Linear C(n) clusters: are they acetylenic or cumulenic?

Uncapped linear Cn clusters have been studied with hybrid density functional theory focusing on the geometry, HOMO-LUMO gap, and the longitudinal optical (LO) vibrational mode. The latter two correlate well with the bond length alternation (BLA) of the optimized geometry. Due to end effects, the BLA is not constant along the chains. The degree of BLA changes continuously with increasing n: starting with essentially nonalternating structures (cumulenic), then turning into strongly alternating (acetylenic) structures. This transition has not yet been described or characterized and occurs at relatively large values of n. The implications for the widely observed characteristic LO vibrational bands of linear carbon clusters are discussed.     

Protein and solvent dynamics: how strongly are they coupled?

Analysis of Raman and neutron scattering spectra of lysozyme demonstrates that the protein dynamics follow the dynamics of the solvents glycerol and trehalose over the entire temperature range measured 100-350 K. The protein's fast conformational fluctuations and low-frequency vibrations and their temperature variations are very sensitive to behavior of the solvents. Our results give insight into previous counterintuitive observations that protein relaxation is stronger in solid trehalose than in liquid glycerol. They also provide insight into the effectiveness of glycerol as a biological cryopreservant.     

When does gold behave as a halogen? Predicted uranium tetraauride and other MAu4 tetrahedral species, (M = Ti,Zr, Hf,Th)

Quantum chemical calculations suggest that a series of molecules with the general formula MAu4 are stable, where M = U, Th, and a group-4 atom. They correspond to Au in the formal valence state -1 and indicate that gold can act as a ligand similar to the halogen series. Of the MAu4 species studied, UAu4, the first predicted mixed gold uranium compound, has a short M-Au bond distance, 2.71 A, which would locate Au between Br and I from the bond length point of view in the U-tetrahalide series. Energetically, the U-Au bond is weaker than the corresponding U-Br and U-I bonds.     

Structures of MAu16 (-) (M=Ag, Li, Na, and K): how far is the endohedral doping?

The structural and electronic properties of MAu16 (-) (M=Ag, Li, Na, and K) have been studied by the scalar relativistic all-electron density-functional calculations, in which particular attention is paid to the stability of the endohedral Au16 (-) cage doped by different dopant atoms. It is found that only the smaller atoms, such as Cu, Li, and Na, can be stably encapsulated in the Au16 (-) cage, while the addition of the larger Ag or K atom prefers to locate in the surface or outside of the cage, which is inconsistent with the previous hypothesis that the Au16 (-) cage could act as a container to hold an arbitrary heterometal atom. The stable endohedral Li@Au16 (-) and Na@Au16 (-) have a large energy gap between the highest occupied molecular orbital and the lowest unoccupied molecular orbital gap, indicating that they are chemically stable and may be used as potential building blocks for designing cluster-assembled materials.     

Freely available conformer generation methods: how good are they?

Conformer generation has important implications in cheminformatics, particularly in computational drug discovery where the quality of conformer generation software may affect the outcome of a virtual screening exercise. We examine the performance of four freely available small molecule conformer generation tools (Balloon, Confab, Frog2, and RDKit) alongside a commercial tool (MOE). The aim of this study is 3-fold: (i) to identify which tools most accurately reproduce experimentally determined structures; (ii) to examine the diversity of the generated conformational set; and (iii) to benchmark the computational time expended. These aspects were tested using a set of 708 drug-like molecules assembled from the OMEGA validation set and the Astex Diverse Set. These molecules have varying physicochemical properties and at least one known X-ray crystal structure. We found that RDKit and Confab are statistically better than other methods at generating low rmsd conformers to the known structure. RDKit is particularly suited for less flexible molecules while Confab, with its systematic approach, is able to generate conformers which are geometrically closer to the experimentally determined structure for molecules with a large number of rotatable bonds (≥10). In our tests RDKit also resulted as the second fastest method after Frog2. In order to enhance the performance of RDKit, we developed a postprocessing algorithm to build a diverse and representative set of conformers which also contains a close conformer to the known structure. Our analysis indicates that, with postprocessing, RDKit is a valid free alternative to commercial, proprietary software.     

Electronic structure and low temperature thermoelectric properties of In₂₄M₈O₄₈ (M = Ge(4+), Sn(4+), Ti(4+), and Zr(4+))

The electronic structure and transport properties of In₂₄M₈O₄₈ (M = Ge⁴⁺, Sn⁴⁺, Ti⁴⁺, and Zr⁴⁺) have been studied by using the full‐potential linearized augmented plane‐wave method and the semiclassical Boltzmann theory, respectively. It is found that the magnitude of powerfactor with respect to relation time follows the order of In₂₄Sn₈O₄₈ > In₂₄Zr₈O₄₈ > In₂₄Ge₈O₄₈ > In₂₄Ti₈O₄₈. The largest powerfactor is 2.7 × 10¹² W/K²ms for In₂₄Sn₈O₄₈ at 60 K, which is nearly thirty times larger than those of conventional n‐type thermoelectric materials. The origin of the different thermoelectric behavior for these compounds is discussed from the electronic structure level. It is found that, at low temperature, the dopant strongly affect the bands near the Fermi level, which consequently leads to their different thermoelectric properties. The electronic configuration and the difference in atomic number between the dopant and the host atom also play an important role on the thermoelectric properties of In₂₄M₈O₄₈. Our calculations give a valuable insight on how to enhance the thermoelectric performance of In₃₂O₄₈. © 2011 Wiley Periodicals, Inc. J Comput Chem, 2011     

MX~4(M=Ti,Zr,Hf;X=Cl,Br)的电子结构研究

本文利用单电子非相对论Hartree-Fock-Slater和完全相对论Dirac-Fock-Slater两种离散变分局域密度泛函方法(DV-Xα), 对MX~4(M=Ti,Zr,Hf;X=Cl,Br)的电子基态和相应于低能UV光谱的激发态进行了计算, 结果与实验符合得较好。用Mulliken布居分析方法研究了分子的共价性质, 发现除HfBr~4外,相对论效应对金属与配体之间的键级影响很小。     

Distribution of N-glycosylation sequons in proteins: how apart are they?

N-glycosylation is a common protein modification process, which affects a number of properties of proteins. Little is known about the distribution of N-glycosylation sequons, for example, the distance between glycosylated sites and their position in the protein primary sequence. Using a large set of experimentally confirmed eukaryotic N-glycoproteins we analyzed the relative position and distribution of sequons. N-Glycosylation probability was found to be lower in the termini of protein sequences compared to the mid region. N-glycosylated sequons were found much farther from C terminus compared to the N-terminus of the protein sequence and this effect was more pronounced for NXS sequons. The distribution of sequons, modeled based on balls-in-boxes classical occupancy, showed a near-maximum probability. Considerable proportion of sequons was found within a distance of ten amino acids, indicating that the steric hindrance was not a key factor in protein N-glycosylation. Interestingly, the distribution of all sequons present in N-glycoproteins showed a pattern very similar to that of glycosylated sequons. The results indicate that protein N-glycosylation chiefly follows a random design.     

All-metal aromatic clusters M4(2-) (M = B, Al, and Ga). Are π-electrons distortive or not?

The π-electrons in benzene, the quintessential aromatic molecule, were previously shown to be distortive, i.e., they prefer localized double bonds alternating with single bonds. It is the σ-electrons that force the double bonds to delocalize, leading to a regular, D(6h) geometry. Herein, we computationally investigate the double-bond localizing or delocalizing propensities of σ- and π-electrons in the archetypal all-metal aromatic cluster Al(4)(2-) and its second- and fourth-period analogs B(4)(2-) and Ga(4)(2-), using Kohn-Sham molecular orbital (MO) theory at BP86/TZ2P in combination with quantitative bond energy decomposition analyses (EDA). We compare the three all-metal aromatic clusters with the structurally related organic species C(4)H(4)(2+), C(4)H(4), and C(4)H(4)(2-). Our analyses reveal that the π-electrons in the group-13 M(4)(2-) molecules have a weak preference for localizing the double bonds. Instead, the σ-electrons enforce the regular D(4h) equilibrium geometry with delocalized double bonds.     

钛,锆和铪羰基化合物M(CO)_n(M=Ti,Zr,Hf;n=4～7)的理论研究

利用密度泛函方法对标题化合物的平衡几何、热化学及振动频率进行了理论预测,发现这3种金属原子都有相似的M(CO)n(n=4～7)结构.全局最低构型对M(CO)7都是单态C3v戴帽八面体7S-1,对M(CO)6都是三重态D3d畸变八面体6T(而对应的单重态M(CO)5仅比它低不到21 kJ·mol-1).对M(CO)n(n=5,4)都是三重态6S-1,其构型分别为从6T中移去1个或2个CO基的衍生物5T和4T.此外,五重态的D3h的三角双锥M(CO)5和单态的Td四面体M(CO)4以及能量更高的含有C和O同时与金属成键的独特配位CO基的M(CO)6和M(CO)3也被发现.最后,给出M(CO)7→M(CO)6+CO反应的离解能.并讨论了金属18价电子的Ti(CO)7存在的可能性.     

Lead-like, drug-like or “Pub-like”: how different are they?

Academic and industrial research continues to be focused on discovering new classes of compounds based on HTS. Post-HTS analyses need to prioritize compounds that are progressed to chemical probe or lead status. We report trends in probe, lead and drug discovery by examining the following categories of compounds: 385 leads and the 541 drugs that emerged from them; "active" (152) and "inactive" (1488) compounds from the Molecular Libraries Initiative Small Molecule Repository (MLSMR) tested by HTS; "active" (46) and "inactive" (72) compounds from Nature Chemical Biology (NCB) tested by HTS; compounds in the drug development phase (I, II, III and launched), as indexed in MDDR; and medicinal chemistry compounds from WOMBAT, separated into high-activity (5,784 compounds with nanomolar activity or better) and low-activity (30,690 with micromolar activity or less). We examined Molecular weight (MW), molecular complexity, flexibility, the number of hydrogen bond donors and acceptors, LogP-the octanol/water partition coefficient estimated by ClogP and ALOGPS), LogSw (intrinsic water solubility, estimated by ALOGPS) and the number of Rule of five (Ro5) criteria violations. Based on the 50% and 90% distribution moments of the above properties, there were no significant difference between leads of known drugs and "actives" from MLSMR or NCB (chemical probes). "Inactives" from NCB and MLSMR were also found to exhibit similar properties. From these combined sets, we conclude that "Actives" (569 compounds) are less complex, less flexible, and more soluble than drugs (1,651 drugs), and significantly smaller, less complex, less hydrophobic and more soluble than the 5,784 high-activity WOMBAT compounds. These trends indicate that chemical probes are similar to leads with respect to some properties, e.g., complexity, solubility, and hydrophobicity.     

Insertion of noble-gas atom (Kr and Xe) into noble-metal molecules (AuF and AuOH): are they stable?

The structure and the stability of a new class of insertion compounds of noble-gas atoms of the type AuNgX (Ng=Kr, Xe and X=F, OH) have been investigated theoretically through ab initio molecular-orbital calculations. All the species are found to have a linear structure with a noble-gas-noble-metal bond, the distance of which is comparable to covalent bond length except the AuKrOH system, for which it lies in between the covalent and van der Waals limits. The dissociation energies corresponding to the lowest-energy fragmentation products, AuX+Ng have been computed to be -166.2, -276.0, -194.4, and -257.6 kJ/mol for AuXeF, AuKrF, AuXeOH, and AuKrOH, respectively, at the MP2 level of theory. The respective barrier heights corresponding to the bent transition states (Au-Ng-X bending mode) have been calculated to be 119.1, 74.9, 160.7, and 141.6 kJ/mol. However, three of these species are found to be metastable in their respective potential-energy surface, and the dissociation energies corresponding to the Au+Ng+X fragments have been calculated to be 112.9, 3.0, and 18.7 kJ/mol for AuXeF, AuKrF, and AuXeOH, respectively, at the same level of theory. An analysis of the nature of interactions involved in the Au-Ng-X systems has been performed using Bader's topological theory of atoms-in-molecules (AIM). Geometric as well as energetic considerations along with AIM results suggest a partial covalent nature of Au-Ng bonds in these systems. This work might have important implications in the preparation of a new class of insertion compounds of noble-gas atoms containing noble-gas-noble-metal bond.     

Filling a Gap: The Coordinatively Saturated Group 4 Carbonyl Complexes TM(CO)8 (TM=Zr,Hf) and Ti(CO)7

Homoleptic Group 4 metal carbonyl cation and neutral complexes were prepared in the gas phase and/or in solid neon matrix. Infrared spectroscopy studies reveal that both zirconium and hafnium form eight-coordinate carbonyl neutral and cation complexes. In contrast, titanium forms only the six-coordinate Ti(CO)₆⁺ and seven-coordinate Ti(CO)₇. Titanium octacarbonyl Ti(CO)₈ is unstable as a result of steric repulsion between the CO ligands. The 20-electron Zr(CO)₈ and Hf(CO)₈ complexes represent the first experimentally observed homoleptic octacarbonyl neutral complexes of transition metals. The molecules still fulfill the 18-electron rule, because one doubly occupied valence orbital does not mix with any of the metal valence atomic orbitals. Zr(CO)₈ and Hf(CO)₈ are stable against the loss of one CO because the CO ligands encounter less steric repulsion than Zr(CO)₇ and Hf(CO)₇. The heptacarbonyl complexes have shorter metal−CO bonds than that of the octacarbonyl complexes due to stronger electrostatic and covalent bonding, but the significantly smaller repulsive Pauli term makes the octacarbonyl complexes stable.     

α-Na3M2(PO4)3 (M = Ti, Fe): absolute cationic ordering in NASICON-type phases

The structure of the fully ordered α-Na(3)Ti(2)(PO(4))(3) NASICON compound was elucidated using high-quality single-crystal data. The cation/vacancy distribution forms a homogeneous 3D arrangement and could represent the absolute cationic ordering available in the full Na(3)M(2)(PO(4))(3) series, as verified for M = Fe. For M = Ti, the reversible α → γ transition was observed at 85 °C, leading to the standard disordered R ?3c γ model. Through JPDF analysis, the most probable Na(+) zigzag M(2)-M(1) diffusion scheme was directly deduced using our accurate crystallographic data.     

Al促进SO~4^2^-/M~xO~y(M=Zr,Ti, Fe)固体强酸的研究

合成与表征了三个系列的Al促进固体强酸样品,并研究了对甲苯的苯甲酰化反应性能。实验表明,向SO~4^2^-/ZrO~2,SO~4^2^-/TiO~2和SO~4^2^-/Fe~2O~3中引入适量的Al~2O~3,有助于稳定样品表面的含硫物种,增加样品表面的有效酸位,提高样品的强酸性和对甲苯的苯甲酰化的反应活性。NH~3吸附微量热结果表明,Al促进样品的强酸性和催化活性的显著提高是由于样品表面的酸位强度分布发生了变化,有利于正丁烷异构化反应和苯甲酰化反应的中强酸位和强酸位的酸量显著增加。     

Al促进SO~4^2^-/M~xO~y(M=Zr, Ti, Fe)固体强酸的研究

合成与表征了三个系列的Al促进固体强酸样品,并研究了对甲苯的苯甲酰化反应性能.实验表明,SO_4~(2-)/ZrO_2,SO_4~(2-)/TiO_2和SO_4~(2-)/Fe_2O_3中引入适量的Al_2O_3,有助于稳定样品表面的含硫物种,增加样品表面的有效酸位,提高样品的强酸性和对甲苯的苯甲酰化的反应活性.NH_3吸附微量热结果表明,Al促进样品的强酸性和催化活性的显著提高是由于样品表面的酸位强度分布发生了变化,有利于正丁烷异构化反应和苯甲酰化反应的中强酸位和强酸位的酸量显著增加.     

Cation distribution in (M′, M)3Se4: II. (V,Ti)3Se4 and (Cr,V)3Se4

The cation distribution among the two crystallographic cation sites of the Cr₃S₄ structure was determined in VTi₂Se₄ and VCr₂Se₄ by high-resolution neutron diffraction, using Rietveld analysis. The results showed a considerable disorder but they nevertheless revealed the site preference of V atoms for the 2(a) site in both compounds. The compositional changes of the lattice parameters and the transition temperatures to the CdI₂-type structure in (V_xTi_1−x)₃Se₄ and (Cr_xV_1−x)₃Se₄ were compared with those in (Cr_xTi_1−x)₃Se₄ and (Fe_xCr_1−x)₃Se₄, and discussed from the viewpoint of the site preference of the cation.     

Expanding molecular transition metal cubane clusters of the form [M4(μ3)-O)4]12+: syntheses, spectroscopic and structural characterizations of molecules M4(μ3-O)4(O2P(Bn)2)4(O4), M = V(V) and W(V)

Oxidizing the trimer V(3)(μ(3)-O)(O(2))(μ(2)-O(2)P(Bn)(2))(6)(H(2)O) in the presence of excess (t)BuOOH results in V(4)(μ(3)-O)(4)(μ(2)-O(2)P(Bn)(2))(4)(O(4)) and heating W(CO)(6) and bis(benzyl)phosphinic acid in 1:1 EtOH/THF at 120 °C produces W(4)(μ(3)-O)(4)(μ(2)-O(2)P(Bn)(2))(4)(O(4)).