The structure and electronic property of the smallest C20‐glycine and Gd‐encapsulated C20‐glycine derivatives with potentially biological activity

Theoretical calculations on interaction of the C₂₀ fullerene (consists solely by pentagons) with the smallest amino acid (glycine) were carried out using density‐functional theory method. The glycine molecule energetically prefers to interact with the Top‐site on the C₂₀ cage via its amino nitrogen (N) active site. The stable ordering of three active sites on glycine molecule is NH₂‐site > O‐site > OH‐site. Moreover, when the Gd atom is encapsulated to the center of C₂₀‐glycine, the cage volume obviously increase ～24.8%; and the endohedral atom induces the generation of two strong bands in the partial density of states spectra, which could cause the effect on optical properties. Additionally, it is also found that the modified C₂₀‐glycine derivative by Gd atom can reduce the thermodynamic and kinetic stabilities. It could be expected that the study may provide a theoretical reference in exploring their intrinsic feature structurally to antitumor activity. © 2012 Wiley Periodicals, Inc.     

Formaldehyde encapsulated in lithium-decorated metal-organic frameworks: a density functional theory study

The stability of monomeric formaldehyde encapsulated in the lithium-decorated metal-organic framework Li-MOF-5 was investigated by means of density functional calculations with the M06-L functional and the 6-31G(d,p) basis set. To assess the efficiency of Li-MOF-5 for formaldehyde preservation, we consider the reaction kinetics and the thermodynamic equilibrium between formaldehyde and its trimerized product, 1,3,5-trioxane. We propose that trimerization of encapsulated formaldehyde takes place in a single reaction step with an activation energy of 34.5 kcal mol(-1). This is 17.2 kcal mol(-1) higher than the corresponding activation energy in the bare system. In addition, the reaction energy of the system studied herein is endothermic by 6.1 kcal mol(-1) and the Gibbs free energy (ΔG) of the reaction becomes positive (11.0 kcal mol(-1)). Consequently, the predicted reverse rate for the trimerization reaction in the Li-MOF-5 is significantly faster than the forward rate. The calculations show that the oligomerization of formaldehyde in Li-MOF-5 is a reversible reaction, suggesting that such a zeolite might be a good candidate material for preserving formaldehyde in its monomeric form.     

From a Si3‐Cyclopropene to a Si3S‐Bicyclo[1.1.0]butane to a Si3S‐Cyclopropene to a Si3S2‐Bicyclo[1.1.0]butane: Back‐and‐Forth,and In‐Between

Compact and highly reactive bicyclo[1.1.0]butanes constitute one of the most fascinating classes of organic compounds. Furthermore, interplay of bicyclo[1.1.0]butanes with their valence isomers, such as buta‐1,3‐dienes and cyclobutenes, is among the fundamental pericyclic transformations in organic chemistry. Herein we report the back‐and‐forth interconversion between the cyclotrisilenes and thiatrisilabicyclo[1.1.0]butanes, allowing for the synthesis of novel representatives of such classes of highly reactive organometallics. The peculiar structural and bonding features of the newly synthesized compounds, as well as the mechanism of their isomerization, were verified both experimentally and computationally.     

Mechanisms for H2O decomposition on the Si(111)‐7 × 7 surface: A DFT cluster model study

The mechanisms for the complete decomposition of water molecules on the Si (111)‐7 × 7 surface were investigated theoretically. The reaction pathways for dissociation of four water molecules over the adatom and rest atom sites were calculated using the density functional theory (DFT) in conjunction with the B3LYP functional. The calculated results demonstrated that the initial O? H bond dissociation from the first H₂O to form the adsorbed OH species is more preferential on the adatom site (Si_a) than the rest atom site (Si_r) of Si (111)‐7 × 7. Four water molecules dissociate successively over the adatom site, backbonds of adatoms which are saturated by OH species can reasonably be the place of insertion of oxygen atoms, yielding a tetrahedral SiO₄ structure with one on top and three inserted oxygen atoms. © 2009 Wiley Periodicals, Inc. Int J Quantum Chem, 2010     

Exploring Electronic Properties of Si20-n H20-n P n Heterofullerenes (N = 1, 2, 5, and 10) Based on NMR and NBO Analysis: A DFT Study

Abstract

Density functional theory (DFT) calculations are performed to characterize Si_20-nH_20-nP_nheterofullerenes (n = 1, 2, 5, and 10), and to examine the stability of encapsulated X@Si_20-nH_20-nP_nwhere X = Li, Na, and K. To this aim, ²⁹Si, ³¹P, and ¹H chemical shielding (CS) tensors as well as natural charges are calculated for the optimized structures. The local structures around silicon as well as phosphorus nuclei are found to show a good correlation with CSs. However, the similar values of ¹H calculated CSs (26–28 ppm) obtained for all the heterofullerenes mean hydrogen atoms do not detect the local structure around the adjacent silicon and also do not distinguish between isomers of heterofullerenes and the number of P dopants. According to calculated endo-hedral inclusion energies (E_inc), formation of the Li@Si_20-nH_20-nP_ncomplexes, unlike the K@Si_20-nH_20-nP_nones, are exothermic while E_incof the Na@Si_20-nH_20-nP_ncomplexes strongly depends on the position and number of P dopants. Moreover, binding energies for the considered models are found to be in the order of Si_20-nH_20-nP_n> Li@Si_20-nH_20-nP_n> Na@Si_20-nH_20-nP_n> K@Si_20-nH_20-nP_nwhile strongly depending on the pattern of P dopants on the surface of the cage.

Supplemental materials are available for this article. Go to the publisher's online edition of Phosphorus, Sulfur, and Silicon and the Related Elements to view the following free supplemental files: Additional figures and tables]     

Guest Modulation of Spin‐Crossover Transition Temperature in a Porous Iron(II) Metal–Organic Framework: Experimental and Periodic DFT Studies

The synthesis, structure, and magnetic properties of three clathrate derivatives of the spin‐crossover porous coordination polymer {Fe(pyrazine)[Pt(CN)₄]} ( 1 ) with five‐membered aromatic molecules furan, pyrrole, and thiophene is reported. The three derivatives have a cooperative spin‐crossover transition with hysteresis loops 14–29 K wide and average critical temperatures T_c=201 K ( 1?fur ), 167 K ( 1?pyr ), and 114.6 K ( 1?thio ) well below that of the parent compound 1 (T_c=295 K), confirming stabilization of the HS state. The transition is complete and takes place in two steps for 1?fur , while 1?pyr and 1?thio show 50 % spin transition. For 1?fur the transformation between the HS and IS (middle of the plateau) phases occurs concomitantly with a crystallographic phase transition between the tetragonal space groups P4/mmm and I4/mmm, respectively. The latter space group is retained in the subsequent transformation involving the IS and the LS phases. 1?pyr and 1?thio display the tetragonal P4/mmm and orthorhombic Fmmm space groups, respectively, in both HS and IM phases. Periodic calculations using density functional methods for 1?fur , 1?pyr , 1?thio , and previously reported derivatives 1?CS₂ , 1?I, 1?bz (benzene), and 1?pz (pyrazine) have been carried out to investigate the electronic structure and nature of the host–guest interactions as well as their relationship with the changes in the LS–HS transition temperatures of 1?Guest . Geometry‐optimized lattice parameters and bond distances in the empty host 1 and 1?Guest clathrates are in general agreement with the X‐ray diffraction data. The concordance between the theoretical results and the experimental data also comprises the guest molecule orientation inside the host and intermolecular distances. Furthermore, a general correlation between experimental T_c and calculated LS–HS electronic energy gap was observed. Finally, specific host–guest interactions were studied through interaction energy calculations and crystal orbital displacement (COD) curve analysis.