Discrimination of isomers by liquid ionization mass spectrometry with techniques of collisional activation and adduct ion formation

Liquid ionization mass spectrometry is a soft ionization technique used with liquid samples under atmospheric pressure. It facilitates the handling of reagents and the observation of ion–molecule reactions in the ion source. The differentiation of isomers by characteristic fragment ions, for example those resulting from asymmetrical cleavage of a cyclobutane ring, and by molecular adduct ion formation was studied. The samples studied were cyclobutane derivatives, alkyl 4-(3-oxo-3-pIienyl-l-aIkenyl)benzoate dimers, and reagents having two functional groups were used to produce adduct ions to clarify the difference between isomers. The reagents act on a sample molecule at two functional groups to form hydrogen bonds. Some correlations were observed between the structure of the sample and the relative abundances of molecular adduct ions and also fragment ions produced by collisionally activated dissociation.     

Prediction of retention indexes. IV. Chain branching in alkylbenzene isomers with C10-13 alkyl chains identified in a scintillator solvent.

Twenty solvent components in a commercial scintillator were identified by chromatography on polar and non-polar columns and by gas chromatography-mass spectrometry (GC-MS) as isomeric 1-(alkyl)m(alkyl)nbenzenes with formulae C16H26, C17H28, C18H30 and C19H32. These isomers occur in four clusters of chromatographic peaks representing ca. 6, 44, 34 and 16% of the total solvent mass. The retention indexes of the isomers are influenced by the lengths of the alkyl chains in the molecule, and their polarity and polarizability can affect the column difference, which is the difference between retention indexes on polar and non-polar columns. 1-Methylalkylbenzenes have higher retention indexes and larger column differences than the evenly distributed isomers, such as 1-butylhexyl-1-pentylhexyl, 1-pentylheptyl- and 1-pentyloctylbenzene. The results demonstrate the effect of structural symmetry on the retention indexes of the isomers. This study shows that the ability to relate GC data and column differences to structures can facilitate the interpretation of GC-MS data in the structure identification of isomers.     

Biscavitands II: Self-Inclusion in a Back-to-Back Connected Biscavitand

A foot-to-foot or `back-to-back' connected biscavitand is prepared directly from a hexadecol resorcinarene precursor. The axial orientation of the biphenyl linker and hence the crown conformation of the hexadecol was established by an X-ray crystal study of the biscavitand. Each cavitand bowl is filled in the crystal by an alkyl `foot' from the next molecule, a self-inclusion which results in polymeric host–guest chains. The new biscavitand differs from previously prepared Z and C isomers of a bowl-to-bowl or `front-to-front' connected host, which crystallize as chains of carcerand-like, solvent-filled cages or as distinct molecules of hemicarceplex, respectively.     

Inclusion Complexes of Gossypol with 2-Pentanone, 3-Pentanone, and 2-Hexanone

Inclusion complexes of gossypol with 2-pentanone, 3-pentanone, and 2-hexanone were prepared by crystallization from the corresponding ketone and hexane, and their structures were determined by low-temperature X-ray diffraction. All three compounds crystallize in monoclinic systems and have a 2:1 gossypol-to-solvent molar ratio. Both gossypol–pentanone complexes crystallize in C2/c space groups, and the solvent cavities in these structures have C₂ symmetry. The 3-pentanone molecule, which has C₂ symmetry, sits symmetrically within the cavity, while the 2-pentanone molecule, which lacks C₂ symmetry, takes two equally probable orientations within the cavity. Both structures are similar to previously reported gossypol inclusion complexes formed with small esters and 3-hexanone. The distal positioning of the carbonyl group in 2-hexanone does not allow it to fit into the same solvent cavity that exists in the pentanone structures. In the gossypol-2-hexanone complex, the solvent cages are skewed, and the C₂ site symmetry is lost. As a result, the structure crystallizes in a Cc space group and has a larger asymmetric unit and unit cell. Although the 2-hexanone structure retains many of the features of the gossypol–pentanone complexes, this is the first report of a gossypol inclusion compound with this extended structure.     

Inclusion Complexes of Gossypol with 2-Pentanone, 3-Pentanone,and 2-Hexanone

Inclusion complexes of gossypol with 2-pentanone, 3-pentanone, and 2-hexanone were prepared by crystallization from the corresponding ketone and hexane, and their structures were determined by low-temperature X-ray diffraction. All three compounds crystallize in monoclinic systems and have a 2:1 gossypol-to-solvent molar ratio. Both gossypol–pentanone complexes crystallize in C2/c space groups, and the solvent cavities in these structures have C₂ symmetry. The 3-pentanone molecule, which has C₂ symmetry, sits symmetrically within the cavity, while the 2-pentanone molecule, which lacks C₂ symmetry, takes two equally probable orientations within the cavity. Both structures are similar to previously reported gossypol inclusion complexes formed with small esters and 3-hexanone. The distal positioning of the carbonyl group in 2-hexanone does not allow it to fit into the same solvent cavity that exists in the pentanone structures. In the gossypol-2-hexanone complex, the solvent cages are skewed, and the C₂ site symmetry is lost. As a result, the structure crystallizes in a Cc space group and has a larger asymmetric unit and unit cell. Although the 2-hexanone structure retains many of the features of the gossypol–pentanone complexes, this is the first report of a gossypol inclusion compound with this extended structure.This revised version was published online in July 2005 with a corrected issue number.     

Effect of molecular symmetry on melting temperature and solubility

Molecular symmetry has a pronounced effect on the melting properties and solubility of organic compounds. As a general rule, symmetrical molecules in crystalline form have higher melting temperatures and exhibit lower solubilities compared with molecules of similar structure but with lower symmetry. Symmetry in a molecule imparts a positive amount of residual entropy in the solid phase (i.e., more possible arrangements leading to the same structure). This means that the entropy of a crystal of symmetric molecules is greater than the entropy of crystal of a similar, but non-symmetric molecule. An analysis is presented relating the enthalpy, entropy and temperature of melting for an idealised system of structural isomers of different molecular symmetries. The analysis presented helps explain why often, yet not always, the crystal of a more symmetric molecule, which has greater entropy to start (closer to that of the liquid), also exhibits a greater gain in entropy upon melting, compared with the crystal of a less symmetrical molecule. The residual entropy due to molecular symmetry has the direct effect of reducing the entropy gain upon melting (a negative effect). However, molecular symmetry also exerts indirect effects on both the entropy and enthalpy of melting. These indirect effects, imposed by the condition of equilibrium melting, are positive, such that it is the balance between the direct and indirect effects what determines the value observed for the entropy of melting of the symmetric molecules. When the indirect effect of molecular symmetry is greater than its direct effect, the observed entropy gain upon melting of the more symmetrical molecule is greater than that of a less symmetrical one.     

Controlled Growth of Porphyrin Wires at a Solid‐Liquid Interface

Bis(zinc porphyrin) scaffolds bearing C₈ or C₁₈ alkyl chains and imidazole end groups self‐assembled in a head‐to‐tail fashion into multi‐porphyrin assemblies on both HOPG and mica. Due to weaker molecule surface‐interactions, longer arrays formed on mica than on HOPG. In both cases, it was essential first to generate monomers that were drop casted on the surface, then to allow time for the bis(zinc porphyrins) to assemble. Although thicker fibrous assemblies were observed with the C₈ alkyl substituents than with the longer chains, noncovalent assemblies up to 1 μm long were observed for each molecule. These investigations provide a reproducible, noncovalent method to grow porphyrin arrays that may be of interest in molecular electronics for charge transport.     

Crystal and molecular structure of 1-phenyl-2-nitroguanidine

The molecular structure of 1-phenyl-2-nitroguanidine is nonplanar, but contains two almost planar fragments: nitroguanyl and phenyl groups. Unlike previously studied nitroguanidines, in 1-phenyl-2-nitroguanidine, the nitro group is turned to the secondary amino group. However, the structural parameters of the nitroguanyl group are little different from those of nitroguanidine and its alkyl derivatives. In the benzene ring, the symmetry in the geometric parameters is not observed, which is explained by the intermolecular interaction with the neighboring molecule.     

Molecular symmetry effects on the stability of highly ordered smectic phases

In an effort to control the phase ranges of highly ordered smectic phases, we examined the impact of molecular symmetry on phase behaviour of a series of 12 symmetrical and unsymmetrical 4,4′-dialkanoyloxybiphenyl derivatives. Combined differential scanning calorimetry, polarised optical microscopy, and X-ray diffraction studies indicated that the compounds studied formed smectic F liquid crystals, and in some cases, G phases at lower temperatures. Although the clearing temperatures were largely unaffected by molecular symmetry, the transitions from the SmF liquid crystals to more ordered phases were consistently lowered upon reducing the molecular symmetry. As a result, unsymmetrical molecules had broader mesophases than their higher symmetry isomers, suggesting a strategy for tuning the phase behaviour of these highly ordered lamellar phases, which have been widely targeted for organic semiconductors.     

An Effective Simulation of Aqueous Micellar Aggregates by Computational Models

Summary We have computationally studied the interaction modes, localization and orientation of a benzene (Bz) molecule on the surface of micelles formed by cetyltrimethylammonium salts CTAX. Experimental ¹H-NMR data on complexation shifts induced by Bz on the polar head hydrogens and on the adjacent methylene hydrogens of CTAX have been interpreted using a computational approach that combines an automatic molecular docking procedure with a calculation module that accounts for NMR complexation shifts due to ring current diamagnetic anisotropy. Three different models were used to reduce the complexity of the micellar system. Computational results, in good agreement with available experimental data, point to a preferential localization of the Bz molecule along the CTAX alkyl tail, about 3.9 Å away from the charged nitrogen. The Bz molecular plane is predicted perpendicular to the C-H bonds of the alkyl tail. The good results obtained with the simplest model suggest that it could be used to study more complex systems involving surfactants endowed with molecular recognition or catalytic abilities.     

Engineering hydrogen-bonded molecular crystals built from derivatives of hexaphenylbenzene and related compounds

Hexakis[4-(2,4-diamino-1,3,5-triazin-6-yl)phenyl]benzene (4) incorporates a disc-shaped hexaphenylbenzene core and six peripheral diaminotriazine groups that can engage in hydrogen bonding according to established motifs. Under all conditions examined, compound 4 crystallizes as planned to give closely related noninterpenetrated three-dimensional networks built from sheets in which each molecule has six hydrogen-bonded neighbors. In the structure of compound 4, the number of hydrogen bonds per molecule and the percentage of volume accessible to guests approach the highest values so far observed in molecular networks. Analogue 5 (which has the same hexaphenylbenzene core but only four diaminotriazine groups at the 1,2,4,5-positions) and analogue 7 (in which the two unsubstituted phenyl groups of compound 5 are replaced by methyl groups) crystallize according to a closely similar pattern. Analogues with flatter pentaphenylbenzene or tetraphenylbenzene cores crystallize differently, underscoring the importance of maintaining a consistent molecular shape in attempts to engineer crystals with predetermined properties.     

Alkylation Effects on the Energy Transfer of Highly Vibrationally Excited Naphthalene

The energy transfer of highly vibrationally excited isomers of dimethylnaphthalene and 2‐ethylnaphthalene in collisions with krypton were investigated using crossed molecular beam/time‐of‐flight mass spectrometer/time‐sliced velocity map ion imaging techniques at a collision energy of approximately 300 cm^?1. Angular‐resolved energy‐transfer distribution functions were obtained directly from the images of inelastic scattering. The results show that alkyl‐substituted naphthalenes transfer more vibrational energy to translational energy than unsubstituted naphthalene. Alkylation enhances the V→T energy transfer in the range ?ΔE_d=?100～?1500 cm^?1 by approximately a factor of 2. However, the maximum values of V→T energy transfer for alkyl‐substituted naphthalenes are about 1500～2000 cm^?1, which is similar to that of naphthalene. The lack of rotation‐like wide‐angle motion of the aromatic ring and no enhancement in very large V→T energy transfer, like supercollisions, indicates that very large V→T energy transfer requires special vibrational motions. This transfer cannot be achieved by the low‐frequency vibrational motions of alkyl groups.     

Enumeration of Isomers of Alkylcyclobutadienes by Means of Alkyl 1,1,1-Triradicals

Previous studies have shown that alkyl 1,1-biradicals could be used to enumerate the constitutional isomers of alkenes [1] and cyclopropanes [2]. In this study, an algorithm of using alkyl 1,1,1-triradicals to enumerate the constitutional isomers of alkylcyclobutadienes is described. An alkylcyclobutadiene molecule is considered to be formed by four alkyl 1,1,1-triradicals by pairing two of the electrons with two of the adjacent alkyl 1,1,1-triradicals, and the remaining unpaired electron with one of the other adjacent alkyl 1,1,1-triradical. This enumeration algorithm showed that the constitutional isomers of the methanol series enumerated by Henze and Blair [3] can be used for enumerating the constitutional isomer of unsaturated cyclic compounds.     

M(o)bius环并苯的分子对称性

一般来说,点群理论认为M(o)bius带环分子最高的对称性只能是C2.本文讨论了由18个苯环组成的环并苯的异构体分子,包括柱面的Hückel型分子(HC-[18])和扭转180°的M(o)bius带环分子(MC-[18]).结果表明除了点对称性外,M(o)bius带环分子还存在一种可称为环面螺旋旋转(TSR)变换的对称性,为此还引用了环面正交曲线坐标系.此外,还讨论了这些分子关于TSR对称性匹配的原子集和原子轨道(AO)集.根据TSR对称性的循环群特征,可以建立此类群的不可约表示及有关特征标.这类分子的分子轨道(MO)关于TSR群的不可约表示是纯的,然而所含的相应的原子轨道对称性匹配的线性组合(SALC-AO)成分可以是多种的.     

Concurrent symmetries: the interplay between local and global molecular symmetries

We analyze in this article the degree to which different groups of atoms retain local symmetries when assembled in a molecule. This study is carried out by applying continuous symmetry measures to several families of mixed sandwiches, a variety of piano-stool molecules, and several organic groups. An analysis of the local symmetry of the electron density shows that, sandwiched between two regions of different symmetry that correspond to the ligand sets, its symmetry is cylindrical at the central metal atom.     

The Fuzzy D2h-symmetries of Ethylene Tetra-halide Molecules and their Molecular Orbitals

Based on our study in relation to the fuzzy symmetry characterization and the application to linear molecule, the fuzzy symmetry of the planar molecules have been analyzed. The prototypical planer molecules we have chosen to study are the C2F3X (X = Cl, Br, and I) and three kinds of C2F2Cl2 isomers. These molecules relate to the fuzzy symmetry in connection with the D2h point group. As we known, the D2h point group includes an identity transformation and seven twofold symmetry transformations but without higher-fold ones. Meanwhile, it is related only to some one-dimensional irreducible representations, but there is not to multi-dimensional irreducible representation. In this paper, the fuzzy symmetries of these molecules and their molecular orbital(MO)s have been studied, such as the membership functions, the representation compositions, the fuzzy correlation diagrams and so on have been analyzed. These analysis methods can be used to analyze the molecular fuzzy symmetries of some other molecule systems, no difficulty.     

Two‐ and Three‐Dimensional Molecular Organization of Schiff‐Base Derivatives

We have designed and synthesized a series of Schiff base derivatives, and studied their structural features in two‐dimensional (2D) and three‐dimensional (3D) states by combining scanning tunneling microscopy (STM) and X‐ray diffraction experiments. The Schiff‐base derivatives with short alkyl chains crystallize easily, which allows a detailed structural analysis by X‐ray diffraction. Due to the strong adsorbate–substrate interactions, those bases with long alkyl chains easily form 2D assemblies on highly oriented pyrolytic graphite (HOPG). The STM images indicate also that the introduction of two methoxy groups into the molecule can change the structure of these 2D assemblies as a result of the increased steric hindrances, for example: the Schiff‐base derivative, bearing both methoxy groups and C₁₆H₃₃ tails, forms 2D Moiré patterns, and an alignment of pairing Schiff‐base molecules may be easily resolved. Conversely, the Schiff base derivative, bearing solely C₁₆H₃₃ tails, forms 2D non‐Moiré patterns. It is demonstrated that the 3D structural features result from the compromise of intermolecular interactions of different molecular moieties. However, there is one more factor, which also governs the 2D structure: the adsorbate‐substrate interaction. The 3D crystal structure may thus help to understand many factors involved in the formation of 2D structures, and would be helpful for designing new molecular assemblies with tailoring functions.     

Motion Capture and Manipulation of a Single Synthetic Molecular Rotor by Optical Microscopy

Single‐molecule imaging and manipulation with optical microscopy have become essential methods for studying biomolecular machines; however, only few efforts have been directed towards synthetic molecular machines. Single‐molecule optical microscopy was now applied to a synthetic molecular rotor, a double‐decker porphyrin (DD). By attaching a magnetic bead (ca. 200 nm) to the DD, its rotational dynamics were captured with a time resolution of 0.5 ms. DD showed rotational diffusion with 90° steps, which is consistent with its four‐fold structural symmetry. Kinetic analysis revealed the first‐order kinetics of the 90° step with a rate constant of 2.8 s^?1. The barrier height of the rotational potential was estimated to be greater than 7.4 kJ mol^?1 at 298 K. The DD was also forcibly rotated with magnetic tweezers, and again, four stable pausing angles that are separated by 90° were observed. These results demonstrate the potency of single‐molecule optical microscopy for the elucidation of elementary properties of synthetic molecular machines.