fluorescence maxima, higher fluorescence quantum yields, and longer fluorescence lifetimes of the polymers, with respect to their corresponding analogous α‐oligothiophenes. © 1999 John Wiley & Sons, Inc. J Polym Sci B: Polym Phys 37: 1873–1880, 1999     

Cooperation of σ–π and σ*–π* Conjugation in the UV/Vis and Fluorescence Spectra of 9,10-Disilylanthracene

In 1996, we reported that silyl groups of 9,10-disilylanthracenes significantly affect the UV/Vis and fluorescence spectra. Although the results indicate that the silyl groups have strong electronic effects on anthracene, the details of the mechanisms responsible for this have not yet been clarified. This article describes the analysis of the UV/Vis and fluorescence spectra of 9,10-bis(diisopropylsilyl)anthracene by theoretical calculations. This study reveals that π conjugation of anthracene is extended by cooperation of σ–π and σ*–π* conjugation between the silyl groups and anthracene. This effect increases the transition moment of the π–π* transition of anthracene. As a result, the molecular extinction coefficient of the ¹L_a band and the fluorescence quantum yield are increased.     

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.