1, 2-, 1, 3- and 1, 4-Cyclohexanedicarboxylates of Cd and Mn with chain and layered structures

A systematic study has been carried out on the three isomeric cyclohexanedicarboxylates (CHDCs) formed by cadmium and manganese with the three isomeric dicarboxylic acids, in the presence or absence of amines. The CHDCs have been prepared under hydrothermal conditions and their structures established by X-ray crystallography. We have been able to isolate two-dimensional layered structures of 1,2-, 1,3- and 1,4-cyclohexanedicarboxylates and chain structures of 1,3- and 1,4-cyclohexanedicarboxylates. The infinite metal-oxygen-metal linkages are observed only in the case of the 1,2-dicarboxylate. In all the three isomeric cyclohexanedicarboxylates, the e,e conformation is most favored, although the 1,4-CHDCs often contain rings in both the e,e and the a,e conformations.     

Global energy minimization by rotational energy embedding

Given a sufficiently good empirical potential function for the internal energy of molecules, prediction of the preferred conformations is nearly impossible for large molecules because of the enormous number of local energy minima. Energy embedding has been a promising method for locating extremely good local minima, if not always the global minimum. The algorithm starts by locating a very good local minimum when the molecule is in a high-dimensional Euclidean space, and then it gradually projects down to three dimensions while allowing the molecule to relax its energy throughout the process. Now we present a variation on the method, called rotational energy embedding, where the descent into three dimensions is carried out by a sequence of internal rotations that are the multidimensional generalization of varying torsion angles in three dimensions. The new method avoids certain kinds of difficulties experienced by ordinary energy embedding and enables us to locate conformations very near the native for avian pancreatic polypeptide and apamin, given only their amino acid sequences and a suitable potential function.     

从头计算研究乙酰胆碱构象和分子静电势

在Hartree－Fock和二级Moller－Plesset微扰理论MP2水平，用6－31G对乙酰胆碱进行了从头计算研究，发现了旁式和反式两种稳定构象．经零点振动能校正后，在Hartree－Fock级别旁式较反式稳定0．24kJ·mol~(-1)；而在MP2级别，反式较旁式稳定2．07kJ·mol~(-1).谐振动频率在HF／6－31G水平计算.还给出了两种构象的MP2分子静电势图.     

Conformational energy surface of 1,2-cyclooctadiene

Boyd's iterative force-field has been used to investigate the conformational energy surface of 1,2-cyclooctadiene. Two energy-minimum conformations with similar strain energies have been found; one has a two-fold axis of symmetry, whereas the other lacks symmetry. The calculated strain-energy barrier for interconversion of the two conformations is 8.8 kcal mol^?1.     

Isomer effects on vibrational energy relaxation in perylene-argon complexes

Fluorescence spectroscopic measurements have been carried out on jet-cooled complexes of perylene with a number of guest species ranging from argon to small hydrocarbons. In the case of argon, a sequence of red-shifted absorption bands is assigned to a group of aggregates involving up to five guest atoms. Calculations using empirical atom-atom pair potentials have allowed unambiguous assignment of eight different perylene-argon complexes. Spectrally dispersed fluorescence measurements have studied the effect of internal energy on the IVR and predissociation processes. In particular, the two perylene diargon isomers are shown to exhibit different rates for IVR.It has been shown that arson forms a series of organised, readily identifiable complexes with perylene in a supersonic jet. On excitation of the different isomeric forms of the 2:1 complex, different rates for vibrational energy redistribution have been found. The greatest difference was observed at low vibrational energies of the parent, which confirmed that low-frequency van der Waals modes were responsible. Although more detailed calculations will appear elsewhere, the most obvious difference between the two isomeric forms is the exchange of two low-frequency x-y plane vibrations (≈5 cm^?1) for a hindered rotation and a substantially higher-frequency (15–30 cm^?1) argon-argon stretching mode. Photodissociation is also readily observed, confirming the computed values for the argon-perylene binding energies. Finally, strong resonance fluorescence is observed, accompanied by (relaxed) emission from the singly dissociated species when either the 1:1 or either 2:1 isomer is excited with a (parent) vibrational energy of 705 cm^?1. Thus, in spite of the presence of the dissociative pathway, all observable emission from the undissociated species appears to originate from a state in the “small molecule” limit, which survives for about 4 ns.     

Structural and energy properties study using the AM1 calculations of aza-azulenes in their ground state

AM1 calculations with complete optimization have been carried out on the azulene molecule and its derivatives such as 1-aza-azulene and 1,3-diaza-azulene. We show that AM1 is an appropriate method for predicting the structure and energy properties of azulene. Experimental values are found with good accuracy and computer results are analogous to those obtained by sophisticated methods such as the ab initio method (6-31G^*). We describe a complete theoretical study of the structural and energy properties of 1-aza-azulene and 1,3-diaza-azulene in their ground states using the same method with full geometry optimization. From the theoretical finding, the most stable conformations are proposed. Otherwise, these geometrical conformations are preserved in order to determine some spectroscopic values of these compounds using the CNDO/M method. Our results are in qualitative agreement with the experimental data.     

Ab initio molecular orbital study of dialuminum-ethylene complexes

The geometries of the various isomeric dialuminum-ethylene complexes Al₂C₂H₄ have been optimized using the STO-3G, 3-21G^(*) and 6-31G^(**) basis sets. Vibrational frequency calculations show that only two out of the six structures examined are thermodynamically stable. Unlike the case of Li₂C₂H₄, 1,2-dialuminoethane is most stable and more ethane-like than 1,2-dilithioethane perhaps due to the larger covalent character of the C---Al bond. Besides, 1,2-dialuminoethane has been found, in contrast to ethane and 1,2-dilithioethane, to have no stable gauche conformer.     

Systematic drug receptor mapping: A new approach to the analysis of conformational energy calculations of flexible molecules with application to dopaminergic and adrenergic agonists

The computer program PRODIS is used to find low energy conformations of flexible molecules by searching the potential energy surface(s) of one or more torsion angles via rigid rotation. The n-dimensional grid of energy versus torsion angles is then converted to a Boltzman probability distribution, with the probability being represented not as a function of torsion angle, but rather a distance between two atoms. These atoms are chosen by comparison with a known, active analogue in which certain atoms have previously been determined as requirements for drug activity. PRODIS produces a list of low energy conformations, their corresponding interatomic distances and the Boltzman probability for each distance ±0.125, as well as the total probability for each conformation. The user also specifies a target interatomic distance and range (usually derived from a more rigid analogue) for which PRODIS lists all conformations and their Boltzman probability that meet this distance.     

The role of internal H-bonding in the conformational preferences of some molecules of the formula CH3CHYCH2X

The conformational energies of 1-amino-2-propanol, 2-amino-1-propanol and 1,2-diaminopropane are studied using ab initio molecular orbital theory employing minimal (STO-3G) and extended (4-31G) basis sets. Calculations at both levels of theory generally favor conformations stabilized by internal H-bonding for all molecules considered. Results are first presented for conformations employing assumed geometries. Since the conformational energy differences as found by the initial set of calculations are in some cases rather small it then becomes necessary to introduce geometry optimizations into the study at the minimal STO-3G level. In addition, to get a better estimate of the energy differences of the various conformations 4-31G calculations are performed on the STO-3G optimized structures. These latter results indicate the following, (a) For 1-amino-2-propanol only one conformation that is stabilized by intramolecular H-bonding is low in energy; this has the methyl and amino groups anti. The other H-bonded conformer, where the methyl and amino groups are gauche, is predicted to be ca. 1.2 kcal mol^?1 less stable. Similar findings for this molecule have recently been provided by micro-wave spectroscopy. (b) For 2-amino-1-propanol the two H-bonded conformers are only separated by about 0.5 kcal mol^?1, with the anti conformer being more stable. Micro-wave spectroscopy again supports these calculations. (c) For 1,2-diaminopropane the gauche conformer is predicted to be of rather high energy (ca. 2.5 kcal mol^?1) compared to the corresponding anti H-bonded conformer. The value of 2.5 kcal mol^?1should be taken as an upper limit, since the geometry optimization of the gauche conformer of 1,2-diaminopropane is incomplete compared to the optimization carried out for the anti conformer.     

Conformational analysis and electronic structure calculations of S-1,2-bis(2-dibutenoyl)glycerol and S-1,2-bis(2,4-hexadienoyl)glycerol,two analogues of 1,2-bis(2,4-octadecadienoyl)-sn-glycero-3-phosphorylcholine

As a model for 1,2-bis(2,4-octadecadienoyl)-sn-glycero-3-phosphorylcholine, a doubly unsaturated membrane-forming lipid molecule, force-field (MMP2) calculations were performed on S-1,2-bis(2-dibutenoyl)glycerol, and CNDO/S-calculations 2

1 CNDO: Complete neglect of differential overlap, a semi-empirical quantum-mechanical method.

on the derived minimum-energy conformations of S-1,2-bis(2,4-hexadienoyl)glycerol. The energy hypersurface especially with respect to the dihedral angles along the C(1)-C(2) and the two C O ester bonds was explored and the rotational strength as a function of these angles was calculated. The two gauche-forms were found to be most stable, with a slight preference for the g⁻-form. The experimental circular dichroism data obtained for 1,2-bis(2,4-hexadienoyl)-sn-glycero-3-phosphorylcholine, the corresponding phosphorylcholine, indicate a dynamic equilibrium between two forms of opposite chirality possibly involving the g⁺-and the g⁻-forms.     

Electronic spectrum of a photochromic diarylethene derivative in a supersonic free jet. Internal conversion from S2(1B) to S1(2A)

The fluorescence excitation and dispersed fluorescence spectra of the open-ring isomer of 1,2-bis(3-methyl-2-thienyl)perfluorocyclopentene have been measured in a supersonic free jet. No vibronic structure has been observed in the excitation spectrum. The intensity of fluorescence gradually increases with the excitation energy in the 25,500–28,700 cm⁻¹ region, indicating that the geometry of the molecule substantially changes upon photoexcitation. The dispersed fluorescence spectrum is anomaly Stokes-shifted with respect to the excitation energy, suggesting that the S₂(1B) state is initially excited followed by rapid internal conversion from the S₂(1B) to S₁(2A) state. The fluorescence is due to the S₁(2A)–S₀(1A) transition. Density functional theory calculations at the B3LYP/6-31G^** level have been carried out to investigate stable conformations responsible for the observed spectra.     

The study of atropoisomers of meso-tetrakis[2.2]paracyclophanylporphyrin

Theoretical considerations of atropoisomers of the title compound have revealed the existence of a large number of stable isomeric species. Syntheses, carried out according to two procedures at widely separated temperatures, resulted in the formation of mixtures of atropoisomers in good yield. Two isomeric fractions have been separated and characterized. Some analytical methods have been worked out and have proved useful in separational techniques.     

高分子链空间构象分布的复杂性——Θ条件下能量与尺寸的分布

通过高分子链的模型的计算来研究高分子链构象的尺寸与能量的分布．结果表明，高分子的链构象在小尺寸范围布居数增多；高分子的链构象在小尺寸范围存在比较稳定的链构象状态；在小尺寸范围比较稳定的链构象多具有类似棒状等非球形结构；高分子的链构象的尺寸与能量的分布显示熵弹性具有不对称性．     

A general treatment of the configuration statistics of polysaccharides.

A treatment of the configurational statistics of polysaccharides is given in the isomeric state approximation. All classes of linear polysaccharides of specifiec chemical sequence are treated simultaneously. Chain tortuosity arising from torsional motions about the chemical bonds of the glycosidic linkages is recognized explicitly as is the possibility for conformational isomerism of the sugar residues. Valence angles and lengths are taken to be fixed at the equilibrium values, and pyranose residues in their chair conformations are treated as inflexible constituents of the skeletal structure. Pyranose and furanose forms capable of pseudorotation may be incorporated as rigid skeletal entities as well, provided suitable attention is given to the selection and interpretation of the conformational isomeric states included. Separation of the configuration energy into independent contributions is shown to be impossible in general. Methods are described for assessing the influence of neighbor interactions on the populations of the several conformers of the sugar residues. The relative conformational free energy of the flexible and chair form conformers of pyranose sugars is discussed, and appropriate measures of polysaccharide chain flexibility and stiffness are suggested.     

DABCO-directed self-assembly of bisporphyrins (DABCO=1,4-diazabicyclo[2.2.2]octane)

Three isomeric zinc bisporphyrins have been prepared by covalently linking together two aminoporphyrins with an isophthalic acid derivative. The porphyrins differ in the substitution pattern on the meso phenyl groups, that is, ortho, meta, or para. Titrations carried out by UV-visible and 1H NMR spectroscopy have been used to map out the stabilities and the stoichiometries of the complexes formed with 1,4-diazabicyclo[2.2.2]octane (DABCO) in chloroform. The ortho- and meta-substituted bisporphyrins form 1:1 intramolecular sandwich complexes. The para-substituted bisporphyrin cannot adopt the cofacial conformation required for this type of complex and forms a higher order 2:2 intermolecular assembly, which is stable over a wide range of DABCO concentrations.     

Molecular fragmentations: Part V. Structures and energies of mass spectral fragments derived from ethyl acetate

Calculations have been made using MINDO/3 of the structures and energies of four conformations of ethyl acetate, of four isomeric forms of its molecular ion, and of all the fragment and rearrangement ions in the mass spectrum together with those of the corresponding neutral fragments.     

Monte Carlo simulations on short single-stranded oligonucleotides. I. Application to RNA trimers

Monte Carlo (MC) structural simulation of short RNA sequences has been carried out by random variations of the nucleotide conformational angles (i.e., phosphodiester chain torsional angles and sugar pucker pseudorotational angles). All of the chemical bond lengths and valence angles remained fixed during the structural simulation, except those of the sugar pucker ring. In this article we present the simulated structures of RNA trimers—r(AAA) and r(AAG)—obtained at 11°C and 70°C. The influence of various initial conformations (selected as starting points in the MC simulations) on the equilibrium conformations has been discussed. The simulated conformational angles have been compared with those estimated by nuclear magnetic resonance (NMR) spectroscopy. For both of the oligonucleotides studied here, the most stable structures are helical conformations with stacked bases, at 11°C and 70°C. However, when the starting point is a stretched chain, it is found that r(AAA) adopts a reverse-stacked structure at low temperature (11°C), in which the A3 base is located between the A1 and A2 bases. Although the energies of these conformations (helical and reverse stacked) are very close to each other, the potential barrier between them is extremely high (close to 30 kcal/mol). This hinders the conformational transition from one structure to the other at a given temperature (and in the course of a same MC simulation). However, it is possible to simulate this structural transition by heating the reverse-stacked structure up to 500°C and cooling down progressively to 70°C and 11°C: Canonical helical structures have been obtained by this procedure. © 1994 by john Wiley & Sons, Inc.     

方酸构象和振动光谱的从头算研究

在6-31G^*^*水平上对方酸(3, 4-二羟基-3-环丁烯-1, 2-二酮)三种构象异构体进行了SCF计算。结果表明ZZ型异构体最稳定, ZE型次之。用等键反应能量分析方酸的稳定性, 并与苯作比较, 讨论方酸的芳香性。在6-31G水平上计算了方酸三种构象的振动频率。     

Hollow cages versus space-filling structures for medium-sized gold clusters: the spherical aromaticity of the Au50 cage

Candidates for the lowest energy structures of medium-sized Au(n), n = 32, 38, 44, 50, and 56, clusters were evaluated using gradient-corrected DFT computations. Both hollow cage and space-filling conformations were considered. The cages were constructed using fullerene-based templates. The space-filling structures were generated by employing a genetic algorithm. We have found that the space-filling isomers were lower in energy except for two notable cases. Like Au(32) [Johansson, M. P.; Sundholm, D.; Vaara, J. Angew. Chem. Int. Ed. 2004, 43, 2678], a hollow cage configuration of Au(50) is more stable than its alternative space-filling isomeric forms. The unusual stabilities of the cage Au(32) and Au(50) can be attributed to spherical aromaticity; both exhibit large negative nucleus-independent chemical shifts and exceptionally large HOMO-LUMO gaps.