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1.
Density functional theory calculations are reported on a set of models of the water‐oxidising complex (WOC) of photosystem II (PSII), exploring structural features revealed in the most recent (1.9 Å resolution) X‐ray crystallographic studies of PSII. Crucially, we find that the variation in the Mn–Mn distances seen between the A and B monomers of this crystal structure can be entirely accounted for, in the low oxidation state (LOS) paradigm, by consideration of the interplay between two hydrogen‐bonding interactions involving proximate amino acid residues with the oxo bridges of the WOC, that is, His337 with O3 (which leads to a general elongation in the Mn–Mn distances between Mn1, Mn2 and Mn3) and Arg357 with O2 (which results in a specific elongation of the Mn2?Mn3 distance).  相似文献   

2.
Three atomic resolution crystal structures of Photosystem II, in the double flashed, nominal S3 intermediate state of its Mn4Ca Water Oxidising Complex (WOC), have now been presented, at 2.25, 2.35 and 2.08 Å resolution. Although very similar overall, the S3 structures differ within the WOC catalytic site. The 2.25 Å structure contains only one oxy species (O5) in the WOC cavity, weakly associated with Mn centres, similar to that in the earlier 1.95 Å S1 structure. The 2.35 Å structure shows two such species (O5, O6), with the Mn centres and O5 positioned as in the 2.25 Å structure and O5−O6 separation of ∼1.5 Å. In the latest S3 variant, two oxy species are also seen (O5, Ox), with the Ox group appearing only in S3, closely ligating one Mn, with O5−Ox separation <2.1 Å. The O5 and O6/Ox groups were proposed to be substrate water derived species. Recently, Petrie et al. (Chem. Phys. Chem., 2017 ) presented large scale Quantum Chemical modelling of the 2.25 Å structure, quantitatively explaining all significant features within the WOC region. This, as in our earlier studies, assumed a ‘low’ Mn oxidation paradigm (mean S1 Mn oxidation level of +3.0, Petrie et al., Angew. Chem. Int. Ed., 2015 ), rather than a ‘high’ oxidation model (mean S1 oxidation level of +3.5). In 2018 we showed (Chem. Phys. Chem., 2018 ) this oxidation state assumption predicted two energetically close S3 structural forms, one with the metal centres and O5 (as OH) positioned as in the 2.25 Å structure, and the other with the metals similarly placed, but with O5 (as H2O) located in the O6 position of the 2.35 Å structure. The 2.35 Å two flashed structure was likely a crystal superposition of two such forms. Here we show, by similar computational analysis, that the latest 2.08 Å S3 structure is also a likely superposition of forms, but with O5 (as OH) occupying either the O5 or Ox positions in the WOC cavity. This highlights a remarkable structural ‘lability’ of the WOC centre in the S3 state, which is likely catalytically relevant to its water splitting function.  相似文献   

3.
Mn(bzimpy)2(1)[bzimpy=2,6-bis(benzimidazol-2-yl)pyridine],a mononuclear manganese(Ⅱ)complex,was synthesized by the reaction of Mn(OOCMe)2 with bzimpy in absolute ethanol.The complex was structurally characterized by elemental analysis,cyclic voltammetry,and X-ray crystallography.In the complex,the manganese-nitrogen distances were different,and the geometry and the metal ion environment showed the distortion.The cyclic voltammetric measurements have been performed to assess its redox characteristics.The presence of oxidation wave at 0.62V and 0.081V vs.SCE or 0.8V and 1.0v vs.NHE suggested that this complex could catalyze the oxidation of water,therefore,simulate the water-oxidizing complex(WOC) of photosystem Ⅱ (PS Ⅱ).The measurements of photoreduction of 2,6-dichlorophenolindophenol (DCPIP),and oxygen evolution in the manganess-depleted and the comples 1-reconstituted PS Ⅱ preparations just support our conjecture.  相似文献   

4.
Density functional theory (DFT) calculations are reported for a set of model compounds intended to represent the structure of the Photosystem II (PSII) water oxidising complex (WOC) as determined by the recent 1.9 ? resolution single crystal X-ray diffraction (XRD) study of Umena et al. In contrast with several other theoretical studies addressing this structure, we find that it is not necessary to invoke photoreduction of the crystalline sample below the S(1)'resting state' in order to rationalise the observed WOC geometry. Our results are consistent with crystallised PSII in the S(1) state, with S(1) corresponding to either (Mn(III))(4) or (Mn(III))(2)(Mn(IV))(2) as required by the two competing paradigms for the WOC oxidation state pattern. Of these two paradigms, the 'low-oxidation-state' paradigm provides a better match for the crystal structure, with the comparatively long Mn(2)-Mn(3) distance in particular proving difficult to reconcile with the 'high-oxidation-state' model. Best agreement with the set of metal-metal distances is obtained with a S(1) model featuring μ-O, μ-OH bridging between Mn(3) and Mn(4) and deprotonation of one water ligand on Mn(4). Theoretical modelling of the 1.9 ? structure is an important step in assessing the validity of this recent crystal structure, with implications for our understanding of the mechanism of water oxidation by PSII.  相似文献   

5.
Metal–organic self‐assembly has proven to be of great use in constructing structures of increasing size and intricacy, but the largest assemblies lack the functions associated with the ability to bind guests. Here we demonstrate the self‐assembly of two simple organic molecules with CdII and PtII into a giant heterometallic supramolecular cube which is capable of binding a variety of mono‐ and dianionic guests within an enclosed cavity greater than 4200 Å3. Its structure was established by X‐ray crystallography and cryogenic transmission electron microscopy. This cube is the largest discrete abiological assembly that has been observed to bind guests in solution; cavity enclosure and coulombic effects appear to be crucial drivers of host–guest chemistry at this scale. The degree of cavity occupancy, however, appears less important: the largest guest studied, bound the most weakly, occupying only 11 % of the host cavity.  相似文献   

6.
We have developed a high‐yielding synthesis of meso‐tetraalkylporphyrins, which previously have been obtained only in lower yields. By employing Montmorrilonite K10 as the acid catalyst and 3 Å molecular sieves as the dehydrating agent, yields that reached 70 % could be achieved with some aliphatic aldehydes. The free‐base porphyrins with decyl ( C10 ) or longer chains were imaged at the single‐molecule level at the solvent/surface interface. Highly oriented pyrolytic graphite (HOPG) was used as a π‐stacking surface, whereas 1‐phenyloctane and 1‐phenylnonane were used as solvents. An odd–even effect was observed from C13 to C16 . For C13 a single‐crystal X‐ray structure allowed an unprecedented insight into how packing from two dimensions is expanded into a three‐dimensional crystal lattice.  相似文献   

7.
We have reinvestigated the synthesis of 1‐methyl‐2,4,5‐trinitroimidazole (MTNI; 1 ), and further characterized its physical properties. It is a promising candidate as an insensitive high explosive. Compound 1 was synthesized from the imidazole ( 2 ), via a 5‐step sequence of reactions, and subjected to various sensitivity tests for explosives. The structure of 1 was characterized by X‐ray diffraction. The crystal is orthorhombic; C4H3N5O6, M = 217.11, Z = 8, Pca21, a = 8.6183(6) Å, b = 17.7119(12) Å, c = 10.6873(7) Å, V = 1631.38(19) Å3, Dc = 1.768 g/cm3. The structure was refined to R = 0.0284 for 3201 independent reflections with I > 2σ(I). The molecular structures calculated by high levels of ab initio and density functional theories were in good agreement with those observed by X‐ray experiment. According to our preliminary sensitivity tests, 1 was characterized to be intermediate in sensitivity between RDX and TNT. The explosive performances were evaluated theoretically, and were found to be comparable to those of RDX. In addition, owing to its low melting point (82 °C), 1 is believed to be an excellent candidate for inclusion in melt‐castable explosives, and may lead to increased explosive power.  相似文献   

8.
Novel Coloring of the α‐Mn Structure Type with Main Group Elements in K5Pb24 – Crystal Structure, Superconductivity, and Structure Property Relationship K5Pb24 was synthesized from the elements in a welded niobium ampoule at 800 °C. The crystal structure was determined from X‐ray single crystal data. Space group I 4 3m, a = 12.358(1) Å, Z = 2, Pearson symbol cI58. The structure of K5Pb24 shows an ordered atomic distribution on the four crystallographic sites of the α‐Mn structure type. The aristotype is decomposed into cluster units consisting of 48 Pb atoms. The structural subunits are built from four 16‐vertex Frank Kasper polyhedra, which consist of 15 Pb and one K atom (K1). The 16‐vertex polyhedra are centered with another K atom (K2). Four such polyhedra share a common corner (K1) and several edges. 18 shared edges form a truncated tetrahedra of twelve Pb atoms. These atoms form together with four K1 atoms (located in the center of the Frank Kasper polyhedra) a Friauf polyhedra. The result is a ‘supratetrahedra‘ of 48 Pb atoms enclosing five K atoms. The body centered arrangement of this units results in a three‐dimensional framework of Pb atoms. The title compound is the lead‐richest phase of the K/Pb system. Superconducting properties are observed from temperature dependent susceptibility measurements. Field dependent measurements reveal a hard type II superconductor. LMTO and EH band structure calculations verify the metallic behavior. An analysis of the density of states with the help of the electron localization function (ELF) shows the presence of lone pairs in this intermetallic phase. The role of lone pairs is discussed with respect to the superconducting property.  相似文献   

9.
The structure of a novel oxido‐aminoxyl (=`nitronyl nitroxide') biradical, 2,2′‐(1‐oxidopyridine‐2,6‐diyl)bis[4,5‐dihydro‐4,4,5,5‐tetramethyl‐3‐oxido‐1H‐imidazol‐1‐oxyl] hydrate ( 1 ⋅H2O) was established by X‐ray analysis in the solid state: monoclinic, space group P21/c, Z=4 with a=12.621(4), b=15.704(5), and c=13.001(4) Å, and β=115.202(6)°. Variable‐temperature magnetic susceptibilities show a weak antiferromagnetic interaction between the two oxido‐substituted aminoxyl moieties of 1 , indicative of a singlet ground state. AM1 Calculations located minima for the possible structure based on the X‐ray crystal structure. A hybride density‐functional‐theory calculation with the UB3LYP method from the X‐ray crystal structure establishes the same spin sign in the two aminoxyl moieties and shows that a small spin density is localized at the C‐atoms of the pyridine moiety. These theoretic results are in good agreement with the determined weak antiferromagnetic interaction of 1 .  相似文献   

10.
Hochtemperatur‐Cs2[PdCl4] — New Results on a “wellknown” Compound Two modifications of Cs2[PdCl4] have been characterized by X‐ray powder and single crystal diffraction, respectively. The crystal structures are described and the group‐subgroup‐relations between these structures are discussed. In addition to the tetragonal (P4/mmm (No. 123), a = 7.4158(8) Å, c = 4.6792(6) Å) and the orthorhombic (Cmcm (No. 63), a = 10.529(1) Å, b = 10.310(1) Å, c = 9.460(1) Å) modification DSC investigations and high‐temperature X‐ray diffraction experiments with synchrotron radiation show the existence of another modification or of yet unknown decomposition products. The phase transformation from the orthorhombic to the tetragonal polymorph is completely finished at 100 °C. The second effect is detected at 319 °C.  相似文献   

11.
The title compound, N′‐benzylidene‐N‐[4‐(3‐methyl‐3‐phenyl‐cyclobutyl)‐thiazol‐2‐yl]‐chloro‐acetic acid hydrazide, has been synthesized and characterized by elemental analysis, IR, 1H and 13C NMR, and X‐ray single crystal diffraction. The compound crystallizes in the orthorhombic space group P 21 21 21 with a = 5.8671 (3) Å, b = 17.7182 (9) Å, and c = 20.6373 (8) Å. Moreover, the molecular geometry from X‐ray experiment, the molecular geometry, vibrational frequencies, and gauge‐including atomic orbital 1H and 13C chemical shift values of the title compound in the ground state have been calculated by using the Hartree–Fock and density functional methods (B3LYP) with 6‐31G(d) and 6‐31G(d,p) basis sets. The results of the optimized molecular structure are exhibited and compared with the experimental X‐ray diffraction. Besides, molecular electrostatic potential, Frontier molecular orbitals, and thermodynamic properties of the title compound were determined at B3LYP/6‐31G(d) levels of theory. © 2011 Wiley Periodicals, Inc. Int J Quantum Chem, 2012  相似文献   

12.
The X‐ray structure of 1,2,4,5‐tetra­hydroxy­benzene (benzene‐1,2,4,5‐tetrol) monohydrate, C6H6O4·H2O, (I), reveals columns of 1,2,4,5‐tetra­hydroxy­benzene parallel to the b axis that are separated by 3.364 (12) and 3.453 (11) Å. Molecules in adjacent columns are tilted relative to each other by 27.78 (8)°. Water mol­ecules fill the channels between the columns and are involved in hydrogen‐bonding interactions with the 1,2,4,5‐tetra­hydroxy­benzene mol­ecules. The crystal structure of the adduct 1,2,4,5‐tetra­hydroxy­benzene–2,5‐di­hydroxy‐1,4‐benzo­quinone (1/1), C6H6O4·C6H4O4, (II), reveals alternating mol­ecules of 1,2,4,5‐tetra­hydroxy­benzene and 2,5‐di­hydroxy‐1,4‐benzo­quinone (both lying on inversion centers), and a zigzag hydrogen‐bonded network connecting mol­ecules in three dimensions. For compound (II), the conventional X‐ray determination, (IIa), is in very good agreement with the synchrotron X‐ray determination, (IIb). When differences in data collection temperatures are taken into account, even the displacement parameters are in very good agreement.  相似文献   

13.
A structurally novel compound was isolated as the main product of tandem Pechmann–dehydration between diethyl 4‐hydroxy‐4‐methyl‐2‐(4′‐nitrophenyl)‐6‐oxocyclohexane‐1,3‐dicarboxylate ( 1 ) and resorcinol in the presence of trifluoroacetic acid. The structure of the product was determined as a racemate of (7R,8R)‐ and (7S,8S)‐ethyl 7,8‐dihydro‐3‐hydroxy‐9‐methyl‐7‐(4′‐nitrophenyl)‐6H‐dibenzo[c]‐pyran‐6‐one‐8‐carboxylate ( 3a ) enantiomers by single crystal X‐ray diffraction analysis. The X‐ray crystal structure revealed that 3a possesses an extended and more stable conjugated aromatic system as a consequence of the stereoselectivity of intramolecular dehydration behavior of Pechmann condensation product 2 . In the crystal superstructure, the (7R,8R)‐ and (7S,8S)‐isomers of 3a respectively self‐assembled into left‐ and right‐handed supramolecular helical chains with a channel size of 3.70 Å × 10.20 Å in virtue of intermolecular hydrogen bonding together with dramatic twisting between carboxylate group at C8 and tricyclic ring framework of 3a , which are then arranged alternatively along the b‐axis direction with a pitch length of 7.894 Å.  相似文献   

14.
The solid and solution structures of a new optically active aminopyridine compound, 2‐[(1S)‐(+)‐10‐camphorsulfonamino]‐6‐aminopyridine [(S)‐csaap], 1 , are reported. Crystal data: space group P21, a = 8.9729 (5), b = 10.9447 (6), c = 36.693 (2) Å, β = 96.435 (1)°, V = 3580.8 (3) Å3, Z = 8, R1 = 0.0673 and wR2 = 0.1600 with I > 2σ(I). This chiral compound shows an unprecedented cocrystallization of four stereoisomers, which are characterized by X‐ray crystallography and NMR spectroscopy.  相似文献   

15.
The porous manganese(II) coordination polymer 1 was prepared via a hydrothermal synthesis approach starting from Mn(NO3)2 and 2,2′‐bipyridine‐4,4′‐dicarboxylic acid in a one to one mixture of ethanol and water at 120 °C. The product was characterized by single crystal X‐ray diffraction, TGA and elemental analysis. Space group: C2/c, Z = 4, unit cell dimensions at –73 °C: a = 11.959(2), b = 14.626(3), c = 9.247(2) Å, β = 127.40(3) R = 0.034, wR2 (all data) = 0.088. The structure determination revealed 1 to be a network which consists of cross linked bis(carboxylato) bridged infinite manganese chains. Water containing open channels with an pore size of 6.87 × 5.86 Å2 are observed.  相似文献   

16.
Crystallization of copper(I) cyanide from piperidine (‘pip’) solution yields an adduct of CuCN : pip (3 : 4) ratio, as established by a single crystal X‐ray structure determination, which also shows the complex to have a single‐stranded ···Cu(CN)Cu(CN)···spine (C,N scrambled), one‐third of the copper atoms carrying a pair of pip ligands, the others only one. Crystallization of silver(I) cyanide from piperidine (‘pip’) or cyclohexylamine (‘CyNH2’) solutions yields adducts of the unusual AgX : unidentate‐N‐base (1 : 2) stoichiometry. The CyNH2 adduct is, unusually for cyanide complexes of this type, mononuclear with a trigonal planar silver atom, [(NC)Ag(H2NCy)2], the AgCN component lying along the intersection of two crystallographic mirror planes which bisect and relate the H2NCy ligands (Ag‐C, N 2.067(3), 2.335(2) Å; N‐Ag‐N, C 80·80(6), 139.60(4)°). In the pip adduct, the immediate silver atom environment is also three‐coordinate (Ag‐C; N, N 2.080(1); 2.288, 2.443(1) Å; N‐Ag‐N 88·34(4), N‐Ag‐C 144.47(4), 125.07(4), (Σ357.9°) perturbed toward two‐coordination, but the silver atom environment geometry is further perturbed from planarity by the parallel approach of an inversion‐related molecule (Ag···C′ 2.926(1) Å (Ag···Ag′ 3.1842(2)°) forming a loose, albeit still discrete, dimer. Key features in the IR spectra of the above compounds and of AgCN : pip (1 : 1) and CuCN : CyNH2 (2 : 3) are assigned and discussed in terms of the structures or of proposed structures in the case of the latter two adducts. The structure of [ClAg(pip)3], adventitiously obtained, is also described (Ag‐Cl 2.471(3); Ag‐N 2.147(13), 2.188(7) (x2) Å; Cl‐Ag‐N 96.1(3), 98.5(2), N‐Ag‐N 116.3(2) (x2), 122.1(3)°).  相似文献   

17.
The organic‐inorganic hybrid nonlinear optical (NLO) material NH4B(d‐ (+)‐C4H4O5)2 · H2O (NBC) was synthesized in a borate‐carboxylic acid system. Its structure was determined by single crystal X‐ray diffraction. It crystallizes in the orthorhombic system, space group Pna21 (No. 33), with cell parameters a = 11.484(6) Å, b = 5.354(3) Å, c = 21.079(12) Å, V = 1296.0(12), Z = 4. It exhibits a three‐dimensional pseudo tunnel structure consisting of fundamental building block [B(d‐ (+)‐C4H4O5)2] anions. The small cavities are occupied by the H2O molecules and NH4+ cations, which stabilize the whole structure by O–H ··· O and N–H ··· O hydrogen bonds. The powder X‐ray diffraction (PXRD) of the crystal was also recorded. Elemental analyses, FT‐IR and FT‐Raman spectra analyses, thermal analysis, and diffuse‐reflectance spectra for the compound are also presented, as are band structures and density of states calculation. Nonlinear optical measurements indicate that the material has second harmonic generation (SHG) properties and is phase‐matchable.  相似文献   

18.
The most recent XRD studies of Photosystem II (PS II) reveal that the His337 residue is sufficiently close to the Mn(4)Ca core of the Water Oxidising Complex (WOC) to engage in H-bonding interactions with the μ(3)-oxo bridge connecting Mn(1), Mn(2) and Mn(3). Such interactions may account for the lengthening of the Mn-Mn distances observed in the most recent and highest resolution (1.9 ?) crystal structure of PS II compared to earlier, lower-resolution (2.9 ? or greater) XRD structures and EXAFS studies on functional PS II. Density functional theory is used to examine the influence on Mn-Mn distances of H-bonding interactions, mediated by the proximate His337 residue, which may lead to either partial or complete protonation of the μ(3)-oxo bridge on models of the WOC. Calculations were performed on a set of minimal-complexity models (in which WOC-ligating amino acid residues are represented as formate and imidazole ligands), and also on extended models in which a 13-peptide sequence (from His332 to Ala344) is treated explicitly. These calculations demonstrate that while the 2.9 ? structure is best described by models in which the μ(3)-oxo bridge is neither protonated nor involved in significant H-bonding, the 1.9 ? XRD structure is better reproduced by models in which the μ(3)-oxo bridge undergoes H-bonding interactions with the His337 residue leading to expansion of the 'close' Mn-Mn distances well known from EXAFS studies at ~ 2.7 ?. Furthermore, full μ(3)-oxo-bridge protonation remains a distinct possibility during the process of water oxidation, as evidenced by the lengthening of the Mn-Mn vectors observed in EXAFS studies of the higher oxidation states of PS II. In this context, the Mn-Mn distances calculated in the protonated μ(3)-oxo bridge structures, particularly for the peptide extended models, are in close agreement with the EXAFS data.  相似文献   

19.
20.
Cyclic disulfide‐rich peptides have exceptional stability and are promising frameworks for drug design. We were interested in obtaining X‐ray structures of these peptides to assist in drug design applications, but disulfide‐rich peptides can be notoriously difficult to crystallize. To overcome this limitation, we chemically synthesized the L ‐ and D ‐forms of three prototypic cyclic disulfide‐rich peptides: SFTI‐1 (14‐mer with one disulfide bond), cVc1.1 (22‐mer with two disulfide bonds), and kB1 (29‐mer with three disulfide bonds) for racemic crystallization studies. Facile crystal formation occurred from a racemic mixture of each peptide, giving structures solved at resolutions from 1.25 Å to 1.9 Å. Additionally, we obtained the quasi‐racemic structures of two mutants of kB1, [G6A]kB1, and [V25A]kB1, which were solved at a resolution of 1.25 Å and 2.3 Å, respectively. The racemic crystallography approach appears to have broad utility in the structural biology of cyclic peptides.  相似文献   

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