Giant motion of La atom inside C82 cage

An anomalous charge density distribution of La atom encapsulated in a C₈₂ cage has been revealed for La@C₈₂ by the maximum entropy method (MEM)/Rietveld analysis using synchrotron powder diffraction data. The obtained La atom charge density shows a feature almost like a bowl or a hemisphere, suggesting that the La atom has a giant motion (large amplitude motion) inside the C₈₂ cage at room temperature. From the obtained MEM charge density, the main results are (1) the cage structure of La@C₈₂ (I) has C_2V symmetry; (2) La atom locates at an off-centered position adjacent to a six-membered ring of the carbon cage; (3) the nearest La–C distance is 2.55(8) and (4) the amount of charge transfer from the La atom to the carbon cage is about 3.2 e, which corresponds to the nominal electronic structure, La³⁺@C₈₂³⁻.     

First-principles study of hydrogen adsorption in metal-doped COF-10

Covalent organic frameworks (COFs), due to their low-density, high-porosity, and high-stability, have promising applications in gas storage. In this study we have explored the potential of COFs doped with Li and Ca metal atoms for storing hydrogen under ambient thermodynamic conditions. Using density functional theory we have performed detailed calculations of the sites Li and Ca atoms occupy in COF-10 and their interaction with hydrogen molecules. The binding energy of Li atom on COF-10 substrate is found to be about 1.0 eV and each Li atom can adsorb up to three H(2) molecules. However, at high concentration, Li atoms cluster and, consequently, their hydrogen storage capacity is reduced due to steric hindrance between H(2) molecules. On the other hand, due to charge transfer from Li to the substrate, O sites provide additional enhancement for hydrogen adsorption. With increasing concentration of doped metal atoms, the COF-10 substrate provides an additional platform for storing hydrogen. Similar conclusions are reached for Ca doped COF-10.     

Neutron elastic scattering studies of biological molecules and complexes

Neutron diffraction can provide very precise stereochemical information about hydrogen bonds and other features involving hydrogen atoms in crystals. This is because, unlike for x rays, the hydrogen atom has a significant scattering amplitude for neutrons relative to other atoms. High-precision studies of a class of molecules, like those on α-amino acids carried out at Brookhaven and Trombay, can provide important information on systematics of the structure, conformation, and hydrogen bonding parameters. Some attempts have also been made to extend these single-crystal studies to some proteins like myoglobin, lysozyme, and trypsin. The large anomalous scattering amplitudes for some stable isotopes like ¹¹³Cd and ¹⁴⁹Sm and the easy variability of neutron wavelength also provides, in principle, a method for solving the phase problem without crystallizing too many heavy atom derivatives. The combination of neutron and x-ray diffraction data, now being used to study charge density distributions in organic molecules and hydrogen bonds, may be extended in the future to larger molecules of biological importance. The small-angle scattering of neutrons is also a powerful technique for studying large biological particles in solution at low resolution to obtain information about sizes, shapes and distribution of constituents.     

The structure of methane hydrate under geological conditions a combined Rietveld and maximum entropy analysis

We present a study of the structure of a fully deuterated methane hydrate under the geological conditions found in the world's oceans. In situ high-resolution neutron diffraction experiments have been performed at temperatures of 220, 275, and 280 K and a pressure of 100 bar, corresponding to the conditions at 1000 m water depth. The data were analyzed with a combination of Rietveld refinement and maximum entropy methods. From the Rietveld refinement, precise atomic parameters of the host lattice could be determined, indicating increasing distortions of the structure of the cages at elevated temperatures and pressures. Debye-Waller factors of the encaged CD(4) molecules have been found to exceed the values of the Debye-Waller factors of the D(2)O molecules considerably. In the large cage of structure type I the thermal center-of-mass displacements of the guests are 5-10 times larger than those of the water molecules. From the maximum entropy analysis maps of the scattering length density have been obtained, showing details of the vibrational amplitudes of the atoms in methane hydrate. The Debye-Waller factors of all molecules have been found to deviate considerably from a simple spherical geometry.     

Crystal structure and electron density of alpha-silicon nitride: experimental and theoretical evidence for the covalent bonding and charge transfer

Crystal structure and electron-density distribution of alpha-silicon nitride (alpha-Si3N4, space group: P31c) have been investigated by a combined technique of the Rietveld method, the maximum-entropy method (MEM), and MEM-based pattern-fitting of high-resolution synchrotron powder diffraction data. In combination with density functional theory calculations, the present experimental electron-density distribution of the alpha-Si3N4 indicates covalent bonds between Si and N atoms and charge transfer from the Si to N atom. The triangular distribution around the N atoms, which is attributable to the nitrogen sp2 hybridization for the nearest silicon and nitrogen pairs, was found in both experimental and theoretical electron density distributions. The minimum electron density in an intralayer Si-N bond was a little lower than that in an interlayer bond, which would be responsible for the inequality between elastic constants, C33 > C11. The present work suggests that the high bulk modulus of the alpha-Si3N4 is attributable to the high minimum electron density of the Si-N bond.     

Interstitial Zn atoms do the trick in thermoelectric zinc antimonide, Zn4Sb3: a combined maximum entropy method X-ray electron density and ab initio electronic structure study

The experimental electron density of the high-performance thermoelectric material Zn4Sb3 has been determined by maximum entropy (MEM) analysis of short-wavelength synchrotron powder diffraction data. These data are found to be more accurate than conventional single-crystal data due to the reduction of common systematic errors, such as absorption, extinction and anomalous scattering. Analysis of the MEM electron density directly reveals interstitial Zn atoms and a partially occupied main Zn site. Two types of Sb atoms are observed: a free spherical ion (Sb3-) and Sb2(4-) dimers. Analysis of the MEM electron density also reveals possible Sb disorder along the c axis. The disorder, defects and vacancies are all features that contribute to the drastic reduction of the thermal conductivity of the material. Topological analysis of the thermally smeared MEM density has been carried out. Starting with the X-ray structure ab initio computational methods have been used to deconvolute structural information from the space-time data averaging inherent to the XRD experiment. The analysis reveals how interstitial Zn atoms and vacancies affect the electronic structure and transport properties of beta-Zn4Sb3. The structure consists of an ideal A12Sb10 framework in which point defects are distributed. We propose that the material is a 0.184:0.420:0.396 mixture of A12Sb10, A11BCSb10 and A10BCDSb10 cells, in which A, B, C and D are the four Zn sites in the X-ray structure. Given the similar density of states (DOS) of the A12Sb10, A11BCSb10 and A10BCDSb10 cells, one may electronically model the defective stoichiometry of the real system either by n-doping the 12-Zn atom cell or by p-doping the two 13-Zn atom cells. This leads to similar calculated Seebeck coefficients for the A12Sb10, A11BCSb10 and A10BCDSb10 cells (115.0, 123.0 and 110.3 microV K(-1) at T=670 K). The model system is therefore a p-doped semiconductor as found experimentally. The effect is dramatic if these cells are doped differently with respect to the experimental electron count. Thus, 0.33 extra electrons supplied to either kind of cell would increase the Seebeck coefficient to about 260 microV K(-1). Additional electrons would also lower sigma, so the resulting effect on the thermoelectric figure of merit of Zn4Sb3 challenges further experimental work.     

Crystal Structure of 〔Aqua(oxalato)(1,10-phenanthroline)(H_2O)〕copper(Ⅱ) Monohydrate

1INTRODUCTIONThemixeda,a'-diimineandoxygendonorligandsofcopper(n)complexesareknowntobepossiblemodelsforenzyme~metalion-substrateandundernumerousin-vestigationst".Themixedoxalato2,2'-bipyridylcomplexesofcopper(I)havebeenwellcharacterizedL2j.Herebywereportthecrystalstructureofits1,lO-phenanthro-lineanalogue.2EXPERIMENTALThetitlecomplexwaspreparedbymixingCuCl,.2H,O,1,lO-phenanthrolineandH,C,o'inmethanol-water(1:lv/v)intheratio1:1:l.Afewdropsoftri-ethylaminewereaddedandtheresultingmi…     

Topology of charge density of flucytosine and related molecules and characteristics of their bond charge distributions

The molecular charge distribution of flucytosine (4-amino-5-fluoro-2-pyrimidone), uracil, 5-fluorouracil, and thymine was studied by means of density functional theory calculations (DFT). The resulting distributions were analyzed by means of the atoms in molecules (AIM) theory. Bonds were characterized through vectors formed with the charge density value, its Laplacian, and the bond ellipticity calculated at the bond critical point (BCP). Within each set of C=O, C-H, and N-H bonds, these vectors showed little dispersion. C-C bonds formed three different subsets, one with a significant degree of double bonding, a second corresponding to single bonds with a finite ellipticity produced by hyperconjugation, and a third one formed by a pure single bond. In N-C bonds, a decrease in bond length (an increase in double bond character) was not reflected as an increase in their ellipticity, as in all C-C bonds studied. It was also found that substitution influenced the N-C, C-O, and C-C bond ellipticity much more than density and its Laplacian at the BCP. The Laplacian of charge density pointed to the existence of both bonding and nonbonding maxima in the valence shell charge concentration of N, O, and F, while only bonding ones were found for the C atoms. The nonbonding maxima related to the sites for electrophilic attack and H bonding in O and N, while sites of nucleophilic attack were suggested by the holes in the valence shell of the C atoms of the carbonyl groups.     

Isotopic effect on the cage-induced quenching of OH(A)/OD(A) inside small argon clusters

In this paper we report on the isotopic effect on the cage-induced excited-state quenching inside small Ar(m) clusters (m<10(2)) solvated in large Ne(N) clusters (N approximately 7.5x10(3)). Excited OH(A)/OD(A) fragments are produced by photodissociation of H2O and D2O molecules and the quenching agents are correspondingly H or D atoms. The decrease of the fluorescence yield with the size of the cluster m>m0 is observed in both cases and it is attributed to the formation of the cage of argon atoms around the doped molecule. Interestingly, more atoms are needed to induce the fluorescence quenching of OD*(A) fragments, m0=21+/-3, compared to the electronically excited state quenching of OH*(A) molecules, 11+/-2. A diffusion model containing two free parameters, the quenching cross section sigmaq and the number of argon atoms forming the cage m0, explains the effect in terms of the residence time of the hydrogen atom inside the cage. We suggest that the melting of the doped rare gas clusters is responsible for the different predissociation dynamics. The quenching cross section obtained from the experimental data is in good agreement with former experiments.     

Ethene insertion into vanadium hydride intermediates formed via vanadium atom reaction with water or ethene: a matrix isolation infrared spectroscopic study

The reaction of V atoms with H2O and various concentrations of C2D4 in argon has been investigated by matrix isolation infrared (IR) spectroscopy. Both C2D6 and CD2H-CD2H are observed as the major products of a set of parallel processes involving hydrogenation of ethene where the formal source of hydrogen is either C2D4 or H2O. Portions of the IR spectrum of CD2H-CD2H isolated in an argon matrix are observed for the first time. For experiments involving low concentrations of C2D4, irradiation of the matrix with light of wavelengths >455 nm results in VH2 formation, with limited observation of ethene hydrogenation. The source of H2 is believed to be due to photoelimination of molecular hydrogen from HO-V-H species, during matrix deposition, with OV as an additional product. Recombination of OV with available H2 in the matrix is proposed as the source of OVH2 under low ethene conditions. No evidence for VD2 formation is observed under our conditions. At higher C2D4 concentrations, VH2 formation is suppressed, while products of ethene hydrogenation are maximized. A second process competing with H2 elimination in which HO-V-H reacts with C2D4 is proposed. Parallel reaction schemes involving V atom insertion into the O-H bonds of water or the photoinduced insertion of V atoms into the C-D bonds of C2D4 are proposed to account for the observed hydrogenation products. In each mechanism, insertion of C2D4 into the V-H or V-D bonds of transient intermediates is followed by photoinduced elimination of the associated ethane isotopomer.     

Cover Picture

The cover picture shows a section of the electron charge density of the first metal carbide endohedral metallofullerene (Sc(2)C(2))@C(84) obtained from a synchrotron X-ray powder diffraction study by the maximum entropy method (MEM). The several density maxima, which correspond to scandium and carbon atoms, are clearly seen inside the C(84) carbon cage. The MEM charge density distribution also reveals that the C(84) cage has D(2d) symmetry (no. 23) and that the C(2) axis is parallel to the <100> face-centered cubic (fcc) direction of the unit cell. As a consequence of the site symmetry being 4mm, the C(2) axis of (Sc(2)C(2))@C(84) is oriented to six equivalent <100> directions and shows a merohedral disorder. The resultant Sc small middle dot small middle dot small middle dotSc distances and C-C bond lengths of the Sc(2)C(2) cluster are 0.429(2) and 0.142(6) nm, respectively. The observed C-C bond length is between that of a typical single and a double bond, and is very close to that of the C-C bond (0.143 nm) combining two pentagons in a C(60) molecule. More about this fascinating structure can be found in the contribution by Shinohara and co-workers on p. 397 ff.     

第一性原理模拟氢气分子在氧化硅团簇上的吸附

基于密度泛函理论,采用广义梯度近似(GGA)分析了H2分子吸附在氧化硅团簇上的几何结构、电子性质以及吸附能.结果发现:H2分子与Si3O4团簇相互作用时,H2分子被分解,游离的H原子优先吸附在末端Si原子上,表明Si3O4团簇体系对氢气的存储主要依赖于末端存在悬挂键的Si原子,接着H2分子才以分子的形式以较小吸附能吸附在Si3O4H4团簇上.氢气分子主要引起与其邻近的原子电荷的重新分布.该团簇体系的红外、拉曼光谱图有效地鉴定了H2分子的吸附状态,为理论上确定团簇的稳定结构和实验上对观测结果的分析提供有力的途径.     

Nb(110)表面氧原子覆盖度对氧分子解离的影响

用基于密度泛函理论的第一性原理方法研究了Nb(110)表面氧原子覆盖度分别为0.25、0.50、0.75 和1.00单层时对氧分子解离的影响. 结果表明, 在氧原子覆盖度不大于0.50单层时, 由于氧分子和表面铌原子的较强相互作用, 使它们能够自发解离. 然而在氧原子覆盖度为0.75单层时, 氧分子只能够在未占据的洞位附近解离, 同时发生严重的晶格畸变. 在形成一个氧原子单层后(1.00 单层), 氧分子只能弱吸附在Nb(100)表面上,此时氧原子向内扩散成为氧分子继续解离的速率决定步骤. 这些结果从理论上解释了在形成一个氧原子单层后, Nb(110)表面氧分子吸收速率迅速下降的原因.     

Crystal structure of {aquaimidazole-[2-(2-carbamoylhydrazone)-propionato]} copper(II) nitrate

The crystal structure of {aquaimidazole[2-(2-carbamoylhydrazone)-propionato]}copper(II) nitrate [Cu(L)Im(H₂O)]NO₃ (I), where HL is the semicarbazone of pyruvic acid, Im is imidazole, is dtermined. The crystal structure of I contains two independent complexes IA and IB in which copper atoms coordinate once deprotonated tridentate HL, imidazole, and water molecules. Outer spheres of the complexes contain nitrate ions. In the compounds studied the coordination polyhedron of the copper atom is a distorted tetragonal pyramid. Its base is composed of carboxyl and carbamide oxygen atoms, azomethine nitrogen of monodeprotonated HL molecules, and the imidazole nitrogen atom. In the crystal, nitrate ions and imidazole molecules link the complexes via hydrogen bonds into 2D networks parallel to the (010) plane. These networks in turn are in pairs arranged into layers along the [010] direction due to hydrogen bonds between water molecules and oxygen atoms of nitrate ions, and also by water molecules and O3 atoms of the neighboring 2D networks. In the crystal, the π-π stacking interaction is observed between the imidazole rings from different layers and there is also a N-O…Cg (π ring) interaction inside the layers.     

Experimental electron density study of a complex between copper(II) and the antibacterial quinolone family member ciprofloxacin

An experimental charge density study of a 1 : 1 complex of Cu-cfx (cfx = ciprofloxacin), 1 [Cu(cfx)(H(2)O)(3)]SO4.2H(2)O, has been performed using single-crystal X-ray diffraction data collected at 100 K using conventional Mo Kalpha radiation. Metal-ligand (ML) bonds and hydrogen bonds (HBs) have been analysed using topological analysis of the electron density with the atoms in molecules (AIM) approach. The copper atom binds to two oxygen atoms in one end of the zwitterionic form of the cfx molecule, in addition to forming bonds with three water molecules, forming a square pyramidal coordination geometry. AIM decomposition of the experimental electron density establishes that the copper atom binds more strongly to the cfx molecule than to the water molecules, suggesting that the latter can be detached leaving behind a reactive, water-free Cu-cfx complex available for interaction with e.g. a macromolecular site. AIM analysis of the extensive hydrogen bond pattern reveals that the positively charged N-end of the zwitterionic cfx forms a relatively strong N-H-O hydrogen bond implying that this region of cfx may play an important role in the docking process in the active site. Visualisation and statistics of selected density derived properties on the molecular surface of the isolated cfx molecule vs its metal complexed counterpart points out regions of potential reactivity. The effect of the fluorine atom is to expand the negative region of the electrostatic potential, while the nitrogen end is heavily electropositive and willingly donates to--for molecular docking purposes--relatively strong hydrogen bonding. The Cu atom is highlighted as a potentially highly reactive site which is likely to interact strongly with any given negative ligand.     

Chemical bonding effect in electron scattering by gaseous molecules

The experimental intensity of 30 keV electron small angle scattering by a gaseous molecule is much different from the calculation using usual independent atom model. This is due to the rearrangement of electron distribution in a molecule by the formation of chemical bonds, and is called chemical bonding effect (CBE). The molecules studied are mainly hydrocarbons such as methane, acetylene, ethane, etc. and some non-hydrocarbons. The measurement was carried out on both elastic and total scattering and the effect was found for not only elastic but also inelastic scattering. The effect is relatively large for hydrogen rich molecules as H₂O, NH₃ and hydrocarbons, but is essentially related to the number of atoms contained in molecules. The origin of CBE will attribute mainly to the concentration of inner atomic electrons resulting from chemical bonding.     

Synchrotron X-ray charge density study of coordination polymer Co3(C8H4O4)4(C4H12N)2(C5H11NO)3 at 16 K

The charge density (CD) of coordination polymer Co3(C8H4O4)4(C4H12N)2(C5H11NO)3 (1) has been determined from multipole modeling of structure factors obtained from single-crystal synchrotron X-ray diffraction measurements at 16 K. The crystal structure formally contains a negatively charged framework with cations and neutral molecules in the voids. However, the CD suggests that the framework is close to neutral, and therefore qualitative conclusions based on formal charge counting, e.g., about guest inclusion properties, will be incorrect. There are considerable differences in the charge distributions of the three unique benzenedicarboxylic acid linkers, which are widely used in coordination polymers. This suggests that the electrostatic properties of coordination polymer cavities, and thereby their inclusion properties, are highly tunable. The electron density topology shows that the tetrahedrally coordinated Co atom has an atomic volume which is 15% larger than that of the octahedrally coordinated Co atom. The crystal structure has both ferromagnetic and antiferromagnetic interactions, but no direct metal-metal bonding is evidenced in the CD. The magnetic ordering therefore takes place through superexchange in the oxygen bridges and the aromatic linkers. Bonding analysis of the experimental CD reveals that two oxygen atoms, O(1) and O(11), have significant covalent contributions to the metal-ligand bonding, whereas all other oxygen atoms have closed-shell interactions with the metals. This indicates that these two oxygen atoms are the key mediators of the magnetic ordering.     

[Ni(CHZ)3]SO4·3H2O的合成、晶体结构及热分解特性

用硫酸镍与碳酰肼(CHZ)反应, 制备得到一种新型含能配合物[Ni(CHZ)3]SO4·3H2O, 通过X射线单晶衍射, 元素分析和傅立叶变换红外(FTIR)光谱对其进行了表征. 晶体结构测试表明, 该化合物晶体属于三斜晶系, P1空间群, a=0.85237(1) nm, b=0.90964(1) nm, c=1.22559(2) nm, β=96.731(2)°, V=0.8849(2) nm3, Z=2, Dc=1.798 g·cm-3. 在该配合物分子中, 碳酰肼作为双齿配体, 以羰基O原子和端基N原子与Ni2+离子发生配位, 形成3个相互垂直的五元平面螯合环. 在氢键、静电引力和范德华力的作用下, 该配合物形成了复杂的三维网状结构. 对碳酰肼分子进行了DFT-B3LYP/6-311+G**量化计算研究, 得到其NBO电荷, 从理论上说明碳酰肼的配位点是羰基O原子和端基N原子. 采用DSC、TG-DTG和FTIR光谱技术对目标化合物的热分解机理进行了研究, 并用Kissinger法和Ozawa-Doyle法对其热分解过程中两个放热峰的非等温反应动力学参数进行了计算. 结果表明, 该配合物具有较高的能量和良好的热稳定性.     

一维链状化合物[Ag(L)]·H2O的合成、晶体结构和荧光性质

The title compound,[Ag(L)]·H2O,1,where HL=4-(isonicotinamido)benzoic acid,was synthesized in methanol solution and its crystal structure was determined by X-ray diffraction analysis.The crystal is of monoclinic.space group P21/c with a=0.571 8(8)nm,b=1.357 2(18)nm,c=1.5580(2)nm,β=91.090(2)°,V=1.2090(3)nm3,Z=4,Dc=2.009 g·cm-3,F(000)=722,Rint=0.042 9,R=0.027 1,wR=0.055 6.In complex 1,the Ag atoms are linearly coordinated by one O atom and one N atom of two ligand molecules.Each I- ligand in turn uses its one carboxylate group and one pyridinyl groups to connect two metal centers,then the one-dimensional (1D) chains is formed.On the other hand,the 1D chains are further connected by O1W-H1WB…O2 hydrogen bonds and Ag-O weak interactions to give a two-dimensional (2D) layer,finally,the 2D net extents to three-dimensional (3D) supramolecular framework by O1W-H1WB…O1 as well as N2-H2…O2 interactions.CCDC:762259.     

Experimental and theoretical electron density distribution and magnetic properties of the butterfly-like complex [Fe(4)O(2)(O(2)CCMe(3))(8)(NC(5)H(4)Me)(2)].2CH(3)CN

The structure and electron density distribution (EDD) of the carboxylate-bridge iron complex [Fe(III)(4)(micro(3)-O)(2)(O(2)CCMe(3))(8)(NC(5)H(4)Me)(2)].2CH(3)CN, 1, has been determined from synchrotron X-ray diffraction data (R(int) = 0.025) collected with the crystal cooled to 16(5) K. At this temperature complex 1 crystallized in the triclinic space group P with cell parameters a = 12.6926(7) A, b = 12.9134(8) A, c = 13.4732(8) A, alpha = 115.372(2) degrees, beta = 107.702(3) degrees, and gamma = 102.731(2) degrees. The theoretical EDD determined from a density functional theory (DFT) single point calculation of an entire molecule of 1 at the experimental geometry has been analyzed and compared to the experimental EDD. The latter is expressed in the framework of a multipolar model with parameters determined by least-squares refinement (R(w)(F(2)) = 0.024) based on the X-ray diffraction data. The central micro(3)-oxygen atom in 1 is significantly out of the plane spanned by the three Fe atoms coordinated to this oxygen. Comparison of measures for the bonding geometry around the iron atoms in 1 with the corresponding values for the iron atoms in relevant trinuclear complexes suggests that there are significant differences in the Fe-(micro(3)-O) bonds in the two cases. Analyses of both the experimental and theoretical EDDs reveal very significant differences between the two Fe-(micro(3)-O) bonds in 1, with one bond being much more directed and stronger than the other bond. A topological analysis of the EDDs using the atoms in molecules approach also reveals very distinct differences between the properties of the two Fe(III) atoms. A clear exponential relationship is found between the Laplacian of the experimental density at the bond critical points in the Fe-ligand bonds and their bond lengths. M?ssbauer spectroscopy of 1 shows two easily separable doublets corresponding to the two different iron sites. Magnetic susceptibility measurements between 4.2 and 300 K indicate antiferromagnetically coupled Fe(III) atoms constituting an S = 0 ground state.