Studies toward the total synthesis of the cytotoxic sponge alkaloid pyrinodemin A

[structure: see text]. The syntheses of the proposed structure of pyrinodemin A (1) and its cis double bond positional isomer (C15'-C16') in racemic form are described. The key reaction involved an intramolecular nitrone/double bond cycloaddition. Our results suggest that neither 1 nor its double positional isomer is the correct structure of pyrinodemin A     

Synthesis of rac-(1R,4aR,9aR)-2-methyl-1,3,4,9a-tetrahydro-2H-1,4a-propanobenzofuro[2,3-c]pyridin-6-ol. An unusual double rearrangement leading to the ortho- and para-f oxide-bridged phenylmorphan isomers

In an attempt to obtain the para-f isomer, rac-(1R,4aR,9aR)-2-methyl-1,3,4,9a-tetrahydro-2H-1,4a-propanobenzofuro[2,3-c]pyridin-6-ol, via mesylation of an intermediate 9[small alpha]-hydroxyphenylmorphan, we obtained, instead, a rearranged chloro compound with a 5-membered nitrogen ring, 7-chloro-3a-(2,5-dimethoxyphenyl)-1-methyl-octahydroindole. This indole underwent a second rearrangement to give us the desired para-f isomer. The structures of the intermediate indole and the final product were unequivocally established by X-ray crystallography. A resynthesis of the known rac-(1R,4aR,9aR)-2-methyl-1,3,4,9a-tetrahydro-2H-1,4a-propanobenzofuro[2,3-c]pyridin-8-ol, the ortho-f isomer, was achieved using the reaction conditions for the para-f isomer, as well as under Mitsunobu reaction conditions where, unusually, the oxide-bridge ring in the 5-phenylmorphan was closed to obtain the desired product. The synthesis of the para-f isomer adds an additional compound to those oxide-bridged phenylmorphans that were initially visualized and synthesized; the establishment of the structure and configuration of 8 of the theoretically possible 12 racemates has now been achieved. The X-ray crystallographic structure analysis of the para-f isomer provides essential data that will be needed to establish the configuration of a ligand necessary to interact with an opioid receptor.     

Structure and stability of B5C and C5B clusters

Geometry optimizations and vibrational frequencies of B5C and C5B clusters were calculated with the Becke-3LYP method using the 6-311+G(d) basis set and some stable configurations of B5C and C5B clusters have been found. The most stable structure of B5C is a planar six-membered ring. However, for C5B clusters, the most stable structure is linear with a boron atom in position 3. Various configurations of B5C clusters containing three-membered boron rings have predominance in energy, whereas various configurations of C5B clusters containing three-membered carbon rings are disadvantageous in energy. In B5C clusters, isomer2 can be converted into isomer1 by surmounting an energy barrier of 43.83 kJ.mol(-1). In C5B clusters, the conversions of isomer5 into isomer2 and isomer7 into isomer2 have energy barriers of 19.66 and 20.57 kJ.mol(-1), respectively.     

Cu2+‐Induced Structural Isomers: Effect of Foreign Metal Ions on the Structure and Properties of Silver Nanoclusters

Metal ions have an important impact on the precise control of the synthesis and atomic structural arrangement of noble metal nanoclusters. In this work, the effect of metal ions on the isomer generation of metal nanoclusters is revealed for the first time. Compared with the previous Ag₂₃ nanoclusters with two face‐centered cubic (fcc) unit cells twisting 27°, the Ag₂₃ isomer had a higher symmetry structure with two fcc unit cells almost overlapping. In addition, the UV/Vis absorption spectrum of the isomer showed a slight redshift of approximately 14 nm. The redshift might be because of the modulation of electronic structure, which is derived from fine‐tuned crystal structure. Based on the experimental results, we provide mechanisms to explain the Cu²⁺ effect on the structural isomer. This work reports a significant finding to tune precisely the crystal structure and understand the mechanism of shape‐controlled synthesis of metal nanoclusters.     

Controlling the isomerization dynamics of iodide acetonitrile dimer complex by optimally designed electromagnetic field: A wave packet based approach

Both symmetric and asymmetric forms of the iodide acetonitrile dimer complex are known to exist with a higher stability shown by the symmetric isomer. Dynamics of this isomerization has been investigated on reduced dimensional surface in absence/presence of external electromagnetic field using Gaussian wave packet as the starting wave function. When the symmetric isomer has been taken as the initial structure, isomerization does not takes place without the external field due to high energy barrier, whereas with the asymmetric isomer as the starting one, isomerization takes place spontaneously with an equal population of both isomers. Our target in this study has been to get a dominant population of asymmetric isomer which is not possible without the application of electromagnetic field. However, it has also been seen that a simple monochromatic field cannot achieve this goal. Only by application of optimally designed polychromatic field the dominating population of asymmetric isomer can be obtained.     

Photocrystallographic structure determination of a new geometric isomer of [Ru(NH3)4(H2O)(eta1-OSO)][MeC6H4SO3]2

The structure of a new metastable geometric isomer of [Ru(NH3)4(H2O)(SO2)][MeC6H4SO3]2 in which the SO2 group is coordinated through a single oxygen in an eta1-OSO bonding mode has been determined at 13 K; the new isomer was obtained as a 36% component of the structure within a single crystal upon irradiation using a tungsten lamp.     

Structural peculiarities of configurational isomers of 1‐styrylpyrroles according to 1Н, 13С and 15N NMR spectroscopy and density functional theory calculations: electronic and steric hindrance for planar structure

Comparative analysis of the ¹Н and ¹³С NMR data for a series of the E and Z‐1‐styrylpyrroles, E and Z‐1‐(1‐propenyl)pyrroles, 1‐vinylpyrroles and styrene suggests that the conjugation between the unsaturated fragments in the former compounds is reduced. This is the result of the mutual influence of the donor p–π and π–π conjugation having opposite directions. According to the NMR data combined with the density functional theory calculations, the Z isomer of 1‐styrylpyrrole has essentially a nonplanar structure because of the steric hindrance. However, the E isomer of 1‐styrylpyrrole is also an out‐of‐plane structure despite the absence of a sterical barrier for the planar one. Deviation of the E isomer from the planar structure seems to be caused by an electronic hindrance produced by a mutual influence of the p–π and π–π conjugation. The structure of the E isomer of the 2‐substituted 1‐styrylpyrroles is similar to that of the 2‐substituted 1‐vinylpyrroles. The steric effects in the Z isomer of the 2‐substituted 1‐styrylpyrroles result in the large increase of the dihedral angle between planes of the pyrrole ring and double bond. Copyright © 2013 John Wiley & Sons, Ltd.     

[Co(pema)(amp)Cl]2^+体系—面式异构体的结构解析及其优势构型

仅合成得到[Co(pema)(amp)Cl]2^+体系配合物的一个面式异构体(pema=N-(2- 吡啶甲基)乙二胺，amp＝2—甲氨基吡啶)．利用二维核磁共振技术与单晶X—ray衍 射法平行解析了该异构体的结构．结果显示结构中存在C—H…π相互作用．用 RHF/LANL2DZ对该体系可能的异构体进行结构、能量优化，可能形成C—H…π相互 作用的异构体具有较好的稳定性．C—H…π相互作用对含吡啶环的[CoN5Cl]^2+系 配合物的异构体的选择性形成及其稳定性具有重要作用．     

Synthetic studies toward spiroleucettadine

Synthetic hydroxydienone precursors to spiroleucettadine and to an isomer thereof resist cyclization to the orthoamide-type functionality present in the proposed structure of the natural product.     

The conversion among various B4C clusters: a density functional theoretical study

Geometry optimizations and vibration frequencies of B4C clusters were performed with Becke-3LYP method using 6-31G(d) basis set. We have found 14 stable isomers, and the most stable structure among them is the five-member ring containing two three-member boron rings. We also analyzed these stable isomers in detail, and the results show that the structures containing three-member boron rings are predominant in energy for B4C clusters. In terms of MO and NBO analysis, the three-centered bond and the pi-electron delocalization play an important role in stabilizing the planar five-member rings of these B4C clusters. Our calculations suggest that isomer4 can be converted into isomer7 with only an energy barrier of 0.31 kJ mol(-1) at the B3LYP/6-311G+(3df) level. Although the planar structures of the five-member rings (isomers12-14) can be converted with each other, the conversions of isomer14 to isomer13 and isomer13 to isomer12 have high-energy barriers of 70.99 and 68.51 kJ mol(-1) at the B3LYP/6-31G(d) level, respectively.     

Photoisomerization mechanism of 4-methylpyridine explored by electronic structure calculations and nonadiabatic dynamics simulations

In the present paper, different electronic structure methods have been used to determine stationary and intersection structures on the ground (S(0)) and (1)ππ? (S(2)) states of 4-methylpyridine, which is followed by adiabatic and nonadiabatic dynamics simulations to explore the mechanistic photoisomerization of 4-methylpyridine. Photoisomerization starts from the S(2)((1)ππ?) state and overcomes a small barrier, leading to formation of the prefulvene isomer in the S(0) state via a S(2)∕S(0) conical intersection. The ultrafast S(2) → S(0) nonradiative decay and low quantum yield for the photoisomerization reaction were well reproduced by the combined electronic structure calculation and dynamics simulation. The prefulvene isomer was assigned as a long-lived intermediate and suggested to isomerize to 4-methylpyridine directly in the previous study, which is not supported by the present calculation. The nonadiabatic dynamics simulation and electronic structure calculation reveal that the prefulvene isomer is a short-lived intermediate and isomerizes to benzvalene form very easily. The benzvalene form was predicted as the stable isomer in the present study and is probably the long-lived intermediate observed experimentally. A consecutive light and thermal isomerization cycle via Dewar isomer was determined and this cycle mechanism is different from that reported in the previous study. It should be pointed out that formation of Dewar isomer from the S(2)((1)ππ?) state is not in competition with the isomerization to the prefulvene form. The Dewar structure observed experimentally may originate from other excited states.     

Isolation and structural analysis of novel conformational isomers of the m-xylylene-bridged calix[6]arenes: the ‘partial cone’ and ‘inverted cone’ isomers

In the benzylation of a m-xylylene-bridged calix[6]arene tetrol, the first example of the ‘partial cone’ isomer of a calix[6]arene was obtained in addition to the corresponding cone and 1,2,3-alternate isomers, and its structure was established by X-ray crystallographic analysis. The synthesis and crystal structure of the ‘inverted cone’ isomer as well as its thermal conversion to the ‘normal cone’ isomer are also described.     

Structure and Electronic Properties of Fullerenes C52q+: Is C522+ an Exception to the Pentagon Adjacency Penalty Rule?

The structure, vibrational spectra and electronic properties of the neutral, singly and doubly charged C52 fullerenes were studied by means of the Hartree-Fock method and density functional theory. Different isomers were considered, in particular those with the lowest possible number (five or six) of adjacent pentagons, and an isomer with a four-atom ring. For neutral and singly charged species, the most stable isomer is that with the lowest number of adjacent pentagons, namely five. However, for C(52)2+, the most stable structure has six adjacent pentagons. This finding, which contradicts the pentagon adjacency penalty rule, is a consequence of complete filling of the HOMO pi shell and the near-perfect sphericity of the most stable isomer. The simulated vibrational spectra show important differences in the positions and intensities of the vibrations for the different isomers.     

Total synthesis of the originally proposed and revised structures of scleritodermin A

The first total synthesis of the originally proposed and revised structure of scleritodermin A, along with an isomer, were achieved by the use of an alpha-azido carboxyl group serving as the key alpha-ketoamide precursor, thus leading to a revision of the structure originally proposed for natural scleritodermin A.     

Stereochemistry in cationic polymerization of alkenyl ethers. III. Effect of the alkoxy group on the steric structure of polymers

Propagation mechanism in the cationic polymerization of alkenyl ethers was investigated through the effect of the bulkiness of alkoxy groups on the steric structure of a polymer. In polymerization with BF₃O(C₂H₅)₂ in toluene at ?78°C, trans-propenyl ethers having less bulky alkoxy groups–methyl, ethyl, and benzyl propenyl ethers–produced a stereoregular polymer having a threo-meso structure, and the cis isomer a nonstereoregular one having threo-meso and racemic structures. On the other hand, in the polymerization of propenyl ethers having bulky alkoxy groups–isopropyl and 1-methylpropyl propenyl ethers–the trans isomer yielded a nonstereoregular polymer with threo-meso and racemic structures, and the cis isomer a stereoregular one with a erythro-meso structure. This result suggests that a bulky alkoxy group plays an important role in determining the steric structure of the polymer by repulsion between the alkoxy groups of a growing chain end and of a monomer. The effect of solvent polarity on the steric structure of a polymer was also studied.     

A disilapentalene and a stable diradical from the reaction of a dilithiosilole with a dichlorocyclopropene

The reaction of 1,1-dilithio-2,3,4,5-tetraphenylsilole (1) with 1,1-dichloro-2,3-diphenylcyclopropene (2) leads to the novel 1,4-disila-1,4-dihydropentalene (4), as well as an exceptionally stable diradical for which the structure 3 is suggested. The diradical is unreactive toward water, methanol, and chloroform; upon heating it transforms into 4. Structure 3 for the paramagnetic species is proposed on the basis of EPR data and theoretical calculations. The trans-trans isomer of diradical 3 was calculated to be more stable than its cis-cis isomer. The strong and stable EPR signal in the reaction mixture is probably due to the trans-trans isomer of diradical 3 in the triplet state. A reaction scheme describing the formation of 3 and 4 is presented.     

NMR study of model compounds of vinyl polymers

Complicated NMR spectra of vinyl polymers provide conformational and configurational knowledge of the polymers in solution. Explicit expressions for the spectral frequencies and intensities are obtained by the analysis of vinyl polymers and their model compounds as weakly coupled systems. The classified spectra expected for common vinyl polymers are presented by using the results of the analysis. The analysis is applied to model compounds of poly(vinyl alcohol) and poly(vinyl acetate) in solution. The results show that conformations of poly(vinyl alcohol) are determined by the intramolecular hydrogen bonding so that the syndiotactic isomer forms a helical structure, the isotactic one a planar zigzag structure. The poly(vinyl acetate) produces a helical structure for isotactic isomer by the repulsion of side chains and a planar zigzag for the syndiotactic isomer.     

Formation and relaxation dynamics of iso-CH2Cl-I in cryogenic matrices

Photolysis of chloroiodomethane (CH(2)ClI) in cryogenic matrices followed by recombination of the nascent radical pair produces an isomer (CH(2)Cl-I) that features a halogen-halogen (Cl-I) bond. Using ultrafast laser pulses, it is possible to follow the formation of this isomer by transient electronic absorption in low-temperature matrices of N(2), CH(4), and Ar. Frequency-domain measurements provide vibrational and electronic spectra, and electronic structure calculations give the structures of the isomers and the minimum energy path that connects them. The ultrafast experiments cleave the C-I bond with a 267-nm photolysis pulse and probe the formation of the isomer at wavelengths between 435 nm and 510 nm. The longest wavelengths preferentially interrogate vibrationally excited molecules, and their transient absorption shows that the highly vibrationally excited isomer appears within 1 to 2 ps, depending on the matrix, likely reflecting the loss of 2000 cm(-1) or more of energy in a strong, inelastic collision of the fragments with the matrix. The subsequent relaxation of the vibrationally excited isomer occurs in 20 to 40 ps, a time that is comparable to those observed for halomethane molecules and their isomers in liquids and in supercritical CO(2). These observations suggest that the formation and initial relaxation of the isomer in dense media do not depend strongly on the identity of the surroundings.     

Effect of isomerization of amino acid residues on the structure of aquaporin

The effect of isomerization of amino acid residues on the structure and water permeability of aquaporin has been investigated. It was established that the equilibrium configuration of the model D isomer is energetically less favorable than that of its natural L isomer. It is shown that the model D isomer of aquaporin is waterproof.