Electronic structure and vibrational spectra of cis-diammine(orotato)platinum(II), a potential cisplatin analogue: DFT and experimental study

Orotic acid (vitamin B₁₃) is a key intermediate in biosynthesis of the pyrimidine nucleotides in living organisms, moreover, it may serve as the biological carrier for some metal ions. cis-Diammine(orotato)platinum(II), cis-[Pt(C₅H₂N₂O₄)(NH₃)₂] can be considered as a new potential cisplatin analogue. The FT-Raman and FT-IR spectra of the title complex are reported, for the first time. The molecular structure, vibrational frequencies, and the theoretical infrared and Raman intensities have been calculated by the density functional mPW1PW91 method. The detailed vibrational assignment has been made on the basis of the calculated potential energy distribution. The theoretically predicted IR and Raman spectra show very good agreement with experiment. Natural bond orbital (NBO) analyses were performed for cisplatin, carboplatin and the title complex. The results provided new data on the nature of platinum–ligand bonding in these compounds. Strong intramolecular hydrogen bond between the orotate ligand and the coordinated ammonia group stabilizes the structure of the platinum(II) complex. Thus, it is suggested that the orotate ligand in the title complex is more inert to the substitution reactions than the chloride ligands in cisplatin.     

小分子硫原子团簇正离子的结构稳定性

用分子图形软件设计出 4 9种硫原子团簇Sn+ (n =3～ 13)的结构 ,使用B3LYP密度泛函进行几何构型优化和振动频率计算 ,根据分子的总能量得出最稳定的同分异构体 .在硫原子团簇正离子中 ,大部分原子为二配位成键 .带有一、三配位的原子结构的总能量较高 .部分最稳定硫原子团簇正离子的构型与最稳定的中性硫原子团簇的构型完全不同 .     

Theoretical insight of adsorption thermodynamics of multifunctional molecules on metal surfaces

Adsorption thermodynamics based on density functional theory (DFT) calculations are exposed for the interaction of several multifunctional molecules with Pt and Au(1 1 0)-(1 × 2) surfaces. The Gibbs free adsorption energy explicitly depends on the adsorption internal energy, which is derived from DFT adsorption energy, and the vibrational entropy change during the chemisorption process. Zero-point energy (ZPE) corrections have been systematically applied to the adsorption energy. Moreover the vibrational entropy change has been computed on the basis of DFT harmonic frequencies (gas and adsorbed phases, clean surfaces), which have been extended to all the adsorbate vibrations and the metallic surface phonons. The phase diagrams plotted in realistic conditions of temperature (from 100 to 400 K) and pressure (0.15 atm) show that the ZPE corrected adsorption energy is the main contribution. When strong chemisorption is considered on the Pt surface, the multifunctional molecules are adsorbed on the surface in the considered temperature range. In contrast for weak chemisorption on the Au surface, the thermodynamic results should be held cautiously. The systematic errors of the model (choice of the functional, configurational entropy and vibrational entropy) make difficult the prediction of the adsorption-desorption phase boundaries.     

Converged properties of clean metal surfaces by all-electron first-principles calculations

All-electron full-potential linearized augmented plane-wave calculations of the surface energy, work function, and interlayer spacings of close-packed metal surfaces are presented, in particular, for the free-electron-like metal surfaces, Mg(0 0 0 1) and Al(1 1 1), and for the transition metal surfaces, Ti(0 0 0 1), Cu(1 1 1), Pd(1 1 1), and Pt(1 1 1). We investigate the convergence of the surface energy as a function of the number of layers in the slab, using the Cu(1 1 1) surface as an example. The results show that the surface energy, as obtained using total energies of the slab and bulk from separate calculations, converges well with respect to the number of layers in the slab. Obviously, it is necessary that bulk and surface calculations are performed with the same high accuracy. Furthermore, we discuss the performance of the local-density and generalized gradient approximations for the exchange-correlation functional in describing the various surface properties.     

Stabilization of valence fluctuations in the cerium solid by the time-dependent collision approach

The collision-generated hybridization which has been found responsible for the on-site mixing of the atomic-likef-state and the band-liked states in mixed valence solids has been studied for the cerium solid. A practical expression which depends on the lattice constant and temperature has been obtained for the collision-generated hybridization. Numerical calculations show that the valence varies continuously with lattice constant and that temperature makes the transition smoother. The collision-generated hybridization is found to be of significant strength in the intermediate valence regime; but over a wide range of the valence near 3.5 it varies rather slowly without preferring a particular valence. Factors which can assist the collision-generated hybridization in stabilizing the mixed valence phase at a particular lattice constant are discussed.     

Density functional theory investigation of the structure of SO2 and SO3 on Cu(1 1 1) and Ni(1 1 1)

Density functional theory (DFT) slab calculations, mainly using the generalised gradient approximation, have been used to investigate the minimum energy structures of molecular SO₂ and SO₃ on Cu(1 1 1) and Ni(1 1 1) surfaces. On Ni(1 1 1) the optimal local adsorption structures are in close agreement with experimental results for both molecular species obtained using the X-ray standing wavefield technique, although for adsorbed SO₂ the energetic difference between two alternative lateral positions of the lying-down molecule on the surface is marginally significant. On Cu(1 1 1) the results for adsorbed SO₂, in particular, were sensitive to the DFT functional used in the calculations, but in all cases failed to reproduce the experimentally-established preference for adsorption with the molecular plane perpendicular to the surface. This result is discussed in the context of previously published DFT results for these species adsorbed on Cu(1 0 0). The optimal geometry found for SO₃ on Cu(1 1 1) is similar to that on Ni(1 1 1), providing agreement with experiment regarding the molecular orientation but not the adsorption site.     

钐(Ⅱ)类卡宾CH_3SmCH_2X(X=Cl、Br和Ⅰ)促进乙烯环丙烷化反应途径的理论研究(英文)

用密度泛函B3LYP方法研究了过渡金属钐类卡宾与乙烯的环丙烷化反应的机理。对三种不同的钐的SS试剂CH_3SmCH_2X(其中X=Cl、Br和Ⅰ)分别和CH_2CH_2反应的各反应物、中间体、过渡态和产物构型的全部结构几何参数进行了优化,用内禀反应坐标(IRC)计算和频率分析方法,对过渡态进行了验证。结果表明：CH_3SmCH_2X(其中X=Cl、Br和Ⅰ)与CH_2CH_2环丙烷化反应按亚甲基转移通道(通道A)和卡宾金属化通道(通道B)都可以进行,与锂类卡宾的反应机理相同,只是按亚甲基转移通道(通道A)进行反应较容易一些,而且此反应在较低的温度下就可以发生。     

The chemisorption of pentacene on Si(0 0 1)-2 × 1

Adsorption structures of the pentacene (C₂₂H₁₄) molecule on the clean Si(0 0 1)-2 × 1 surface were investigated by scanning tunneling microscopy (STM) in conjunction with density functional theory calculations and STM image simulations. The pentacene molecules were found to adsorb on four major sites and four minor sites. The adsorption structures of the pentacene molecules at the four major sites were determined by comparison between the experimental and the simulated STM images. Three out of the four theoretically identified adsorption structures are different from the previously proposed adsorption structures. They involve six to eight Si-C covalent chemical bonds. The adsorption energies of the major four structures are calculated to be in the range 67-128 kcal/mol. It was also found that the pentacene molecule hardly hopped on the surface when applying pulse bias voltages on the molecule, but was mostly decomposed.     

New feature in the Auger peak of adsorbed oxygen

Recent joint theoretical and experimental investigations of Auger core-core-valence spectra of alkali adatoms on simple metals have revealed that such technique is capable to ascertain contributions from different adsorption environments in the signal [M.I. Trioni, S. Caravati, G.P. Brivio, L. Floreano, F. Bruno, A. Morgante, Phys. Rev. Lett. 93 (2004) 206802]. Consequently, to verify if such an effect is present also for other chemical species, we study theoretically the KLV transition of oxygen either as a bulk impurity or as an adsorbate in/on Al and Ag (jellium-like). We make use of the Fermi golden rule in which the matrix elements of the interaction are calculated within DFT. We verify that the relevant physical quantity of this phenomenon is the excited local density of states (LDOS), calculated within a region centered on the core ionized atom. The Auger rate for oxygen in Ag bulk displays a single asymmetric peak, while for adsorbed oxygen a second smaller feature at lower energies, and very close to the first one, appears. This unexpected result follows from the removal of the degeneracy of the m quantum number of the 2p states of oxygen at the surface. It is only displayed on the electronically less dense metal (Ag), but not on Al.     

Chemical Reactivity of Tetrasulfur Tetranitride: Synthesis,Physical Properties,and Structural Characterization of the Amorphous Phase Cu7S4N4

Tetrasulfur tetranitride, S₄N₄, reacts with elemental Cu within inert solvents to a black‐blue material of approximate composition Cu₇S₄N₄ which is totally amorphous to X‐rays and which cannot be made crystalline by either thermal treatment or electron radiation. Cu₇S₄N₄ explodes if heated above 234 °C or when subjected to mechanical shock to eventually yield copper(I) sulfide; this together with the characteristic infrared spectrum of Cu₇S₄N₄ indicates the presence of molecular S₄N₄ units inside the amorphous phase. The metastable nature of Cu₇S₄N₄ is also mirrored by electron microscopy which furthermore allows the structural characterization of its degradation products. Based on experimental EXAFS data offering characteristic Cu—N and Cu—S distances, a theoretical crystalline approximant of Cu₇S₄N₄ was suggested and structurally optimized by density‐functional total‐energy calculations including periodic boundary conditions. This model incorporates a central S₄N₄ unit bonded to three shells of Cu atoms of different functionalities; in addition, a partial rupture of the S₄N₄ unit is likely to allow for a lowering of the total energy of the metastable phase. The latter observation supports the impossibility to make Cu₇S₄N₄ crystallize using ₄N₄ crystallize using whatever kind of measures.