Synthesis and structure of new types of organogermanium compounds containing α‐amino acid or α‐aminophosphonic acid moieties

A series of germasesquioxides and germatranes containing α‐amino acid or α‐aminophosphonic acid moieties was synthesized by the reaction of β‐trichlorogermylpropionyl chloride with α‐amino acid esters or α‐aminophosphonates. The structures of all products were confirmed by ¹H NMR, ³¹P NMR, and IR spectra, and elemental analyses. The intramolecular monocyclic penta‐coordinated structure of the trichlorogermyl intermediate was determined by X‐ray diffraction. The X‐ray analyses showed that the geometry about the germanium atom was a slightly distorted trigonal bipyramid, and a coordinate covalent bond exists between the oxygen and the germanium atoms. © 1999 John Wiley & Sons, Inc. Heteroatom Chem 10: 73–78, 1999     

Differentiation of α‐COOH from β‐COOH in aspartic acids by N‐phosphorylation

The biomimic reactions of N‐phosphoryl amino acids, which involved intramolecular penta‐coordinate phosphoric‐carboxylic mixed anhydrides, are very important in the study of many biochemical processes. The reactivity difference between the α‐COOH group and β‐COOH in phosphoryl amino acids was studied by experiments and theoretical calculations. It was found that the α‐COOH group, and not β‐COOH, was involved in the ester exchange on phosphorus in experiment. From MNDO calculations, the energy of the penta‐coordinate phosphoric intermediate containing five‐member ring from α‐COOH was 35 kJ/mol lower than that of the six‐member one from β‐COOH. This result was in agreement with that predicted by HF/6‐31G** and B3LYP/6‐31G** calculations. Theoretical three‐dimensional potential energy surface for the intermediates predicted that the transition states 4 and 5 involving α‐COOH or β‐COOH group had energy barriers of ΔE=175.8 kJ?mol^?1 and 210.4 kJ?mol^?1, respectively. So the α‐COOH could be differentiated from β‐COOH intramolecularly in aspartic acids by N‐phosphorylation. © 2001 John Wiley & Sons, Inc. Int J Quant Chem 83: 41–51, 2001     

Self‐assembly properties of Salamo‐type trinuclear Cu(II) and Co(II) complexes based on the regulation of H+/OHˉ

A novel naphthalenediol‐based bis(salamo)‐type tetraoxime compound (H₄L) was designed and synthesized. Two new supramolecular complexes, [Cu₃(L)(μ‐OAc)₂] and [Co₃(L)(μ‐OAc)₂(MeOH)₂]·4CHCl₃ were synthesized by the reaction of H₄L with Cu(II) acetate dihydrate and Co(II) acetate dihydrate, respectively, and were characterized by elemental analyses and X‐ray crystallography. In the Cu(II) complex, Cu1 and Cu2 atoms located in the N₂O₂ sites, and are both penta‐coordinated, and Cu3 atom is also penta‐coordinated by five oxygen atoms. All the three Cu(II) atoms have geometries of slightly distorted tetragonal pyramid. In the Co(II) complex, Co1 and Co3 atoms located in the N₂O₂ sites, and are both penta‐coordinated with geometries of slightly distorted triangular bipyramid and distorted tetragonal pyramid, respectively, while Co2 atom is hexa‐coordinated by six oxygen atoms with a geometry of slightly distorted octahedron. These self‐assembling complexes form different dimensional supramolecular structures through inter‐ and intra‐molecular hydrogen bonds. The coordination bond cleavages of the two complexes have occurred upon the addition of the H⁺, and have reformed again via the neutralization effect of the OH^?. The changes of the two complexes response to the H⁺/OH^? have observed in the UV–Vis and ¹H NMR spectra.     

Crystallographic report: 2‐Furfurylgermatrane

The germanium atom is penta‐coordinated and adopts a trigonal bipyramidal geometry. The 2‐furfuryl group and the nitrogen atom each occupy an apical position with a transannular N→Ge bond distance of 2.173(3) Å. Copyright © 2004 John Wiley & Sons, Ltd.     

Force constant decomposition for penta‐coordinated XH3Cl2‐ (X = C,Si, Ge) structures

Based on the energy decomposition analysis of an interacting system, we propose a method for force constant decomposition analysis with respect to the specific normal coordinate. Using the presented method, we examined the penta‐coordinated system (X = C, Si, Ge), which possesses a three‐center four‐electron bond. The origin of the difference in the stability of the penta‐coordinated D_3h structures was clearly shown to be the effect of electron delocalization–polarization term. © 2018 Wiley Periodicals, Inc.     

Crystallographic report: The crystal structure of 2‐benzo[b]thienylgermatrane

The germanium atom is penta‐coordinated and adopts trigonal bipyramidal geometry. The 2‐benzo[b]thienyl group and the nitrogen atom each occupy an apical position with the transannular N → Ge bond distance being 2.180(4) Å. Copyright © 2003 John Wiley & Sons, Ltd.     

Crystallographic report: 1‐[4‐(2‐Thienyl)phenyl]germatrane

In the title compound, germanium is penta‐coordinated and adopts a trigonal bipyramidal geometry. The (2‐thienyl)phenyl group and the nitrogen atom each occupy an apical position with a transannular N→Ge bond distances of 2.247(4) and 2.219(4) Å for the two independent molecules. Copyright © 2005 John Wiley & Sons, Ltd.     

Syntheses,characterizations and crystal structures of new triorganotin complexes with 2‐mercaptopyrimidine and 4‐amino‐2‐mercaptopyrimidine

Four triorganotin(IV) complexes with 2‐mercaptopyrimidine (HSpym) and 4‐amino‐2‐mercaptopyrimidine (HSapym) of the type, R₃SnL (L= Spym, R=Ph, 1; R=PhCH₂, 2; L=Sapym, R=Ph, 3; R=PhCH₂, 4), were synthesized. All the complexes 1–4 have been characterized by elemental, IR, ¹H NMR, and X‐ray crystallography diffraction analyses, which revealed that the structures of 1–4 are penta‐coordinated with R₃Sn‐coordinated to the thiol S and heterocyclic N atoms, and the structural distortion for each is a displacement from tetragonal toward trigonal bipyramidal geometry. The complex 1 is a one‐dimensional chain complex, while compounds 3 and 4 are dimers due to the existence of N···H hydrogen bonding. © 2005 Wiley Periodicals, Inc. Heteroatom Chem 16:69–75, 2005; Published online in Wiley InterScience (www.interscience.wiley.com). DOI 10.1002/hc.20068     

Verallgemeinerung der Aminopentadienal‐Umlagerung

Generalization of the Aminopentadienal Rearrangement Contrary to the rearrangement of 3‐amino‐3‐X‐prop‐2‐enals 2 (R=H), which easily give 3‐X‐prop‐2‐enamides 3 at low temperature, the postulated rearrangement (Scheme 1) of the vinylogous 5‐amino‐5‐X‐penta‐2,4‐dienals 6 (R=H) normally stops at the level of 2‐aminopyrylium salts 7 . The main reason is that the charge in salts of type 7 is highly delocalized, leading to low‐energy species, which make addition of weak nucleophiles difficult. In this paper, two concepts for increasing the chances of the `aminopentadienal rearrangement' 6 →→ 8 are presented and substantiated by typical experiments. On one side, the easily available 2‐aminopyrylium chlorides 7 (X=Cl) are reacted with a twofold excess of secondary amines (Scheme 2) to give 5‐(dialkylamino)penta‐2,4‐dienamides of type 9 and 10 . On the other hand, after replacing the amino groups of 6 by PhO and EtO groups, the corresponding 5‐chloro‐5‐phenoxy‐ ( 13b ) and 5‐chloro‐5‐ethoxypenta‐2,4‐dienals ( 13a ) easily rearrange at low temperature to give 5‐chloropenta‐2,4‐diene‐1‐carboxylates 18a and 18b , respectively, which are now obviously lower in energy than the corresponding pyrylium‐salt intermediates 16 (Scheme 4).     

Penta-coordinated phosphorus structure analysis on kinases

Phosphorus element was discovered in organismin the 17th century. In the past decades, it has beenfound that phosphorus plays crucial roles in many as-pects of bio-systems. For example, many biologicalprocesses are regulated by the phosphorylation anddephosphorylation of amino acid residues in proteins[1].However, there are still some unsolved problems[2],such as whether the process goes through a penta-co-ordinated phosphorus or a metaphosphate dianionicintermediate. The X-ray crystals struc…     

Organotin(IV) carboxylates of cyclopropane carboxylic acid and 3‐cyclohexylpropanoic acid: synthesis,characterization and biological activity. The crystal structure of bis(cyclopropanecarboxylato) tetramethyldistannoxane

A series of tri‐ and di‐organotin(IV) derivatives of the types R₃SnL, R₂SnL₂ and [(R₂SnL)₂O]₂ have been synthesized by the reaction of tri‐ and di‐organotin(IV) chloride(s) with sodium cyclopropane carboxylate and sodium 3‐cyclohexylpropanoate. Based on spectroscopic evidence (IR and NMR), all the triorganotin carboxylates were found to be penta‐coordinated in the solid state (except the tricyclohexyltin derivative, which was found to be four‐coordinated) and four‐coordinated in the solution state. Attempted reaction of Me₂SnCl₂ with sodium cyclopropane carboxylate in 1:2 stoichiometry afforded a bis(dicarboxylato tetraorganodistannoxane) complex, {[Me₂Sn(cyclo‐CH₂)₂CHCOO]₂O}₂. The X‐ray diffraction of this ‘dimethyltin(IV) complex’ shows that the compound possesses a tetranuclear aggregate with one bridging bidentate and other free organic ester type monodentate carboxylate groups in which each Sn atom has a five‐coordinated geometry. These complexes were also screened for their antifungal activities. Copyright © 2008 John Wiley & Sons, Ltd.     

Density functional theory calculation of cyclic carboxylic phosphorus mixed anhydrides as possible intermediates in biochemical reactions: Implications for the Pro‐Tide approach

Cyclic acyl phosphoramidates (CAPAs) are important components in several fundamental biological reactions such as protein synthesis and phosphorylation. These structures are particularly interesting in the nucleotide pro‐drug approach, Pro‐Tide, since they are putative intermediates in one of the hydrolysis steps required for activation. The central role played by the amino acid carboxylate function suggests first the formation of a cyclic mixed phosphorus anhydride, rapidly followed by water attack. To investigate such speculations, we performed quantum mechanical calculations using the B3LYP/6‐311+G** level of theory for the plausible mechanisms of action considered. In the five‐membered ring case, transition state theory demonstrated how the overall, gas‐phase, mechanism of action could be split into two in‐line addition–elimination (A–E) steps separated by a penta‐coordinate phosphorane intermediate. The difference between five‐membered and six‐membered ring first A–E was also explored, revealing a single step, unimolecular reaction for the six‐membered ring A–E profile. Implicit solvent contribution further confirmed the importance of CAPAs as reactive intermediates in such kind of reactions. Lastly, the second A–E pathway was analyzed to understand the complete pathway of the reaction. This analysis is the first attempt to clarify the putative mechanism of action involved in the activation of Pro‐Tides and casts light also on the possible mechanism of action involved in primordial protein syntheses, strengthening the hypothesis of a common cyclic mixed phosphorus anhydride species as a common intermediate. © 2012 Wiley Periodicals, Inc.     

Synthesis of bis‐ and tris‐organophosphorus substituted amines and amino acids with PCH2N Fragments

The aminomethylation of the derivatives of trivalent organophosphorus acids, containing PH and POSiMe₃ fragments with various bis‐ and tris(alkoxymethyl)amines and bis(alkoxymethyl)amino acids, is proposed as a convenient method for the synthesis of new bis‐ and trisphosphorylated amines and amino acids as well as their derivatives with four and five coordinated phosphorus. Also the three‐components systems of phosphorous acid, paraformaldehyde, and amines are thoroughly investigated via the treatment of reaction mixtures with bis(trimethylsilyl)amine. © 2010 Wiley Periodicals, Inc. Heteroatom Chem 21:430–440, 2010; View this article online at wileyonlinelibrary.com . DOI 10.1002/hc.20616     

Structural and Spectral Studies on the Ni(II) Complexes of 1,5‐Diazacyclooctane (DACO) Bearing Heterocyclic Pendants: Formation of a Two‐dimensional Network via Hydrogen Bonds and π‐π Stacking Interactions

A penta‐coordinated Ni(II) complex with a 1,5‐diazacyclooctane (DACO) ligand functionalized by two imidazole donor pendants, [NiL¹Cl] (ClO₄) H₂O (1) (where L¹ = 1,5‐bis (imidazol‐4‐ylmethyl)‐l,5‐diazacyclooctane) has been synthesized and characterized by X‐ray diffraction, infrared spectra, elemental analyses, conductance, thermal analyses and UV‐Vis techniques. Complex 1 crystallizes in triclinic crystal system, P‐l space group with a = 0.74782(7), b = 1.15082 (10), c = 1.23781(11) nm, α = 82.090(2), β = 73.011(2), γ = 83.462(2)°, V = 1.00603(16) nm³, M, = 486.00, Z = 2, D_c = 1.604 g/cm³, final R = 0.0435, and wR = 0.1244. The structures of 1 and its related complexes show that in all the three mononuclear complexes, each Ni(II) center is penta‐coordinated with a near regular square pyramid (RSP) to distorted square‐pyramidal (DSP) coordination environment due to the boat/chair configuration of DACO ring in these complexes, and the degree of distortion increases with the augment of the size of the heterocyclic pendants. In addition, the most striking feature of complex 1 resides in the formation of a two‐dimensional network structure through hydrogen bonds and stabilized by π‐π stacking. The solution behaviors of the Ni(II) complexes are also discussed in detail.     

Ring‐opening polymerization of rac‐lactide catalyzed by Al(III) and Zn(II) complexes incorporating Schiff base ligands derived from pyrrole‐2‐carboxaldehyde

A series of Al(III) chloride [LAl‐Cl]; Al(III) alkoxide [LAl‐OR]₂; and Zn(II) [LZn]₂ complexes with Schiff base ligands were obtained. ¹H NMR and X‐ray diffraction studies indicate that [LAl‐Cl] complexes have C_s symmetry and the Al center is penta‐coordinated. The Al(III) alkoxide complex [L⁵Al‐OⁱPr]₂ is a dimer bridged by OⁱPr^? with the Al center in a distorted octahedral environment. Zn complexes [LZn]₂ are double helix dimers with tetra‐coordinated Zn centers. The catalytic activity for the ring‐opening polymerization of rac‐lactide was evaluated. The best activity in this series is shown by the aluminium chloride complex with a flexible three‐carbon bridge; more flexible four‐carbon bridges lower the activity.     

Derivatives of Coenzyme F430 with a Covalently Attached α‐Axial Ligand. Part I

X‐Ray structures of the enzyme methyl‐coenzyme M reductase show that the Ni‐center in the prosthetic group coenzyme F430 is penta‐ or hexacoordinated with the carboxamide group of a glutamine residue occupying the axial coordination site on the α‐side of the macrocycle. To obtain diastereoselectively coordinated complexes for mechanistic and spectroscopic studies of the free coenzyme in solution, we aimed to prepare partial‐synthetic derivatives of coenzyme F430 that have a coordinating group attached via a linker to one of the propanoic acid side chains. By using molecular‐mechanics calculations and two different conformational search methods, a set of 50 structures containing imidazole or pyridine units as potential ligands were computationally tested according to geometric criteria defining coordinating conformations. The best candidates proved to be proline‐containing tri‐ and tetrapeptides with a methyl‐histidine as the C‐terminal residue. These linkers were synthesized, and their conformation was determined by NMR. Refinement of the molecular modeling by using the experimentally determined geometric restraints allowed us to decide that the tripeptide Pro‐Pro‐His(π‐Me)‐OMe ( 10 ) was the most promising of all tested structures for attachment to the side chain at C(3) or C(13) of F430.     

Effect of water on zinc (II), cadmium (II) complexes with pyridylimidazole: Theoretical study of stability and electronic spectrum

The geometry structures of complexes such as [Zn(PIm)₂(H₂O)] and [Cd(PIm)₂(H₂O)₂] [PIm = (2‐(2′‐pyridyl) imidazole)] are optimized by density functional theory (DFT) B3LYP methods. On the basis of their stable structures, the stability of the coordinated water existing in the complexes is analyzed quantitatively in terms of the interaction between the central metal and the coordinated water. The interaction energy of the Zn pyridylimidazole complex increased obviously by considering the intermolecular hydrogen bond (O? H…N). The theoretical calculation well explained penta‐ and hexa‐coordinated conformation, respectively, in Zn and Cd pyridylimidazole complexes. The spectral properties of the Zn Cd complexes have been studied by time‐dependent density functional theory (TD‐DFT). The calculation results show that the coordinated waters in Cd complexes have little effect on their spectral properties. While the axially coordinated waters in Zn pyridylimidazole cause a red shift in the absorption wavelength and change the pattern of charge transfer as a result of the effect of polarization from intermolecular hydrogen bond. © 2005 Wiley Periodicals, Inc. Int J Quantum Chem, 2006     

Two Aluminophosphate Molecular Sieves Built from Pairs of Enantiomeric Structural Building Units

Herein we report the synthesis and structures of two new small‐pore aluminophosphate molecular sieves PST‐13 and PST‐14 with mutually connected 8‐ring channels. The structure of PST‐13, synthesized using diethylamine as an organic structure‐directing agent, contains penta‐coordinated framework Al atoms bridged by hydroxy groups and thus edge‐sharing 3‐ and 5‐rings. Upon calcination, PST‐13 undergoes a transformation to PST‐14 with loss of bridging hydroxy groups and occluded organic species. The structures of both materials consist “nonjointly” of pairs of previously undiscovered 1,5‐ and 1,6‐open double 4‐rings (d4rs) which are mirror images of each other. We also present a series of novel chemically feasible hypothetical structures built from 1‐open d4r (sti) or 1,3‐open d4r (nsc) units, as well as from these two enantiomeric structural building units.     

(CH_3C_5H_4)_3Ln·THF(Ln=Sm,Ho,Tb,Yb)与环戊二烯生成(C_5H_5)_3Ln·THF的新反应

研究了(CH_3C_5H_4)_3Ln·THF (Ln = Sm,Ho,Tb,Yb)与环戊二烯高产率生成 (C_5H_5)_3Ln·THF的新反应。反应产物经过了元素分析、质谱和X射线的表征。产 物(C_5H_5)_3Ln·THF的特征结构参数,如五元碳环的碳原子与中心金属的平均距 离,五元碳环质心与中心金属距离,配位的四氢呋喃氧原子与中心金属距离,由于 “镧系收缩现象”,随着中心原子序数的增加而减小。     

Preparation and characterization of phosphorus‐containing Mannich‐type bases as curing agents for epoxy resin

Two novel phosphorus‐containing Mannich‐type bases, [(2‐{[(diethoxy‐phosphoryl)‐phenyl‐methyl]‐amino}‐ ethylamino)‐phenyl‐methyl]‐phosphonic acid diethyl ester (PEDA) and ({2‐[2‐(2‐{[(diethoxy‐phosphoryl)‐phenyl‐methyl]– amino}‐ethylamino)‐ethylamino]‐ethylamino}‐phenyl‐methyl)‐phosphonic acid diethyl ester (PTTA) were prepared and employed as curing agents in an attempt to prepare flame retardant epoxy systems. Through a curing reaction, phosphorus was incorporated in the backbone of the epoxy polymer. The processing characteristic of these systems was studied in terms of gel time at different temperatures. Thermal and flame retardancy properties of the cured epoxy thermosets were characterized by differential scanning calorimetry (DSC), thermogravimetric analysis (TGA), and flammability test. The degradation activation energy was calculated by Kissinger's model. The results showed that the gel time of the phosphorus‐containing epoxy systems was prolonged; the glass transition temperature (T_g) was increased due to the introduction of phosphorus and the initial degradation activation energy of phosphorus‐containing epoxy systems was lower than phosphorus‐free epoxy systems. High char yield (23–27 wt%) and limiting oxygen index (LOI) values of 28–30 were observed for the phosphorus‐containing epoxy thermosets, indicating their improvement in flame retardancy. Copyright © 2008 John Wiley & Sons, Ltd.