This paper describes the synthesis and characterization of the first series of hydrogen bonding-driven hydrazide foldamers and their recognition for alkyl saccharides in chloroform. Oligomers 1, 2-4, 5, 6, and 7, which contain one, two, four, six, or twelve repeated dibenzoyl hydrazide residues, respectively, have been prepared. The rigid and planar conformations of 1 and 2 or 4 have been established with X-ray analysis and (1)H NMR spectroscopy, whereas the folding and helical conformations of 5-7 have been evidenced by the 1D and 2D (1)H NMR and IR spectroscopy and molecular mechanics calculations. Molecular mechanics calculations also revealed that 5, 6, and 7 possess a rigid cavity with size of ca. 10.6 to 11.1 A, and half of the carbonyl groups in the folding conformations are orientated inwardly inside the cavity. (1)H NMR and CD experiments revealed that 5-7 efficiently complex alkylated mono- and disaccharides 32-35 in chloroform. The association constants (K(assoc)) of the complexes have been determined with the (1)H NMR and fluorescent titration methods. The energy-minimized conformation of 6.34 has been obtained with molecular mechanics calculation. The hydrazide-based folding structures described here represent novel examples of hydrogen bonding-driven foldamers that act as artificial receptors for selective molecular recognition.

This paper describes the synthesis, self-assembly, and characterization of a new class of highly stable hydrazide-based quadruply hydrogen-bonded heterodimers. All of the hydrazide-derived heterodimers possess the complementary ADDA-DAAD hydrogen-bonding sequences. Hydrazide derivatives 1, which has two intramolecular S(6) RO.H-N hydrogen bonds, and 2 complex to afford two fastly exchanging isomeric heterodimers 1.2 and 1.2' in chloroform, as a result of two different conformational arrangements of 2. An average binding constant K(assoc) of 4.7 x 10(4) M(-)(1) was determined for heterodimer 1.2 and 1.2' by (1)H NMR titration of 1 with changing 2 in chloroform-d. In contrast, 1 binds 11 and 12, both of which are introduced with two intramolecular S(6) hydrogen bonds, to exclusively afford heterodimers 1.11 and 1.12, with K(assoc) values of 1.8 x 10(4) and 5.0 x 10(2) M(-)(1), respectively. Fluorine-containing 19, which has a hydrazide skeleton identical to that of 1 but two intramolecular S(6) F.H-N hydrogen bonds, can also complex with 2, 11, and 12, to afford heterodimers 19.2, 19.2', 19.11, and 19.12, with K(assoc) values of of 1.2 x 10(4) (average value for 19.2 and 19.2'), 5.4 x 10(3), and 1.9 x 10(2) M(-)(1), respectively. The structures of the new heterodimers have been proven with NOESY, IR, and VPO (for some of the heterodimers) experiments. Moreover, 1 and 19 can also strongly bind 2,7-dilauroylamido-1,8-naphthyridine 23 to afford dimers 1.23 and 19.23 with K(assoc) values of 6.0 x 10(5) and 1.4 x 10(5) M(-)(1), respectively. Adding 1 to the 1:1 solution of 23 and 1-octyl-3-(4-oxo-3,4-dihydro-pyrido[2,3-d]pyrimidin-2-yl)urea 24 or 1-octyl-3-(4-oxo-1,4-dihydro-pyrimidin-2-yl)urea 25, which had been developed initially by Zimmerman and Meijer, respectively, induces dimers 23.24 and 23.25 to dissociate, leading to the formation of dimers 1.23 and 24.24 or 25.25, respectively. The new hydrazide-based hydrogen-bonding modules described are useful building blocks for self-assembly and open a new avenue to recognition between discrete supramolecular species.

We employed computational techniques, including molecular docking, energy minimization, and molecular dynamics simulation, to investigate the ice-binding surface of fish type III antifreeze protein (AFP). The putative ice-binding site was previously identified by mutagenesis, structural analysis, and flatness evaluation. Using a high-resolution x-ray structure of fish type III AFP as a model, we calculated the ice-binding interaction energy of 11 surface patches chosen to cover the entire surface of the protein. These various surface patches exhibit small but significantly different ice-binding interaction energies. For both the prism ice plane and an "ice" plane in which water O atoms are randomly positioned, our calculations show that a surface patch containing 14 residues (L19, V20, T18, S42, V41, Q9, P12, A16, M21, T15, Q44, I13, N14, K61) has the most favorable interaction energy and corresponds to the previously identified ice-binding site of type III AFP. Although in general agreement with the earlier studies, our results also suggest that the ice-binding site may be larger than the previously identified "core" cluster that includes mostly hydrophilic residues. The enlargement mainly results from the inclusion of peripheral hydrophobic residues and K61.

The monomer and dimer structures of cyclo[(-L-Phe 1 -D-Ala 2 ) n -] and cyclo[(-L-Phe 1 -D-Me N-Ala 2 ) n -] (n ) 3-6) were studied by using the semiempirical molecular orbital AM1 method and the density functional B3LYP method. The structural characteristics of these molecules were revealed, some of which are not yet confirmed experimentally. The influences of the substituents and ring size on molecular structure and the self-assembly process are discussed in detail. The inherent impetus for these molecules to self-assemble to polypeptide nanotubes is discussed.

Link to publicationCitation for published version (APA): Li, X., Sproviero, E. M., Ryde, U., Batista, V. S., & Chen, G. (2013). Theoretical EXAFS studies of a model of the oxygen-evolving complex of photosystem II obtained with the quantum cluster approach. International Journal of Quantum Chemistry, 113(4), 474-478. DOI: 10.1002/qua.24143 General rights Copyright and moral rights for the publications made accessible in the public portal are retained by the authors and/or other copyright owners and it is a condition of accessing publications that users recognise and abide by the legal requirements associated with these rights.• Users may download and print one copy of any publication from the public portal for the purpose of private study or research.• You may not further distribute the material or use it for any profit-making activity or commercial gain • You may freely distribute the URL identifying the publication in the public portal ABSTRACTThe oxygen-evolving complex (OEC) of photosystem II is the only natural system that can form O 2 from water and sunlight and it consists of a Mn 4 Ca cluster. In a series of publications, Siegbahn has developed a model of the OEC with the quantum mechanical (QM) cluster approach that is compatible with available crystal structures, able to form O 2 with a reasonable energetic barrier, and has a significantly lower energy than alternative models. In this investigation, we present a method to restrain a QM geometry optimization towards experimental polarized EXAFS data. With this method, we show that the cluster model is compatible with the EXAFS data and we obtain a refined cluster model that is an optimum compromise between QM and polarized EXAFS data.

Two artificial water oxidation catalysts, the blue dimer and the Llobet catalyst, have been studied using hybrid DFT methods. The results are compared to those for water oxidation in the natural photosystem II enzyme. Studies on the latter system have now reached a high level of understanding, at present much higher than the one for the artificial systems. A recent high resolution X-ray structural investigation of PSII has confirmed the main features of the structure of the oxygen evolving complex (OEC) suggested by previous DFT cluster studies. The O-O bond formation mechanism suggested is of direct coupling (DC) type between an oxygen radical and a bridging oxo ligand. A similar DC mechanism is found for the Llobet catalyst, while an acid-base (AB) mechanism is preferred for the blue dimer. All of them require at least one oxygen radical. Full energy diagrams, including both redox and chemical steps, have been constructed illustrating similarities and differences to the natural system. Unlike previous DFT studies, the results of the present study suggest that the blue dimer is rate-limited by the initial redox steps, and the Llobet catalyst by O(2) release. The results could be useful for further improvement of the artificial systems.

We describe theoretical insights into the mechanism of Hg-C bond protonolysis in methyl mercury coordinated by the tris(2-mercapto-1-tert-butylimidazolyl)hydroborato ligand, the structural and functional analogue of the organomercurial lyase MerB. Different cleavage pathways including both frontside and backside attack transition states were systematically studied by the hybrid density functional method B3LYP. Dependence of Hg-C bond activation on the primary sulfur coordination number of mercury was elaborated, and conceptual DFT indexes were suggested to be more appropriate than gross charge of atom sites in interpreting the dependence. Furthermore, absence of configurational inversion in MerB-catalyzed reactions was accounted for by examinations of the backside protonolysis pathways in the present system. Lastly, a rationalization was provided about the choice between different characteristics of transition states including both four-center and six-center ones.

The DNA binding and cross-linking modes of a trinuclear platinum complex [Pt(3)Cl(3)(hptab)][ClO(4)](3) (1; hptab = N,N,N',N',N'',N''-hexakis(2-pyridylmethyl)-1,3,5-tris(aminomethyl)benzene) and its dinuclear analogue [Pt(2)Cl(2)(m-tpxa)]Cl(2) (2; m-tpxa = N,N,N',N'-tetra(2-pyridylmethyl)-m-xylylene diamine) are reported and compared. The adducts of 1 and 2 with 18-mer duplex N1, 5'-d(GAAGAAGTCACAAAATGT)-3'5'-d(ACATTTTGTGACTTCTTC)-3', have been characterized by means of denaturing polyacrylamide gels, Maxam-Gilbert sequencing, and MALDI-TOF mass spectrometry combined with enzymatic degradation to obtain insights into structural features responsible for the differences in their antitumor activities. The cytotoxic-active complex 1 readily forms various DNA adducts, such as through 1,3- and 1,4-intrastrand cross-links, and in particular, the unique and unprecedented interstrand cross-linked triadducts. In contrast, the cytotoxic-inactive complex 2 preferentially forms 1,4-intrastrand rather than 1,3-intra- and -interstrand cross-links. Digestion of the DNA adducts of 1 shows that the cleavage is completely blocked at one nucleotide before the cross-linked guanine residues on the opposite strand, a feature that appears to be unprecedented in antitumor platinum complexes. In the case of 2, the cleavage bypasses the first platinated guanine site and stops at one nucleotide prior to the second platinated site, confirming that very few 1,3-intrastrand cross-links are formed by 2. These results are supported by molecular-modeling studies of intra- and interstrand cross-links of duplex N1 with 1 and 2. The remarkable differences between 1 and 2 in DNA binding and cross-linking provide mechanistic insights into their different cytotoxicity against the tumor cell lines; these insights are useful for designing future antitumor agents.