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Building supramolecular helical structures is a challenge due to difficulties in the design and control of competitive noncovalent forces.

Human serum transferrin binds ferric ions with high affinity and delivers them into cellsivia/ireceptor-mediated endocytosis upon a decrease in pH in the endosome. Protonation events and conformational changes are known to play an important role in iron-release though the release is not yet fully understood. Human serum transferrin consists of two similar lobes which release iron at different rates. In this study, we investigate the iron binding sites of N- and C-lobes using quantum mechanical tools, particularly, the quantum chemical cluster approach. This study supports the inevitable role of axial tyrosine for the release of iron in quantum chemical models and provides valuable information about the proton transfer pathways for the protonation of Tyr188 and Tyr517 in N- and C-lobes, respectively. The calculations show that the release process is similar in both lobes; however, the energetic differences of the release process in N- and C-lobes, demonstrated for the first time, indicated that the release of iron in the N-lobe is thermodynamically favorable, in contrast to the one in the C-lobe.

In this study, the efficiency of halogen⋯halogen interactions to control supramolecular assemblies of boron dipyrromethene (BODIPY) (B1–B5) derivatives was explored.

The energetic viability of the previously proposed biogenetic pathway for the formation of two unique monoterpenoid indole alkaloids, voacafricine A and B, which are present in the fruits of Voacanga africana, was investigated using density functional theory computations. The results of these calculations indicate that not only is the previously suggested pathway not energetically viable but also that an alternative biosynthetic precursor is likely.

The energetic viability of the previously proposed biogenetic pathway for the formation of two unique monoterpenoid indole alkaloids, voacafricine A and B, which are present in the fruits of

In this study, the efficiency of halogen bonding strategies to control over the supramolecular assemblies of boron dipyrromethene (BODIPY) (B-1, B-2, and B-3) derivatives was explored. BODIPY cores were decorated with iodine (XB donor) and pyridine (XB acceptor) groups to promote halogen bonding formations. Single crystal X-ray diffraction analysis revealed the formation of I⋯X (N, F) XB, which led to the impressive halogen-bonded supramolecular self-assembly of 2-D layers (B-1), 1-D ladder-like chains (B-2), and helical assembly (B-3). The molecular electrostatic potential (MEP) showed the presence of σ holes on the outer tip of the iodine for all compounds. The SAPT analysis clarified the decomposition of interaction energies. The results revealed that the electrostatic forces have the largest contributions to XB in dimers of B-2, whereas dispersion components are the major source of XB interactions in dimers of B-1 and B-3. The additional AIM theory analysis showed the bond critical points (BCPs) between I⋯N, F which also confirm the presence of halogen bonding in B-1, B-2, and B-3.

Here, we present the first example of sp3 hybridized carbon centered (Csp3) tetrel bonding mediated 3D BODIPY assembly via the exceptional synergy of Csp3⋯N and Csp3⋯F pair interactions. The carbon tetrel bond interaction energies of Csp3⋯N and Csp3⋯F are amplified significantly as the size of the 1D chain grows from dimer to tetramer BODIPY units.

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.

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.

The asymmetric desymmetrization of meso-cyclic anhydrides catalyzed by the pseudoenantiomeric pairs of cinchona alkaloids, quinine (QN) and quinidine (QD), has been subjected to a computational study employing density functional theory (DFT) to understand the origin of the experimentally observed stereoselectivity. The spatial placement of the catalyst with respect to the anhydride, which resembles a molecular tweezer, was found to be the primary reason for the stabilization of the oxyanion forming in the transition states, as well as the oxyanion intermediate observed along the reaction coordinate. The distortion–interaction model has been employed to rationalize the experimentally observed enantiomeric ratios. The assistance of solvent molecules was essential in the prediction of experimental enantioselectivities.

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.

ConspectusRemarkable 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 st...

In this paper the aggregates of the chiral organolithium N-Boc-2-lithiopiperidine [Boc=CO2C(CH3)3], which play an important role in the formation of chiral 2-substituted piperidines found in many alkaloid structures and medicinal compounds, have been investigated within the framework of Density Functional Theory (DFT) calculations. In the complex structures, the lithium atoms are tetra-coordinated, the diaminoalkoxide ligand is tridentate to one lithium atom and forms a chelate with the substrate which is stabilized by the solvent diethyl ether. The same type of bonding was observed for all the different ligand-bound structures; for ligands 6 and 7, which have bulky substituents, selectivity was in agreement with experiment. The results shed light on the microscopic structures of these species and suggest a potential ligand, 11, to yield high enantioselectivity.

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.

Poly(silafluorene-phenylenedivinylene)s and poly((tetraphenyl)-silole- phenylenedivinylene)s are promising materials to be used as chemical sensors for explosives detection. The optoelectronic properties of these polymers as well as their constituent units have been investigated by modeling the properties of their excited states. Natural Transition Orbital analysis and topological φS descriptor assessment have been used to qualitatively and quantitatively characterize the physical nature of the transitions constituting the absorption spectra. The main transitions observed in all oligomers are associated to be a π-π∗ transition of the bridging moiety. Lower energy transitions of charge transfer character are further considered to understand the fluorescence quenching mechanism upon the complexation of these polymers with the analytes. Indeed the charge-transfer character of the first excited state leads to the emergence of thermal deactivation channels and hence to luminescence quenching.

Poly(silafluorene-phenylenedivinylene)s and poly((tetraphenyl)-silole-phenylenedivinylene)s are promising materials for use in explosives detection. Monomers and dimers of silafluorene- and silole-containing polymers for the detection of nitro-containing explosives are modeled with M062X/6-31G(d). The geometric features of silafluorene- and silole-containing dimers optimized with M062X/6-31G(d) agree well with experimental findings. The binding properties of explosive and nonexplosive materials have been differentiated by comparing the relative stabilities of their complexes with silafluorene- and silole-containing dimers. The interactions that promote binding in the complexation of silafluorene- and silole-containing polymers with explosives are studied with a small model to shed light on the origin of the stability of the complexes. The topology of the electron density was analyzed using the quantum theory of atoms in molecules (QTAIM) methodology to understand the nature of the noncovalent interactions that are responsible for analyte-polymer binding. The carbon and germanium analogues of silafluorene-containing dimers are modeled to better understand the role of silicon in these polymeric systems. The calculated HOMO-LUMO energy differences of the complexes of dimers with explosives correlate well with the stability of the complexes; both (HOMO-LUMO and stability) support the selectivities of silafluorene- and silole-containing polymers. The stabilities of the complexes have shown that silafluorene-containing polymer detects the analytes in the order of 2,4,6-trinitrotoluene (TNT) similar to picric acid (PA) > 2,6-dinitrotoluene (DNT) > cyclotrimethylenetrinitramine (RDX) > nitrobenzene (NB), while the silole-containing polymer is able to detect the aromatic TNT but is not responsive to the nonaromatic RDX.

A capto-dative monomer, 2-acetamidoacrylic acid (AAA), was homopolymerized through RAFT polymerization method using 2-(2-cyanopropanyl dithiobenzoate) (CPDB) as a chain transfer agent and AIBN free radical initiator in DMF at 70 °C. DFT calculations were performed in the selection of the CTA for this unique monomer as well as to elucidate the influence of cd-stabilized growing radical on the kinetic parameters in comparison to methacrylic acid (MAA) and N-(prop-1-en-2-yl)acetamide (NPAA), which represent the captive and dative groups of AAA, respectively. Keq for these three monomers is in the order of AAA k−add for NPAA and MAA, for AAA k−add is about four orders of magnitude larger than kβ. This is the major disadvantage in the RAFT process of AAA using CPDB. Yet, poly(AAA) could be achieved with PDI as low as 1.49. Molecular weight of the polymer can be tuned by the monomer/AIBN ratio. First block copolymers of AAA with MAA and MMA using poly(AAA) as a macro-CTA were also synthesized, indicating the presence of active chain ends.

Above its critical aggregation concentration the tfa salt of the peptide A6K self-assembles into micron long, hollow nanotubes with uniform diameters of 52 nm and crystalline order. Here we combine the use of SAXS with cryoTEM and cryo-electron tomography (cryoET, 3D cryoTEM) to study the formation process of the 2D crystalline A6K nanotubes. This study reveals that the formation of these tubes in fact is a crystal growth process, involving different mechanisms depending on the conditions used. Inorganic crystals have been demonstrated to form not only through ion-by-ion addition but also through non-classical mechanisms including oriented attachment. Here we show an organic crystalline material that can form through molecule-by-molecule growth as well as through oriented attachment. We discuss the mechanisms in relation to the supersaturation levels of the peptide solutions and the molecular interactions between the peptide molecules in the tubular assemblies. The proposed mechanisms are supported by semi-empirical molecular orbital calculations and time resolved dissolution experiments. This article was originally published with incorrect page numbers (p. 3463-3470)

The alcoholysis of cyclic meso-anhydrides catalyzed by β-amino alcohols has been investigated with DFT quantum mechanics to determine the mechanism of this reaction. Both nucleophilic catalysis and general base catalysis pathways are explored for methanol-induced ring opening of an anhydride catalyzed by a chiral amino alcohol. The nucleophilic pathway involves a late transition state with a high energy barrier. In this mechanism, methanolysis is expected to take place following the amine-induced ring opening of the anhydride. In the base-catalyzed mechanism, methanol attack on one carbonyl group of the meso-anhydride is assisted by the β-amino alcohol; the amine functionality abstracts the methanol proton. The chiral amino alcohol also catalyzes the reaction by stabilizing the oxyanion that forms upon ring opening of the anhydride by hydrogen bonding with its alcoholic moiety. Both stepwise and concerted pathways have been studied for the general base catalysis route. Transition structures for both are found to be lower in energy than in the nucleophilic mechanism. Overall this study has shed light on the mechanism of the β-amino alcohol-catalyzed alcoholysis of cyclic meso-anhydrides, showing that the nucleophilic pathway is approximately 100 kJ mol(-1) higher in energy than the general base pathway.