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Calculations were partially performed at the TUBITAK ULAKBIM, High Performance and Grid Computing Center (TRUBA resources) as well as the computational resources at CCBG (www.ccbg.chem.boun.edu.tr) funded by the Bogazici University Research Fund (BAP Project No: 5156 and BAP-SUP Project No: 8245). B.D thanks Gebze Technical University Research Fund (BAP Project No: 2018-A105-32) for the financial support. The authors thank Assist. Prof. Yunus Emre Turkmen (Bilkent University, Ankara, Turkey) for fruitful discussions

The ability to tune optical features of BODIPY materials is essential for their photo-related application. However, it is challenging to efficiently tune the crystal packing of BODIPY derivatives because of their complex nature. In this study, such control of BODIPY supramolecular assemblies was achieved by designing a BODIPY containing a halogen bond (XB) acceptor (–NO2) and donor (I, Br) to mediate halogen bonding interactions. The mono halogenated 2 and 4 was unable to form XB, whereas 3 and 5 formed isostructural mono-coordinate motif 3, 5-I (1D tubular structure) and symmetric bifurcated motif 5-II (1D zig-zag chains structure) via N-O···I,Br XB interactions. The results show that the dispersion and electrostatic component are the major source of 3, 5-I and 5-II XB formations. The XB interaction between –NO2 and X (I, Br) promote singlet-to-triplet intersystem crossing and triplet-to-singlet reverse intersystem crossing due to delocalization of oxygen electrons partially onto the Br and I. Then this interaction leads to unexpected fluorescence enhancement of 5-II. Finally, the indirect optical band gaps of the 3, 5-I and 5-II were able to be tuned in the range of 1.9–2.50 eV via XB driven crystal packings.

Monocarboxylic acid substituted phthalonitrile derivatives (PN1 and PN2) have been synthesized and their molecular geometries and hydrogen bond interactions investigated with single cystal X-ray diffraction analysis. PN1-a and PN2 crystal structures linked by a pair of O–H⋯O hydrogen bonds form classical carboxylic acid inversion dimers, whilst PN1-b crystal structure stabilized by classical O–H⋯O and O–H⋯N hydrogen bonding interactions. Spectral characterizations of PN1-a and PN2 structures have been performed by FT-IR, 1H-13C NMR and UV-Vis techniques. Molecular structure optimization and structural properties of PN1 and PN2 in the forms of monomer and dimer have been studied with the DFT approach, B3LYP functional and 6-311++G(d,p) basis set. The effects of dimeric forms of structures on geometrical and spectral parameters have been evaluated together with the values of monomeric forms and experimental ones. Concepts specific to electronic absorption spectra such as absorption wavelengths and major contributions to electronic transitions and FMOs energy values have been determined by TD-DFT approach. Some reactivity properties of the monomer PN1-a and PN2 structures have been evaluated through global, local parameter values and MEP visuals. It was shown that PN2 monomer structure which has both a low HOMO-LUMO energy gap (ΔE=3.83 eV) and a higher chemical softness value (S=0.52 eV−1) is more reactive than PN1-a monomer. The potentials of being nonlinear optical (NLO) material and some thermodynamic parameters that are thought to contribute to their structural properties have been determined theoretically for PN1-a and PN2 monomeric forms. Furthermore, it is determined that PN2 has superior properties compared to PN1 based on the electrical characterization of the compounds.

The reactions between low-valent Rh(I) and Ir(I) metal-carbonyl complexes and arylnitrile oxides possess the electronic and structural features of 1,3-dipolar cycloadditions. Density functional theory (DFT) calculations on these reactions, involving both cyclopentadienyl and carboranyl ligands on the metal carbonyl, explain the ease of the chemical processes and the stabilities of the resulting metallaisoxazolin-5-ones. The metal-carbonyl bond has partial double bond character according to the Wiberg index calculated through NBO analysis, and so the reaction can be considered a normal 1,3-dipolar cycloaddition involving M═C bonds. The rates of formation of the metallacycloadducts are controlled by distortion energy, analogous to their organic counterparts. The superior ability of anionic Ir complexes to share their electron density and accommodate higher oxidation states explains their calculated higher reactivity toward cycloaddition, as compared to Rh analogues.

With the advances in three-dimensional structure determination techniques, high quality structures of the iron transport proteins transferrin and the bacterial ferric binding protein (FbpA) have been deposited in the past decade. These are proteins of relatively large size, and developments in hardware and software have only recently made it possible to study their dynamics using standard computational resources. We review computational techniques towards understanding the equilibrium and kinetic properties of iron transport proteins under different environmental conditions. At the level of detail that requires quantum chemical treatments, the octahedral geometry around iron has been scrutinized and it has been established that the iron coordinating tyrosines are in an unusual deprotonated state. At the atomistic level, both the N-lobe and the full bilobal structure of transferrin have been studied under varying conditions of pH, ionic strength and binding of other metal ions by molecular dynamics (MD) simulations. These studies have allowed questions to be answered, among others, on the function of second shell residues in iron release, the role of synergistic anions in preparing the active site for iron binding, and the differences between the kinetics of the N- and the C-lobe. MD simulations on FbpA have led to the detailed observation of the binding kinetics of phosphate to the apo form, and to the conformational preferences of the holo form under conditions mimicking the environmental niches provided by the periplasmic space. To study the dynamics of these proteins with their receptors, one must resort to coarse-grained methodologies, since these systems are prohibitively large for atomistic simulations. A study of the complex of human transferrin (hTf) with its pathogenic receptor by such methods has revealed a potential mechanistic explanation for the defense mechanism that arises in evolutionary warfare. Meanwhile, the motions in the transferrin receptor bound hTf have been shown to disfavor apo hTf dissociation, explaining why the two proteins remain in complex during the recycling process from the endosome to the cell surface. Open problems and possible technological applications related to metal ion binding-release in iron transport proteins that may be handled by hybrid use of quantum mechanical, MD and coarse-grained approaches are discussed.

Remarkable progress in the area of asymmetric organocatalysis has been achieved in the last decades. Cinchona alkaloids and their derivatives have emerged as powerful organocatalysts owing to their reactivities leading to high enantioselectivities. The widespread usage of cinchona alkaloids has been attributed to their nontoxicity, ease of use, stability, cost effectiveness, recyclability, and practical utilization in industry. The presence of tunable functional groups enables cinchona alkaloids to catalyze a broad range of reactions. Excellent experimental studies have extensively contributed to this field, and highly selective reactions were catalyzed by cinchona alkaloids and their derivatives. Computational modeling has helped elucidate the mechanistic aspects of cinchona alkaloid catalyzed reactions as well as the origins of the selectivity they induce. These studies have complemented experimental work for the design of more efficient catalysts. This Account presents recent computational studies on cinchona alkaloid catalyzed organic reactions and the theoretical rationalizations behind their effectiveness and ability to induce selectivity. Valuable efforts to investigate the mechanisms of reactions catalyzed by cinchona alkaloids and the key aspects of the catalytic activity of cinchona alkaloids in reactions ranging from pharmaceutical to industrial applications are summarized. Quantum mechanics, particularly density functional theory (DFT), and molecular mechanics, including ONIOM, were used to rationalize experimental findings by providing mechanistic insights into reaction mechanisms. B3LYP with modest basis sets has been used in most of the studies; nonetheless, the energetics have been corrected with higher basis sets as well as functionals parametrized to include dispersion M05-2X, M06-2X, and M06-L and functionals with dispersion corrections. Since cinchona alkaloids catalyze reactions by forming complexes with substrates via hydrogen bonds and long-range interactions, the use of split valence triple-ζ basis sets including diffuse and polarization functions on heavy atoms and polarization functions on hydrogens are recommended. Most of the studies have used the continuum-based models to mimic the condensed phase in which organocatalysts function; in some cases, explicit solvation was shown to yield better quantitative agreement with experimental findings. The conformational behavior of cinchona alkaloids is also highlighted as it is expected to shed light on the origin of selectivity and pave the way to a comprehensive understanding of the catalytic mechanism. The ultimate goal of this Account is to provide an up-to-date overlook on cinchona alkaloid catalyzed chemistry and provide insight for future studies in both experimental and theoretical fields.

WOS:000448348600049 Organogelators have a wide range of use in everyday life including drug delivery and controlled release, surface coating and paper industry. In this study, a series of model bisamides have been analyzed as potential organogelators. These molecules are connected by odd and even numbered methylene units (n) in length ranging from 2 to 9. By constructing layers of those molecules along the growth direction we provide an insight into the self-assembly process. A complete systematic analysis of the computational results with B3LYP/6-311+G** suggests that the self-assembly of these potential organogelators is influenced by the odd-even effect, the relative direction of amide carbonyl groups, the bridging spacer chain length and the presence of a chiral alpha carbon. The aforementioned factors alter the strength of the intermolecular hydrogen bonds as well as the van der Waals interactions, which in turn may affect the self-assembly process of gelation and result in the formation of aggregates with different shapes. It is found that molecules with short central chains have an energetic preference for antiparallel arrangement over their parallel analogues as a result of stronger hydrogen bonding interactions. As the central chain elongates, the free energy difference between antiparallel and parallel structures decreases suggesting a compromise between hydrogen bonding and van der Waals interactions. The complete structural analysis suggests ribbon-like structures for achiral even-antiparallel and woven-like structures for odd-parallel systems, respectively. Upon creation of asymmetry on the alpha carbon, a twisted ribbon-like and a coiled coil-like structure are observed for even and odd systems, respectively. Our computational results are in accordance with the experimental results and provide an insight into the self-assembly of layers of bisamides.

Two different groups of methacrylates containing Type I or Type II photoinitiating moieties were synthesized and evaluated for use in UV curing applications. The first, a novel group of monomeric photoinitiators (MPIs) were synthesized by reactions of tert-butyl alpha-bromomethacrylate (TBBr) with 2-hydroxy-1-[4-(2-hydroxyethoxy)phenyl]-2-methyl-1-propanone (Irgacure 2959), 1-hydroxy-cyclo-hexyl-phenyl-ketone (Irgacure 184) and 4-hydroxyacetophenone to give monomers MPI1, MPI3 and MPI4 respectively; and conversion of MPI1 to MPI2 by cleavage of tert-butyl ester groups with trifluoroacetic acid. The second group of photoinitiators were synthesized by reaction of 2-isocyanatoethyl methacrylate (IEM) with Irgacure 2959 (MPI5) and 4-hydroxybenzophenone (MPI6). All these MPIs' absorption range in the UV region was found to be similar to their nonmonomeric analogs. Their photoinitiating abilities in the polymerizations of hexane-1,6-diol diacrylate (HDDA), 2-hydroxyethyl methacrylate (HEMA) and trimethylolpropane triacrylate (TMPTA) were studied using photodifferential scanning calorimeter and the kinetic parameters were correlated with the structures of the photoinitiating systems. Photoinitiating activities of investigated Type I photoinitiators, including small molecule commercial analogs, during polymerizations of HDDA and TMPTA are very slightly influenced by MPIs structure. However, the MPI structure is found to be important for the curing of HEMA, and some of the synthesized MPIs have better efficiency than commercial ones tested. The MPIs based on Irgacure 2959; Irgacure 184 and benzophenone (BP), with similar or increased photoinitiating activity compared to their commercial precursors, appear to be promising photoinitiators. An extra advantage of MPIs is their incorporation into the final formulations, reducing undesired migration of small molecules. (C) 2016 Elsevier B.V. All rights reserved.