Theoretical study on cooperative effects between X⋯N and X⋯Carbene halogen bonds (X = F,Cl,Br and I)

Quantum chemical calculations are performed to study the interplay between halogen?nitrogen and halogen?carbene interactions in NCX?NCX?CH₂ complexes, where X?=?F, Cl, Br and I. Molecular geometries and interaction energies of dyads and triads are investigated at the MP2/aug-cc-pVTZ level of theory. It is found that the X?N and X?C_carbene interaction energies in the triads are larger than those in the dyads, indicating that both the halogen bonding interactions are enhanced. The estimated values of cooperative energy E _coop are all negative with much larger E _coop in absolute value for the systems including iodine. The nature of halogen bond interactions of the complexes is analyzed using parameters derived from the quantum theory atoms in molecules methodology and energy decomposition analysis.

The competition of C-X⋯O=P halogen bond and π-hole⋯O=P bond between halopentafluorobenzenes C6F5X (X=F, Cl, Br, I) and triethylphosphine oxide

Calculation predicted the interacting forms of halopentafluorobenzene C₆F₅X (X=F, Cl, Br, I) with triethylphosphine oxide which is biologically interested and easily detected by ³¹P NMR. The interaction energy and geometric parameters of resultant halogen or π-hole bonding complexes were estimated and compared. Moreover, the bonding constants were determined by ³¹P NMR. Both theory and experiments indicated the C₆F₆ and C₆F₅Cl interact with triethylphosphine oxide by π-hole bonding pattern, while C₆F₅I by halogen/σ-hole bonding form. For C₆F₅Br, two interactions are comparative and should coexist competitively. The calculated interaction energies of σ-hole bonding complexes, ?5.07 kcal mol^?1 for C₆F₅Br?O=P and ?8.25 kcal mol^?1 for C₆F₅I?O=P, and π-hole bonding complexes, ?7.29 kcal mol^?1 for C₆F₆?O=P and ?7.24 kcal mol^?1 for C₆F₅Cl?O=P, are consistent with the changing tendency of bonding constants measured by ³¹P NMR, 4.37, 19.7, 2.42 and 2.23 M^?1, respectively.

DFT study of (17)O, (1)H and (13)C NMR chemical shifts in two forms of native cellulose, I(α) and I(β)

This computational study is intended to shed light on the crystalline and molecular structure, together with the hydrogen bonding (H-bonding) differences between two forms of native cellulose. DFT calculations were carried out to characterize the ¹⁷O, ¹H and ¹³C nuclear magnetic resonance (NMR) parameters in cellulose I_α and I_β with the B3LYP functional employing the 6–311++G7 and 6–31+G1 basis sets. Geometry optimization revealed that the average HB length is shortened by 0.01–0.08 Å when the chains are aligned, whereas the average bond angle increases by about 4–8° exhibiting the enhancement of HB strength. For the isolated cellotetramer chains, the isotropic ¹⁷O–H chemical shifts were plotted as a function of HB length. Our results indicated that as the HB length in cellotetramer I_α increases, the ¹⁷O–H chemical shift isotropy increases, but this parameter changes in the opposite direction for the other structure. Moreover, B3LYP/6–311++G7 calculations reveal that there is an acceptable correlation between the calculated ¹³C chemical shifts of the two structures and their experimental values.     

Synthesis, crystal structures and spectroscopic properties of copper(I) complexes containing β-dialdiminato supporting ligands

Two mononuclear neutral copper(I) complexes, Cu(L¹)PPh₃ (1), Cu(L²)(PPh₃)₂ (2) ([L¹]⁻ = [{N(C₆H₃ⁱPr₂-2,6)C(H)}₂CPh]⁻; [L²]⁻ = [{N(C₆H₅)C(H)}₂CPh]⁻) have been synthesized and structurally characterized by X-ray crystallography. In complex 1, the copper(I) atom is in a distorted three-coordinate trigonal planar environment, whereas in complex 2 with the less sterically hindered β-dialdiminato ligand, the copper(I) atom is the centre of a four-coordinate distorted tetrahedron. At room temperature complexes 1 and 2 in a film of PMMA exhibit green emission at 543 and 549 nm with lifetimes of 5.28 and 5.32 ns, respectively.     

Interplay between halogen bonds and hydrogen bonds in OH/SH···HOX···HY (X = Cl, Br; Y = F, Cl, Br) complexes

The character of the cooperativity between the HOX···OH/SH halogen bond (XB) and the Y―H···(H)OX hydrogen bond (HB) in OH/SH···HOX···HY (X = Cl, Br; Y = F, Cl, Br) complexes has been investigated by means of second-order Møller?Plesset perturbation theory (MP2) calculations and “quantum theory of atoms in molecules” (QTAIM) studies. The geometries of the complexes have been determined from the most negative electrostatic potentials (V _S,min) and the most positive electrostatic potentials (V _S,max) on the electron density contours of the individual species. The greater the V _S,max values of HY, the larger the interaction energies of halogen-bonded HOX···OH/SH in the termolecular complexes, indicating that the ability of cooperative effect of hydrogen bond on halogen bond are determined by V _S,max of HY. The interaction energies, binding distances, infrared vibrational frequencies, and electron densities ρ at the BCPs of the hydrogen bonds and halogen bonds prove that there is positive cooperativity between these bonds. The potentiation of hydrogen bonds on halogen bonds is greater than that of halogen bonds on hydrogen bonds. QTAIM studies have shown that the halogen bonds and hydrogen bonds are closed-shell noncovalent interactions, and both have greater electrostatic character in the termolecular species compared with the bimolecular species.

Formation of the Si-B bond: insertion reactions of silylenes into B-X(X = F,Cl, Br,O, and N) bonds

The insertion reactions of the silylene H₂Si with H₂BXH_n-1 (X?=?F, Cl, Br, O, N; n?=?1, 1, 1, 2, 3) have been studied by DFT and MP2 methods. The calculations show that the insertions occur in a concerted manner, forming H₂Si(BH₂)(XH_n-1). The essences of H₂Si insertions with H₂BXH_n-1 are the transfers of the σ electrons on the Si atom to the positive BH₂ group and the electrons of X into the empty p orbital on the Si atom in H₂Si. The order of reactivity in vacuum shows the barrier heights increase for the same-family element X from up to down and the same-row element X from right to left in the periodic table. The energies relating to the B-X bond in H₂BXH_n-1, and the bond energies of Si-X and Si-B in H₂Si(BH₂)(XH_n-1) may determine the preference of insertions of H₂Si into B-X bonds for the same-column element X or for the same-row element X. The insertion reactions in vacuum are similar to those in solvents, acetone, ether, and THF. The barriers in vacuum are lower than those in solvents and the larger polarities of solvents make the insertions more difficult to take place. Both in vacuum and in solvents, the silylene insertions are thermodynamically exothermic.

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Graphical Abstract The insertion process of H₂Si and H₂BXH_n-1(X?=?F, Cl, Br, O, and N; n?=?1, 1 , 1, 2, 3).

     

1H, 15N and 13C backbone chemical shift assignment of titin domains A59–A60 and A60 alone

The giant protein titin is the third most abundant protein of vertebrate striated muscle. The titin molecule is >1 μm long and spans half the sarcomere, from the Z-disk to the M-line, and has important roles in sarcomere assembly, elasticity and intracellular signaling. In the A-band of the sarcomere titin is attached to the thick filaments and mainly consists immunoglobulin-like and fibronectin type III-like domains. These are mostly arranged in long-range patterns or ‘super-repeats’. The large super-repeats each contain 11 domains and are repeated 11 times, thus forming nearly half the titin molecule. Through interactions with myosin and C-protein, they are involved in thick filament assembly. The importance of titin in muscle assembly is highlighted by the effect of mutations in the A-band portion, which are the commonest cause of dilated cardiomyopathy, affecting ~1 in 250 (Herman et al. in N Engl J Med 366:619–628, 2012). Here we report backbone ¹⁵N, ¹³C and ¹H chemical shift and ¹³Cβ assignments for the A59–A60 domain tandem from the titin A59–A69 large super-repeat, completed using triple resonance NMR. Since, some regions of the backbone remained unassigned in A60 domain of the complete A59–A60 tandem, a construct containing a single A60 domain, A60sd, was also studied using the same methods. Considerably improved assignment coverage was achieved using A60sd due to its lower mass and improved molecular tumbling rate; these assignments also allowed the analysis of inter-domain interactions using chemical shift mapping against A59–A60.     

The structure of N δ -( N ′-sulfodiaminophosphinyl)- l -ornithine and its binding to ornithine transcarbamoylase: A quantum chemical study

The structure of N i -( N '-Sulfodiaminophosphinyl)- l -ornithine (PSOrn) in complex with the enzyme ornithine transcarbamoylase (OTCase) was recently characterised by Langley et al. [D.B. Langley, M.D. Templeton, B.A. Fields, R.E. Mitchell and C.A. Collyer, J. Biol. Chem., 275 (2000) 20012] using X-ray diffraction techniques. In this work, the interaction of PSOrn with the arginine residues of OTCase is modelled using density functional theory, with an emphasis on characterising the mechanism of binding between PSOrn, an inhibitor, and the enzyme. For the purposes of this study, the interaction of PSO, an analogue of PSOrn (obtained by replacing a (CH 2 ) 3 CH( CO 2 m )( NH 3 + ) side chain by methyl) with one and two arginine (Arg) molecules are investigated. The PSO > (Arg) 2 trimer is found to be strongly bound, by ～171 kJ mol m 1 , due to the presence of four hydrogen bonds in addition to a large ionic interaction between a dinegative PSO 2 m and protonated arginines. The computed geometry is consistent with the X-ray structure and the large binding energy is consistent with the observation that PSOrn is a powerful inhibitor. Furthermore, in agreement with the proposals of Langley et al. , the most stable bound form of PSO is found to be an imino type tautomer. The population analyses that were carried out on PSO suggest that PN, PO, SN and SO bonds, as in a range of other systems, are generally either single or semipolar bonds.     

Pt(II) complexes with (N,N′) or (C,N,E)− (E = N,S) ligands: Cytotoxic studies,effect on DNA tertiary structure and structure–activity relationships

The cytotoxic activity of two series of platinum(II) complexes containing the polyfunctional imines R¹–CHN–R² [R¹ = phenyl or ferrocenyl unit and R² = (CH₂)_n–CH₂–NMe₂ where n = 1 or 2) (1 and 2) or C₆H₄-2-SMe (3)] acting as a bidentate (N,N′) (4–7) or terdentate [C(phenyl or ferrocenyl),N,N′]^? (8–10) or [C(ferrocenyl),N,S]^? ligand (11) in front of A549 lung, MDA-MB231 breast and HCT116 colon human adenocarcinoma cell lines is reported. The results reveal that most of the platinum(II) complexes are active against the three assayed lines and compounds 6, 7 and the platinacycles 10 and 11 exhibit a remarkable antiproliferative activity, even greater than cisplatin itself, in the cisplatin resistant HCT116 human cancer cell line. Electrophoretic DNA migration studies showed that most of them modify the DNA tertiary structure in a similar way as the reference cisplatin. Solution studies of a selection of the most relevant complexes have also been performed in order to test: (a) their stability in the aqueous biological medium and/or the formation of biologically active species and (b) their proclivity to react with 9-methylguanine (9-MeG), as a model nucleobase. Computational studies at DFT level have also been performed in order to explain the different solution behaviour of the complexes and their proclivity to react with the nucleobase.     

Uric acid salts of magnesium: crystal and molecular structures and thermal analysis of two phases of Mg(C5H3N4O3)2 · 8H2O

Two structurally different phases of a uric acid salt of magnesium, Mg(hydrogenurate)₂ · 8H₂O, have been prepared by crystallization from solution at pH = 7.5–8.0 and were investigated by x-ray crystallography, thermal analysis, and ir spectroscopy. Both phases are monoclinic, space group P2₁/c with a = 9.573(2), b = 14.627(3), c = 7.170(1) Å, β = 101.91(1)° (phase I) and a = 10.397(2), b = 14.306(3), c = 6.732(1) Å, β = 104.64(2)° (phase II). The crystal structures of both phases (R = 0.053 and 0.051, respectively) contain isolated octahedral [Mg(H₂O)₆]²⁺ cations, hydrogenurate monoanions, and two molecules of water of crystallization per formula unit. The structural formula representing these facts is [Mg(H₂O)₆] (hydrogenura-te)₂·2H₂O. The tautomeric form of the hydrogenurate molecule corresponds to the tri-keto form of uric acid deprotonated at N(3). Differences in bond length between uric acid and the hydrogenurate molecule may be described in terms of three additional resonance structures distributing the formal negative charge at N(3) within the pyrimidine (but not the imidazole) ring. Deprotonation at N(3) significantly decreases the internal C-N-C angle at N(3). Alternating pairs of medium-strong intermolecular N-HO hydrogen bonds lead to infinite chains of hydrogenurate molecules extending along the b axis of the unit cells in both phases. The main difference between the two phases lies in their stacking pattern of the hydrogenurate molecules. Infrared data confirm the hydrogen bonding characteristics resulting from the crystal structure analysis. Thermogravimetric measurements and differential scanning calorimetry data show that the dehydration of both phases occurs in two distinct steps with Mg(hydrogenurate)₂.6H₂O as an intermediate phase. The first dehydration step (−2H₂O) is a topotactic reaction with three-dimensional preservation of the main structure elements of the octahydrate in the structure of the hexahydrate.     

Atomic structures of excited state A–T Hoogsteen base pairs in duplex DNA by combining NMR relaxation dispersion,mutagenesis, and chemical shift calculations

NMR relaxation dispersion studies indicate that in canonical duplex DNA, Watson–Crick base pairs (bps) exist in dynamic equilibrium with short-lived low abundance excited state Hoogsteen bps. N1-methylated adenine (m¹A) and guanine (m¹G) are naturally occurring forms of damage that stabilize Hoogsteen bps in duplex DNA. NMR dynamic ensembles of DNA duplexes with m¹A–T Hoogsteen bps reveal significant changes in sugar pucker and backbone angles in and around the Hoogsteen bp, as well as kinking of the duplex towards the major groove. Whether these structural changes also occur upon forming excited state Hoogsteen bps in unmodified duplexes remains to be established because prior relaxation dispersion probes provided limited information regarding the sugar-backbone conformation. Here, we demonstrate measurements of C3′ and C4′ spin relaxation in the rotating frame (R1ρ) in uniformly ¹³C/¹⁵N labeled DNA as sensitive probes of the sugar-backbone conformation in DNA excited states. The chemical shifts, combined with structure-based predictions using an automated fragmentation quantum mechanics/molecular mechanics method, show that the dynamic ensemble of DNA duplexes containing m¹A–T Hoogsteen bps accurately model the excited state Hoogsteen conformation in two different sequence contexts. Formation of excited state A–T Hoogsteen bps is accompanied by changes in sugar-backbone conformation that allow the flipped syn adenine to form hydrogen-bonds with its partner thymine and this in turn results in overall kinking of the DNA toward the major groove. Results support the assignment of Hoogsteen bps as the excited state observed in canonical duplex DNA, provide an atomic view of DNA dynamics linked to formation of Hoogsteen bps, and lay the groundwork for a potentially general strategy for solving structures of nucleic acid excited states.     

Interplay between halogen and chalcogen bonding in the XCl∙∙∙OCS∙∙∙NH3 (X = F,OH, NC,CN, and FCC) complex

The interplay between halogen and chalcogen bonding in the XCl???OCS and XCl???OCS???NH₃ (X = F, OH, NC, CN, and FCC) complex was studied at the MP2/6-311++G(d,p) computational level. Cooperative effect is observed when halogen and chalcogen bonding coexist in the same complex. The effect is studied by means of binding distance, interaction energy, and cooperative energy. Molecular electrostatic potential calculation reveals the electrostatic nature of the interactions. Cooperative effect is explained by the difference of the electron density. Second-order stabilization energy was calculated to study the orbital interaction in the complex. Atoms in molecules analysis was performed to analyze the enhancement of the electron density in the bond critical point.     

Stabilization of a hydrated ketone by metal complexation. The crystal and molecular structures of bis-2,2′,N,N′-bipyridyl ketone-hydrate nickel(II) sulfate,copper(II) chloride and copper(II) nitrate

The crystal structure of the complexes (I)Ni[C₁₁N₈N₂(OH)₂]₂SO₄, (II) Cu[C₁₁H₈N₂(OH)₂]₂Cl₂· 4H₂O and (III) Cu[C₁₁H₈N₂(OH)₂]₂(NO₃)₂·2H₂O have been determined by three-dimensional X-ray analysis methods. Crystal data are: (I), monoclinic, space group C2/c, Z = 4, a = 19.666(4), b = 7.994(2), c = 16.045(6) /rA, /gb = 111.231(9)°, (II), monoclinic, space group C2/c, Z = 4, a = 14.504(4), b = 12.333(8), c = 14.630(3) Å, /gb = 90.92°; and (IIl), monoclinic, space group P2₁/n, Z = 2, a = 7.601(5), b = 11.977(4), c = 14.463(6) Å, β = 93.10(8)°. These structural investigations clearly demonstrate that in each case hydration occurs across the ketone double bond in the ligand and that the resulting hydroxyl group coordinates to the metal. Two di-2-pyridyl ketone ligands are thus bonded to the metal atom in a tridentate fashion. In the nickel complex (I), all six coordination interactions appear to have approximately the same strength. However, in the copper complexes (II) and (III), the pyridyl nitrogens are strongly coordinating to the metal in the equatorial plane, while the hydroxyl groups are more weakly coordinating in the axial direction. The metal to ligand bond distances are: (I) d_Ni−O = 2.098(4), d_NiN = 2.062(4), 2.087(4) Å, (II) d_CuO = 2.465(5), d_CuN = 1.994(5), 2.006(5) Å, (III) d_CuO = 2.464(5), d_CuN = 1.990(5), 2.036(5) Å. The neutral diol that results from hydrolysis of di-2-pyridyl ketone is stabilized by coordination to the metal and such coordination is little affected by changes in the metal, the anion or the extent of hydration.     

Elemental (C,N, P) and isotopic (δ13C, δ15N) signature of primary producers and their contribution to the organic matter in coastal lagoon sediment

Estuarine ecosystems are easily deteriorated by organic pollution because of its high primary productivity. To identify chemical proxies for the possible sources of autochthonous organic matter [phytoplankton-derived particulate organic material (POM), macroalgae and seagrass], we measured C:N:P and the ratios of carbon and nitrogen stable isotopes (δ¹³C and δ¹⁵N values) in two estuarine environments, the polyhaline lagoon, Lake Nakaumi, and the oligohaline lagoon, Lake Shinji, in Japan. Due to vigorous photosynthesis, the δ¹³C of phytoplankton-derived POM in Lake Nakaumi was larger than what would normally be expected from estuarine salinity gradients. Concentrations of nitrogen and phosphorus did not affect the δ¹³C of phytoplankton-derived POM. The δ¹⁵N of all plants was uniform and was higher than the δ¹⁵N of sediments. The seagrass showed a higher C:N ratio than POM and macroalgae, while the macroalgae showed a higher N:P ratio. Thus, simultaneous evaluation of C:N and N:P ratios would distinguish these three plant groups, and it would be possible to identify the source plants from the elemental ratios of the sediments.     

Large 13C/12C and small 15N/14N isotope fractionation in an experimental detrital foodweb (litter–fungi–collembolans)

Correctly estimating the trophic fractionation factors (Δ¹⁵N and Δ¹³C) in controlled laboratory conditions is essential for the application of stable isotope analysis in studies on the trophic structure of soil communities. Laboratory experiments usually suggest large ¹⁵N/¹⁴N and small ¹³C/¹²C trophic fractionation, but in field studies litter-dwelling microarthropods and other invertebrates are consistently enriched in ¹³C relative to plant litter. In the present study, we report data from two laboratory experiments investigating both fungi–collembolans and litter–fungi–collembolans systems. In the fungi–collembolans system, Δ¹⁵N and Δ¹³C averaged 1.4 ± 0.1 and 1.0 ± 0.2 ‰, respectively. In microcosms with fungi-inoculated litter, the difference in δ¹⁵N between collembolans and plant litter averaged 1.5 ± 0.2 ‰, confirming the relatively small ¹⁵N/¹⁴N trophic fractionation at the basal level of detrital foodwebs reported in numerous field studies. In full agreement with field observations, the difference in δ¹³C between bulk litter and collembolans in laboratory microcosms averaged 3.6 ± 0.1 ‰ and only little depended on collembolan species identities or the presence of water-soluble compounds in the litter. We conclude that increased δ¹³C values typical of litter-dwelling decomposers are largely determined by an increased ¹³C content in saprotrophic microorganisms.