Open-chain Structure Research Articles

Crystal structure of sodium (1S)-d-mannit-1-yl-sulfonate.

The title salt, Na+·C6H13O9S- [systematic name: sodium (1S,2S,3S,4R,5R)-1,2,3,4,5,6-hexa-hydroxy-hexane-1-sulfonate], is formed by reaction of d-mannose with sodium bis-ulfite (sodium hydrogen sulfite) in water. The anion has an open-chain structure with the S atom and the C atoms of the carbohydrate chain forming an essentially planar zigzag chain in which the absolute values of the torsion angles lie between 173.6 (2) and 179.9 (3)°. The sodium cations are penta--coordinated by O atoms, with one link to a carbohydrate O atom and four to O atoms of sulfonate residues in separate anions, thus creating a three-dimensional network. The carbohydrate anions are arranged in a head (-SO3-) to head (-SO3-) arrangement, thereby forming two parallel sheets linked through coordination to sodium ions, with each sheet containing inter-molecular hydrogen bonds between the anionic residues. Unusually, the double sheets are not connected to neighbouring sets of double sheets, either by ion coordination or inter-molecular hydrogen bonding.

Control of Selectivity in Palladium(II)-Catalyzed Oxidative Transformations of Allenes.

Oxidation reactions play a central role in organic synthesis, and it is highly desirable that these reactions are mild and occur under catalytic conditions. In Nature, oxidation reactions occur under mild conditions via cascade processes, and furthermore, they often occur in an enantioselective manner with many of them involving molecular oxygen or hydrogen peroxide as the terminal oxidant. Inspired by the reactions in Nature, we have developed a number of Pd(II)-catalyzed cascade reactions under mild oxidative conditions. These reactions have an intrinsic advantage of step economy and rely on selectivity control in each step. In this Account, we will discuss the control of chemo-, regio-, and diastereoselectivity in Pd(II)-catalyzed dehydrogenative cascade coupling reactions. The enantioselective version of this methodology has also been addressed, and new chiral centers have been introduced using a catalytic amount of a chiral phosphoric acid (CPA). Research on this topic has provided access to important compounds attractive for synthetic and pharmaceutical chemists. These compounds include carbocyclic, heterocyclic, and polycyclic systems, as well as polyunsaturated open-chain structures. Reactions leading to these compounds are initiated by coordination of an allene and an unsaturated π-bond moiety, such as olefin, alkyne, or another allene, to the Pd(II) center, followed by allene attack involving a C(sp3)-H cleavage under mild reaction conditions. Recent progress within our research group has shown that weakly coordinating groups (e.g., hydroxyl, alkoxide, or ketone) could also initiate the allene attack on Pd(II), which is essential for the oxidative carbocyclization. Furthermore, a highly selective palladium-catalyzed allenic C(sp3)-H bond oxidation of allenes in the absence of an assisting group was developed, which provides a novel and straightforward synthesis of [3]dendralene derivatives. For the oxidative systems, benzoquinone (BQ) and its derivatives are commonly used as oxidants or catalytic co-oxidants (electron transfer mediators, ETMs) together with molecular oxygen. A variety of transformations including carbocyclization, acetoxylation, arylation, carbonylation, borylation, β-hydride elimination, alkynylation, alkoxylation, and olefination have been demonstrated to be compatible with this Pd(II)-based catalytic oxidative system. Recently, several challenging synthetic targets, such as cyclobutenes, seven-membered ring carbocycles, spirocyclic derivatives, functional cyclohexenes, and chiral cyclopentenone derivatives were obtained with high selectivity using these methods. The mechanisms of the reactions were mainly studied by kinetic isotope effects (KIEs) or DFT computations, which showed that in most cases the C(sp3)-H cleavage is the rate-determining step (RDS) or partially RDS. This Account will describe our efforts toward the development of highly selective and atom-economic palladium(II)-catalyzed oxidative transformation of allenes (including enallenes, dienallenes, bisallenes, allenynes, simple allenes, and allenols) with a focus on overcoming the selectivity problem during the reactions.

Tandem Mass Spectrometry and Ion Mobility Reveals Structural Insight into Eicosanoid Product Ion Formation.

Ion mobility measurements of product ions were used to characterize the collisional cross section (CCS) of various complex lipid [M-H]- ions using traveling wave ion mobility mass spectrometry (TWIMS). TWIMS analysis of various product ions derived after collisional activation of mono- and dihydroxy arachidonate metabolites was found to be more complex than the analysis of intact molecular ions and provided some insight into molecular mechanisms involved in product ion formation. The CCS observed for the molecular ion [M-H]- and certain product ions were consistent with a folded ion structure, the latter predicted by the proposed mechanisms of product ion formation. Unexpectedly, product ions from [M-H-H2O-CO2]- and [M-H-H2O]- displayed complex ion mobility profiles suggesting multiple mechanisms of ion formation. The [M-H-H2O]- ion from LTB4 was studied in more detail using both nitrogen and helium as the drift gas in the ion mobility cell. One population of [M-H-H2O]- product ions from LTB4 was consistent with formation of covalent ring structures, while the ions displaying a higher CCS were consistent with a more open-chain structure. Using molecular dynamics and theoretical CCS calculations, energy minimized structures of those product ions with the open-chain structures were found to have a higher CCS than a folded molecular ion structure. The measurement of product ion mobility can be an additional and unique signature of eicosanoids measured by LC-MS/MS techniques. Graphical Abstract ᅟ.

Straightening out complex stereochemistry

When chemists at the University of Bristol set out to make a pair of natural products with antimicrobial activity, it seemed like a quick and easy way to highlight some synthetic methodology their lab had developed. But after finishing their 10-step syntheses of baulamycins A and B, the researchers noticed that the NMR spectra of the molecules they made didn’t match those originally reported for the natural material. It turns out that the stereochemistry of the natural compounds had been incorrectly assigned, and the Bristol team had been making the wrong molecules all along. The team, led by Varinder K. Aggarwal, Eddie L. Myers, and Craig P. Butts, now reports a method to figure out the correct stereochemistry of baulamycins A and B and other complex molecules. It’s not so easy, Aggarwal says. Baulamycins A and B have an open chain structure with seven stereocenters. “It was very daunting to

Photoelectron spectroscopy and density functional theory studies of (fructose + (H2O)n)- (n = 1-5) anionic clusters.

Photoelectron spectroscopy (PES) and density functional theory (DFT) based calculations are executed to characterize gas phase, isolated (fructose + (H2O)n)- (n = 1-5) anionic species produced using a matrix assisted laser desorption ionization (MALDI) method. Gas phase, isolated (fructose + (H2O)n)- (n = 1-5) cluster anions mainly exist as open chain structures with conformational and positional isomers in the present experiments. Some cyclic structures of (fructose + (H2O)n)- (n = 3, 4) are apparently present in the experiments and their VDEs can contribute to the lower energy shoulders of PES features observed for (fructose + (H2O)n)- (n = 3, 4). Cyclic (fructose + (H2O)n)- (n = 1-5) clusters have the added electron as dipole bound, whereas open chain structures have the added electron in a valence orbital. Water molecules in open chain anions predominantly interact with the (1)C side (including (1)OH, (2)O, and (3)OH) of fructose-: they finally form a quasi-cubic structure with OH groups and carbonyl O in the most stable structures for (fructose + (H2O)4)- and (fructose + (H2O)5)- cluster anions. Water molecules solvating cyclic anions form water-water hydrogen bond networks that preferentially interact with OH groups at the (1), (2), and (3) positions of fructose pyranose anions, and the (3), (4), and (6) positions of fructose furanose anions. Structures of neutral (fructose + (H2O)n) (n = 1-5) have pyranose structures as the lower energy isomers rather than open chain structures: this observation is consistent with the fructose solution tautomeric equilibrium with neutral fructose pyranose being the preponderant species. Water molecules also tend to form water-water hydrogen bond networks, interacting with OH groups at (1), (2), and (3) positions for neutral pyranose conformations.

Anionic fructose-related conformational and positional isomers assigned through PES experiments and DFT calculations.

Gas phase, isolated fructose anionic species, fructose-, (fructose-H)-, (fructose-OH)-, and (fructose-H2O)-, are investigated employing anionic photoelectron spectroscopy (PES) combined with density functional theory (DFT) calculations. The PES vertical detachment energies (VDEs) for these anions are determined and, based on these experimental values, their calculated anionic structures are assigned. Generation of these four species through the matrix assisted laser desorption ionization (MALDI) process is sample desorption substrate dependent. The parent anion fructose- exists as a single, dominant open chain structure in the gas phase, with substrate dependent specific conformational isomers. (Fructose-H)- and (fructose-OH)- are mainly produced from the laser ablation process rather than from fragmentation reaction pathways associated with the parent anion species. Both conformational and positional isomers are identified in the gas phase for these latter anions. (Fructose-H2O)- has two types of positional isomers, both of which contribute to two different components of the observed PES feature. The fixed positions for losing an OH group and an H atom, in addition to thermodynamic calculations, provide reaction pathways for generating a dehydration product (open chain structures) from the parent anion (open chain and furanose structures), further demonstrating the active nature of fructose upon capturing an extra electron.

Kinematic Modeling for a Class of Free-Floating Space Robots

This paper investigates the kinematics of free-floating space robots during motion planning for target capture. First, generalized kinematic mapping of free-floating space robots with open-chain multibody structures is established. To predict the reaction movement of spacecraft caused by the motions of its manipulators, a dynamic coupling matrix concept, the main contribution of this paper, is proposed to explicitly express position kinematics. The feasibility and effectiveness of the presented numerical implementation algorithms are then verified by solving forward and inverse kinematics problems. Then, applications in workspace analysis and motion planning are described. Finally, a discussion of the framework is presented.

Silver compounds based on N,N,N-tridentate pyridylpyrazolate ligands. An opportunity to build cyclic trimetallic and oligomeric luminescent liquid crystals

Silver pyrazolate complexes [Ag(μ-pzR(n)py)]3 [R(n)=C6H4OCnH2n+1; 3 (n=1); 4 (n=10); 5 (n=12); 6 (n=16) and 7 (n=18)] have been prepared by reaction of Ag2O with 3-(4-n-alkyloxyphenyl)-5-(pyridin-2-yl)pyrazole ligands [HpzR(n)py]. The presence of the pyridine as substituent group on the ligand seems to favour the formation of silver cyclic trimers which were isolated in the solid state, as it was supported by the X-ray single crystal structure of the derivative bearing the shortest alkyl chain [Ag(μ-pzR(1)py)]3 (3). By contrast, in CDCl3 or CD2Cl2 solution, the formation of one-dimensional coordination oligomers [Ag(μ-pzR(n)py)]x is proposed. The lability and interchange of AgN pyrazolic bonds of the trimeric structures in polar solvents appear to be responsible for the self-organization of Ag/μ-pzR(n)py motifs into open-chain oligomers. However, in C6D6 solution, the presence of only one set of signals led us to consider that apolar solvents may not affect the AgN pyrazolic bonds, so that the cyclic trimeric structure found in the solid state could be maintained in solution. Complexes bearing the longest chains [5 (n=12); 6 (n=16) and 7 (n=18)] exhibited liquid crystal behaviour showing smectic A (SmA) mesophases in agreement with the open-chain oligomeric structure proposed for the mesomorphic state. Photophysical studies performed on [Ag(μ-pzR(12)py)]3 (5), chosen as a representative example of the series, reveal the presence of luminescence in solution at room temperature for these materials.

A New Allotrope of Nitrogen as High-Energy Density Material.

A new allotrope of nitrogen in which the atoms are connected to form a novel N6 molecule is predicted to exist at ambient conditions. The N6 molecule is a charge-transfer complex with an open-chain structure containing both single and triple bonds. The charge transfer induces ionic characteristics in the intermolecular interactions and leads to a much higher cohesive energy for the predicted crystal compared to solid N2. The N6 solid is also more stable than a previously reported polymeric solid of nitrogen. Because of the kinetic stability of the molecules and strong intermolecular interactions, the N6 crystal is shown by metadynamics simulations to be dynamically stable around room temperature and to only dissociate to N2 molecules above 700 K. The N6 crystal can likely be synthesized under high-pressure high-temperature conditions, and the considerable metastability may allow for an ambient-pressure recovery of the crystal. Because of the large energy difference between the single and triple bonds, the dissociation of the N6 crystal is expected to release a large amount of energy, placing it among the most efficient energy materials known today.

Crystal structure of sodium (1S)-d-lyxit-1-yl-sulfonate.

The title compound, Na(+)·C5H11O8S(-) [systematic name: sodium (1S,2S,3S,4R)-1,2,3,4,5-penta-hydroxy-pentane-1-sulfonate], is formed by reaction of d-lyxose with sodium bis-ulfite (sodium hydrogen sulfite) in water. The anion has an open-chain structure in which one of the oxygen atoms of the sulfonate residue, the S atom, the C atoms of the sugar chain and the O atom of the hy-droxy-methyl group form an essentially planar zigzag chain with the corresponding torsion angles lying between 179.80 (11) and 167.74 (14)°. A three-dimensional bonding network exists in the crystal structure involving hexa-coordination of sodium ions by O atoms, three of which are provided by a single d-lyxose-sulfonate unit and the other three by two sulfonate groups and one hy-droxy-methyl group, each from separate units of the adduct. Extensive inter-molecular O-H⋯O hydrogen bonding supplements this bonding network.

Determination of joint reactions in a rigid multibody system, two different approaches

In this paper two different methods for determination of frictionless joint reaction forces and moments are presented. The considered multibody system has an open kinematic chain structure. The first method refers to the determination of resultant joint reaction forces and moments based on the Rodrigues approach suitable for computation in a symbolic form. The second method presented is the method based on the so-called vectors of the body mass moments and vector rotators coupled for a pole and oriented axes. Both approaches are presented and discussed on the three- like rigid multibody system.

Quantum chemical study of dissociative electron attachment to d-ribose and d-fructose

We performed quantum chemistry calculations using long-range corrected density-functional theory to understand the interaction of an excess electron with d-ribose/d-fructose. Previous experimental studies have shown that these sugar molecules undergo dissociative electron attachment to form various fragments upon capture of a nearly zero-energy electron. First, we studied doorway states, including dipole-bound and valence-bound anions in pyranose, furanose, and open-chain structures. Subsequently, we explored the reaction pathways on the anionic potential energy surfaces for selected structures to understand the detailed reaction mechanisms of dissociative electron attachment to these sugar molecules.

From the (1B) Spectroscopic State to the Photochemical Product of the Ultrafast Ring-Opening of 1,3-Cyclohexadiene: A Spectral Observation of the Complete Reaction Path.

All stages of the electrocyclic ring-opening of 1,3-cyclohexadiene (CHD) were observed by time-resolved photoionization-photoelectron spectroscopy. Spectra of the 1B state, previously unobserved using time-resolved methods, were obtained upon optical excitation using ultrashort laser pulses at 4.60 or 4.65 eV, followed by ionization with pulses at 3.81, 3.85, and 4.10 eV, revealing a 1B lifetime of 30 fs. In an experiment using 3.07 eV probe photons and a 4.69 eV pump, we observed a time-sequenced progression of Rydberg states that includes s, p, and d states of the series n = 3 to 6. The sequentiality of the Rydberg signals points to an ionization mechanism that captures the molecule on different points along the reaction path in 2A. A dynamic fit of the Rydberg signals, coupled with MS-CASPT2 calculations, reveals that as the wavepacket moves down the potential energy surface it acquires kinetic energy at a rate of 28 eV/ps before reaching the conical intersection to the 1A ground state. During the reaction, the terminal carbon atoms separate at a speed of 16 Å/ps. A deconvolution of the Rydberg signals from a broad feature assigned to structurally disperse 1,3,5-hexatriene (HT) shows the formation of the open-chain hexatriene structure with an onset 142 fs after the initial absorption of a pump photon. The experimental observations are discussed in the context of recent ultrafast X-ray scattering experiments and theoretical quantum dynamics simulations.

Crystal structure of potassium (1S)-d-lyxit-1-yl-sulfonate monohydrate.

The title compound, K(+)·C5H11O8S(-)·H2O [systematic name: potassium (1S,2S,3S,4R)-1,2,3,4,5-penta-hydroxy-pentane-1-sulfonate monohydrate], formed by reaction of d-lyxose with potassium hydrogen sulfite in water, crystallizes as colourless square prisms. The anion has an open-chain structure in which the S atom, the C atoms of the sugar chain and the oxygen atom of the hy-droxy-methyl group form an essentially all-trans chain with the corresponding torsion angles lying between 178.61 (12) and 157.75 (10)°. A three-dimensional bonding network exists in the crystal structure involving coordination of two crystallographically independent potassium ions by O atoms (one cation being hexa- and the other octa-coordinate, with each lying on a twofold rotation axis), and extensive inter-molecular O-H⋯O hydrogen bonding.

In vitro and in silico toxicity evaluation of bioactive 4′-aminochalcone derivatives

The 4′-aminochalcones compounds are open-chain flavonoids structures which have shown a known array of pharmacological activities, such as antibacterial, antifungal, anti-inflammatory and antitumor effects. There is little toxicological information available about these compounds in the literature. Therefore, the investigation of toxic effects of three 4′-aminochalcone derivatives was performed using in silico and in vitro assays. In silico provided results that indicated the occurrence of mutagenic and genotoxic effects. In vitro tests, using Cellular Proliferation and Viability, Micronucleus, and DNA damage by Comet assay, showed that the compounds studied also present mutagenic and genotoxic effects, which confirm the result determined by the in silico analysis. The use of experimental and computational models is complementary to each other and the results determined for 4′-aminochalones suggest that the chalcones should also be carefully considered since they show some risks to cause toxic effects to human cells.

Vibrational study of 5-azacytosine and propanedinitrile under high pressure

The effect of high pressure on the vibrational modes of 5-azacytosine (C3H4N4O) and propanedinitrile (CH2(CN)2) was investigated at room temperature using a diamond anvil cell (DAC). In situ infrared and Raman spectroscopy results indicated that the ring structure of 5-azacytosine remained preserved and the band shifts induced by high pressure were fully reversible up to 13GPa. For the open-chain structure of propanedinitrile, a polymerization reaction was observed by infrared spectroscopy almost instantly at about 15GPa at room temperature. The same pressure-induced polymerization was observed after a week at 1GPa, at room temperature.

Rethinking aromaticity in H-bonded systems. Caveats for transition structures involving hydrogen transfer and π-delocalization.

Monoaza- and diaza-derivatives of malondialdehydes, in short aminoacroleins and vinamidines, are prototypical examples of open-chain structures prone to π-electron delocalization, for which intramolecular hydrogen bonding enhances (or diminishes) their pseudoaromaticity depending on the substitution pattern. This interplay is illustrated herein by DFT-based calculations of aromaticity indices in the gas phase and polar solvents. Elucidation of transition structures involved in tautomeric conversions helps to solve how the intramolecular hydrogen transfer occurs. While TSs exhibit a high degree of aromaticity, the dichotomy between forward and backward pathways points to a complex trajectory. Addition of thermal corrections to the electronic energy decreases both the enthalpy and free energy leading to negative ΔH(‡) and ΔG(‡) values. This variational effect accounts for the otherwise elusive distinction between transition structures and saddle points (usually overlooked for high electronic barriers). Also, this rationale fits well within the framework of Marcus' theory.

Crystal structure of potassium (1R)-d-ribit-1-yl-sulfonate.

The title compound, K(+)·C5H11O8S(-) [systematic name: potassium (1R,2R,3R,4R)-1,2,3,4,5-penta-hydroxy-pentane-1-sulfonate], formed by reaction of d-ribose with potassium hydrogen sulfite in water, crystallizes as colourless plates. The anion has an open-chain structure in which the S atom and the C atoms of the sugar chain, excepting that of the hy-droxy-methyl group, form an essentially all-trans chain; the C atom of the hy-droxy-methyl group lies in a gauche relationship with the three contiguous C atoms. Through complex cation coordination (through seven oxygen atoms of six different anions) and inter-molecular O-H⋯O hydrogen bonding, a three-dimensional bonding network exists in the crystal structure.

Cyclic and acyclic fructose conformers in the gas phase: a large-scale second-order perturbation theory study.

We performed large-scale second-order perturbation theory gas-phase calculations to study about five hundred structures of D-fructose. The two lowest energy fructose structures identified are β-pyranoses possessing (2)C5 chair, with ΔG(298 K) of 6 kJ/mol, differing in orientation of the equatorially positioned hydroxymethyl group, gt and g'g, where the gt rotamer is the global minimum, consistent with the recent microwave spectroscopy study. We have found that interconversions from the fructose global minimum to the second and third most stable β-pyranose rotamers involve the energy barriers of ca. 30 kJ/mol. Among numerous fructofuranose conformers discovered (about 250), a pair of the ((3)T2) α- and (E3) β-anomers are energetically most preferred and lie at least 12 kJ/mol above the global minimum. We also found that the fructose open-chain structures lie significantly higher in energy than the most stable cyclic species. The commonly used M06-2X density functional performs well compared to MP2 and G4 theory at identifying the low-energy fructose minima, including the global one, and at reproducing their intramolecular H-bond geometric parameters. The lowest-energy gas-phase pyranose and furanose structures of fructose benefit from stabilization due to the cooperative or quasi-linear H-bonding and both endo and exo anomeric effects.

Experimental and theoretical investigations of energy transfer and hydrogen-bond breaking in small water and HCl clusters.

Water is one of the most pervasive molecules on earth and other planetary bodies; it is the molecule that is searched for as the presumptive precursor to extraterrestrial life. It is also the paradigm substance illustrating ubiquitous hydrogen bonding (H-bonding) in the gas phase, liquids, crystals, and amorphous solids. Moreover, H-bonding with other molecules and between different molecules is of the utmost importance in chemistry and biology. It is no wonder, then, that for nearly a century theoreticians and experimentalists have tried to understand all aspects of H-bonding and its influence on reactivity. It is somewhat surprising, therefore, that several fundamental aspects of H-bonding that are particularly important for benchmarking theoretical models have remained unexplored experimentally. For example, even the binding strength between two gas-phase water molecules has never been determined with sufficient accuracy for comparison with high-level electronic structure calculations. Likewise, the effect of cooperativity (nonadditivity) in small H-bonded networks is not known with sufficient accuracy. An even greater challenge for both theory and experiment is the description of the dissociation dynamics of H-bonded small clusters upon acquiring vibrational excitation. This is because of the long lifetimes of many clusters, which requires running classical trajectories for many nanoseconds to achieve dissociation. In this Account, we describe recent progress and ongoing research that demonstrates how the combined and complementary efforts of theory and experiment are enlisted to determine bond dissociation energies (D0) of small dimers and cyclic trimers of water and HCl with unprecedented accuracy, describe dissociation dynamics, and assess the effects of cooperativity. The experimental techniques rely on IR excitation of H-bonded X-H stretch vibrations, measuring velocity distributions of fragments in specific rovibrational states, and determining product state distributions at the pair-correlation level. The theoretical methods are based on high-level ab initio potential energy surfaces used in quantum and classical dynamical calculations. We achieve excellent agreement on D0 between theory and experiments for all of the clusters that we have compared, as well as for cooperativity in ring trimers of water and HCl. We also show that both the long-range and the repulsive parts of the potential must be involved in bond breaking. We explain why H-bonds are so resilient and hard to break, and we propose that a common motif in the breaking of cyclic trimers is the opening of the ring following transfer of one quantum of stretch excitation to form open-chain structures that are weakly bound. However, it still takes many vibrational periods to release one monomer fragment from the open-chain structures. Our success with water and HCl dimers and trimers led us to embark on a more ambitious project: studies of mixed water and HCl small clusters. These clusters eventually lead to ionization of HCl and serve as prototypes of acid dissociation in water. Measurements and calculations of such ionizations are yet to be achieved, and we are now characterizing these systems by adding monomers one at a time. We describe our completed work on the HCl-H2O dimer and mention our recent theoretical results on larger mixed clusters.