Photoisomerization of alfa calcidol by a sensitized quantum chain reaction.

PubMed

Estruch, Gastón A; Aramendía, Pedro F

2012-01-01

The production of vitamin D3 is a pharmaceutically relevant process, producing high added-value products. Precursors are extracts from vegetal origin but bearing mainly an E geometry in the 5,6 double bond. The synthesis of vitamin D3 (5-E-α-calcidol) with the correct Z stereochemistry in the 5,6 double bond from the E isomer using anthracene and triethylamine (TEA) as the sensitizer system was studied from the kinetic and mechanistic point of view. The sensitized isomerization of E-calcidol by irradiation of anthracene takes place only in deoxygenated solution and yields the Z isomer in ca 5% yield in the photostationary state. When TEA is added to the system, the E-Z reaction is not inhibited by oxygen any more, the quantum yield of photoisomerization to the Z isomer grows linearly with the concentration of E-calcidol, while conversions higher than 95% to the Z isomer are reached in the photostationary state and E-Z quantum yields as high as 45 at [E-calcidol] = 25 mM are reached. If TEA is replaced by 1,4-diazabicyclo[2.2.2]octane, the reaction rate drops to one-third at the same amine concentration. The observations can be explained by a quantum chain reaction mechanism. The high conversion achieved eliminates the need of isomer separation. © 2011 Wiley Periodicals, Inc. Photochemistry and Photobiology © 2011 The American Society of Photobiology.

Relaxation dynamics of C60

NASA Astrophysics Data System (ADS)

Walsh, Tiffany R.; Wales, David J.

1998-10-01

The relaxation dynamics of C60 from high-energy isomers to Buckminsterfullerene is examined using a master equation approach. An exhaustive catalog of the C60 fullerene isomers containing only five- and six-membered rings is combined with knowledge of the Stone-Wales rearrangements that connect all such isomers. Full geometry optimizations have been performed for all the minima and the transition states which connect them up to six Stone-Wales steps away from the global minimum. A density-functional tight-binding potential was employed to provide a quantum mechanical description of the bonding. The resulting picture of the potential energy landscape reveals a "weeping willow" structure which offers a clear explanation for the relatively long relaxation times observed experimentally. We also predict the most important transient local minima on the annealing pathway.

The structure and photochemical transformation of cyclopropylacetylene radical cation as revealed by matrix EPR and quantum chemical study

NASA Astrophysics Data System (ADS)

Shiryaeva, Ekaterina S.; Tyurin, Daniil A.; Feldman, Vladimir I.

2012-05-01

The primary radical cation of cyclopropylacetylene was first characterized by EPR spectroscopy in low-temperature freon matrices. The assignment was confirmed by specific deuteration and quantum-chemical calculations at PBE0 and CCSD(T) levels. Photolysis with visible light led to irreversible transformation of the initial species to a ring-open structure. Detailed computational analysis of energy and magnetic resonance parameters of possible reaction products justified formation of pent-3-en-1-yne radical cation (presumably, a (Z)-isomer). This conclusion was also supported by the effect of specific deuteration.

Competition between drum and quasi-planar structures in RhB18 –: motifs for metallo-boronanotubes and metallo-borophenes† †Electronic supplementary information (ESI) available: The photoelectron spectrum of RhB18 – at 266 nm; the top 42 low-lying isomers of RhB18 –; the relative Gibbs free energies, valence molecular orbitals, and coordinates of the two most stable isomers of RhB18 –. See DOI: 10.1039/c6sc02623k Click here for additional data file.

PubMed Central

Jian, Tian; Li, Wan-Lu; Chen, Xin; Chen, Teng-Teng; Lopez, Gary V.

2016-01-01

Metal-doped boron clusters provide new opportunities to design nanoclusters with interesting structures and bonding. A cobalt-doped boron cluster, CoB18 –, has been observed recently to be planar and can be viewed as a motif for metallo-borophenes, whereas the D 9d drum isomer as a motif for metallo-boronanotubes is found to be much higher in energy. Hence, whether larger doped boron drums are possible is still an open question. Here we report that for RhB18 – the drum and quasi-planar structures become much closer in energy and co-exist experimentally, revealing a competition between the metallo-boronanotube and metallo-borophene structures. Photoelectron spectroscopy of RhB18 – shows a complicated spectral pattern, suggesting the presence of two isomers. Quantum chemistry studies indicate that the D 9d drum isomer and a quasi-planar isomer (C s) compete for the global minimum. The enhanced stability of the drum isomer in RhB18 – is due to the less contracted Rh 4d orbitals, which can have favorable interactions with the B18 drum motif. Chemical bonding analyses show that the quasi-planar isomer of RhB18 – is aromatic with 10 π electrons, whereas the observed RhB18 – drum cluster sets a new record for coordination number of eighteen among metal complexes. The current finding shows that the size of the boron drum can be tuned by appropriate metal dopants, suggesting that even larger boron drums with 5d, 6d transition metal, lanthanide or actinide metal atoms are possible. PMID:28451138

An Unusual Conformational Isomer of Verrucosidin Backbone from a Hydrothermal Vent Fungus, Penicillium sp. Y-50-10.

PubMed

Pan, Chengqian; Shi, Yutong; Auckloo, Bibi Nazia; Chen, Xuegang; Chen, Chen-Tung Arthur; Tao, Xinyi; Wu, Bin

2016-08-18

A new verrucosidin derivative, methyl isoverrucosidinol (1), was isolated from the marine fungus Penicillium sp. Y-50-10, dwelling in sulfur rich sediment in the Kueishantao hydrothermal vents off Taiwan. The structure was established by spectroscopic means including HRMS and 2D-NMR spectroscopic analysis. The absolute configuration was defined mainly by comparison of quantum chemical TDDFT calculated and experimental ECD spectra. Among hitherto known compounds with a verrucosidine backbone isolated from natural resource, compound 1 represents the first example of a new conformational isomer of its skeleton, exhibiting antibiotic activity against Bacillus subtilis with MIC value 32 μg/mL.

Quantum chemical study of small AlnBm clusters: Structure and physical properties

NASA Astrophysics Data System (ADS)

Loukhovitski, Boris I.; Sharipov, Alexander S.; Starik, Alexander M.

2017-08-01

The structure and physical properties, including rotational constants, characteristic vibrational temperatures, collision diameter, dipole moment, static polarizability, the energy gap between the highest occupied molecular orbital (HOMO) and the lowest unoccupied molecular orbital (LUMO), and formation enthalpy of the different isomeric forms of AlnBm clusters with n + m ⩽ 7 are studied using density functional theory. The search of the structure of isomers has been carried employing multistep hierarchical algorithm. Temperature dependencies of thermodynamic functions, such as enthalpy, entropy, and specific heat capacity, have been determined both for the individual isomers and for the ensembles with equilibrium and frozen compositions for the each class of clusters taking into account the anharmonicity of cluster vibrations and the contribution of their excited electronic states. The prospects of the application of small AlnBm clusters as the components of energetic materials are also considered.

Triplet and ground state potential energy surfaces of 1,4-diphenyl-1,3-butadiene: theory and experiment.

PubMed

Saltiel, J; Dmitrenko, O; Pillai, Z S; Klima, R; Wang, S; Wharton, T; Huang, Z-N; van de Burgt, L J; Arranz, J

2008-05-01

Relative energies of the ground state isomers of 1,4-diphenyl-1,3-butadiene (DPB) are determined from the temperature dependence of equilibrium isomer compositions obtained with the use of diphenyl diselenide as catalyst. Temperature and concentration effects on photostationary states and isomerization quantum yields with biacetyl or fluorenone as triplet sensitizers with or without the presence of O(2), lead to significant modification of the proposed DPB triplet potential energy surface. Quantum yields for ct-DPB formation from tt-DPB increase with [tt-DPB] revealing a quantum chain process in the tt --> ct direction, as had been observed for the ct --> tt direction, and suggesting an energy minimum at the (3)ct* geometry. They confirm the presence of planar and twisted isomeric triplets in equilibrium (K), with energy transfer from planar or quasi-planar geometries (quantum chain events from tt and ct triplets) and unimolecular decay (k(d)) from twisted geometries. Starting from cc-DPB, varphi(cc-->tt) increases with increasing [cc-DPB] whereas varphi(cc-->ct) is relatively insensitive to concentration changes. The concentration and temperature dependencies of the decay rate constants of DPB triplets in cyclohexane are consistent with the mechanism deduced from the photoisomerization quantum yields. The experimental DeltaH between (3)tt-DPB* and (3)tp-DPB*, 2.7 kcal mol(-1), is compared with the calculated energy difference [DFT with B3LYP/6-31+G(d,p) basis set]. Use of the calculated DeltaS = 4.04 eu between the two triplets gives k(d) = (2.4-6.4) x 10(7) s(-1), close to 1.70 x 10(7) s(-1), the value for twisted stilbene triplet decay. Experimental and calculated relative energies of DPB isomers on the ground and triplet state surfaces agree and theory is relied upon to deduce structural characteristics of the equilibrated conformers in the DPB triplet state.

Quantum-Chemical ab initio Calculations on the Three Isomers of Diborabenzene (C4H4B2)

NASA Astrophysics Data System (ADS)

Singh, Jaswinder; Wang, Yuekui; Raabe, Gerhard

2010-01-01

Quantum-chemical ab initio calculations up to the ZPE+CCSD(T)/aug-cc-pVTZ//MP2/6- 311++G** level were performed on three possible structural isomers of diborabenzene (C4H4B2). All three molecules were found to be local minima on the C4H4B2 energy surface and to have closed shell singlet ground states. While the ground states of the 1,3- and 1,4-isomer are planar and of C2v and D2h symmetry, respectively, 1,2-diborabenzene is non-planar with a C2 axis passing through the center of the BB bond and the middle of the opposite carbon-carbon bond as the only symmetry element. The energetically most favourable 1,3-diborabenzene was found to be about 19 and 36 kcal/mol lower in energy than the 1,2- and the 1,4-isomer. Planar 1,3- and 1,4-diborabenzene have three doubly occupied π orbitals while non-planar 1,2-diborabenzene has also three doubly occupied orbitals which can be derived from the π orbitals of its 3.7 kcal/mol energetically less favourable planar form ("π-like" orbitals). The lowest unoccupied orbitals of all three isomers have σ symmetry with large coefficients at the two boron atoms. These orbitals are lower in energy than the lowest unoccupied molecular orbitals (LUMOs) of e. g. benzene and pyridine and might cause pronounced acceptor properties which could be one of the reasons for the elusiveness of the title compounds. The results of bond separation reactions show that cyclic conjugation stabilizes all three diborabenzenes relative to their isolated fragments. The most effective stabilization energy of about 24 kcal/mol was found for the energetically lowest 1,3-isomer. This value amounts to approximately one third of the experimental value for the bond separation energy of pyridine. In all cases the energetically lowest triplet states are significantly (16 - 24 kcal/mol) higher in energy than the singlet ground states. Also among the triplets the 1,3-isomer is the energetically most fabourable species.

Hydrogen-bonded ring closing and opening of protonated methanol clusters H(+)(CH3OH)(n) (n = 4-8) with the inert gas tagging.

PubMed

Li, Ying-Cheng; Hamashima, Toru; Yamazaki, Ryoko; Kobayashi, Tomohiro; Suzuki, Yuta; Mizuse, Kenta; Fujii, Asuka; Kuo, Jer-Lai

2015-09-14

The preferential hydrogen bond (H-bond) structures of protonated methanol clusters, H(+)(MeOH)n, in the size range of n = 4-8, were studied by size-selective infrared (IR) spectroscopy in conjunction with density functional theory calculations. The IR spectra of bare clusters were compared with those with the inert gas tagging by Ar, Ne, and N2, and remarkable changes in the isomer distribution with the tagging were found for clusters with n≥ 5. The temperature dependence of the isomer distribution of the clusters was calculated by the quantum harmonic superposition approach. The observed spectral changes with the tagging were well interpreted by the fall of the cluster temperature with the tagging, which causes the transfer of the isomer distribution from the open and flexible H-bond network types to the closed and rigid ones. Anomalous isomer distribution with the tagging, which has been recently found for protonated water clusters, was also found for H(+)(MeOH)5. The origin of the anomaly was examined by the experiments on its carrier gas dependence.

An Unusual Conformational Isomer of Verrucosidin Backbone from a Hydrothermal Vent Fungus, Penicillium sp. Y-50-10

PubMed Central

Pan, Chengqian; Shi, Yutong; Auckloo, Bibi Nazia; Chen, Xuegang; Chen, Chen-Tung Arthur; Tao, Xinyi; Wu, Bin

2016-01-01

A new verrucosidin derivative, methyl isoverrucosidinol (1), was isolated from the marine fungus Penicillium sp. Y-50-10, dwelling in sulfur rich sediment in the Kueishantao hydrothermal vents off Taiwan. The structure was established by spectroscopic means including HRMS and 2D-NMR spectroscopic analysis. The absolute configuration was defined mainly by comparison of quantum chemical TDDFT calculated and experimental ECD spectra. Among hitherto known compounds with a verrucosidine backbone isolated from natural resource, compound 1 represents the first example of a new conformational isomer of its skeleton, exhibiting antibiotic activity against Bacillus subtilis with MIC value 32 μg/mL. PMID:27548192

A spectroscopic study on the coordination and solution structures of the interaction systems between biperoxidovanadate complexes and the pyrazolylpyridine-like ligands.

PubMed

Yu, Xian-Yong; Deng, Lin; Zheng, Baishu; Zeng, Bi-Rong; Yi, Pinggui; Xu, Xin

2014-01-28

In order to understand the substitution effects of pyrazolylpyridine (pzpy) on the coordination reaction equilibria, the interactions between a series of pzpy-like ligands and biperoxidovanadate ([OV(O2)2(D2O)](-)/[OV(O2)2(HOD)](-), abbrv. bpV) have been explored using a combination of multinuclear ((1)H, (13)C, and (51)V) magnetic resonance, heteronuclear single quantum coherence (HSQC), and variable temperature NMR in a 0.15 mol L(-1) NaCl D2O solution that mimics the physiological conditions. Both the direct NMR data and the equilibrium constants are reported for the first time. A series of new hepta-coordinated peroxidovanadate species [OV(O2)2L](-) (L = pzpy-like chelating ligands) are formed due to several competitive coordination interactions. According to the equilibrium constants for products between bpV and the pzpy-like ligands, the relative affinity of the ligands is found to be pzpy > 2-Ester-pzpy ≈ 2-Me-pzpy ≈ 2-Amide-pzpy > 2-Et-pzpy. In the interaction system between bpV and pzpy, a pair of isomers (Isomers A and B) are observed in aqueous solution, which are attributed to different types of coordination modes between the metal center and the ligands, while the crystal structure of NH4[OV(O2)2(pzpy)]·6H2O (CCDC 898554) has the same coordination structure as Isomer A (the main product for pzpy). For the N-substituted ligands, however, Isomer A or B type complexes can also be observed in solution but the molar ratios of the isomer are reversed (i.e., Isomer B type is the main product). These results demonstrate that when the N atom in the pyrazole ring has a substitution group, hydrogen bonding (from the H atom in the pyrazole ring), the steric effect (from alkyl) and the solvation effect (from the ester or amide group) can jointly affect the coordination reaction equilibrium.

Tautomeric preferences of the cis and trans isomers of axitinib

NASA Astrophysics Data System (ADS)

Mirzaei, M. Saeed; Taherpour, Avat Arman

2018-05-01

The tautomeric preferences of axitinib, a potent anticancer drug, as tyrosine kinase inhibitor have been investigated using quantum chemical calculations and docking methods. The energy differences between the two tautomers of trans-isomer are around 4 and 3 kcal mol-1 in vacuo and water, respectively, and for its cis-isomer (major photochemical isomerization product) this equilibrium reversed completely in favour of the second tautomer (not considered previously), which is about 7-8 kcal mol-1 more stable in both gas and aqueous media. The results indicate a very high activation energy for proton exchange for both [1,2] and [1,5] H-shift (around 50 kcal mol-1) in the gas phase, but inclusion of protic solvents (e.g. water) decrease this barrier to around 14 and 35 kcal mol-1 for the both hydrogen shift processes, respectively. In order to have better insight about the electronic structure of axitinib tautomers, the NBO, HOMO-LUMO, NICS and molecular electrostatic potential surfaces (MESP) calculations have been carried out. Docking investigations on the two more stable tautomers revealed that binding of the trans isomer of tautomer I to the active site of the receptor is the most favourable in the terms of energy and structure. This more stability could be attributed to the more hydrogen bonding of this tautomer with the protein residues in comparison to the second tautomer.

Quantum chemical calculations of anion complex [B12Hx(CF3)12-x]2-, x = 9 - 12

NASA Astrophysics Data System (ADS)

Koblova, Elena A.; Saldin, Vitaly I.; Ustinov, Alexander Yu.

2016-12-01

The geometric, energetic, spectral and electronic properties of the most stable isomers of B12Hx(CF3)12-X2- anion complex with x = 9 - 12 have been studied using Density Functional Theory (B3LYP/6-311++G**). It was shown that these isomers are characterized by the preference to form the most symmetric structures with uniformly distributed charge densities. However, when replacing a hydrogen atom with fluoromethyl group, an inductive effect occurs. Blue shifts in the IR spectrum compared to the vibrations of the free CF3 molecule are in the range of 2 - 69 cm-1 and points to the stability of B12Hx(CF3)12-x2- anions.

Discrimination of nuclear spin isomers exploiting the excited state dynamics of a quinodimethane derivative

DOE Office of Scientific and Technical Information (OSTI.GOV)

Obaid, Rana; Faculty of Pharmacy, Al-Quds University, Abu Dis, Palestine; Kinzel, Daniel

2014-10-28

Despite the concept of nuclear spin isomers (NSIs) exists since the early days of quantum mechanics, only few approaches have been suggested to separate different NSIs. Here, a method is proposed to discriminate different NSIs of a quinodimethane derivative using its electronic excited state dynamics. After electronic excitation by a laser field with femtosecond time duration, a difference in the behavior of several quantum mechanical operators can be observed. A pump-probe experimental approach for separating these different NSIs is then proposed.

Experimental and Quantum-Chemical Study of Electronically Excited States of Protolytic Isovanillin Species

NASA Astrophysics Data System (ADS)

Vusovich, O. V.; Tchaikovskaya, O. N.; Sokolova, I. V.; Vasil'eva, N. Yu.

2014-05-01

Methods of electronic spectroscopy and quantum chemistry are used to compare protolytic vanillin and isovanillin species. Three protolytic species: anion, cation, and neutral are distinguished in the ground state of the examined molecules. Vanillin and isovanillin in the ground state in water possess identical spectral characteristics: line positions and intensities in the absorption spectra coincide. Minima of the electrostatic potential demonstrate that the deepest isomer minimum is observed on the carbonyl oxygen atom. However, investigations of the fluorescence spectra show that the radiative properties of isomers differ. An analysis of results of quantum-chemical calculations demonstrate that the long-wavelength ππ* transition in the vanillin absorption spectra is formed due to electron charge transfer from the phenol part of the molecule to oxygen atoms of the methoxy and carbonyl groups, and in the isovanillin absorption spectra, it is formed only on the oxygen atom of the methoxy group. The presence of hydroxyl and carbonyl groups in the structure of the examined molecules leads to the fact that isovanillin in the ground S0 state, the same as vanillin, possesses acidic properties, whereas in the excited S1 state, they possess basic properties. A comparison of the рKа values of aqueous solutions demonstrates that vanillin possesses stronger acidic and basic properties in comparison with isovanillin.

Quantum size effects in the size-temperature phase diagram of gallium: structural characterization of shape-shifting clusters.

PubMed

Steenbergen, Krista G; Gaston, Nicola

2015-02-09

Finite temperature analysis of cluster structures is used to identify signatures of the low-temperature polymorphs of gallium, based on the results of first-principle Born-Oppenheimer molecular dynamics simulations. Pre-melting structural transitions proceed from either the β- and/or the δ-phase to the γ- or δ-phase, with a size- dependent phase progression. We relate the stability of each isomer to the electronic structures of the different phases, giving new insight into the origin of polymorphism in this complicated element. © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Detailed solvent, structural, quantum chemical study and antimicrobial activity of isatin Schiff base

NASA Astrophysics Data System (ADS)

Brkić, Dominik R.; Božić, Aleksandra R.; Marinković, Aleksandar D.; Milčić, Miloš K.; Prlainović, Nevena Ž.; Assaleh, Fathi H.; Cvijetić, Ilija N.; Nikolić, Jasmina B.; Drmanić, Saša Ž.

2018-05-01

The ratios of E/Z isomers of sixteen synthesized 1,3-dihydro-3-(substituted phenylimino)-2H-indol-2-one were studied using experimental and theoretical methodology. Linear solvation energy relationships (LSER) rationalized solvent influence of the solvent-solute interactions on the UV-Vis absorption maxima shifts (νmax) of both geometrical isomers using the Kamlet-Taft equation. Linear free energy relationships (LFER) in the form of single substituent parameter equation (SSP) was used to analyze substituent effect on pKa, NMR chemical shifts and νmax values. Electron charge density was obtained by the use of Quantum Theory of Atoms in Molecules, i.e. Bader's analysis. The substituent and solvent effect on intramolecular charge transfer (ICT) were interpreted with the aid of time-dependent density functional (TD-DFT) method. Additionally, the results of TD-DFT calculations quantified the efficiency of ICT from the calculated charge-transfer distance (DCT) and amount of transferred charge (QCT). The antimicrobial activity was evaluated using broth microdilution method. 3D QSAR modeling was used to demonstrate the influence of substituents effect as well as molecule geometry on antimicrobial activity.

Site-specific binding of a water molecule to the sulfa drugs sulfamethoxazole and sulfisoxazole: a laser-desorption isomer-specific UV and IR study.

PubMed

Uhlemann, Thomas; Seidel, Sebastian; Müller, Christian W

2018-03-07

To determine the preferred water molecule binding sites of the polybasic sulfa drugs sulfamethoxazole (SMX) and sulfisoxazole (SIX), we have studied their monomers and monohydrated complexes through laser-desorption conformer-specific UV and IR spectroscopy. Both the SMX and SIX monomer adopt a single conformer in the molecular beam. On the basis of their conformer-specific IR spectra in the NH stretch region, these conformers were assigned to the SMX and SIX global minimum structures, both exhibiting a staggered sulfonamide group and an intramolecular C-HO[double bond, length as m-dash]S hydrogen bond. The SMX-H 2 O and SIX-H 2 O complexes each adopt a single isomer in the molecular beam. Their isomeric structures were determined based on their isomer-specific IR spectra in the NH/OH stretch region. Quantum Theory of Atoms in Molecules analysis of the calculated electron densities revealed that in the SMX-H 2 O complex the water molecule donates an O-HN hydrogen bond to the heterocycle nitrogen atom and accepts an N-HO hydrogen bond from the sulfonamide NH group. In the SIX-H 2 O complex, however, the water molecule does not bind to the heterocycle but instead donates an O-HO[double bond, length as m-dash]S hydrogen bond to the sulfonamide group and accepts an N-HO hydrogen bond from the sulfonamide NH group. Both water complexes are additionally stabilized by a C ph -HOH 2 hydrogen bond. Interacting Quantum Atoms analysis suggests that all intermolecular hydrogen bonds are dominated by the short-range exchange-correlation contribution.

The boron conundrum: Bonding in the bowl B30 and B36, fullerene B40 and triple ring B42 clusters

NASA Astrophysics Data System (ADS)

Pham, Hung Tan; Duong, L. V.; Tam, Nguyen Minh; Pham-Ho, M. P.; Nguyen, Minh Tho

2014-07-01

Geometries and bonding of B30, B36, B40 and B42 clusters were studied using quantum chemical computations. The bowl B30 and B36 and planar B42 clusters exhibit disk aromaticity. Diatropic ring current is strong in B30 and weaker in B42. A fullerene-like B40 (D2d) having two hexagons and four heptagons was found as the lowest-lying isomer. Such a fullerene whose MOs closely mimic those of the buckyball B80, represents novel structural feature of boron clusters. The most stable B42 (C2h) isomer is a triple ring tube with consistent σ + π diatropic magnetic responses making it a tubular aromatic species.

Non-conjugated, phenyl assisted coupling in through bond electron transfer in a perylenemonoimide-triphenylamine system.

PubMed

Bell, Toby D M; Stefan, Alina; Lemaur, Vincent; Bernhardt, Stefan; Müllen, Klaus; Cornil, Jérôme; Beljonne, David; Hofkens, Johan; Van der Auweraer, Mark; De Schryver, Frans C

2007-04-01

Two donor-bridge-acceptor compounds containing triphenylamine (TPA) donors and perylenemonoimide (PMI) acceptors have been studied by spectroscopic techniques and quantum chemical computation. Both systems have been observed to emit prompt and delayed fluorescence under certain conditions indicating that forward and reverse electron transfer (ET) processes can occur between the locally excited and the charge separated states. The experimental and computational results show that the TPA and PMI chromophores are better coupled by almost 50% in the meta isomers which undergo ET more readily than the para isomers. Quantum chemical calculations indicate that this unexpected situation is the result of a phenyl group on the side of the bridge being advantageously positioned in the meta isomers. This leads to more extensive delocalisation of the TPA HOMO into the bridge enhancing the total through bond electronic coupling between the TPA and PMI chromophores. The calculations also indicate a strong angle dependence of the total coupling in both isomers. The experimental results are discussed in the context of the high temperature limit of Marcus's theory of non-adiabatic ET.

Quantum-chemical insights from deep tensor neural networks

PubMed Central

Schütt, Kristof T.; Arbabzadah, Farhad; Chmiela, Stefan; Müller, Klaus R.; Tkatchenko, Alexandre

2017-01-01

Learning from data has led to paradigm shifts in a multitude of disciplines, including web, text and image search, speech recognition, as well as bioinformatics. Can machine learning enable similar breakthroughs in understanding quantum many-body systems? Here we develop an efficient deep learning approach that enables spatially and chemically resolved insights into quantum-mechanical observables of molecular systems. We unify concepts from many-body Hamiltonians with purpose-designed deep tensor neural networks, which leads to size-extensive and uniformly accurate (1 kcal mol−1) predictions in compositional and configurational chemical space for molecules of intermediate size. As an example of chemical relevance, the model reveals a classification of aromatic rings with respect to their stability. Further applications of our model for predicting atomic energies and local chemical potentials in molecules, reliable isomer energies, and molecules with peculiar electronic structure demonstrate the potential of machine learning for revealing insights into complex quantum-chemical systems. PMID:28067221

Quantum-chemical insights from deep tensor neural networks.

PubMed

Schütt, Kristof T; Arbabzadah, Farhad; Chmiela, Stefan; Müller, Klaus R; Tkatchenko, Alexandre

2017-01-09

Learning from data has led to paradigm shifts in a multitude of disciplines, including web, text and image search, speech recognition, as well as bioinformatics. Can machine learning enable similar breakthroughs in understanding quantum many-body systems? Here we develop an efficient deep learning approach that enables spatially and chemically resolved insights into quantum-mechanical observables of molecular systems. We unify concepts from many-body Hamiltonians with purpose-designed deep tensor neural networks, which leads to size-extensive and uniformly accurate (1 kcal mol -1 ) predictions in compositional and configurational chemical space for molecules of intermediate size. As an example of chemical relevance, the model reveals a classification of aromatic rings with respect to their stability. Further applications of our model for predicting atomic energies and local chemical potentials in molecules, reliable isomer energies, and molecules with peculiar electronic structure demonstrate the potential of machine learning for revealing insights into complex quantum-chemical systems.

Quantum-chemical insights from deep tensor neural networks

NASA Astrophysics Data System (ADS)

Schütt, Kristof T.; Arbabzadah, Farhad; Chmiela, Stefan; Müller, Klaus R.; Tkatchenko, Alexandre

2017-01-01

Learning from data has led to paradigm shifts in a multitude of disciplines, including web, text and image search, speech recognition, as well as bioinformatics. Can machine learning enable similar breakthroughs in understanding quantum many-body systems? Here we develop an efficient deep learning approach that enables spatially and chemically resolved insights into quantum-mechanical observables of molecular systems. We unify concepts from many-body Hamiltonians with purpose-designed deep tensor neural networks, which leads to size-extensive and uniformly accurate (1 kcal mol-1) predictions in compositional and configurational chemical space for molecules of intermediate size. As an example of chemical relevance, the model reveals a classification of aromatic rings with respect to their stability. Further applications of our model for predicting atomic energies and local chemical potentials in molecules, reliable isomer energies, and molecules with peculiar electronic structure demonstrate the potential of machine learning for revealing insights into complex quantum-chemical systems.

Isomer-specific vibronic structure of the 9-, 1-, and 2-anthracenyl radicals via slow photoelectron velocity-map imaging

PubMed Central

DeVine, Jessalyn A.; Levine, Daniel S.; Kim, Jongjin B.; Neumark, Daniel M.

2016-01-01

Polycyclic aromatic hydrocarbons, in various charge and protonation states, are key compounds relevant to combustion chemistry and astrochemistry. Here, we probe the vibrational and electronic spectroscopy of gas-phase 9-, 1-, and 2-anthracenyl radicals (C14H9) by photodetachment of the corresponding cryogenically cooled anions via slow photoelectron velocity-map imaging (cryo-SEVI). The use of a newly designed velocity-map imaging lens in combination with ion cooling yields photoelectron spectra with <2 cm−1 resolution. Isomer selection of the anions is achieved using gas-phase synthesis techniques, resulting in observation and interpretation of detailed vibronic structure of the ground and lowest excited states for the three anthracenyl radical isomers. The ground-state bands yield electron affinities and vibrational frequencies for several Franck–Condon active modes of the 9-, 1-, and 2-anthracenyl radicals; term energies of the first excited states of these species are also measured. Spectra are interpreted through comparison with ab initio quantum chemistry calculations, Franck–Condon simulations, and calculations of threshold photodetachment cross sections and anisotropies. Experimental measures of the subtle differences in energetics and relative stabilities of these radical isomers are of interest from the perspective of fundamental physical organic chemistry and aid in understanding their behavior and reactivity in interstellar and combustion environments. Additionally, spectroscopic characterization of these species in the laboratory is essential for their potential identification in astrochemical data. PMID:26792521

Isomer-specific vibronic structure of the 9-, 1-, and 2-anthracenyl radicals via slow photoelectron velocity-map imaging

DOE Office of Scientific and Technical Information (OSTI.GOV)

Weichman, Marissa L.; DeVine, Jessalyn A.; Levine, Daniel S.

Polycyclic aromatic hydrocarbons, in various charge and protonation states, are key compounds relevant to combustion chemistry and astrochemistry. In this paper, we probe the vibrational and electronic spectroscopy of gas-phase 9-, 1-, and 2-anthracenyl radicals (C 14H 9) by photodetachment of the corresponding cryogenically cooled anions via slow photoelectron velocity-map imaging (cryo-SEVI). The use of a newly designed velocity-map imaging lens in combination with ion cooling yields photoelectron spectra with <2 cm -1 resolution. Isomer selection of the anions is achieved using gas-phase synthesis techniques, resulting in observation and interpretation of detailed vibronic structure of the ground and lowest excitedmore » states for the three anthracenyl radical isomers. The ground-state bands yield electron affinities and vibrational frequencies for several Franck–Condon active modes of the 9-, 1-, and 2-anthracenyl radicals; term energies of the first excited states of these species are also measured. Spectra are interpreted through comparison with ab initio quantum chemistry calculations, Franck–Condon simulations, and calculations of threshold photodetachment cross sections and anisotropies. Experimental measures of the subtle differences in energetics and relative stabilities of these radical isomers are of interest from the perspective of fundamental physical organic chemistry and aid in understanding their behavior and reactivity in interstellar and combustion environments. Finally and additionally, spectroscopic characterization of these species in the laboratory is essential for their potential identification in astrochemical data.« less

Isomer-specific vibronic structure of the 9-, 1-, and 2-anthracenyl radicals via slow photoelectron velocity-map imaging

DOE PAGES

Weichman, Marissa L.; DeVine, Jessalyn A.; Levine, Daniel S.; ...

2016-01-20

Polycyclic aromatic hydrocarbons, in various charge and protonation states, are key compounds relevant to combustion chemistry and astrochemistry. In this paper, we probe the vibrational and electronic spectroscopy of gas-phase 9-, 1-, and 2-anthracenyl radicals (C 14H 9) by photodetachment of the corresponding cryogenically cooled anions via slow photoelectron velocity-map imaging (cryo-SEVI). The use of a newly designed velocity-map imaging lens in combination with ion cooling yields photoelectron spectra with <2 cm -1 resolution. Isomer selection of the anions is achieved using gas-phase synthesis techniques, resulting in observation and interpretation of detailed vibronic structure of the ground and lowest excitedmore » states for the three anthracenyl radical isomers. The ground-state bands yield electron affinities and vibrational frequencies for several Franck–Condon active modes of the 9-, 1-, and 2-anthracenyl radicals; term energies of the first excited states of these species are also measured. Spectra are interpreted through comparison with ab initio quantum chemistry calculations, Franck–Condon simulations, and calculations of threshold photodetachment cross sections and anisotropies. Experimental measures of the subtle differences in energetics and relative stabilities of these radical isomers are of interest from the perspective of fundamental physical organic chemistry and aid in understanding their behavior and reactivity in interstellar and combustion environments. Finally and additionally, spectroscopic characterization of these species in the laboratory is essential for their potential identification in astrochemical data.« less

Structure, spectroscopy, and dynamics of the phenol-(water)2 cluster at low and high temperatures

NASA Astrophysics Data System (ADS)

Samala, Nagaprasad Reddy; Agmon, Noam

2017-12-01

Aqueous solutions are complex due to hydrogen bonding (HBing). While gas-phase clusters could provide clues on the solution behavior, most neutral clusters were studied at cryogenic temperatures. Recent results of Shimamori and Fujii provide the first IR spectrum of warm phenol-(H2O)2 clusters. To understand the temperature (T) effect, we have revisited the structure and spectroscopy of phenol-(H2O)2 at all T. While older quantum chemistry work concluded that the cyclic isomers are the most stable, the inclusion of dispersion interactions reveals that they are nearly isoenergetic with isomers forming π-HBs with the phenyl ring. Whereas the OH-stretch bands were previously assigned to purely local modes, we show that at low T they involve a concerted component. We have calculated the (static) anharmonic IR spectra for all low-lying isomers, showing that at the MP2 level, one can single out one isomer (udu) as accounting for the low-T spectrum to 3 cm-1 accuracy. Yet no isomer can explain the substantial blueshift of the phenyl-OH band at elevated temperatures. We describe the temperature effect using ab initio molecular dynamics with a density functional and basis-set (B3LYP-D3/aug-cc-pVTZ) that provide a realistic description of OH⋯O vs. OH⋯π HBing. From the dipole moment autocorrelation function, we obtain good description for both low- and high-T spectra. Trajectory visualization suggests that the ring structure remains mostly intact even at high T, with intermittent switching between OH⋯O and OH⋯π HBing and lengthening of all 3 HBs. The phenyl-OH blueshift is thus attributed to strengthening of its OH bond. A model for three beads on a ring suggests that this shift is partly offset by the elimination of coupling to the other OH bonds in the ring, whereas for the two water molecules these two effects nearly cancel.

Analysis of the isomer ratios of polymethylated-DOTA complexes and the implications on protein structural studies

PubMed Central

Opina, Ana Christina L.; Strickland, Madeleine; Lee, Yong-Sok; Tjandra, Nico; Byrd, R. Andrew; Swenson, Rolf E.; Vasalatiy, Olga

2016-01-01

A rigidified and symmetrical polymethylated 1,4,7,10-tetraazacyclododecane-1,4,7,10-tetraacetic acid (DOTA) ligand bearing four SSSS methyl groups in both the tetraaza ring and the acetate arms (SSSS-SSSS-M4DOTMA) was prepared. The isomer ratio of SSSS-SSSS-M4DOTMA complexed with a series of lanthanide ions was carefully investigated using RP-HPLC and NMR. A square antiprismatic (SAP) configuration was exclusively observed for the early lanthanides, while the twisted square antiprismatic (TSAP) geometry was preferred as the lanthanide ion size decreases. The late lanthanides preferentially adopted the TSAP geometry. One of the pendant arms was modified with a pyridyl disulfide group (SSSS-SSSS-M8SPy) for cysteine attachment and displayed a similar isomer trend as the parent compound, Ln-SSSS-SSSS-M4DOTMA. Covalent attachment to the ubiquitin S57C mutant showed resonances whose intensities are in agreement with the isomeric population observed by HPLC. Furthermore, the NOE experiments combined with quantum chemical calculations have unequivocally demonstrated that the SAP of Pr-SSSS-SSSS-M4DOTMA and Pr-SSSS-SSSS-M8SPy, as well as the TSAP of Yb-SSSS-SSSS-M8SPy are more stable than their corresponding isomers. PMID:26857249

Association Mechanisms of Unsaturated C2 Hydrocarbons with Their Cations: Acetylene and Ethylene

NASA Technical Reports Server (NTRS)

Bera, Partha P.; Head-Gordon, Martin; Lee, Timothy J.

2013-01-01

The ion-molecule association mechanism of acetylene and ethylene with their cations is investigated by ab initio quantum chemical methods to understand the structures, association energies, and the vibrational and electronic spectra of the products. Stable puckered cyclic isomers are found as the result of first forming less stable linear and bridge isomers. The puckered cyclic complexes are calculated to be strongly bound, by 87, 35 and 56 kcal/mol for acetylene-acetylene cation, ethylene-ethylene cation and acetylene-ethylene cation, respectively. These stable complexes may be intermediates that participate in further association reactions. There are no association barriers, and no significant inter-conversion barriers, so the initial linear and bridge encounter complexes are unlikely to be observable. However, the energy gap between the bridged and cyclic puckered isomers greatly differs from complex to complex: it is 44 kcal/mol in C4H4 +, but only 6 kcal/mol in C4H8 +. The accurate CCSD(T) calculations summarized above are also compared against less computationally expensive MP2 and density functional theory (DFT) calculations for structures, relative energies, and vibrational spectra. Calculated vibrational spectra are compared against available experiments for cyclobutadiene cation. Electronic spectra are also calculated using time-dependent DFT.

Exploration of the Ca2+ interaction modes of the nifedipine calcium channel antagonist.

PubMed

Liu, Huichun; Zhang, Liang; Li, Ping; Cukier, Robert I; Bu, Yuxiang

2007-02-02

A comprehensive study is carried out using quantum chemical computation and molecular dynamics (MD) simulations to gain insight into the interaction between Ca(2+) ions and the most important class of calcium channel antagonists--nifedipine. First, the chelating structures and energetic characters of nifedipine-Ca(2+) in the gas phase are explored, and 25 isomers are found. The most favorable chelating mode is a tridentate one, that is, Ca(2+) binds to two carbonyl O atoms and one nitryl O atom, where Ca(2+) is above the plane of the three O atoms to form a pyramidal structure. Accurate geometric structures, relative stabilities, vertical and adiabatic binding energies, and charge distributions are discussed. The differences in the geometries and energies among these isomers are analyzed from the contributions of chelating sites, electrostatics and polarizations, steric repulsions, and charge distributions. The interconversions among isomers with similar geometries and energies are also investigated because of the importance of the geometric transformation in the biological system. Furthermore, certain numbers of water molecules are added to the nifedipine-Ca(2+) system to probe the effect of water. A detailed study is performed on the hydrated geometries on the basis of the most stable isomer 1. Stepwise hydration can weaken the nifedipine-Ca(2+) interaction, and the chelating sites of nifedipine are gradually replaced by the added water molecules. Hexacoordination is found to be the most favorable geometry no matter how many water molecules were added, which can be verified by the MD simulations. The transfer of water molecules from the inner shell to the outer shell is also supported by MD simulations of the hexahydrated complexes.

Quantum chemical calculations of anion complex [B12Hx(NF2)12-x]2-, x = 9 - 12

NASA Astrophysics Data System (ADS)

Koblova, E. A.; Saldin, V. I.; Ustinov, A. Yu

2017-01-01

The geometric, energetic, spectral and electronic properties of various isomers of B12Hх(NF2)12-х 2- anion complex with x = 9 - 12 have been studied using Density Functional Theory (B3LYP/6-311++G**). It was shown that the most stable isomers are characterized by the preference to form the most symmetric structures with uniformly distributed charge densities. However, when replacing a hydrogen atom with difluoramino group, an inductive effect occurs. NF2 group pulls a part of electron density that leads to the polarization of the boron core. Blue shifts in the IR spectrum compared to the vibrations of the free radical NF2 ranging from 5 to 69 cm-1 for the most stable isomers with the minimum total energy are characteristic and points to the stability of B12Hх(NF2)12-х 2- anions. The obtained results broaden the idea of aromaticity of B12H12 2- anion and will be useful in synthesis of new B12H12 2- derivatives.

Influence of pH on the cis- trans isomerization of Valine-Proline dipeptide: An integrated NMR and theoretical investigation

NASA Astrophysics Data System (ADS)

Ivanova, Galya; Yakimova, Boryana; Angelova, Silvia; Stoineva, Ivanka; Enchev, Venelin

2010-06-01

The pH influence on the cis- trans isomerization of the Valine-Proline dipeptide was investigated by means of NMR spectral techniques and quantum chemical calculations at different computational levels. It was found that the process of isomerization is strongly pH dependent. The trans-isomer of Val-Pro is the more abundant isomer when the amino group is protonated, while an approximately equal distribution between the cis and trans-isomers for the neutral and anion forms of the dipeptide was confirmed.

Theoretical and experimental NMR study of protopine hydrochloride isomers.

PubMed

Tousek, Jaromír; Malináková, Katerina; Dostál, Jirí; Marek, Radek

2005-07-01

The 1H and 13C NMR chemical shifts of cis- and trans-protopinium salts were measured and calculated. The calculations of the chemical shifts consisted of conformational analysis, geometry optimization (RHF/6-31G** method) and shielding constants calculations (B3LYP/6-31G** method). Based on the results of the quantum chemical calculations, two sets of experimental chemical shifts were assigned to the particular isomers. According to the experimental results, the trans-isomer is more stable and its population is approximately 68%. Copyright 2005 John Wiley & Sons, Ltd

[Ortho/para spin-isomers of H2O molecules as a factor responsible for formation of two structural motifs in water].

PubMed

Zakharov, S D

2013-01-01

According to the last results obtained by small-angle X-ray scattering and X-ray spectroscopy it was suggested that water within the nanometer scale represents a fluctuating mixture of clusters with tetrahedral structure and a subphase with partially broken hydrogen bonds whereas the nuclear configuration of the H20 molecule corresponds to single tetrahedral coordination. The basic reason of such structural partition is not clear until now. Here we show that it can be associated with the existence of two nuclear H2O spin-isomers which have different probability to be in one or another subphase. The para-molecule can transfer an excess of its rotational energy to the environment up to the complete stopping of rotation because its rotational quantum number J = 0 in the basic state. This property is favorable for the formation of clusters with closed H-bonds. Ortho-molecules with odd-numbered J states lack for this property and thus should be predominantly present in the surrounding with distorted bonds.

Versatile Indolocarbazole-Isomer Derivatives as Highly Emissive Emitters and Ideal Hosts for Thermally Activated Delayed Fluorescent OLEDs with Alleviated Efficiency Roll-Off.

PubMed

Zhang, Dongdong; Song, Xiaozeng; Cai, Minghan; Kaji, Hironori; Duan, Lian

2018-02-01

Maintaining high efficiency at high brightness levels is an exigent challenge for real-world applications of thermally activated delayed fluorescent organic light-emitting diodes (TADF-OLEDs). Here, versatile indolocarbazole-isomer derivatives are developed as highly emissive emitters and ideal hosts for TADF-OLEDs to alleviate efficiency roll-off. It is observed that photophysical and electronic properties of these compounds can be well modulated by varying the indolocarbazole isomers. A photoluminescence quantum yield (η PL ) approaching unity and a maximum external quantum efficiency (EQE max ) of 25.1% are obtained for the emitter with indolo[3,2-a]carbazolyl subunit. Remarkably, record-high EQE/power efficiency of 26.2%/69.7 lm W -1 at the brightness level of 5000 cd m -2 with a voltage of only 3.74 V are also obtained using the same isomer as the host in a green TADF-OLED. It is evident that TADF hosts with high η PL values, fast reverse intersystem crossing processes, and balanced charge transport properties may open the path toward roll-off-free TADF-OLEDs. © 2018 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Phototransformation of azoxystrobin fungicide in organic solvents. Photoisomerization vs. photodegradation.

PubMed

Chastain, Jeoffrey; ter Halle, Alexandra; de Sainte Claire, Pascal; Voyard, Guillaume; Traikïa, Mounir; Richard, Claire

2013-12-01

Azoxystrobin is a systemic fungicide that has a tendency to accumulate at the surface of crop leaves or inside their cuticle where it undergoes photodegradation. Its photochemistry was investigated in n-heptane and isopropanol to mimic the polarity of wax leaves. Using analytical and kinetic data, we demonstrate that azoxystrobin (isomer E) undergoes efficient photoisomerization into the isomer Z with a quantum yield of 0.75 ± 0.08. This value is 30-fold higher than that reported in aqueous solution. The photoisomerization of isomer Z into azoxystrobin is more efficient with a chemical yield of 0.95 ± 0.1. In addition, a pseudo photostationary equilibrium is reached when the ratio [azoxystrobin]/[isomer Z] is 2.0 ± 0.1. Photodegradation also takes place from azoxystrobin (quantum yield = 0.073 ± 0.008). Photoproducts mainly arise from bond cleavage between rings and from demethylation of the ether with or without saturation of the acrylate double bond. Theoretical calculations were undertaken to investigate the photoisomerization mechanism and the solvent effect. These data show that the photochemical reactivity of azoxystrobin is enhanced when the solvent polarity decreases and thus should be significant in leaf waxes.

Møller-Plesset perturbation theory gradient in the generalized hybrid orbital quantum mechanical and molecular mechanical method

NASA Astrophysics Data System (ADS)

Jung, Jaewoon; Sugita, Yuji; Ten-no, S.

2010-02-01

An analytic gradient expression is formulated and implemented for the second-order Møller-Plesset perturbation theory (MP2) based on the generalized hybrid orbital QM/MM method. The method enables us to obtain an accurate geometry at a reasonable computational cost. The performance of the method is assessed for various isomers of alanine dipepetide. We also compare the optimized structures of fumaramide-derived [2]rotaxane and cAMP-dependent protein kinase with experiment.

Ab initio electron correlated studies on the intracluster reaction of NO+ (H2O)(n) → H3O+ (H2O)(n-2) (HONO) (n = 4 and 5).

PubMed

Asada, Toshio; Nagaoka, Masataka; Koseki, Shiro

2011-01-28

Hydrated nitrosonium ion clusters NO(+)(H(2)O)(n) (n = 4 and 5) were investigated by using MP2/aug-cc-pVTZ level of theory to clarify isomeric reaction pathways for formation of HONO and fully hydrated hydride ions. We found some new isomers and transition state structures in each hydration number, whose lowest activation energies of the intracluster reactions were found to be 4.1 and 3.4 kcal mol(-1) for n = 4 and n = 5, respectively. These thermodynamic properties and full quantum mechanical molecular dynamics simulation suggest that product isomers with HONO and fully hydrated hydride ions can be obtained at n = 4 and n = 5 in terms of excess hydration binding energies which can overcome these activation barriers.

Theoretical studies on absorption, emission, and resonance Raman spectra of Coumarin 343 isomers

NASA Astrophysics Data System (ADS)

Wu, Wenpeng; Cao, Zexing; Zhao, Yi

2012-03-01

The vibrationally resolved spectral method and quantum chemical calculations are employed to reveal the structural and spectral properties of Coumarin 343 (C343), an ideal candidate for organic dye photosensitizers, in vacuum and solution. The results manifest that the ground-state energies are dominantly determined by different placements of hydrogen atom in carboxylic group of C343 conformations. Compared to those in vacuum, the electronic absorption spectra in methanol solvent show a hyperchromic property together with the redshift and blueshift for the neutral C343 isomers and their deprotonated anions, respectively. From the absorption, emission, and resonance Raman spectra, it is found that the maximal absorption and emission come from low-frequency modes whereas the high-frequency modes have high Raman activities. The detailed spectra are further analyzed for the identification of the conformers and understanding the potential charge transfer mechanism in their photovoltaic applications.

Probing photochromic properties by correlation of UV-visible and infra-red absorption spectroscopy: a case study with cis-1,2-dicyano-1,2-bis(2,4,5-trimethyl-3-thienyl)ethene.

PubMed

Spangenberg, Arnaud; Piedras Perez, Jose Alejandro; Patra, Abhijit; Piard, Jonathan; Brosseau, Arnaud; Métivier, Rémi; Nakatani, Keitaro

2010-02-01

Quantification of the relative composition of the isomers in a photochromic system at any irradiation time interval is a critical issue in determining absolute quantum yields. For this purpose, we have developed a simple and convenient protocol involving combination of UV-visible and infra-red absorption spectroscopy. Photochromic cyclization reaction of cis-l,2-dicyano-l,2-bis(2,4,5-trimethyl-3-thieny1)ethene (CMTE) is analyzed to demonstrate the efficiency of the proposed methodology. This approach is based on the fact that the two isomers show distinctive infra-red bands. Detailed investigations of the UV-visible and infra-red spectra of the mixture obtained at different irradiation times in CCl(4) supported by quantum chemical computations lead to the unambiguous estimation of molar absorption coefficients of the closed isomer (epsilon(CF) = 4650 L mol(-1) cm(-1) at 512 nm). It facilitates the first determination of absolute quantum yields of this reversible photochromic reaction in CCl(4) by fitting the UV-visible spectral data (Phi(OF-->CF) = 0.41 +/- 0.05 and Phi(CF-->OF) = 0.12 +/- 0.02 at 405 nm and 546 nm, respectively).

SASS: A symmetry adapted stochastic search algorithm exploiting site symmetry

NASA Astrophysics Data System (ADS)

Wheeler, Steven E.; Schleyer, Paul v. R.; Schaefer, Henry F.

2007-03-01

A simple symmetry adapted search algorithm (SASS) exploiting point group symmetry increases the efficiency of systematic explorations of complex quantum mechanical potential energy surfaces. In contrast to previously described stochastic approaches, which do not employ symmetry, candidate structures are generated within simple point groups, such as C2, Cs, and C2v. This facilitates efficient sampling of the 3N-6 Pople's dimensional configuration space and increases the speed and effectiveness of quantum chemical geometry optimizations. Pople's concept of framework groups [J. Am. Chem. Soc. 102, 4615 (1980)] is used to partition the configuration space into structures spanning all possible distributions of sets of symmetry equivalent atoms. This provides an efficient means of computing all structures of a given symmetry with minimum redundancy. This approach also is advantageous for generating initial structures for global optimizations via genetic algorithm and other stochastic global search techniques. Application of the SASS method is illustrated by locating 14 low-lying stationary points on the cc-pwCVDZ ROCCSD(T) potential energy surface of Li5H2. The global minimum structure is identified, along with many unique, nonintuitive, energetically favorable isomers.

[H2O ortho-para spin conversion in aqueous solutions as a quantum factor of Konovalov paradox].

PubMed

Pershin, S M

2014-01-01

Recently academician Konovalov and co-workers observed an increase in electroconductivity and biological activity simultaneously with diffusion slowing (or nanoobject diameter increasing) and extremes of other parameters (ζ-potential, surface tension, pH, optical activity) in low concentration aqueous solutions. This phenomenon completely disappeared when samples were shielded against external electromagnetic fields by a Faraday cage. A conventional theory of water and water solutions couldn't explain "Konovalov paradox" observed in numerous experiments (representative sampling about 60 samples and 7 parameters). The new approach was suggested to describe the physics of water and explain "Konovalov paradox". The proposed concept takes into account the quantum differences of ortho-para spin isomers of H2O in bulk water (rotational spin-selectivity upon hydration and spontaneous formation of ice-like structures, quantum beats and spin conversion induced in the presence of a resonant electromagnetic radiation). A size-dependent self-assembly of amorphous complexes of H2O molecules more than 275 leading to the ice Ih structure observed in the previous experiments supports this concept.

Intramolecular interactions, isomerization and vibrational frequencies of two paracetamol analogues: A spectroscopic and a computational approach

NASA Astrophysics Data System (ADS)

Viana, Rommel B.; Ribeiro, Gabriela L. O.; Santos, Sinara F. F.; Quintero, David E.; Viana, Anderson B.; da Silva, Albérico B. F.; Moreno-Fuquen, Rodolfo

2016-06-01

The aim of this investigation was to determine the molecular properties and provide an interpretation of the vibrational mode couplings of these two paracetamol analogues: 2-bromo-2-methyl-N-(4-nitrophenyl)-propanamide and 2-bromo-2-methyl-N-p-tolyl-propanamide. E/Z isomers, keto/enol unimolecular rearrangement and prediction of the transition state structures in each mechanism were also assessed using the Density Functional Theory (DFT). The DFT estimates a high energy gap between E and Z isomers (9-11 kcal·mol- 1), with barrier heights ranging from 16 to 19 kcal·mol- 1. In contrast, the barrier energies on the keto/enol isomerization are almost 10 kcal·mol- 1 higher than those estimated for the E/Z rearrangement. The kinetic rate constant was also determined for each reaction mechanism. Natural bond orbital analysis and the quantum theory of atoms in molecules were used to interpret the intramolecular hydrogen bonds and to understand the most important interactions that govern the stabilization of each isomer. Furthermore, an analysis of the atomic charge distribution using different population methodologies was also performed.

Structure-biodegradability relationship of nonylphenol isomers during biological wastewater treatment process.

PubMed

Hao, Ruixia; Li, Jianbing; Zhou, Yuwen; Cheng, Shuiyuan; Zhang, Yi

2009-05-01

The relationship between nonylphenol (NP) isomer structure and its biodegradability within the wastewater treatment process of sequencing batch reactor (SBR) was investigated. The GC-MS method was used for detecting the NP isomers existing in the SBR influent, activated sludge and effluent. Fifteen NP isomers were detected in the influent, with significant biodegradability variations being observed among these isomers. It was found that the NP isomers associated with retention time of 10.553, 10.646, 10.774, and 10.906 min in the GC-MS analysis showed higher biodegradability, while the isomers with retention time of 10.475, 10.800, and 10.857 min illustrated lower biodegradability. Through analyzing the mass spectrograms, the chemical structures of four selected NP isomers in the wastewater were further deduced. The higher correlation coefficients of 0.9421 and 0.9085 were observed between the NP isomer biodegradation rates and the molecular connectivity indexes with the order of two and four, respectively. Such correlation analysis indicated that a more complex side branch structure (such as a larger side carbon-chain branch or more branches in the nonyl) of NP isomer would lead to lower biodegradability, and a longer nonyl chain of the isomer would result in a higher biodegradability.

Structures of cage, prism, and book isomers of water hexamer from broadband rotational spectroscopy.

PubMed

Pérez, Cristóbal; Muckle, Matt T; Zaleski, Daniel P; Seifert, Nathan A; Temelso, Berhane; Shields, George C; Kisiel, Zbigniew; Pate, Brooks H

2012-05-18

Theory predicts the water hexamer to be the smallest water cluster with a three-dimensional hydrogen-bonding network as its minimum energy structure. There are several possible low-energy isomers, and calculations with different methods and basis sets assign them different relative stabilities. Previous experimental work has provided evidence for the cage, book, and cyclic isomers, but no experiment has identified multiple coexisting structures. Here, we report that broadband rotational spectroscopy in a pulsed supersonic expansion unambiguously identifies all three isomers; we determined their oxygen framework structures by means of oxygen-18-substituted water (H(2)(18)O). Relative isomer populations at different expansion conditions establish that the cage isomer is the minimum energy structure. Rotational spectra consistent with predicted heptamer and nonamer structures have also been identified.

Substitution effects on the absorption spectra of nitrophenolate isomers.

PubMed

Wanko, Marius; Houmøller, Jørgen; Støchkel, Kristian; Suhr Kirketerp, Maj-Britt; Petersen, Michael Åxman; Nielsen, Mogens Brøndsted; Nielsen, Steen Brøndsted; Rubio, Angel

2012-10-05

Charge-transfer excitations highly depend on the electronic coupling between the donor and acceptor groups. Nitrophenolates are simple examples of charge-transfer systems where the degree of coupling differs between ortho, meta and para isomers. Here we report the absorption spectra of the isolated anions in vacuo to avoid the complications of solvent effects. Gas-phase action spectroscopy was done with two different setups, an electrostatic ion storage ring and an accelerator mass spectrometer. The results are interpreted on the basis of CC2 quantum chemical calculations. We identified absorption maxima at 393, 532, and 399 nm for the para, meta, and ortho isomer, respectively, with the charge-transfer transition into the lowest excited singlet state. In the meta isomer, this π-π* transition is strongly redshifted and its oscillator strength reduced, which is related to the pronounced charge-transfer character, as a consequence of the topology of the conjugated π-system. Each isomer's different charge distribution in the ground state leads to a very different solvent shift, which in acetonitrile is bathochromic for the para and ortho, but hypsochromic for the meta isomer.

Combined experimental and computational investigation of the absorption spectra of E- and Z-cinnamic acids in solution: The peculiarity of Z-cinnamics.

PubMed

Salum, María L; Arroyo Mañez, Pau; Luque, F Javier; Erra-Balsells, Rosa

2015-07-01

Cinnamic acids are present in all kinds of plant tissues and hence in herbs and derived medicines, cosmetics and foods. The interest in their role in plants and their therapeutic applications has grown exponentially. Because of their molecular structure they can exist in E- and Z-forms, which are both found in plants. However, since only the E-forms are commercially available, very few in vitro and in vivo studies of the Z-form have been reported. In this work the physico-chemical properties of Z-cinnamic acids in solution have been examined by means of UV-absorption spectroscopy and high-level quantum mechanical computations. For each isomer similar absorption spectra were obtained in methanol and acetonitrile. However, distinct trends were found for Z- and E forms of cinnamic acids in water, where a higher hypsochromic shift of the Z-isomer relative to the E-form was observed. In general the wavelength of maximal absorption of the Z-form is dramatically blue shifted (-30 to -40 nm) to λ<280 nm, while a slightly blue shift of the absorption maxima for the corresponding E-form (+3 to -4 nm) was observed. This difference is associated with the non-planar, largely distorted, Z-structure and to the almost complete flat structure of the E-form. The results provide a basis for the study of functional and biotechnological roles of cinnamic acids and for the analysis of samples containing mixture of both geometric isomers. Copyright © 2015 Elsevier B.V. All rights reserved.

A new approach to highly sensitive determination of retinoic acid isomers by preconcentration with CdSe quantum dots.

PubMed

Torabi, Behzad; Shemirani, Farzaneh

2014-03-01

Unusual amounts of retinoic acid (RA) isomers play an important role in abnormal morphological development of mammals; such as rat embryos. Each isomer of RA has a unique function in first steps of embryonic life. In the current study, a new method for preconcentration and simultaneous determination of all-trans retinoic acid, 13-cis retinoic acid, 9-cis retinoic acid and 9,13-di-cis retinoic acid in rat whole rudimentary embryo culture (RWEC) has been developed. RA isomers were extracted from samples by conjugation to appropriate amount of surface modified CdSe quantum dots (QDs) prior to HPLC/UV determination. In order to quickly release of the analytes with unchanged form, separated RA-QD conjugation were irradiated by intensive near infrared wavelength (NIR). Low energy NIR irradiation results in maintaining the primary forms of RA isomers during the release. The conjugation and release mechanisms were described and experimental parameters were investigated in detail. Under optimized conditions, the method was linear in the range of 0.040-34.600 pmol g(-1) for all-trans RA (R(2)=0.9996), 0.070-34.200 pmol g(-1) for 13-cis RA (R(2)=0.9992), 0.050-35.300 pmol g(-1) for 9,13-di-cis RA (R(2)=0.9998) and 0.050-32.900 pmol g(-1) for 9-cis RA (R(2)=0.9990). The present method can be useful for retinoic acid monitoring in clinical studies. © 2013 Published by Elsevier B.V.

Structure, Stabilities, Thermodynamic Properties, and IR Spectra of Acetylene Clusters (C2H2)n=2-5.

PubMed

Karthikeyan, S; Lee, Han Myoung; Kim, Kwang S

2010-10-12

There are no clear conclusions over the structures of the acetylene clusters. In this regard, we have carried out high-level calculations for acetylene clusters (C2H2)2-5 using dispersion-corrected density functional theory (DFT-D), Møller-Plesset second-order perturbation theory (MP2); and coupled-cluster theory with single, double, and perturbative triple excitations [CCSD(T)] at the complete basis set limit. The lowest energy structure of the acetylene dimer has a T-shaped structure of C2v symmetry, but it is nearly isoenergetic to the displaced stacked structure of C2h symmetry. We find that the structure shows the quantum statistical distribution for configurations between the T-shaped and displaced stacked structures for which the average angle (|θ̃|) between two acetylene molecules would be 53-78°, close to the T-shaped structure. The trimer has a triangular structure of C3h symmetry. The tetramer has two lowest energy isomers of S4 and C2h symmetry in zero-point energy (ZPE)-uncorrected energy (ΔEe), but one lowest energy isomer of C2v symmetry in ZPE-corrected energy (ΔE0). For the pentamer, the global minimum structure is C1 symmetry with eight sets of T-type π-H interactions and a set of π-π interactions. Our high-level ab initio calculations are consistent with available experimental data.

Bioinspired Orientation of β-Substituents on Porphyrin Antenna Ligands Switches Ytterbium(III) NIR Emission with Thermosensitivity.

PubMed

Ning, Yingying; Ke, Xian-Sheng; Hu, Ji-Yun; Liu, Yi-Wei; Ma, Fang; Sun, Hao-Ling; Zhang, Jun-Long

2017-02-20

"Configurational isomerism" is an important approach found in naturally occurring chlorophylls to modulate light harvesting function without significant structural changes; however, this feature has been seldom applied in design of antenna ligands for lanthanide (Ln) sensitization. In this work, we introduced a bioinspired approach by orientation of β-dilactone moieties on porphyrinates, namely cis-/trans-porphodilactones, to modulate the energy transfer process from the lowest triplet excited state of the ligand (T 1 ) to the emitting level of ytterbium(III) ( 2 F 5/2 , Yb*). Interestingly, near-infrared (NIR) emission of Yb(III) could be switched "on" by the cis-porphodilactone ligand, while the trans-isomer renders Yb(III) emission "off" and the ratio of quantum yields is ∼8. Analysis of the structure-photophysical properties relationship suggests that the significant emission difference is correlated to the energy gaps between T 1 and Yb* (1152 cm -1 in the cis- vs -25 cm -1 in the trans-isomer). More interestingly, due to back energy transfer (BEnT), the Yb(III) complex of cis-porphodilactone exhibits NIR emission with high thermosensitivity (4.0%°C -1 in solution and 4.9%°C -1 in solid state), comparable to previously reported terbium (Tb) and europium (Eu) visible emitters, in contrast to the trivial emission changes of the trans-isomer and porphyrin and porpholactone analogues. This work opens up new access to design NIR emissive Ln complexes by bioinspired modification of antenna ligands.

A complete vibrational study on a potential environmental toxicant agent, the 3,3',4,4'-tetrachloroazobenzene combining the FTIR, FTRaman, UV-Visible and NMR spectroscopies with DFT calculations.

PubMed

Castillo, María V; Pergomet, Jorgelina L; Carnavale, Gustavo A; Davies, Lilian; Zinczuk, Juan; Brandán, Silvia A

2015-01-05

In this study 3,3',4,4'-tetrachloroazobenzene (TCAB) was prepared and then characterized by infrared, Raman, multidimensional nuclear magnetic resonance (NMR) and ultraviolet-visible spectroscopies. The density functional theory (DFT) together with the 6-31G(*) and 6-311++G(**) basis sets were used to study the structures and vibrational properties of the two cis and trans isomers of TCAB. The harmonic vibrational wavenumbers for the optimized geometries were calculated at the same theory levels. A complete assignment of all the observed bands in the vibrational spectra of TCAB was performed combining the DFT calculations with the scaled quantum mechanical force field (SQMFF) methodology. The molecular electrostatic potentials, atomic charges, bond orders and frontier orbitals for the two isomers of TCAB were compared and analyzed. The comparison of the theoretical ultraviolet-visible spectrum with the corresponding experimental demonstrates a good concordance while the calculated (1)H and (13)C chemicals shifts are in good conformity with the corresponding experimental NMR spectra of TCAB in solution. The npp(*) transitions for both forms were studied by natural bond orbital (NBO) while the topological properties were calculated by employing Bader's Atoms in the Molecules (AIM) theory. This study shows that the cis and trans isomers exhibit different structural and vibrational properties and absorption bands. Copyright © 2014. Published by Elsevier B.V.

Photochemical Generation of H_{2}NCNX, H_{2}NNCX, H_{2}NC(NX) (x = O, s) in Low-Temperature Matrices

NASA Astrophysics Data System (ADS)

Voros, Tamas; Lajgut, Gyozo Gyorgy; Magyarfalvi, Gabor; Tarczay, Gyorgy

2017-06-01

The [NH_{2}, C, N, O] and the [NH_{2}, C, N, S] systems were investigated by quantum-chemical computations and matrix-isolation spectroscopic methods. The equilibrium structures of the isomers and their relative energies were determined by CCSD(T) method. This was followed by the computation of the harmonic and anharmonic vibrational wavenumbers, infrared intensities, relative Raman activities and UV excitation energies. These computed data were used to assist the identification of products obtained by UV laser photolysis of 3,4-diaminofurazan, 3,4-diaminothiadiazole and 1,2,4-thiadiazole-3,5-diamine in low-temperature Ar and Kr matrices. Experimentally, first the precursors were studied by matrix-isolation IR and UV spectroscopic methods. Based on these UV spectra, different wavelengths were selected for photolysis. The irradiations, carried out by a tunable UV laser-light source, resulted in the decomposition of the precursors, and in the appearance of new bands in the IR spectra. Some of these bands were assigned to cyanamide (H_{2}NCN) and its isomer, the carbodiimide molecule (HNCNH), generated from H_{2}NCN. By the analysis of the relative absorbance vs. photolysis time curves, the other bands were grouped to three different species both for the O- and the S-containing systems. In the case of the O-containing isomers, these bands were assigned to the H_{2}NNCO:H_{2}NCN, and H_{2}NCNO:H_{2}NCN complexes, and to the ring-structure H_{2}NC(NO) isomer. In a similar way, the complexes of H_{2}NNCS and H_{2}NCNS with the H_{2}NCN, and H_{2}NC(NS) were also identified. 1,2,4-thiadiazole-3,5-diamine was also investigated in similar way like the above mentioned precursors. The results of this study also support the identification of the new S-containing isomers. Except for H_{2}NNCO and H_{2}NCNS, these molecules were not identified previously. It is expected that at least some of these species, like the methyl isocyanate (CH_{3}CNO) isomer, are present and could be identified in astrophysical objects. T. Voros, Gy. Gy. Lajgut, G. Magyarfalvi, Gy. Tarczay, J. Chem. Phys., 146, 024305, 2017. D. T. Halfen, V. V. Ilyushin, L. M. Ziurys, Astrophys. J., 812, L5, 2015. J. Cernicharo et. al., Astron. Astrophys., 587, L4, 2016.

Zero kinetic energy photoelectron spectroscopy of tryptamine and the dissociation pathway of the singly hydrated cation cluster.

PubMed

Gu, Quanli; Knee, J L

2012-09-14

The relative ionization energies of tryptamine conformations are determined by zero kinetic energy photoelectron spectroscopy and photoionization efficiency measurements. The relative cationic conformational stabilities are compared to the published results for the neutral molecule. In the cation, the interaction strength changes significantly between amino group and either the phenyl or the pyrrole moiety of the indole chromophore where most of the positive charge is located, leading to different conformational structures and relative conformer energies in the cation. In particular, the measured adiabatic ionization potential of isomer B is 60,928 ± 5 cm(-1), at least 400 cm(-1) higher than any of the 6 other tryptamine isomers which all have ionization potentials within 200 cm(-1) of each other. In addition to the monomer, measurements were made on the A conformer of the tryptamine(+)-H(2)O complex including the ionization threshold and cation dissociation energy measured using a threshold photoionization fragmentation method. The water cluster exhibits an unexpectedly high ionization potential of 60,307 ± 100 cm(-1), close to the conformer A monomer of 60 320 ± 100 cm(-1). It also exhibits surprisingly low dissociation energy of 1750 ± 150 cm(-1) compared to other H-bonding involved cation-H(2)O complexes which are typically several thousands of wavenumbers higher. Quantum chemical calculations indicate that upon ionization the structure of the parent molecule in the water complex remains mostly unchanged due to the rigid intermolecular double hydrogen bonded water molecule bridging the monomer backbone and its side chain thus leading to the high ionization potential in the water cluster. The surprisingly low dissociation energy measured in the cationic water complex is attributed to the formation of a much more stable structural isomer H(+) in the exit channel.

Influence of photoisomers in bilirubin determinations on Kodak Ektachem and Hitachi analysers in neonatal specimens study of the contribution of structural and configurational isomers.

PubMed

Gulian, J M; Dalmasso, C; Millet, V; Unal, D; Charrel, M

1995-08-01

We compared data obtained with the Kodak Ektachem and Hitachi 717 Analysers and HPLC from 83 neonates under phototherapy. Total bilirubin values determined with the Kodak and Hitachi are in good agreement, but we observed a large discrepancy in the results for conjugated (Kodak) and direct (Hitachi) bilirubin. HPLC revealed that all the samples contained configurational isomers, while only 7.7% and 30.8% contained conjugated bilirubin and structural isomers, respectively. We developed a device for the specific and quantitative production of configurational or structural isomers, by irradiation with blue or green light. In vitro, total bilirubin values are coherent for the routine analysers in the presence of configurational or structural isomers. With configurational isomers, unconjugated bilirubin (Kodak) is lower than total bilirubin (Kodak), and conjugated bilirubin (Kodak) is always equal to zero, so the apparatus gives a false positive response for delta bilirubin. In contrast, the direct bilirubin (Hitachi) is constant. Furthermore, in the presence of structural isomers, unconjugated bilirubin (Kodak) is unexpectedly higher than total bilirubin (Kodak), conjugated bilirubin (Kodak) is proportional to the quantity of these isomers, and direct bilirubin (Hitachi) is constant. The contribution of photoisomers in bilirubin measurements is discussed.

The effect of meta coupling on colour purity, quantum yield, and exciton utilizing efficiency in deep-blue emitters from phenanthroimidazole isomers.

PubMed

Wang, Zhiming; Li, Xueying; Zhang, Wanyu; Zhang, Shitong; Li, Hui; Yu, Zhenqiang; Chen, Yanming; Lu, Ping; Chen, Ping

2015-12-21

meta-Coupling isomers usually exhibit bluer emission than do the para-isomers, but the loss of efficiency with respect to photoluminescence (PL) and electroluminescence (EL) is an inevitable result in most cases, particularly for deep blue emitters. In this study, three blue emitting isomers, 4,4'-bis(1-phenyl-phenanthro[9,10-d]imidazol-2-yl)biphenyl (BPPI), 3,4'-bis(1-phenyl-phenanthro[9,10-d]-imidazol-2-yl)biphenyl (L-BPPI) and 3,3'-bis(1-phenyl-phenanthro[9,10-d]-imidazol-2-yl)biphenyl (Z-BPPI), were chosen as model compounds to investigate the essential reason behind the meta-coupling effect due to their different coupling forms, viz. para-para, para-meta, and meta-meta, respectively, in similar dimeric phenanthroimidazole frameworks. A combination of detailed photophysical data, device performance and DFT calculations for the excited state provided valuable information. In particular, the relationship between certain key parameters in calculations as well as PL or EL properties was confirmed, such as oscillator strength and quantum yield, among others, which could effectively reduce the issues related to synthesis and characterisation using prior computer simulations. Good agreement was observed in the results obtained from calculation and experiments, and it was concluded that meta-tuning barely realised improvement in EL, unless some special excited states formed or an exciton conversion channel appeared, as in the case of reverse intersystem crossing.

Far-infrared spectra of yttrium-doped gold clusters Au(n)Y (n=1-9).

PubMed

Lin, Ling; Claes, Pieterjan; Gruene, Philipp; Meijer, Gerard; Fielicke, André; Nguyen, Minh Tho; Lievens, Peter

2010-06-21

The geometric, spectroscopic, and electronic properties of neutral yttrium-doped gold clusters Au(n)Y (n=1-9) are studied by far-infrared multiple photon dissociation (FIR-MPD) spectroscopy and quantum chemical calculations. Comparison of the observed and calculated vibrational spectra allows the structures of the isomers present in the molecular beam to be determined. Most of the isomers for which the IR spectra agree best with experiment are calculated to be the energetically most stable ones. Attachment of xenon to the Au(n)Y cluster can cause changes in the IR spectra, which involve band shifts and band splittings. In some cases symmetry changes, as a result of the attachment of xenon atoms, were also observed. All the Au(n)Y clusters considered prefer a low spin state. In contrast to pure gold clusters, which exhibit exclusively planar lowest-energy structures for small sizes, several of the studied species are three-dimensional. This is particularly the case for Au(4)Y and Au(9)Y, while for some other sizes (n=5, 8) the 3D structures have an energy similar to that of their 2D counterparts. Several of the lowest-energy structures are quasi-2D, that is, slightly distorted from planar shapes. For all the studied species the Y atom prefers high coordination, which is different from other metal dopants in gold clusters.

Structural Elucidation of cis / trans Dicaffeoylquinic Acid Photoisomerization Using Ion Mobility Spectrometry-Mass Spectrometry

DOE Office of Scientific and Technical Information (OSTI.GOV)

Zheng, Xueyun; Renslow, Ryan S.; Makola, Mpho M.

Due to the recently uncovered health benefits and anti-HIV activities of dicaffeoylquinic acids (diCQAs), understanding their structures and functions is of great interest for drug discovery efforts. DiCQAs are analytically challenging to identify and quantify since they commonly exist as a diverse mixture of positional and geometric (cis/trans) isomers. In this work, we utilized ion mobility spectrometry coupled with mass spectrometry to separate the various isomers before and after UV irradiation. The experimental collision cross sections were then compared with theoretical structures to differentiate and identify the diCQA isomers. Our analyses found that naturally the diCQAs existed predominantly as trans/transmore » isomers, but after 3 h of UV irradiation, cis/cis, cis/trans, trans/cis, and trans/trans isomers were all present in the mixture. This is the first report of successful differentiation of cis/trans diCQA isomers individually, which shows the great promise of IMS coupled with theoretical calculations for determining the structure and activity relationships of different isomers in drug discovery studies.« less

Lipid and glycolipid isomer analyses using ultra-high resolution ion mobility spectrometry separations

DOE PAGES

Wojcik, Roza; Webb, Ian K.; Deng, Liulin; ...

2017-01-18

Understanding the biological mechanisms related to lipids and glycolipids is challenging due to the vast number of possible isomers. Mass spectrometry (MS) measurements are currently the dominant approach for studying and providing detailed information on lipid and glycolipid structures. However, difficulties in distinguishing many structural isomers (e.g. distinct acyl chain positions, double bond locations, as well as glycan isomers) inhibit the understanding of their biological roles. Here we utilized ultra-high resolution ion mobility spectrometry (IMS) separations based upon the use of traveling waves in a serpentine long path length multi-pass Structures for Lossless Manipulations (SLIM) to enhance isomer resolution. Themore » multi-pass arrangement allowed separations ranging from ~16 m (1 pass) to ~470 m (32 passes) to be investigated for the distinction of lipids and glycolipids with extremely small structural differences. Lastly, these ultra-high resolution SLIM IMS-MS analyses provide a foundation for exploring and better understanding isomer specific biological and disease processes.« less

Revealing the structure of isolated peptides: IR-IR predissociation spectroscopy of protonated triglycine isomers

NASA Astrophysics Data System (ADS)

Voss, Jonathan M.; Fischer, Kaitlyn C.; Garand, Etienne

2018-05-01

We report an isomer specific IR-IR double resonance study of the mass-selected protonated triglycine peptide. Comparison of experimental spectra with calculations reveals the presence of two isomers, with protonation occurring at either the terminal amine site or one of the amide oxygen sites. The amine protonated isomer identified in our experiment contains an atypical cis amide configuration as well as a more typical trans amide. The amide protonated peptide, on the other hand, contains two trans amide moieties. Both isomers are found to be the lowest energy structures for their respective protonation site, but it is unclear, from experiments and calculations, which one is the global minimum. The presence of both in our experiments likely points to kinetic trapping of a higher energy structure. Finally, the observed frequencies of the Nsbnd H and Osbnd H stretch vibrations are used to estimate the hydrogen-bond strengths present in each isomer, accounting for the relative stabilities of these structures.

Revealing the structure of isolated peptides: IR-IR predissociation spectroscopy of protonated triglycine isomers

DOE Office of Scientific and Technical Information (OSTI.GOV)

Voss, Jonathan M.; Fischer, Kaitlyn C.; Garand, Etienne

Here, we report an isomer specific IR-IR double resonance study of the mass-selected protonated triglycine peptide. Comparison of experimental spectra with calculations reveals the presence of two isomers, with protonation occurring at either the terminal amine site or one of the amide oxygen sites. The amine protonated isomer identified in our experiment contains an atypical cis amide configuration as well as a more typical trans amide. The amide protonated peptide, on the other hand, contains two trans amide moieties. Both isomers are found to be the lowest energy structures for their respective protonation site, but it is unclear, from experimentsmore » and calculations, which one is the global minimum. The presence of both in our experiments likely points to kinetic trapping of a higher energy structure. Lastly, the observed frequencies of the NH and OH stretch vibrations are used to estimate the hydrogen-bond strengths present in each isomer, accounting for the relative stabilities of these structures.« less

Revealing the structure of isolated peptides: IR-IR predissociation spectroscopy of protonated triglycine isomers

DOE PAGES

Voss, Jonathan M.; Fischer, Kaitlyn C.; Garand, Etienne

2018-03-08

Here, we report an isomer specific IR-IR double resonance study of the mass-selected protonated triglycine peptide. Comparison of experimental spectra with calculations reveals the presence of two isomers, with protonation occurring at either the terminal amine site or one of the amide oxygen sites. The amine protonated isomer identified in our experiment contains an atypical cis amide configuration as well as a more typical trans amide. The amide protonated peptide, on the other hand, contains two trans amide moieties. Both isomers are found to be the lowest energy structures for their respective protonation site, but it is unclear, from experimentsmore » and calculations, which one is the global minimum. The presence of both in our experiments likely points to kinetic trapping of a higher energy structure. Lastly, the observed frequencies of the NH and OH stretch vibrations are used to estimate the hydrogen-bond strengths present in each isomer, accounting for the relative stabilities of these structures.« less

Study on Separation of Structural Isomer with Magneto-Archimedes method

NASA Astrophysics Data System (ADS)

Kobayashi, T.; Mori, T.; Akiyama, Y.; Mishima, F.; Nishijima, S.

2017-09-01

Organic compounds are refined by separating their structural isomers, however each separation method has some problems. For example, distillation consumes large energy. In order to solve these problems, new separation method is needed. Considering organic compounds are diamagnetic, we focused on magneto-Archimedes method. With this method, particle mixture dispersed in a paramagnetic medium can be separated in a magnetic field due to the difference of the density and magnetic susceptibility of the particles. In this study, we succeeded in separating isomers of phthalic acid as an example of structural isomer using MnCl2 solution as the paramagnetic medium. In order to use magneto-Archimedes method for separating materials for food or medicine, we proposed harmless medium using oxygen and fluorocarbon instead of MnCl2 aqueous solution. As a result, the possibility of separating every structural isomer was shown.

C5H9N isomers: pointers to possible branched chain interstellar molecules

NASA Astrophysics Data System (ADS)

Etim, Emmanuel E.; Gorai, Prasanta; Das, Ankan; Arunan, Elangannan

2017-04-01

The astronomical observation of isopropyl cyanide further stresses the link between the chemical composition of the interstellar medium (ISM) and molecular composition of the meteorites in which there is a dominance of branched chain amino acids as compared to the straight. However, observations of more branched chain molecules in ISM will firmly establish this link. In the light of this, we have considered C5H9N isomeric group in which the next higher member of the alkyl cyanide and other branched chain isomers belong. High-level quantum chemical calculations have been employed in estimating accurate energies of these isomers. From the results, the only isomer of the group that has been astronomically searched, n-butyl cyanide is not the most stable isomer and therefore, which might explain why its search could only yield upper limits of its column density without a successful detection. Rather, the two most stable isomers of the group are the branched chain isomers; tert-butylnitrile and isobutyl cyanide. Based on the rotational constants of these isomers, it is found that the expected intensity of tert-butylnitrile is the maximum among this isomeric group. Thus, this is proposed as the most probable candidate for astronomical observation. A simple LTE (local thermodynamic equilibrium) modelling has also been carried out to check the possibility of detecting tert-butyl cyanide in the millimetre-wave region. Contribution to the Topical Issue "Low-Energy Interactions related to Atmospheric and Extreme Conditions", edited by S. Ptasinska, M. Smialek-Telega, A. Milosavljevic and B. Sivaraman.

Chiral Tagging of Verbenone with 3-BUTYN-2-OL for Establishing Absolute Configuration and Determining Enantiomeric Excess

NASA Astrophysics Data System (ADS)

Evangelisti, Luca; Mayer, Kevin J.; Holdren, Martin S.; Smart, Taylor; West, Channing; Pate, Brooks; Sedo, Galen; Marshall, Frank E.; Grubbs, G. S., II

2017-06-01

Chiral analysis of a commercial sample of (1S)-(-)-verbenone has been performed using the chiral tag approach. The chirped-pulse Fourier transform microwave spectrum of the verbenone-butynol complex is measured in the 2-8 GHz frequency range. Verbenone is placed in a nozzle reservoir heated to 333K (about 1 Torr vapor pressure). The complex is formed by using a carrier gas of neon with approximately 0.1% butynol. The expansion pressure is about 2 atm. A measurement using racemic butynol is performed to identify isomers of both diastereomer complexes. Quantum chemistry calculations using the B3LYP-D3BJ method with the def2TZVP basis set provided estimated spectroscopic constants for the homochiral and heterochiral complexes. This analysis included 8 isomers for each diastereomer. Four rotational spectra are identified for isomers of the homochiral complex and correspond to the four lowest energy isomers from the theoretical study. Three heterochiral complexes are identified and also correspond to the lowest energy isomers from theory. Subsequent measurements were made with enantiopure tag (both (R)-(+)-3-buty-2-nol and (S)-(-)-3-butyn-2-ol) to establish the absolute configuration of verbenone. The sensitivity of the measurement was sufficient to perform ^{13}C-isotopologue analysis of three of the homochiral complexes and two of the heterochiral complexes. These results provide definitive structures of verbenone with correct stereochemistry. The commercial sample has relatively low enantiomeric excess with the certificate of analysis reporting an EE of 53.6%. Using the intensities of assigned transitions of the chiral tag complexes, the enantiomeric excess was determined from the broadband rotational spectrum through the ratio of the intensities of pairs of transitions. A total of 2617 pairs of transitions were analyzed. The average EE was found to be 53.6% with a standard deviation of 2%.

On the Relative Stability of Cumulenone and Aldehyde Isomers: when we HEAT345(Q) Things UP

NASA Astrophysics Data System (ADS)

Lee, Kelvin; McCarthy, Michael C.; Stanton, John F.

2017-06-01

Isomers of H_2C_{2n+1}O are examples of complex organic molecules that are either known or proposed to exist in the interstellar medium. For the smallest of these chains (H_2C_3O) only two of three isomers are observed in space: propynal (HC(O)CCH) and cyclopropenone (c-C_3H_2O), while evidence for the remaining isomer propadienone (H_2C_3O) is currently lacking. Potentially, this behaviour may be rationalised by a thermodynamic argument: several studies have provided quantum chemical calculations in an effort to determine the relative thermodynamic stability between these three isomers. An early study by Radom, at the SCF/6-31G** level ranked HC(O)CCH as the thermodynamic minimum, followed by H_2C_3O, and c-C_3H_2O. The most recent determination by Karton and Talbi, using W2-F12 theory, places H_2C_3O as the lowest energy isomer; 2.5 kJ mol^{-1} lower than the HC(O)CCH form. In an attempt to resolve this long-standing ambiguity, we were motivated to provide high level calculations based on the HEAT protocol. In this talk, we will discuss the relative stability of H_2C_3O and H_2C_5O isomers, along with their sulfur analogues, as revealed by HEAT345(Q) theory.

Photoelectron spectroscopy and theoretical study of M(IO3)2(-) (M = H, Li, Na, K): structural evolution, optical isomers, and hyperhalogen behavior.

PubMed

Hou, Gao-Lei; Wu, Miao Miao; Wen, Hui; Sun, Qiang; Wang, Xue-Bin; Zheng, Wei-Jun

2013-07-28

H(IO3)2(-) and M(IO3)2(-) (M = Li, Na, K) anions were successfully produced via electrospray ionization of their corresponding bulk salt solutions, and were characterized by combining negative ion photoelectron spectroscopy and quantum chemical calculations. The experimental vertical detachment energies (VDEs) of M(IO3)2(-) (M = H, Li, Na, K) are 6.25, 6.57, 6.60, and 6.51 eV, respectively, and they are much higher than that of IO3(-) (4.77 eV). The theoretical calculations show that each of these anions has two energetically degenerate optical isomers. It is found that the structure of H(IO3)2(-) can be written as IO3(-)(HIO3), in which the H atom is tightly bound to one of the IO3(-) groups and forms an iodic acid (HIO3) molecule; while the structures of M(IO3)2(-) can be written as (IO3(-))M(+)(IO3(-)), in which the alkali metal atoms interact with the two IO3(-) groups almost equally and bridge the two IO3(-) groups via two O atoms of each IO3(-) with the two MOOI planes nearly perpendicular to each other. In addition, the high VDEs of M(IO3)2(-) (M = Li, Na, K) can be explained by the hyperhalogen behavior of their neutral counterparts.

1-Formyl-3-phenyl-5-(4-isopropylphenyl)-2-pyrazoline: Synthesis, characterization, antimicrobial activity and DFT studies

NASA Astrophysics Data System (ADS)

Sid, Assia; Messai, Amel; Parlak, Cemal; Kazancı, Nadide; Luneau, Dominique; Keşan, Gürkan; Rhyman, Lydia; Alswaidan, Ibrahim A.; Ramasami, Ponnadurai

2016-10-01

The structure of 1-formyl-3-phenyl-5-(4-isopropylphenyl)-2-pyrazoline synthesized as single crystal was investigated by FTIR, NMR, XRD. Experimental data were complemented by quantum mechanical calculations. XRD data show that the compound crystallizes in the triclinic system (P-1) via trans isomer (a = 6.4267(4) Å, b = 10.9259(12) Å, c = 12.4628(9) Å and α = 102.894(8)°, β = 102.535(6)°, γ = 101.633(7)°). Anti-microbial screening results indicate that the compound shows promising activity. The theoretically predicted and experimentally obtained parameters reveal further insight into pyrazoline systems.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Wojcik, Roza; Webb, Ian K.; Deng, Liulin

Understanding the biological mechanisms related to lipids and glycolipids is challenging due to the vast number of possible isomers. Mass spectrometry (MS) measurements are currently the dominant approach for studying and providing detailed information on lipid and glycolipid structures. However, difficulties in distinguishing many structural isomers (e.g. distinct acyl chain positions, double bond locations, as well as glycan isomers) inhibit the understanding of their biological roles. Here we utilized ultra-high resolution ion mobility spectrometry (IMS) separations based upon the use of traveling waves in a serpentine long path length multi-pass Structures for Lossless Manipulations (SLIM) to enhance isomer resolution. Themore » multi-pass arrangement allowed separations ranging from ~16 m (1 pass) to ~470 m (32 passes) to be investigated for the distinction of lipids and glycolipids with extremely small structural differences. Lastly, these ultra-high resolution SLIM IMS-MS analyses provide a foundation for exploring and better understanding isomer specific biological and disease processes.« less

229Thorium-doped calcium fluoride for nuclear laser spectroscopy.

PubMed

Dessovic, P; Mohn, P; Jackson, R A; Winkler, G; Schreitl, M; Kazakov, G; Schumm, T

2014-03-12

The (229)thorium isotope presents an extremely low-energy isomer state of the nucleus which is expected around 7.8 eV, in the vacuum ultraviolet (VUV) regime. This unique system may bridge between atomic and nuclear physics, enabling coherent manipulation and precision spectroscopy of nuclear quantum states using laser light. It has been proposed to implant (229)thorium into VUV transparent crystal matrices to facilitate laser spectroscopy and possibly realize a solid-state nuclear clock. In this work, we validate the feasibility of this approach by computer modelling of thorium doping into calcium fluoride single crystals. Using atomistic modelling and full electronic structure calculations, we find a persistent large band gap and no additional electronic levels emerging in the middle of the gap due to the presence of the dopant, which should allow direct optical interrogation of the nuclear transition.Based on the electronic structure, we estimate the thorium nuclear quantum levels within the solid-state environment. Precision laser spectroscopy of these levels will allow the study of a broad range of crystal field effects, transferring Mössbauer spectroscopy into the optical regime.

Chromophore twisting in the excited state of a photoswitchable fluorescent protein captured by time-resolved serial femtosecond crystallography

NASA Astrophysics Data System (ADS)

Coquelle, Nicolas; Sliwa, Michel; Woodhouse, Joyce; Schirò, Giorgio; Adam, Virgile; Aquila, Andrew; Barends, Thomas R. M.; Boutet, Sébastien; Byrdin, Martin; Carbajo, Sergio; de La Mora, Eugenio; Doak, R. Bruce; Feliks, Mikolaj; Fieschi, Franck; Foucar, Lutz; Guillon, Virginia; Hilpert, Mario; Hunter, Mark S.; Jakobs, Stefan; Koglin, Jason E.; Kovacsova, Gabriela; Lane, Thomas J.; Lévy, Bernard; Liang, Mengning; Nass, Karol; Ridard, Jacqueline; Robinson, Joseph S.; Roome, Christopher M.; Ruckebusch, Cyril; Seaberg, Matthew; Thepaut, Michel; Cammarata, Marco; Demachy, Isabelle; Field, Martin; Shoeman, Robert L.; Bourgeois, Dominique; Colletier, Jacques-Philippe; Schlichting, Ilme; Weik, Martin

2018-01-01

Chromophores absorb light in photosensitive proteins and thereby initiate fundamental biological processes such as photosynthesis, vision and biofluorescence. An important goal in their understanding is the provision of detailed structural descriptions of the ultrafast photochemical events that they undergo, in particular of the excited states that connect chemistry to biological function. Here we report on the structures of two excited states in the reversibly photoswitchable fluorescent protein rsEGFP2. We populated the states through femtosecond illumination of rsEGFP2 in its non-fluorescent off state and observed their build-up (within less than one picosecond) and decay (on the several picosecond timescale). Using an X-ray free-electron laser, we performed picosecond time-resolved crystallography and show that the hydroxybenzylidene imidazolinone chromophore in one of the excited states assumes a near-canonical twisted configuration halfway between the trans and cis isomers. This is in line with excited-state quantum mechanics/molecular mechanics and classical molecular dynamics simulations. Our new understanding of the structure around the twisted chromophore enabled the design of a mutant that displays a twofold increase in its off-to-on photoswitching quantum yield.

Chromophore twisting in the excited state of a photoswitchable fluorescent protein captured by time-resolved serial femtosecond crystallography

DOE PAGES

Coquelle, Nicolas; Sliwa, Michel; Woodhouse, Joyce; ...

2017-09-11

Chromophores absorb light in photosensitive proteins and thereby initiate fundamental biological processes such as photosynthesis, vision and biofluorescence. An important goal in their understanding is the provision of detailed structural descriptions of the ultrafast photochemical events that they undergo, in particular of the excited states that connect chemistry to biological function. Here in this paper we report on the structures of two excited states in the reversibly photoswitchable fluorescent protein rsEGFP2. We populated the states through femtosecond illumination of rsEGFP2 in its non-fluorescent off state and observed their build-up (within less than one picosecond) and decay (on the several picosecondmore » timescale). Using an X-ray free-electron laser, we performed picosecond time-resolved crystallography and show that the hydroxybenzylidene imidazolinone chromophore in one of the excited states assumes a near-canonical twisted configuration halfway between the trans and cis isomers. This is in line with excited-state quantum mechanics/molecular mechanics and classical molecular dynamics simulations. Our new understanding of the structure around the twisted chromophore enabled the design of a mutant that displays a twofold increase in its off-to-on photoswitching quantum yield.« less

Chromophore twisting in the excited state of a photoswitchable fluorescent protein captured by time-resolved serial femtosecond crystallography

DOE Office of Scientific and Technical Information (OSTI.GOV)

Coquelle, Nicolas; Sliwa, Michel; Woodhouse, Joyce

Chromophores absorb light in photosensitive proteins and thereby initiate fundamental biological processes such as photosynthesis, vision and biofluorescence. An important goal in their understanding is the provision of detailed structural descriptions of the ultrafast photochemical events that they undergo, in particular of the excited states that connect chemistry to biological function. Here in this paper we report on the structures of two excited states in the reversibly photoswitchable fluorescent protein rsEGFP2. We populated the states through femtosecond illumination of rsEGFP2 in its non-fluorescent off state and observed their build-up (within less than one picosecond) and decay (on the several picosecondmore » timescale). Using an X-ray free-electron laser, we performed picosecond time-resolved crystallography and show that the hydroxybenzylidene imidazolinone chromophore in one of the excited states assumes a near-canonical twisted configuration halfway between the trans and cis isomers. This is in line with excited-state quantum mechanics/molecular mechanics and classical molecular dynamics simulations. Our new understanding of the structure around the twisted chromophore enabled the design of a mutant that displays a twofold increase in its off-to-on photoswitching quantum yield.« less

Molecules in Laboratory and in Interstellar Space?

NASA Astrophysics Data System (ADS)

Thimmakondu, Venkatesan S.

2016-06-01

In this talk, the quantum chemistry of astronomically relevant molecules will be outlined with an emphasis on the structures and energetics of C_7H_2 isomers, which are yet to be identified in space. Although more than 100's of isomers are possible for C_7H_2, to date only 6 isomers had been identified in the laboratory. The equilibrium geometries of heptatriynylidene (1), cyclohepta-1,2,3,4-tetraen-6-yne (2), and heptahexaenylidene (3), which we had investigated theoretically will be discussed briefly. While 1 and 3 are observed in the laboratory, 2 is a hypothetical molecule. The theoretical data may be useful for the laboratory detection of 2 and astronomical detection of 2 and 3. THIS WORK IS SUPPORTED BY A RESEARCH GRANT (YSS/2015/00099) FROM SERB, DST, GOVERNMENT OF INDIA. Apponi, A. P.; McCarthy, M. C.; Gottlieb, C. A.; Thaddeus, P. Laboratory Detection of Four New Cumulene Carbenes: H_2C_7, H_2C_8, H_2C_9, and D_2C10, Astrophys. J. 2000, 530, 357-361 Ball, C. D; McCarthy, M. C.; Thaddeus, P. Cavity Ringdown Spectroscopy of the Linear Carbon Chains HC_7H, HC_9H, HC11H, and HC13H. J. Chem. Phys. 2000, 112, 10149-10155 Dua, S.; Blanksby, S. J.; Bowie, J. H. Formation of Neutral C_7H_2 Isomers from Four Isomeric C_7H_2 Radical Anion Precursors in the Gas Phase. J. Phys. Chem. A, 2000, 104, 77-85. Thimmakondu, V. S. The equilibrium geometries of heptatriynylidene, cyclohepta-1,2,3,4-tetraen-6-yne, and heptahexaenylidene, Comput. Theoret. Chem. 2016, 1079, 1-10

Importance of many-body dispersion and temperature effects on gas-phase gold cluster (meta)stability

NASA Astrophysics Data System (ADS)

Goldsmith, Bryan R.; Gruene, Philipp; Lyon, Jonathan T.; Rayner, David M.; Fielicke, André; Scheffler, Matthias; Ghiringhelli, Luca M.

Gold clusters in the gas phase exhibit many structural isomers that are shown to intercovert frequently, even at room temperature. We performed ab initio replica-exchange molecular dynamics (REMD) calculations on gold clusters (of sizes 5-14 atoms) to identify metastable states and their relative populations at finite temperature, as well as to examine the importance of temperature and van der Waals (vdW) on their isomer energetic ordering. Free energies of the gold cluster isomers are optimally estimated using the Multistate Bennett Acceptance Ratio. The distribution of bond coordination numbers and radius of gyration are used to address the challenge of discriminating isomers along their dynamical trajectories. Dispersion effects are important for stabilizing three-dimensional structures relative to planar structures and brings isomer energetic predictions to closer quantitative agreement compared with RPA@PBE calculations. We find that higher temperatures typically stabilize metastable three-dimensional structures relative to planar/quasiplanar structures. Computed IR spectra of low free energy Au9, Au10, and Au12 isomers are in agreement with experimental spectra obtained by far-IR multiple photon dissociation in a molecular beam at 100 K.

Structural Identification of 19 Purified Isomers of the OPV Acceptor Material bisPCBM by 13C NMR and UV-Vis Absorption Spectroscopy and High-Performance Liquid Chromatography.

PubMed

Liu, Tong; Abrahams, Isaac; Dennis, T John S

2018-04-26

The molecular structures of 19 purified isomers of bis-phenyl-C 62 -butyric acid methyl ester were identified by a combination of 13 C NMR and UV-vis absorption spectroscopies and high-performance liquid chromatography (HPLC) retention time analysis. All 19 isomers are dicyclopropafullerenes (none are homofullerenes). There were seven isomers with C 1 molecular point-group symmetry, four with C s , six with C 2 , one with C 2 v , and one with C 2 h symmetry. The C 2 h , C 2 v , and all five nonequatorial C 1 isomers were unambiguously assigned to their respective HPLC fractions. For the other 12 isomers, the 13 C NMR and UV-vis spectra placed them in six groups of two same-symmetry isomers. On the basis of the widely spaced HPLC retention times of the two isomers within each of these six groups, and the empirical inverse correlation between retention time and addend spacing, each isomer was assigned to its corresponding HPLC fraction. In addition, the missing trans-1 isomer was found, purified, and characterized.

Discrimination of Isomers of Released N- and O-Glycans Using Diagnostic Product Ions in Negative Ion PGC-LC-ESI-MS/MS

NASA Astrophysics Data System (ADS)

Ashwood, Christopher; Lin, Chi-Hung; Thaysen-Andersen, Morten; Packer, Nicolle H.

2018-03-01

Profiling cellular protein glycosylation is challenging due to the presence of highly similar glycan structures that play diverse roles in cellular physiology. As the anomericity and the exact linkage type of a single glycosidic bond can influence glycan function, there is a demand for improved and automated methods to confirm detailed structural features and to discriminate between structurally similar isomers, overcoming a significant bottleneck in the analysis of data generated by glycomics experiments. We used porous graphitized carbon-LC-ESI-MS/MS to separate and detect released N- and O-glycan isomers from mammalian model glycoproteins using negative mode resonance activation CID-MS/MS. By interrogating similar fragment spectra from closely related glycan isomers that differ only in arm position and sialyl linkage, product fragment ions for discrimination between these features were discovered. Using the Skyline software, at least two diagnostic fragment ions of high specificity were validated for automated discrimination of sialylation and arm position in N-glycan structures, and sialylation in O-glycan structures, complementing existing structural diagnostic ions. These diagnostic ions were shown to be useful for isomer discrimination using both linear and 3D ion trap mass spectrometers when analyzing complex glycan mixtures from cell lysates. Skyline was found to serve as a useful tool for automated assessment of glycan isomer discrimination. This platform-independent workflow can potentially be extended to automate the characterization and quantitation of other challenging glycan isomers. [Figure not available: see fulltext.

The Dewar Isomer of 1,2-Dihydro-1,2-azaborinines: Isolation, Fragmentation, and Energy Storage.

PubMed

Edel, Klara; Yang, Xinyu; Ishibashi, Jacob S A; Lamm, Ashley N; Maichle-Mössmer, Cäcilia; Giustra, Zachary X; Liu, Shih-Yuan; Bettinger, Holger F

2018-05-04

The photochemistry of 1,2-dihydro-1,2-azaborinine derivatives was studied under matrix isolation conditions and in solution. Photoisomerization occurs exclusively to the Dewar valence isomers upon irradiation with UV light (>280 nm) with high quantum yield (46 %). Further photolysis with UV light (254 nm) results in the formation of cyclobutadiene and an iminoborane derivative. The thermal electrocyclic ring-opening reaction of the Dewar valence isomer back to the 1,2-dihydro-1-tert-butyldimethylsilyl-2-mesityl-1,2-azaborinine has an activation barrier of (27.0±1.2) kcal mol -1 . In the presence of the Wilkinson catalyst, the ring opening occurs rapidly and exothermically (ΔH=(-48±1) kcal mol -1 ) at room temperature. © 2018 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

Separating para and ortho water.

PubMed

Horke, Daniel A; Chang, Yuan-Pin; Długołęcki, Karol; Küpper, Jochen

2014-10-27

Water exists as two nuclear-spin isomers, para and ortho, determined by the overall spin of its two hydrogen nuclei. For isolated water molecules, the conversion between these isomers is forbidden and they act as different molecular species. Yet, these species are not readily separated, and no pure para sample has been produced. Accordingly, little is known about their specific physical and chemical properties, conversion mechanisms, or interactions. The production of isolated samples of both spin isomers is demonstrated in pure beams of para and ortho water in their respective absolute ground state. These single-quantum-state samples are ideal targets for unraveling spin-conversion mechanisms, for precision spectroscopy and fundamental symmetry-breaking studies, and for spin-enhanced applications, for example laboratory astrophysics and astrochemistry or hypersensitized NMR experiments. © 2014 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Theoretical study of mixed LiLnX4 (Ln = La, Dy; X = F, Cl, Br, I) rare earth/alkali halide complexes.

PubMed

Groen, C P; Oskam, A; Kovács, A

2000-12-25

The structure, bonding and vibrational properties of the mixed LiLnX4 (Ln = La, Dy; X = F, Cl, Br, I) rare earth/alkali halide complexes were studied using various quantum chemical methods (HF, MP2 and the Becke3-Lee-Yang-Parr exchange-correlation density functional) in conjunction with polarized triple-zeta valence basis sets and quasi-relativistic effective core potentials for the heavy atoms. Our comparative study indicated the superiority of MP2 theory while the HF and B3-LYP methods as well as less sophisticated basis sets failed for the correct energetic relations. In particular, f polarization functions on Li and X proved to be important for the Li...X interaction in the complexes. From the three characteristic structures of such complexes, possessing 1-(C3v), 2-(C2v), or 3-fold coordination (C3v) between the alkali metal and the bridging halide atoms, the bi- and tridentate forms are located considerably lower on the potential energy surface then the monodentate isomer. Therefore only the bi- and tridentate isomers have chemical relevance. The monodentate isomer is only a high-lying local minimum in the case of X = F. For X = Cl, Br, and I this structure is found to be a second-order saddle point. The bidentate structure was found to be the global minimum for the systems with X = F, Cl, and Br. However, the relative stability with respect to the tridentate structure is very small (1-5 kJ/mol) for the heavier halide derivatives and the relative order is reversed in the case of the iodides. The energy difference between the three structures and the dissociation energy decrease in the row F to I. The ionic bonding in the complexes was characterized by natural charges and a topological analysis of the electron density distribution according to Bader's theorem. Variation of the geometrical and bonding characteristics between the lanthanum and dysprosium complexes reflects the effect of "lanthanide contraction". The calculated vibrational data indicate that infrared spectroscopy may be an effective tool for experimental investigation and characterization of LiLnX4 molecules.

Configuration and energy landscape of the benzonitrile anion

NASA Astrophysics Data System (ADS)

Kirnosov, Nikita; Adamowicz, Ludwik

2017-05-01

Quantum chemical calculations are employed to study the configurational isomers of the anion formed by benzene substituted with a cyano group. It is found that an excess electron can form dipole-bound (DB) states with benzonitrile and phenyl-isocyanide isomers. It can also attach to the cyano group, if this group is separated from the benzene ring by some distance, forming a covalent CN- anion. There are four positions at peripherals of the benzene ring where this anion can localize and form stable complexes with the benzene radical. In these complexes CN- is connected to the benzene radical via non-covalent interactions.

Theoretical and experimental vibrational spectroscopy study on rotational isomer of 4-phenylbutylamine

NASA Astrophysics Data System (ADS)

Ünal, A.; Okur, M.

2017-02-01

The possible four stable rotational isomers of 4-phenylbutylamine (4PBA) molecule were experimentally and theoretically studied by vibrational spectroscopy. The FT-IR (4000-400 cm-1) and Raman (3700-60 cm-1) spectra of 4PBA were recorded at room temperature in liquid phase. The complete vibrational wavenumbers and corresponding vibrational assignments of 4PBA molecule were discussed assisted with B3LYP/6-311++G(d,p) level of theory along with scaled quantum mechanics force field (SQM-FF) method. Results from experimental and theoretical data the most stable form of 4PBA molecule was obtained.

The C4H7+ cation. A theoretical investigation

NASA Technical Reports Server (NTRS)

Koch, W.; Liu, B.; DeFrees, D. J.

1988-01-01

The potential energy surface of the C4H7+ cation has been investigated with ab initio quantum chemical theory. Extended basis set calculations, including electronic correlation, show that cyclobutyl and cyclopropylcarbinyl cation are equally stable isomers. The saddle point connecting these isomers lies 0.6 kcal/mol above the minima. The global C4H7+ minimum corresponds to the 1-methylallyl cation, which is 9.0 kcal/mol more stable than the cyclobutyl and the cyclopropylcarbinyl cation and 9.5 kcal/mol below the 2-methylallyl cation. These results are in excellent agreement with experimental data.

Complexes of Small Chiral Molecules: Propylene Oxide and 3-BUTYN-2OL

NASA Astrophysics Data System (ADS)

Evangelisti, Luca; West, Channing; Coles, Ellie; Pate, Brooks

2017-06-01

Complexes of propylene oxide with 3-butyn-2-ol were observed in the molecular rotational spectra, and isotopologue analysis allowed for structural determination of the complexes. Using a gas mixture of 0.1% propylene oxide and 0.1% 3-butyn-2-ol in neon, the broadband rotational spectrum was measured in the 2-8 GHz frequency range using a chirped-pulse Fourier transform microwave spectrometer. Four isomers of each diastereomer pair, formed by a hydrogen bond between the two monomers, are identified in quantum chemistry study of the complex using B3LYP-D3BJ with the def2TZVP basis set. The initial measurement used racemic samples of both molecules in order to obtain all possible isomers of the complex in the pulsed jet expansion. A total of six distinct spectra were assigned in the racemic measurement - three for both the homochiral and heterochiral complex. Substitution structures for the most intense homochiral and heterochiral complexes were obtained. These complexes use the two lowest energy conformations of butynol despite conformational cooling of the monomer, resulting in a single identified isomer. This result shows that a wide range monomer conformational geometries need to be examined when performing searches for the lowest energy geometry. Analysis of the diastereomer spectra was used to develop a method for determining the enantiomeric excess of 3-butyn-2-ol and propylene oxide for use as a chiral tag, which could be used in subsequent measurements to determine enantiomeric excess. The sensitivity limits for enantiomeric excess determination and the linearity of the rotational spectroscopy signals as a function of sample enantiomeric excess will be presented.

Preparation, Separation, and Conformational Analysis of Differentially Sulfated Heparin Octasaccharide Isomers using Ion Mobility Mass Spectrometry

PubMed Central

Seo, Youjin; Andaya, Armann; Leary, Julie A.

2012-01-01

Heparin is a linear sulfated polysaccharide widely used in medicine because of its anticoagulant properties. The various sulfation and/or acetylation patterns on heparin impart different degrees of conformational change around the glycosidic bonds and subsequently alter its function as an anticoagulant, anticancer, or antiviral drug. Characterization of these structures is important for eventual elucidation of its function but presents itself as an analytical challenge due to the inherent heterogeneity of the carbohydrates. Heparin octasaccharide structural isomers of various sulfation patterns were investigated using ion mobility mass spectrometry (IMMS). In addition to distinguishing the isomers, we report the preparation and tandem mass spectrometry analysis for multiple sulfated or acetylated oligosaccharides. Herein, our data indicate that heparin octasaccharide isomers were separated based on their structural conformations in the ion mobility cell. Subsequent to this separation, isomers were further distinguished using product ions resulting from tandem mass spectrometry. Overall, IMMS analysis was used to successfully characterize and separate individual isomers and subsequently measure their conformations. PMID:22283665

Communication: Gas-phase structural isomer identification by Coulomb explosion of aligned molecules

NASA Astrophysics Data System (ADS)

Burt, Michael; Amini, Kasra; Lee, Jason W. L.; Christiansen, Lars; Johansen, Rasmus R.; Kobayashi, Yuki; Pickering, James D.; Vallance, Claire; Brouard, Mark; Stapelfeldt, Henrik

2018-03-01

The gas-phase structures of four difluoroiodobenzene and two dihydroxybromobenzene isomers were identified by correlating the emission angles of atomic fragment ions created, following femtosecond laser-induced Coulomb explosion. The structural determinations were facilitated by confining the most polarizable axis of each molecule to the detection plane prior to the Coulomb explosion event using one-dimensional laser-induced adiabatic alignment. For a molecular target consisting of two difluoroiodobenzene isomers, each constituent structure could additionally be singled out and distinguished.

ENVIRONMENTAL ANALYSIS BY AB INITIO QUANTUM MECHANICAL COMPUTATION AND GAS CHROMATOGRAPHY/FOURIER TRANSFORM INFRARED SPECTROMETRY.

EPA Science Inventory

Computational chemistry, in conjunction with gas chromatography/mass spectrometry/Fourier transform infrared spectrometry (GC/MS/FT-IR), was used to tentatively identify seven tetrachlorobutadiene (TCBD) isomers detected in an environmental sample. Computation of the TCBD infrare...

The [(AI 2O 3) 2] - Anion Cluster: Electron Localization-Delocalization Isomerism

DOE Office of Scientific and Technical Information (OSTI.GOV)

Sierka, Marek; Dobler, Jens; Sauer, Joachim

2009-10-05

Three-dimensional bulk alumina and its two-dimensional thin films show great structural diversity, posing considerable challenges to their experimental structural characterization and computational modeling. Recently, structural diversity has also been demonstrated for zerodimensional gas phase aluminum oxide clusters. Mass-selected clusters not only make systematic studies of the structural and electronic properties as a function of size possible, but lately have also emerged as powerful molecular models of complex surfaces and solid catalysts. In particular, the [(Al 2O 3) 3-5] + clusters were the first example of polynuclear maingroup metal oxide cluster that are able to thermally activate CH 4. Over themore » past decades gas phase aluminum oxide clusters have been extensively studied both experimentally and computationally, but definitive structural assignments were made for only a handful of them: the planar [Al 3O 3] - and [Al 5O 4] - cluster anions, and the [(Al 2O 3) 1-4(AlO)] + cluster cations. For stoichiometric clusters only the atomic structures of [(Al 2O 3) 4] +/0 have been nambiguously resolved. Here we report on the structures of the [(Al 2O 3) 2] -/0 clusters combining photoelectron spectroscopy (PES) and quantum chemical calculations employing a genetic algorithm as a global optimization technique. The [(Al 2O 3) 2] - cluster anion show energetically close lying but structurally distinct cage and sheet-like isomers which differ by delocalization/localization of the extra electron. The experimental results are crucial for benchmarking the different computational methods applied with respect to a proper description of electron localization and the relative energies for the isomers which will be of considerable value for future computational studies of aluminum oxide and related systems.« less

Structural Characterization of Monomers and Oligomers of D-Amino Acid-Containing Peptides Using T-Wave Ion Mobility Mass Spectrometry

NASA Astrophysics Data System (ADS)

Pang, Xueqin; Jia, Chenxi; Chen, Zhengwei; Li, Lingjun

2017-01-01

The D-residues are crucial to biological function of D-amino acid containing peptides (DAACPs). Previous ion mobility mass spectrometry (IM-MS) studies revealing oligomerization patterns of amyloid cascade demonstrated conversion from native soluble unstructured assembly to fibril ß-sheet oligomers, which has been implicated in amyloid diseases, such as Alzheimer's disease and type 2 diabetes. Although neuropeptides are typically present at very low concentrations in circulation, their local concentrations could be much higher in large dense core vesicles, forming dimers or oligomers. We studied the oligomerization of protonated and metal-adducted achatin I and dermorphin peptide isomers with IM-MS. Our results suggested that dimerization, oligomerization, and metal adduction augment the structural differences between D/L peptide isomers compared to protonated monomers. Dimers and oligomers enhanced the structural differences between D/L peptide isomers in both aqueous and organic solvent system. Furthermore, some oligomer forms were only observed for either D- or L-isomers, indicating the importance of chiral center in oligomerization process. The oligomerization patterns of D/L isomers appear to be similar. Potassium adducts were detected to enlarge the structural differences between D/L isomers.

Two conformers of 10,11-dihydro-5H-dibenzo[a,d]cycloheptene spiro-linked with homobenzoquinone epoxide.

PubMed

Asahara, Haruyasu; Koizumi, Takuya; Mochizuki, Eiko; Oshima, Takumi

2006-03-01

The crystal structures of the two thermally equilibrated conformational isomers of the epoxide 1',5'-dimethylspiro[10,11-dihydro-5H-dibenzo[a,d]cycloheptene-5,8'-4'-oxatricyclo[5.1.0.0(3,5)]octane]-2',6'-dione, C23H20O3, have been determined by X-ray diffraction. In the tricyclic dione skeleton, the oxirane and cyclopropane rings adopt an anti structure with respect to the conjunct quinone frame. The spiro-linked 10,11-dihydro-5H-dibenzo[a,d]cycloheptene ring of the major isomer has a fairly twisted boat form, folding opposite to the adjoining cyclopropane methyl substituent, whereas the seven-membered ring of the minor isomer has an almost ideal twist-boat form, inversely folding to the side of the relevant methyl group. The conformational structures of these isomers have been compared with those of the corresponding isomers of the unepoxidized homobenzoquinone.

Preparation and characterization of six calixarene bonded stationary phases for high performance liquid chromatography.

PubMed

Ding, Chenghua; Qu, Kang; Li, Yongbo; Hu, Kai; Liu, Hongxia; Ye, Baoxian; Wu, Yangjie; Zhang, Shusheng

2007-11-02

Six calixarene bonded silica gel stationary phases were prepared and characterized by elemental analysis, infrared spectroscopy and thermal analysis. Their chromatographic performance was investigated by using PAHs, aromatic positional isomers and E- and Z-ethyl 3-(4-acetylphenyl) acrylate isomers as probes. Separation mechanism based on the different interactions between calixarenes and analytes were discussed. The chromatographic behaviors of those analytes on the calixarene columns were influenced by the supramolecular interaction including pi-pi interaction, space steric hindrance and hydrogen bonding interaction between calixarenes and analytes. Notably, the presence of polar groups (-OH, -NO(2) and -NH(2)) in the aromatic isomers could improve their separation selectivity on calixarene phase columns. The results from quantum chemistry calculation using DFT-B3LYP/STO-3G* base group were consistent with the retention behaviors of PHAs on calix[4]arene column.

Investigations of the Rg-BrCl (Rg = He, Ne, Ar, Kr, Xe) binary van der Waals complexes: ab initio intermolecular potential energy surfaces, vibrational states and predicted pure rotational transition frequencies

NASA Astrophysics Data System (ADS)

Li, Song; Zheng, Rui; Chen, Shan-Jun; Chen, Yan; Chen, Peng

2017-03-01

The intermolecular potential energy surfaces (PESs) of the ground electronic state for the Rg-BrCl (Rg = He, Ne, Ar, Kr, Xe) van der Waals complexes have been constructed by using the coupled-cluster method in combination with the augmented quadruple-zeta correlation-consistent basis sets supplemented with an additional set of bond functions. The features of the anisotropic PESs for these complexes are remarkably similar, which are characterized by three minima and two saddle points between them. The global minimum corresponds to a collinear Rg-Br-Cl configuration. Two local minima, correlate with an anti-linear Rg-Cl-Br geometry and a nearly T-shaped structure, can also be located on each PES. The quantum bound state calculations enable us to investigate intermolecular vibrational states and rotational energy levels of the complexes. The transition frequencies are predicted and are fitted to obtain their corresponding spectroscopic constants. In general, the periodic trends are observed for this complex family. Comparisons with available experimental data for the collinear isomer of Ar-BrCl demonstrate reliability of our theoretical predictions, and our results for the other two isomers of Ar-BrCl as well as for other members of the complex family are also anticipated to be trustable. Except for the collinear isomer of Ar-BrCl, the data presented in this paper would be beneficial to improve our knowledge for these experimentally unknown species.

Sequential picosecond isomerizations in a photochromic ruthenium sulfoxide complex triggered by pump-repump-probe spectroscopy.

PubMed

King, Albert W; Jin, Yuhuan; Engle, James T; Ziegler, Christopher J; Rack, Jeffrey J

2013-02-18

The complex [Ru(bpy)(2)(bpSO)](PF(6))(2), where bpy is 2,2'-bipydine and bpSO is 1,2-bis(phenylsulfinyl)ethane, exhibits three distinct isomers which are accessible upon metal-to-ligand charge-transfer (MLCT) irradiation. This complex and its parent, [Ru(bpy)(2)(bpte)](PF(6))(2), where bpte is 1,2-bis(phenylthio)ethane, have been synthesized and characterized by UV-visible spectroscopy, NMR, X-ray crystallography, and femtosecond transient absorption spectroscopy. A novel method of 2-color Pump-Repump-Probe spectroscopy has been employed to investigate all three isomers of the bis-sulfoxide complex. This method allows for observation of the isomerization dynamics of sequential isomerizations of each sulfoxide from MLCT irradiation of the S,S-bonded complex to ultimately form the O,O-bonded metastable complex. One-dimensional (1-D) and two-dimensional (2-D) (COSY, NOESY, and TOCSY) (1)H NMR data show the thioether and ground state S,S-bonded sulfoxide complexes to be rigorously C(2) symmetric and are consistent with the crystal structures. Transient absorption spectroscopy reveals that the S,S to S,O isomerization occurs with an observed time constant of 56.8 (±7.4) ps. The S,O to O,O isomerization time constant was found to be 59 (±4) ps by pump-repump-probe spectroscopy. The composite S,S- to O,O-isomer quantum yield is 0.42.

Bond-bending isomerism of Au 2I 3 -: Competition between covalent bonding and aurophilicity

DOE PAGES

Li, Wan -Lu; Liu, Hong -Tao; Jian, Tian; ...

2015-10-13

We report a joint photoelectron spectroscopy and theoretical investigation of the gaseous Au 2I 3 – cluster, which is found to exhibit two types of isomers due to competition between Au–I covalent bonding and Au–Au aurophilic interactions. The covalent bonding favors a bent IAuIAuI – structure with an obtuse Au–I–Au angle (100.7°), while aurophilic interactions pull the two Au atoms much closer, leading to an acutely bent structure (72.0°) with an Au–Au distance of 3.08 Å. The two isomers are separated by a small barrier and are nearly degenerate with the obtuse isomer being slightly more stable. At low temperature,more » only the obtuse isomer is observed; distinct experimental evidence is observed for the co-existence of a combination of isomers with both acute and obtuse bending angles at room temperature. As a result, the two bond-bending isomers of Au 2I 3 – reveal a unique example of one molecule being able to oscillate between different structures as a result of two competing chemical forces.« less

Bond-bending isomerism of Au 2I 3 -: Competition between covalent bonding and aurophilicity

DOE Office of Scientific and Technical Information (OSTI.GOV)

Li, Wan -Lu; Liu, Hong -Tao; Jian, Tian

We report a joint photoelectron spectroscopy and theoretical investigation of the gaseous Au 2I 3 – cluster, which is found to exhibit two types of isomers due to competition between Au–I covalent bonding and Au–Au aurophilic interactions. The covalent bonding favors a bent IAuIAuI – structure with an obtuse Au–I–Au angle (100.7°), while aurophilic interactions pull the two Au atoms much closer, leading to an acutely bent structure (72.0°) with an Au–Au distance of 3.08 Å. The two isomers are separated by a small barrier and are nearly degenerate with the obtuse isomer being slightly more stable. At low temperature,more » only the obtuse isomer is observed; distinct experimental evidence is observed for the co-existence of a combination of isomers with both acute and obtuse bending angles at room temperature. As a result, the two bond-bending isomers of Au 2I 3 – reveal a unique example of one molecule being able to oscillate between different structures as a result of two competing chemical forces.« less

High-K isomers and rotational structures in {sup 174}W

DOE Office of Scientific and Technical Information (OSTI.GOV)

Tandel, S.K.; Chowdhury, P.; Seabury, E.H.

2006-04-15

High-spin states in {sup 174}W (Z = 74) have been populated using the reaction {sup 128}Te({sup 50}Ti, 4n){sup 174}W at beam energies of 215 and 225 MeV. The Gammasphere array was used to detect the {gamma} rays emitted by the evaporation residues. Four previously known collective band structures have been extended, and 16 new rotational sequences observed. Two are built upon isomeric states, one corresponding to a two-quasiparticle K = 8 isomer, the other to a four-quasiparticle K = 12 isomer, with the latter exhibiting strong K-violating {delta}K=12 decays to the ground state band. Nucleonic configurations for the two- andmore » four-quasiparticle excitations are proposed, and Woods-Saxon cranking calculations are presented to understand the rotational structures. Decay mechanisms of multi-quasiparticle K isomers are discussed in terms of the prevalent phenomenological models, with special emphasis on {gamma}-tunneling calculations. Surprisingly, the latter underpredict the decay hindrance for the K = 12 isomer by three orders of magnitude, unlike all other isomer decays in this mass region.« less

Competition between quasi-planar and cage-like structures in the B29- cluster: photoelectron spectroscopy and ab initio calculations.

PubMed

Li, Hai-Ru; Jian, Tian; Li, Wei-Li; Miao, Chang-Qing; Wang, Ying-Jin; Chen, Qiang; Luo, Xue-Mei; Wang, Kang; Zhai, Hua-Jin; Li, Si-Dian; Wang, Lai-Sheng

2016-10-26

Size-selected boron clusters have been found to be predominantly planar or quasi-planar (2D) in the small size regime with the appearance of three-dimensional (3D) borospherene cages of larger sizes. A seashell-like B 28 - cluster was previously shown to be the smallest borospherene, which competes with a quasi-planar isomer for the global minimum. Here we report a study on the structures and bonding of the B 29 - and B 29 clusters using photoelectron spectroscopy (PES) and first-principles calculations and demonstrate the continued competition between the 2D and borospherene structures. The PES spectrum of B 29 - displays a complex pattern with evidence of low-lying isomers. Global-minimum searches and extensive theoretical calculations revealed a complicated potential energy surface for B 29 - with five low-lying isomers, among which the lowest three were shown to contribute to the experimental spectrum. A 3D seashell-like C s (2, 1 A') isomer, featuring two heptagons on the waist and one octagon at the bottom, is the global minimum for B 29 - , followed by a 2D C 1 (3, 1 A) isomer with a hexagonal hole and a stingray-shaped 2D C s (1, 1 A') isomer with a pentagonal hole. However, by taking into account the entropic effects, the stingray-shaped isomer 1 was shown to be the lowest in energy at room temperature and was found to dominate the PES spectrum. Isomers 2 and 3, which have lower electron binding energies, were also found to be present in the experiment. Chemical bonding analyses showed that isomer 1 is an all-boron analogue of benzo[ghi]fluoranthene (C 18 H 10 ), whereas the borospherene isomer 2 possesses 18π electrons, conforming to the 2(N + 1) 2 electron counting rule for spherical aromaticity. For the B 29 neutral cluster, the seashell-like borospherene isomer is the global minimum, significantly lower in energy than the stingray-shaped quasi-planar structure.

Roles of dynamical symmetry breaking in driving oblate-prolate transitions of atomic clusters

DOE Office of Scientific and Technical Information (OSTI.GOV)

Oka, Yurie, E-mail: ok-yu@fuji.waseda.jp; Yanao, Tomohiro, E-mail: yanao@waseda.jp; Koon, Wang Sang, E-mail: koon@cds.caltech.edu

2015-04-07

This paper explores the driving mechanisms for structural transitions of atomic clusters between oblate and prolate isomers. We employ the hyperspherical coordinates to investigate structural dynamics of a seven-atom cluster at a coarse-grained level in terms of the dynamics of three gyration radii and three principal axes, which characterize overall mass distributions of the cluster. Dynamics of gyration radii is governed by two kinds of forces. One is the potential force originating from the interactions between atoms. The other is the dynamical forces called the internal centrifugal forces, which originate from twisting and shearing motions of the system. The internalmore » centrifugal force arising from twisting motions has an effect of breaking the symmetry between two gyration radii. As a result, in an oblate isomer, activation of the internal centrifugal force that has the effect of breaking the symmetry between the two largest gyration radii is crucial in triggering structural transitions into prolate isomers. In a prolate isomer, on the other hand, activation of the internal centrifugal force that has the effect of breaking the symmetry between the two smallest gyration radii is crucial in triggering structural transitions into oblate isomers. Activation of a twisting motion that switches the movement patterns of three principal axes is also important for the onset of structural transitions between oblate and prolate isomers. Based on these trigger mechanisms, we finally show that selective activations of specific gyration radii and twisting motions, depending on the isomer of the cluster, can effectively induce structural transitions of the cluster. The results presented here could provide further insights into the control of molecular reactions.« less

Roles of dynamical symmetry breaking in driving oblate-prolate transitions of atomic clusters

NASA Astrophysics Data System (ADS)

Oka, Yurie; Yanao, Tomohiro; Koon, Wang Sang

2015-04-01

This paper explores the driving mechanisms for structural transitions of atomic clusters between oblate and prolate isomers. We employ the hyperspherical coordinates to investigate structural dynamics of a seven-atom cluster at a coarse-grained level in terms of the dynamics of three gyration radii and three principal axes, which characterize overall mass distributions of the cluster. Dynamics of gyration radii is governed by two kinds of forces. One is the potential force originating from the interactions between atoms. The other is the dynamical forces called the internal centrifugal forces, which originate from twisting and shearing motions of the system. The internal centrifugal force arising from twisting motions has an effect of breaking the symmetry between two gyration radii. As a result, in an oblate isomer, activation of the internal centrifugal force that has the effect of breaking the symmetry between the two largest gyration radii is crucial in triggering structural transitions into prolate isomers. In a prolate isomer, on the other hand, activation of the internal centrifugal force that has the effect of breaking the symmetry between the two smallest gyration radii is crucial in triggering structural transitions into oblate isomers. Activation of a twisting motion that switches the movement patterns of three principal axes is also important for the onset of structural transitions between oblate and prolate isomers. Based on these trigger mechanisms, we finally show that selective activations of specific gyration radii and twisting motions, depending on the isomer of the cluster, can effectively induce structural transitions of the cluster. The results presented here could provide further insights into the control of molecular reactions.

Photoswitchable Fluorescent Diarylethene Derivatives with Thiophene 1,1-Dioxide Groups: Effect of Alkyl Substituents at the Reactive Carbons

PubMed Central

Sumi, Takaki; Irie, Masahiro

2017-01-01

Photoswitching and fluorescent properties of sulfone derivatives of 1,2-bis(2-alkyl-4-methyl-5-phenyl-3-thienyl)perfluorocyclopentene, 1–5, having methyl, ethyl, n-propyl, i-propyl, and i-butyl substituents at the reactive carbons (2- and 2′-positions) of the thiophene 1,1-dioxide rings were studied. Diarylethenes 1–5 underwent isomerization reactions between open-ring and closed-ring forms upon alternate irradiation with ultraviolet (UV) and visible light and showed fluorescence in the closed-ring forms. The alkyl substitution at the reactive carbons affects the fluorescent property of the closed-ring isomers. The closed-ring isomers 2b–5b with ethyl, n-propyl, i-propyl, and i-butyl substituents show higher fluorescence quantum yields than 1b with methyl substituents. In polar solvents, the fluorescence quantum yield of 1b markedly decreases, while 2b–5b maintain the relatively high fluorescence quantum yields. Although the cycloreversion quantum yields of the derivatives with methyl, ethyl, n-propyl, and i-propyl substituents are quite low and in the order of 10−5, introduction of i-butyl substituents was found to increase the yield up to the order of 10−3. These results indicate that appropriate alkyl substitution at the reactive carbons is indispensable for properly controlling the photoswitching and fluorescent properties of the photoswitchable fluorescent diarylethenes, which are potentially applicable to super-resolution fluorescence microscopies. PMID:28869489

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

PubMed

Bowes, Katharine F; Cole, Jacqueline M; Husheer, Shamus L G; Raithby, Paul R; Savarese, Teresa L; Sparkes, Hazel A; Teat, Simon J; Warren, John E

2006-06-21

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.

A strategy to improve the identification reliability of the chemical constituents by high-resolution mass spectrometry-based isomer structure prediction combined with a quantitative structure retention relationship analysis: Phthalide compounds in Chuanxiong as a test case.

PubMed

Zhang, Qingqing; Huo, Mengqi; Zhang, Yanling; Qiao, Yanjiang; Gao, Xiaoyan

2018-06-01

High-resolution mass spectrometry (HRMS) provides a powerful tool for the rapid analysis and identification of compounds in herbs. However, the diversity and large differences in the content of the chemical constituents in herbal medicines, especially isomerisms, are a great challenge for mass spectrometry-based structural identification. In the current study, a new strategy for the structural characterization of potential new phthalide compounds was proposed by isomer structure predictions combined with a quantitative structure-retention relationship (QSRR) analysis using phthalide compounds in Chuanxiong as an example. This strategy consists of three steps. First, the structures of phthalide compounds were reasonably predicted on the basis of the structure features and MS/MS fragmentation patterns: (1) the collected raw HRMS data were preliminarily screened by an in-house database; (2) the MS/MS fragmentation patterns of the analogous compounds were summarized; (3) the reported phthalide compounds were identified, and the structures of the isomers were reasonably predicted. Second, the QSRR model was established and verified using representative phthalide compound standards. Finally, the retention times of the predicted isomers were calculated by the QSRR model, and the structures of these peaks were rationally characterized by matching retention times of the detected chromatographic peaks and the predicted isomers. A multiple linear regression QSRR model in which 6 physicochemical variables were screened was built using 23 phthalide standards. The retention times of the phthalide isomers in Chuanxiong were well predicted by the QSRR model combined with reasonable structure predictions (R 2 =0.955). A total of 81 peaks were detected from Chuanxiong and assigned to reasonable structures, and 26 potential new phthalide compounds were structurally characterized. This strategy can improve the identification efficiency and reliability of homologues in complex materials. Copyright © 2018 Elsevier B.V. All rights reserved.

Terahertz Spectroscopy and Solid-State Density Functional Theory Calculations of Cyanobenzaldehyde Isomers.

PubMed

Dash, Jyotirmayee; Ray, Shaumik; Nallappan, Kathirvel; Kaware, Vaibhav; Basutkar, Nitin; Gonnade, Rajesh G; Ambade, Ashootosh V; Joshi, Kavita; Pesala, Bala

2015-07-23

Spectral signatures in the terahertz (THz) frequency region are mainly due to bulk vibrations of the molecules. These resonances are highly sensitive to the relative position of atoms in a molecule as well as the crystal packing arrangement. To understand the variation of THz resonances, THz spectra (2-10 THz) of three structural isomers: 2-, 3-, and 4-cyanobenzaldehyde have been studied. THz spectra obtained from Fourier transform infrared (FTIR) spectrometry of these isomers show that the resonances are distinctly different especially below 5 THz. For understanding the intermolecular interactions due to hydrogen bonds, four molecule cluster simulations of each of the isomers have been carried out using the B3LYP density functional with the 6-31G(d,p) basis set in Gaussian09 software and the compliance constants are obtained. However, to understand the exact reason behind the observed resonances, simulation of each isomer considering the full crystal structure is essential. The crystal structure of each isomer has been determined using X-ray diffraction (XRD) analysis for carrying out crystal structure simulations. Density functional theory (DFT) simulations using CRYSTAL14 software, utilizing the hybrid density functional B3LYP, have been carried out to understand the vibrational modes. The bond lengths and bond angles from the optimized structures are compared with the XRD results in terms of root-mean-square-deviation (RMSD) values. Very low RMSD values confirm the overall accuracy of the results. The simulations are able to predict most of the spectral features exhibited by the isomers. The results show that low frequency modes (<3 THz) are mediated through hydrogen bonds and are dominated by intermolecular vibrations.

Three isomers detected for the whisky lactone: 5-butyl-4-methyl tetrahydrofuran-2-one by Fourier transform microwave spectroscopy and quantum chemical calculations

NASA Astrophysics Data System (ADS)

Kawashima, Yoshiyuki; Katsuragi, Ryusuke; Hirota, Eizi

2017-05-01

The ground-state rotational spectra of the whisky lactone (WL) : 5-butyl-4-methyl tetrahydrofuran-2-one were observed and analyzed by molecular beam Fourier transform microwave spectroscopy combined with quantum chemical calculations. We have detected three stereo-isomers: the trans-TTT form with a methyl CH3 group attached to C(4) in an equatorial position (eq) and a butyl C4H9 group to C(5) in an eq position, for which 110 b-type and 113 a-type transitions were assigned, the cis-TTT form with a CH3 to C(4) in an axial position (ax) and a C4H9 to C(5) in eq, for which 96 a-type, 101 b-type, and 45 c-type transitions were observed, and the cis-GTT form with a CH3 to C(4) in ax and a C4H9 to C(5) in eq, for which 158 a-type, 52 b-type, and 17 c-type transitions were observed, where TTT and GTT denote the conformations about the C(6)sbnd C(5), C(7)sbnd C(6), and C(8)sbnd C(7) bonds, with T and G designating trans and gauche, respectively. The rotational constants thus derived agree with the predictions made by quantum chemical calculations, MP2/6-311++G(d, p) within 1.2%. The trans-TTT form was calculated to be the most stable. The splittings due to internal rotation of the terminal methyl in the butyl group were observed for all the three stereo-isomers and were analyzed by the XIAM program to determine the threefold potential barrier V3 to be 966.4 (25), 978.8 (11), and 1098.7 (48) in cm-1 for the trans-TTT (eq, eq), the cis-TTT (ax, eq), and the cis-GTT (ax, eq) forms, respectively, to be compared with quantum chemically calculated values: 1055, 1055, and 1053 in cm-1.

Population and decay of a Kπ=8- two-quasineutron isomer in 244Pu

NASA Astrophysics Data System (ADS)

Hota, S. S.; Tandel, S. K.; Chowdhury, P.; Ahmad, I.; Carpenter, M. P.; Chiara, C. J.; Greene, J. P.; Hoffman, C. R.; Jackson, E. G.; Janssens, R. V. F.; Kay, B. P.; Khoo, T. L.; Kondev, F. G.; Lakshmi, S.; Lalkovski, S.; Lauritsen, T.; Lister, C. J.; McCutchan, E. A.; Moran, K.; Peterson, D.; Shirwadkar, U.; Seweryniak, D.; Stefanescu, I.; Toh, Y.; Zhu, S.

2016-08-01

The decay of a Kπ=8- isomer in 244Pu and the collective band structures populating the isomer were studied using deep inelastic excitations with 47Ti and 208Pb beams, respectively. Precise measurements of M 1 /E 2 branching ratios in the band confirm a 9 /2-[734] ν⊗7 /2+[624] ν configuration assignment for the isomer, validating the systematics of Kπ=8- , two-quasineutron isomers observed in even-Z , N =150 isotones. These isomers around the deformed shell gap at N =152 provide critical benchmarks for theoretical predictions of single-particle energies in this gateway region to superheavy nuclei.

Structural characterization of cevimeline and its trans-impurity by single crystal XRD.

PubMed

Stepanovs, Dmitrijs; Tetere, Zenta; Rāviņa, Irisa; Kumpiņš, Viktors; Zicāne, Daina; Bizdēna, Ērika; Bogans, Jānis; Novosjolova, Irina; Grigaloviča, Agnese; Meri, Remo Merijs; Fotins, Juris; Čerkasovs, Maksims; Mishnev, Anatoly; Turks, Māris

2016-01-25

Cevimeline is muscarinic receptor agonist which increases secretion of exocrine glands. Cevimeline base is a liquid (m.p. 20-25 °C) at ambient conditions, therefore its pharmaceutical formulation as a solid hydrochloride hemihydrate has been developed. The synthesis of cevimeline yields its cis- and trans-isomers and only the cis-isomer is recognized as the API and used in the finished formulation. In this study structural and physicochemical investigations of hydrochloride hemihydrates of cis- and trans-cevimelines have been performed. Single crystal X-ray analyses of both cis- and trans-isomers of cevimeline are reported here for the first time. It was found that the cis-isomer, the API, has less dense crystal packing, lower melting point and higher solubility in comparison to the trans-isomer. Copyright © 2015 Elsevier B.V. All rights reserved.

First hyperpolarizability of isomers of pyridinium N-phenoxide betaine dye in solution using the ASEC-FEG method

NASA Astrophysics Data System (ADS)

Torres, E. M.; Georg, H. C.; Fonseca, T. L.; Castro, M. A.

2018-05-01

The linear and nonlinear properties of isomeric forms of pyridinium-N-phenoxide betaine dye were investigated in protic and aprotic solvents using atomistic simulations. We employed the sequential Quantum Mechanics/Molecular Mechanics (S-QM/MM) and the free energy gradient (FEG) methods to optimize the geometry of each isomer in chloroform, acetonitrile, methanol and water. The results show a complex dependence of the first hyperpolarizability with respect to the solvent nature and isomeric form, with a marked effect of conformational changes for para-betaine. Large contrasts of the first hyperpolarizability show a clear distinction between isomeric forms in solution that could be experimentally detected.

Molecular spinning by a chiral train of short laser pulses

NASA Astrophysics Data System (ADS)

Floß, Johannes; Averbukh, Ilya Sh.

2012-12-01

We provide a detailed theoretical analysis of molecular rotational excitation by a chiral pulse train, a sequence of linearly polarized pulses with the polarization direction rotating from pulse to pulse by a controllable angle. Molecular rotation with a preferential rotational sense (clockwise or counterclockwise) can be excited by this scheme. We show that the directionality of the rotation is caused by quantum interference of different excitation pathways. The chiral pulse train is capable of selective excitation of molecular isotopologs and nuclear spin isomers in a mixture. We demonstrate this using 14N2 and 15N2 as examples for isotopologs and para- and ortho-nitrogen as examples for nuclear-spin isomers.

Characterization of a distonic isomer C6H5C+(OH)OCH2 of methyl benzoate radical cation by associative ion-molecule reactions

NASA Astrophysics Data System (ADS)

Dechamps, Noémie; Flammang, Robert; Gerbaux, Pascal; Nam, Pham-Cam; Nguyen, Minh Tho

2006-03-01

The C6H5C+(OH)OCH2 radical cation, formally a distonic isomer of ionized methyl benzoate, has been prepared by dissociative ionization of neopentyl benzoate, as earlier suggested by Audier et al. [H.E. Audier, A. Milliet, G. Sozzi, S. Hammerum, Org. Mass. Spectrom. 25 (1990) 44]. Its distonic character has now been firmly established by its high reactivity towards neutral methyl isocyanide (ionized methylene transfer) producing N-methyl ketenimine ions. Other mass spectrometric experiments and ab initio quantum chemical calculations also concur with each other pointing toward the existence of a stable distonic radical cation.

Investigations of the Rg-BrCl (Rg=He, Ne, Ar, Kr, Xe) binary van der Waals complexes: ab initio intermolecular potential energy surfaces, vibrational states and predicted pure rotational transition frequencies.

PubMed

Li, Song; Zheng, Rui; Chen, Shan-Jun; Chen, Yan; Chen, Peng

2017-03-05

The intermolecular potential energy surfaces (PESs) of the ground electronic state for the Rg-BrCl (Rg=He, Ne, Ar, Kr, Xe) van der Waals complexes have been constructed by using the coupled-cluster method in combination with the augmented quadruple-zeta correlation-consistent basis sets supplemented with an additional set of bond functions. The features of the anisotropic PESs for these complexes are remarkably similar, which are characterized by three minima and two saddle points between them. The global minimum corresponds to a collinear Rg-Br-Cl configuration. Two local minima, correlate with an anti-linear Rg-Cl-Br geometry and a nearly T-shaped structure, can also be located on each PES. The quantum bound state calculations enable us to investigate intermolecular vibrational states and rotational energy levels of the complexes. The transition frequencies are predicted and are fitted to obtain their corresponding spectroscopic constants. In general, the periodic trends are observed for this complex family. Comparisons with available experimental data for the collinear isomer of Ar-BrCl demonstrate reliability of our theoretical predictions, and our results for the other two isomers of Ar-BrCl as well as for other members of the complex family are also anticipated to be trustable. Except for the collinear isomer of Ar-BrCl, the data presented in this paper would be beneficial to improve our knowledge for these experimentally unknown species. Copyright © 2016 Elsevier B.V. All rights reserved.

Topologically guided tuning of Zr-MOF pore structures for highly selective separation of C6 alkane isomers

DOE PAGES

Wang, Hao; Dong, Xinglong; Lin, Junzhong; ...

2018-05-01

As an alternative technology to energy intensive distillations, adsorptive separation by porous solids offers lower energy cost and higher efficiency. Herein we report a topology-directed design and synthesis of a series of Zr-based metal-organic frameworks with optimized pore structure for efficient separation of C6 alkane isomers, a critical step in the petroleum refining process to produce gasoline with high octane rating. Zr 6O 4(OH) 4(bptc) 3 adsorbs a large amount of n-hexane but excluding branched isomers. The n-hexane uptake is ~70% higher than that of a benchmark adsorbent, zeolite-5A. A derivative structure, Zr 6O 4(OH) 8(H 2O) 4(abtc) 2, ismore » capable of discriminating all three C6 isomers and yielding a high separation factor for 3-methylpentane over 2,3-dimethylbutane. This property is critical for producing gasoline with further improved quality. Multicomponent breakthrough experiments provide a quantitative measure of the capability of these materials for separation of C6 alkane isomers. A detailed structural analysis reveals the unique topology, connectivity and relationship of these compounds.« less

Resolving Structural Isomers of Monosaccharide Methyl Glycosides Using Drift Tube and Traveling Wave Ion Mobility Mass Spectrometry

PubMed Central

Li, Hongli; Giles, Kevin; Bendiak, Brad; Kaplan, Kimberly; Siems, William F.; Hill, Herbert H.

2013-01-01

Monosaccharide structural isomers including sixteen methyl-D-glycopyranosides and four methyl-N-acetylhexosamines were subjected to ion mobility measurements by electrospray ion mobility mass spectrometry. Two ion mobility-MS systems were employed: atmospheric pressure drift tube ion mobility time-of-flight mass spectrometry and a Synapt G2 HDMS system which incorporates a low pressure traveling wave ion mobility separator. All the compounds were investigated as [M+Na]+ ions in the positive mode. A majority of the monosaccharide structural isomers exhibited different mobility drift times in either system, depending on differences in their anomeric and stereochemical configurations. In general, drift time patterns (relative drift times of isomers) matched between the two instruments. Higher resolving power was observed using the atmospheric pressure drift tube. Collision cross section values of monosaccharide structural isomers were directly calculated from the atmospheric pressure ion mobility experiments and a collision cross section calibration curve was made for the traveling wave ion mobility instrument. Overall, it was demonstrated that ion mobility-mass spectrometry using either drift tube or traveling wave ion mobility is a valuable technique for resolving subtle variations in stereochemistry among the sodium adducts of monosaccharide methyl glycosides. PMID:22339760

Topologically guided tuning of Zr-MOF pore structures for highly selective separation of C6 alkane isomers

DOE Office of Scientific and Technical Information (OSTI.GOV)

Wang, Hao; Dong, Xinglong; Lin, Junzhong

As an alternative technology to energy intensive distillations, adsorptive separation by porous solids offers lower energy cost and higher efficiency. Herein we report a topology-directed design and synthesis of a series of Zr-based metal-organic frameworks with optimized pore structure for efficient separation of C6 alkane isomers, a critical step in the petroleum refining process to produce gasoline with high octane rating. Zr 6O 4(OH) 4(bptc) 3 adsorbs a large amount of n-hexane but excluding branched isomers. The n-hexane uptake is ~70% higher than that of a benchmark adsorbent, zeolite-5A. A derivative structure, Zr 6O 4(OH) 8(H 2O) 4(abtc) 2, ismore » capable of discriminating all three C6 isomers and yielding a high separation factor for 3-methylpentane over 2,3-dimethylbutane. This property is critical for producing gasoline with further improved quality. Multicomponent breakthrough experiments provide a quantitative measure of the capability of these materials for separation of C6 alkane isomers. A detailed structural analysis reveals the unique topology, connectivity and relationship of these compounds.« less

Failures of fractional crystallization: ordered co-crystals of isomers and near isomers.

PubMed

Kelley, Steven P; Fábián, László; Brock, Carolyn Pratt

2011-02-01

A list of 270 structures of ordered co-crystals of isomers, near isomers and molecules that are almost the same has been compiled. Searches for structures containing isomers could be automated by the use of IUPAC International Chemical Identifier (InChI™) strings but searches for co-crystals of very similar molecules were more labor intensive. Compounds in which the heteromolecular A···B interactions are clearly better than the average of the homomolecular A···A and B···B interactions were excluded. The two largest structural classes found include co-crystals of configurational diastereomers and of quasienantiomers (or quasiracemates). These two groups overlap. There are 114 co-crystals of diastereomers and the same number of quasiracemates, with 71 structures being counted in both groups; together the groups account for 157 structures or 58% of the total. The large number of quasiracemates is strong evidence for inversion symmetry being very favorable for crystal packing. Co-crystallization of two diastereomers is especially likely if a 1,1 switch of a methyl group and an H atom, or of an inversion of a [2.2.1] or [2.2.2] cage, in one of the diastereomers would make the two molecules enantiomers.

Determination of ortho-cresyl phosphate isomers of tricresyl phosphate used in aircraft turbine engine oils by gas chromatography and mass spectrometry.

PubMed

De Nola, G; Kibby, J; Mazurek, W

2008-07-25

Tricresyl phosphate (TCP) is used as an anti-wear additive in aircraft turbine engine oil. Concerns about its toxicity are largely based on the tri-o-cresyl phosphate isomer content. However, the presence of other and more toxic isomers has been previously suggested. In this work, the structural isomers of TCP have been determined by two methods (experimental and semi-theoretical). First, the TCP isomers were separated by gas chromatography (GC) and identified by mass spectrometry (MS). Second, after base cleavage of TCP, GC was used to quantify the cresol precursors. These results were used to calculate the TCP isomer distribution based on the assumption of a statistical distribution of the TCP isomers. The results from the two determinations showed reasonable agreement for three of the four oils studied. The o-cresyl isomers were found to be present almost exclusively as the more toxic mono-o-cresyl isomers in the concentration range 13-150 mg/L. The ability to analyse for the mono-o-cresyl isomers allows the toxicity of TCP to be based on the latter isomers rather than on the less toxic tri-o-cresyl phosphate isomer.

[Quantum differences of ortho/para H2O2 spin-isomers as a factor of the femtosecond charge separation kinetics modulation in reaction centers of purple bacteria].

PubMed

Pishchal'nikov, R Iu; Pershin, S M; Bunkin, A F

2012-01-01

We have proposed the mechanism of coherent modulations of the P* state in the transient absorption spectra of the reaction center isolated from purple bacteria. Two water molecules, located between special pair, Ba, Bb chlorophylls and histidine L173 and M202, are supposed to be ortho-H2O and para-H2O isomers with different magnetic properties. The distinctive modulation frequencies were labeling as rotational resonances of ortho-H2O. According to our assumption, the interaction of rotational modes of water isomers with the charge-transfer states is a reason of coherent modulations of kinetics. We have modified a Hamiltonian system in order to take into account the rotational modes of ortho-H2O. Evolution of the density matrix was calculated in Liouville space. The Redfield relaxation theory for molecular aggregates was used to model kinetics up to 3 ps.

Electrical detection of ortho–para conversion in fullerene-encapsulated water

PubMed Central

Meier, Benno; Mamone, Salvatore; Concistrè, Maria; Alonso-Valdesueiro, Javier; Krachmalnicoff, Andrea; Whitby, Richard J.; Levitt, Malcolm H.

2015-01-01

Water exists in two spin isomers, ortho and para, that have different nuclear spin states. In bulk water, rapid proton exchange and hindered molecular rotation obscure the direct observation of two spin isomers. The supramolecular endofullerene H2O@C60 provides freely rotating, isolated water molecules even at cryogenic temperatures. Here we show that the bulk dielectric constant of this substance depends on the ortho/para ratio, and changes slowly in time after a sudden temperature jump, due to nuclear spin conversion. The attribution of the effect to ortho–para conversion is validated by comparison with nuclear magnetic resonance and quantum theory. The change in dielectric constant is consistent with an electric dipole moment of 0.51±0.05 Debye for an encapsulated water molecule, indicating the partial shielding of the water dipole by the encapsulating cage. The dependence of bulk dielectric constant on nuclear spin isomer composition appears to be a previously unreported physical phenomenon. PMID:26299447

Ab initio study of the chlorine nitrate protonation reaction - Implications for loss of ClONO2 in the stratosphere

NASA Technical Reports Server (NTRS)

Lee, Timothy J.; Rice, Julia E.

1993-01-01

Ab initio quantum mechanical methods, including coupled-cluster theory, are used to determine the equilibrium geometries, dipole moments, and harmonic vibrational frequencies of ClONO2, NO2(+), and four isomers of protonated ClONO2. It was found that, for the equilibrium structures and harmonic frequencies of ClONO2, HOCl, and NO2(+), the highest-level theoretical predictions are consistent with the available experimental information concerning the reactions of ClONO2 and HOCl with HCl on the surface of polar stratospheric clouds (PSCs). The study supports a recent hypothesis that the reaction of ClONO2 on the surface of PSCs is proton catalyzed, although the mechanism is different.

The Scent of Roses and beyond: Molecular Structures, Analysis, and Practical Applications of Odorants

ERIC Educational Resources Information Center

Mannschreck, Albrecht; von Angerer, Erwin

2011-01-01

A few odorous compounds found in roses are chosen to arouse the reader's interest in their molecular structures. This article differs from some similar reports on odorants mainly by combining the structural description with the presentation of the following types of isomers: constitutional isomers, enantiomers, and diastereomers. The preparation…

Population and decay of a K π = 8 – two-quasineutron isomer in Pu 244

DOE PAGES

Hota, S. S.; Tandel, S. K.; Chowdhury, P.; ...

2016-08-22

Here, the decay of a K π = 8 – isomer in 244Pu and the collective band structures populating the isomer were studied using deep inelastic excitations with 47Ti and 208Pb beams, respectively. Precise measurements of M1/E2 branching ratios in the band confirm a 9/2 –[734] νⓍ7/2 +[624] ν configuration assignment for the isomer, validating the systematics of K π = 8 –, two-quasineutron isomers observed in even-Z, N = 150 isotones. These isomers around the deformed shell gap at N = 152 provide critical benchmarks for theoretical predictions of single-particle energies in this gateway region to superheavy nuclei.

Population and decay of a K π = 8 – two-quasineutron isomer in Pu 244

DOE Office of Scientific and Technical Information (OSTI.GOV)

Hota, S. S.; Tandel, S. K.; Chowdhury, P.

Here, the decay of a K π = 8 – isomer in 244Pu and the collective band structures populating the isomer were studied using deep inelastic excitations with 47Ti and 208Pb beams, respectively. Precise measurements of M1/E2 branching ratios in the band confirm a 9/2 –[734] νⓍ7/2 +[624] ν configuration assignment for the isomer, validating the systematics of K π = 8 –, two-quasineutron isomers observed in even-Z, N = 150 isotones. These isomers around the deformed shell gap at N = 152 provide critical benchmarks for theoretical predictions of single-particle energies in this gateway region to superheavy nuclei.

Structural isomers of C2N(+) - A selected-ion flow tube study

NASA Technical Reports Server (NTRS)

Knight, J. S.; Petrie, S. A. H.; Freeman, C. G.; Mcewan, M. J.; Mclean, A. D.

1988-01-01

Reactivities of the structural isomers CCN(+) and CNC(+) were examined in a selected-ion flow tube at 300 + or - 5 K. The less reactive CNC(+) isomer was identified as the product of the reactions of C(+) + HCN and C(+) + C2N2; in these reactions only CNC(+) can be produced because of energy constraints. Rate coefficients and branching ratios are reported for the reactions of each isomer with H2, CH4, NH3, H2O, C2H2, HCN, N2, O2, N2O, and CO2. Ab initio calculations are presented for CCN(+) and CNC(+); a saddle point for the reaction CCN(+) yielding CNC(+) is calculated to be 195 kJ/mol above CNC(+). The results provide evidence that the more reactive CCN(+) isomer is unlikely to be present in measurable densities in interstellar clouds.

New isomer in 96Y marking the onset of deformation at N = 57

NASA Astrophysics Data System (ADS)

Iskra, Ł. W.; Fornal, B.; Leoni, S.; Bocchi, G.; Petrovici, A.; Porzio, C.; Blanc, A.; De France, G.; Jentschel, M.; Köster, U.; Mutti, P.; Régis, J.-M.; Simpson, G.; Soldner, T.; Ur, C. A.; Urban, W.; Bazzacco, D.; Benzoni, G.; Bottoni, S.; Bruce, A.; Cieplicka-Oryńczak, N.; Crespi, F. C. L.; Fraile, L. M.; Korten, W.; Kröll, T.; Lalkovski, S.; Márginean, N.; Michelagnoli, C.; Melon, B.; Mengoni, D.; Million, B.; Nannini, A.; Napoli, D.; Podolyák, Zs.; Regan, P. H.; Szpak, B.

2017-01-01

The level scheme of 96Y was significantly extended and a new 201 ns isomer was located at 1655 keV excitation energy, with spin-parity assignment of 5± or 6-. The isomer decays to spherical low-spin structure by transitions with large hindrance and is fed by a short cascade which resembles the beginning of a rotational band. This is in analogy with the feeding and decay pattern of the 4- isomer in 98Y, here confirmed, by lifetime analysis, as a bandhead of a rotational structure with sizable deformation. It is suggested that the new isomer in 96Y arises from a shape change between deformed and spherical configurations, which indicates the appearance of deformation already at N = 57 in the yttrium chain. The experimental findings for 96Y are strengthened by theoretical calculations based on the complex Excited Vampir model.

Energetics of the S 2 state spin isomers of the oxygen-evolving complex of Photosystem II

DOE Office of Scientific and Technical Information (OSTI.GOV)

Vinyard, David J.; Khan, Sahr; Askerka, Mikhail

Here, the S 2 redox intermediate of the oxygen-evolving complex in Photosystem II is present as two spin isomers. The S = 1/2 isomer gives rise to a multiline EPR signal at g = 2, while the S = 5/2 isomer exhibits a broad EPR signal at g = 4.1. The electronic structures of these isomers are known, but their role in the catalytic cycle of water oxidation remains unclear. We show that formation of the S = 1/2 state from the S = 5/2 state is exergonic at temperatures above 160 K. However, the S = 1/2 isomer decaysmore » to S 1 more slowly than the S = 5/2 isomer. These differences support the hypotheses that the S 3 state is formed via the S 2 state S = 5/2 isomer and that the stabilized S 2 state S = 1/2 isomer plays a role in minimizing S 2Q A- decay in light-limiting conditions.« less

Energetics of the S 2 state spin isomers of the oxygen-evolving complex of Photosystem II

DOE PAGES

Vinyard, David J.; Khan, Sahr; Askerka, Mikhail; ...

2017-01-12

Here, the S 2 redox intermediate of the oxygen-evolving complex in Photosystem II is present as two spin isomers. The S = 1/2 isomer gives rise to a multiline EPR signal at g = 2, while the S = 5/2 isomer exhibits a broad EPR signal at g = 4.1. The electronic structures of these isomers are known, but their role in the catalytic cycle of water oxidation remains unclear. We show that formation of the S = 1/2 state from the S = 5/2 state is exergonic at temperatures above 160 K. However, the S = 1/2 isomer decaysmore » to S 1 more slowly than the S = 5/2 isomer. These differences support the hypotheses that the S 3 state is formed via the S 2 state S = 5/2 isomer and that the stabilized S 2 state S = 1/2 isomer plays a role in minimizing S 2Q A- decay in light-limiting conditions.« less

Infrared photodissociation spectroscopy of protonated neurotransmitters in the gas phase

NASA Astrophysics Data System (ADS)

MacLeod, N. A.; Simons, J. P.

2007-03-01

Protonated neurotransmitters have been produced in the gas phase via a novel photochemical scheme: complexes of the species of interest, 1-phenylethylamine, 2-amino-1-phenylethanol and the diastereo-isomers, ephedrine and pseudoephedrine, with a suitable proton donor, phenol (or indole), are produced in a supersonic expansion and ionized by resonant two photon ionization of the donor. Efficient proton transfer generates the protonated neurotransmitters, complexed to a phenoxy radical. Absorption of infrared radiation, and subsequent evaporation of the phenoxy tag, coupled with time of flight mass spectrometry, provides vibrational spectra of the protonated (and also hydrated) complexes for comparison with the results of quantum chemical computation. Comparison with the conformational structures of the neutral neurotransmitters (established previously) reveals the effect of protonation on their structure. The photochemical proton transfer strategy allows spectra to be recorded from individual laser shots and their quality compares favourably with that obtained using electro-spray or matrix assisted laser desorption ion sources.

Molecular structure and spectroscopic investigation of sodium(E)-2-hydroxy-5-((4-sulfonatophenyl)diazenyl)benzoate: A DFT study

NASA Astrophysics Data System (ADS)

Shahab, Siyamak; Kumar, Rakesh; Darroudi, Mahdieh; Yousefzadeh Borzehandani, Mostafa

2015-03-01

Quantum-chemical calculations using the Density Functional Theory (DFT) approach for structural analysis of new azodye sodium(E)-2-hydroxy-5-((4-sulfonatophenyl)diazenyl) (trans isomer) is carried out using B3LYP methods with 6-31G∗ basis set. The comparison of measured UV-Vis data, IR and NMR spectra of the molecule with the experimental data were also described which allowed assignment of major spectral features of title molecule. The optimized geometrical parameters obtained by B3LYP methods show a good agreement with experimental data. On the basis of polyvinyl alcohol (PVA) and the dichroic synthesized dye polarizer absorbing in the UV region of the spectrum (λmax = 353 nm) with the effect of polarization in the absorption maximum 96% was developed. The spectral-polarization parameters of stretched PVA-films were calculated.

Azide derivatized anticancer agents of Vitamin K 3: X-ray structural, DSC, resonance spectral and API studies

NASA Astrophysics Data System (ADS)

Badave, Kirti; Patil, Yogesh; Gonnade, Rajesh; Srinivas, Darbha; Dasgupta, Rajan; Khan, Ayesha; Rane, Sandhya

2011-12-01

Compound 1 [1-imino (acetyl hydrazino)-Vitamin K 3], displays valence tautomerically related electronic isomers as Form I and Form II. Form I exhibits 2D packing fragment with 1D ribbon chains of N-H⋯O hydrogen bonds and shows EPR silent features. While Form II is EPR active and exhibits biradical nature with double quantum transitions at g = 2.0040. 1H NMR of compound 2, [1-imino (hydrazino carboxylate)-Vitamin K 3] and Form II exhibit π delocalization via resonance assisted H-bonding [RAHB] effect compared to Form I. Molecular interactions in Form I and II are visualized by DSC. The electronic structures of compounds 1 and 2 have been correlated to their API values by measuring anticancer activities, mitochondrial potentials and DNA shearing patterns. Form II and compound 2 indicate mitochondria mediated apoptosis (˜75% cell death) while Form I causes 35% cell death.

C 90 temperature effects on relative stabilities of the IPR isomers

NASA Astrophysics Data System (ADS)

Slanina, Zdeněk; Zhao, Xiang; Lee, Shyi-Long; Ōsawa, Eiji

1997-07-01

The complete set of 46 isolated-pentagon-rule (IPR) isomers of C 90 is treated by the SAMI quantum-chemical method (Semi-Ab-Initio Model 1), and their energetics is also checked by ab initio SCF computations (HF/3-21G, HF/4-31G) and the AM1 and PM3 semiempirical methods. All the methods point out a C2 species as the system state (with an exception at the HF/3-21G level). However, the energetics itself is not able to produce a good agreement with recent observations (one C2 v, three C2, and one C1, separeted into three HPLC fractions). The symmetries of the five SAM1 lowest-energy structures are: C2, C2 v, Cs, D5 h, C1. In order to respect temperature effects on relative stabilities, entropy contributions are also computed and significant changes are found. The symmetries of the five structures most populated in a high-temperature region are according to the SAM1 computations: two times C2, Cs, C2 v, C1. One of the recently reported HPLC fractions shows 70 lines in the 13C NMR spectrum, assigned to a C2 species (45 lines) and C2 v species (25 lines, 5 weaker). There is however an alternative interpretation of the spectrum: a Cs (46 lines, 2 weaker) and a C2 v species (24 lines, 3 weaker). The last two structures are indeed present in the SAM1 high-temperature stability set so that agreement between observations and calculations can be achieved.

SEPARATION OF ISOMERS OF NONYLPHENOL AND SELECT NONPHENYL POLYETHOXYLATES BY HIGH-PERFORMANCE LIQUID CHROMATOGRAPHY ON A GRAPHITIC CARBON COLUMN

EPA Science Inventory

p-Nonylphenol (NP) is ubiquitous degradation product of nonylphenol polyethoxylate (NPE) surfactants and has been reported to be an endocrine disrupter. It is composed of numerous structural isomers resulting from ;the various branching patterns of the C-9 group. Twenty-two isome...

High-spin structure, K isomers, and state mixing in the neutron-rich isotopes 173Tm and 175Tm

NASA Astrophysics Data System (ADS)

Hughes, R. O.; Lane, G. J.; Dracoulis, G. D.; Byrne, A. P.; Nieminen, P. H.; Watanabe, H.; Carpenter, M. P.; Chowdhury, P.; Janssens, R. V. F.; Kondev, F. G.; Lauritsen, T.; Seweryniak, D.; Zhu, S.

2012-11-01

High-spin states in the odd-proton thulium isotopes 173Tm and 175Tm have been studied using deep-inelastic reactions and γ-ray spectroscopy. In 173Tm, the low-lying structure has been confirmed and numerous new states have been identified, including a three-quasiparticle Kπ= 19/2- isomer with a lifetime of τ=360(100) ns at 1906 keV and a five-quasiparticle Kπ=35/2- isomer with a lifetime of τ= 175(40) ns at 4048 keV. The Kπ=35/2- state is interpreted as a t-band configuration that shows anomalously fast decays. In 175Tm, the low-lying structure has been reevaluated, a candidate state for the 9/2-[514] orbital has been identified at 1175 keV, and the 7/2-[523] bandhead has been measured to have a lifetime of τ= 460(50) ns. Newly identified high-K structures in 175Tm include a Kπ=15/2- isomer with a lifetime of τ= 64(3) ns at 947 keV and a Kπ= 23/2+ isomer with a lifetime of τ= 30(20) μs at 1518 keV. The Kπ=15/2- isomer shows relatively enhanced decays to the 7/2-[523] band that can be explained by chance mixing with the 15/2- member of the 7/2- band. Multiquasiparticle calculations have been performed for 173Tm and 175Tm, the results of which compare well with the experimentally observed high-spin states.

a Chiral Tag Study of the Absolute Configuration of Camphor

NASA Astrophysics Data System (ADS)

Pratt, David; Evangelisti, Luca; Smart, Taylor; Holdren, Martin S.; Mayer, Kevin J.; West, Channing; Pate, Brooks

2017-06-01

The chiral tagging method for rotational spectroscopy uses an established approach in chiral analysis of creating a complex with an enantiopure tag so that enantiomers of the molecule of interest are converted to diastereomer complexes. Since the diastereomers have distinct structure, they give distinguishable rotational spectra. Camphor was chosen as an example for the chiral tag method because it has spectral properties that could pose challenges to the use of three wave mixing rotational spectroscopy to establish absolute configuration. Specifically, one of the dipole moment components of camphor is small making three wave mixing measurements challenging and placing high accuracy requirements on computational chemistry for calculating the dipole moment direction in the principal axis system. The chiral tag measurements of camphor used the hydrogen bond donor 3-butyn-2-ol. Quantum chemistry calculations using the B3LYP-D3BJ method and the def2TZVP basis set identified 7 low energy isomers of the chiral complex. The two lowest energy complexes of the homochiral and heterochiral complexes are observed in a measurement using racemic tag. Absolute configuration is confirmed by the use of an enantiopure tag sample. Spectra with ^{13}C-sensitivity were acquired so that the carbon substitution structure of the complex could be obtained to provide a structure of camphor with correct stereochemistry. The chiral tag complex spectra can also be used to estimate the enantiomeric excess of the sample and analysis of the broadband spectrum indicates that the sample enantiopurity is higher than 99.5%. The structure of the complex is analyzed to determine the extent of geometry modification that occurs upon formation of the complex. These results show that initial isomer searches with fixed geometries will be accurate. The reduction in computation time from fixed geometry assumptions will be discussed.

Isomer spectroscopy using RI beam

NASA Astrophysics Data System (ADS)

Odahara, Atsuko

2009-10-01

We have studied systematically high-spin oblate shape isomers in the N=83 isotones, which have revealed the characteristics of nuclear structure, such as the preserving pairing interactions at high-spin states, decrease of Z=64 proton shell gap energy as the decrease of proton number from 64 to 60 and so on. Recently, it became possible to search for isomers by the secondary fusion reaction at high-spin states in nuclei, which could not be populated by the stable beam and stable target, using RCNP RI beam line at Osaka University. RI beams enable us to study high-spin states in nuclei in wide mass region. By using the RI beams delivered by RIBF and the high-efficiency γ-ray detection system GRETINA, it will be possible to investigate nuclei far from the stability line. Single-particle energies and nucleon-nucleon interactions of these nuclei close to drip line are expected to be the test ground of nuclear models, such as shell structures. We have a plan to search for isomers with half lives of ˜μsec to ˜msec and to explore the decay mechanism of isomers in the proton-rich nuclei along N=Z line with 80< A<100. Moreover we try to search for nuclei beyond the proton drip line, which could be defined that isomeric states would be bound by the centrifugal potential although the ground states would be unbound against the proton emission. Isomers are expected to reveal the following characteristics of these nuclei. (1) Existence of isomers could prove the magicity of N=Z=50 and the large neutron-proton interaction, as one of the candidates of isomers is spin-gap isomer which is caused by the lowering of excitation energies resulting from the stretch coupling of spins of high-j (g9/2) holes of the ^100Sn core. (2) Isomers could prove the nuclear deformation which is caused by the evolution of shell structure. One of spin-gap isomers in ^94Ag was reported to have large prolate deformation. (3) This mass region is on the way of the rapid proton (rp) synthesis pass. Recently, neutrino reactions in the super novae were reported to play a role of the synthesis of the rp-process nuclei. In the case of no path or slow down of rp process, isomers could contribute to synthesis of rp-nuclei with larger Z, although the production rates of isomers are small.

Ar(n)HF van der Waals clusters revisited: II. Energetics and HF vibrational frequency shifts from diffusion Monte Carlo calculations on additive and nonadditive potential-energy surfaces for n=1-12.

PubMed

Jiang, Hao; Xu, Minzhong; Hutson, Jeremy M; Bacić, Zlatko

2005-08-01

The ground-state energies and HF vibrational frequency shifts of Ar(n)HF clusters have been calculated on the nonadditive potential-energy surfaces (PESs) for n=2-7 and on the pairwise-additive PESs for the clusters with n=1-12, using the diffusion Monte Carlo (DMC) method. For n>3, the calculations have been performed for the lowest-energy isomer and several higher-lying isomers which are the closest in energy. They provide information about the isomer dependence of the HF redshift, and enable direct comparison with the experimental data recently obtained in helium nanodroplets. The agreement between theory and experiment is excellent, in particular, for the nonadditive DMC redshifts. The relative, incremental redshifts are reproduced accurately even at the lower level of theory, i.e., the DMC and quantum five-dimensional (rigid Ar(n)) calculations on the pairwise-additive PESs. The nonadditive interactions make a significant contribution to the frequency shift, on the order of 10%-12%, and have to be included in the PESs in order for the theory to yield accurate magnitude of the HF redshift. The energy gaps between the DMC ground states of the cluster isomers are very different from the energy separation of their respective minima on the PES, due to the considerable variations in the intermolecular zero-point energy of different Ar(n)HF isomers.

Silacyanogen

NASA Astrophysics Data System (ADS)

Ignatyev, Igor S.; Schaefer, Henry F., III

1997-10-01

Structures of all possible linear isomers of the Si-substituted cyanogen were optimized at the SCF, B3LYP, MP2, and CCSD levels of theory. At all levels of theory the most stable isomer was found to be SiNCN, while for cyanogen the most stable structure is well known to be NCCN. The theoretical ordering of the stability of the acyclic structures is SiNCN>SiNNO>NSiCN>NSiNC. The difference in the order of stability of silacyanogen and cyanogen isomers is rationalized, taking into account the position of the unpaired electron on carbon in the CN radical and that on nitrogen in the SiN radical.

Investigation on structure, electronic and magnetic properties of Cr doped (ZnO)12 clusters: First-principles calculations

NASA Astrophysics Data System (ADS)

Liu, Huan; Zhang, Jian-Min

2018-05-01

The structural, electronic, and magnetic properties of (ZnO)12 clusters doped with Cr atoms have been investigated by using spin-polarized first-principles calculations. The exohedral a3 isomer is favorable than endohedral a2 isomer. The isomer a1 and a5 respectively have the narrowest and biggest gap between highest unoccupied molecular orbital and the lowest unoccupied molecular orbital (HOMO-LUMO) of 0.473 and 1.291 eV among these five monodoped isomers. The magnetic moment may be related to the local environment around the Cr atom that the a2 isomer whose total magnetic moment is 6 μB while the other monodoped isomers which all isomers have nearly total magnetic moments 4 μB . For Cr-doped (ZnO)12 on a1 or a3 isomer, the DOS of spin-up channel cross the Fermi level EF showing a finite magnitude near the Fermi level which might be useful for half metallic character. For the bidoped cases, the exohedral isomers are found to be most favorable. Including all bipoed isomers of substitutional, exohedral and endohedral bidoped clusters, the total magnetic moment of the ferromagnetic (antiferromagnetic) state is 8 (0) μB and the HOMO-LUMO gap of antiferromagnetic state is slightly larger than that of ferromagnetic state. The magnetic coupling between the Cr atoms in bidoped configurations is mainly governed by the competition between direct Cr and Cr atoms antiferromagnetic interaction and the ferromagnetic interaction between two Cr atoms via O atom due to strong p-d hybridization. Most importantly, we show that the exohedral bidoped (ZnO)12 clusters favor the ferromagnetic state, which may have the future applications in spin-dependent magneto-optical and magneto-electrical devices.

NTO-Picryl Constitutional Isomers—A DFT Study

NASA Astrophysics Data System (ADS)

Türker, Lemi; Çelik Bayar, Çağlar

2012-01-01

The quantum chemical properties and the detonation performance of some new explosives, 5-nitro-4-picryl-2,4-dihydro-3H-1,2,4-triazol-3-one (class A) and 5-nitro-2-picryl-2,4-dihydro-3H-1,2,4-triazol-3-one (class B), and their constitutional isomers have been investigated theoretically using the density functional theory (DFT) 6-31G(d,p) method. All of the constitutional isomers were found to be more sensitive than 5-nitro-2,4-dihydro-3H-1,2,4-triazol-3-one (NTO) and TNT but more insensitive than RDX and HMX. Their detonation performance is higher than that of NTO and TNT and all except two had lower detonation performance than RDX and HMX.

Synthesis, characterization and cellular location of cytotoxic constitutional organometallic isomers of rhenium delivered on a cyanocobalmin scaffold.

PubMed

Santoro, Giuseppe; Zlateva, Theodora; Ruggi, Albert; Quaroni, Luca; Zobi, Fabio

2015-04-21

Constitutional isomers of cyanocobalamin adducts based on a fluorescent rhenium tris-carbonyl diimine complex were prepared, characterized and tested against PC-3 cancer cells. The adducts differ only in the relative binding position of the organometallic species which is either bound at the cyano or the 5'-hydroxo group of vitamin B12. When tested for their cytotoxic potency, the species showed IC50 values in the low μM rage. Upon conjugation to the vitamin an energy transfer process causes an extremely low quantum yield of fluorescence emission, making the conjugates unsuitable for fluorescence imaging. However, by exploiting the vibrational signature of the fac-[Re(CO)3](+) core, their cellular distribution was evaluated via FTIR spectromicroscopy.

Photodegradation of sulfathiazole under simulated sunlight: Kinetics, photo-induced structural rearrangement, and antimicrobial activities of photoproducts.

PubMed

Niu, Xi-Zhi; Glady-Croué, Julie; Croué, Jean-Philippe

2017-11-01

Photolysis is a core natural process impacting the fate of some sulfonamide antibiotics in sunlit waters. In this study, sunlight-induced phototransformation of sulfathiazole was investigated. A photolytic quantum yield of 0.079 was obtained in buffered water (pH = 8.0). Different natural organic matter isolates inhibited the photolysis of sulfathiazole by light screening effect. A kinetic model was developed to predict the photodegradation rate of sulfathiazole using the light screening correction factor of the water matrix in the wavelength range of 300-350 nm. An isomeric photoproduct of sulfathiazole with a longer retention time was observed on liquid chromatography. Based on its MS/MS spectra and absorption characteristics, the isomer was postulated as 2-imino-3-(p-aminobenzenesulfinyl-oxy)-thiazole. A reaction mechanism for the photo-cleavage and photo-induced structural rearrangement was proposed. The formation mechanism of the isomer was supported by photochemical experiments spiking synthetic 2-aminothiazole; while the formation kinetics were treated with a partly-diffusion-controlled model. The three identified products showed significantly enhanced photo-stability. Antimicrobial assay of irradiated sulfathiazole solutions with Escherichia coli indicated little antimicrobial potency ascribed to photoproducts. This study demonstrates the efficacy of sunlight in rapidly degrading sulfathiazole at a predictable rate, leading to photoproducts of low antimicrobial potency. The mass spectrometry and mechanistic work described here are new insights into the photochemistry of sulfonamides. Copyright © 2017 Elsevier Ltd. All rights reserved.

Identification of absolute geometries of cis and trans molecular isomers by Coulomb Explosion Imaging.

PubMed

Ablikim, Utuq; Bomme, Cédric; Xiong, Hui; Savelyev, Evgeny; Obaid, Razib; Kaderiya, Balram; Augustin, Sven; Schnorr, Kirsten; Dumitriu, Ileana; Osipov, Timur; Bilodeau, René; Kilcoyne, David; Kumarappan, Vinod; Rudenko, Artem; Berrah, Nora; Rolles, Daniel

2016-12-02

An experimental route to identify and separate geometric isomers by means of coincident Coulomb explosion imaging is presented, allowing isomer-resolved photoionization studies on isomerically mixed samples. We demonstrate the technique on cis/trans 1,2-dibromoethene (C 2 H 2 Br 2 ). The momentum correlation between the bromine ions in a three-body fragmentation process induced by bromine 3d inner-shell photoionization is used to identify the cis and trans structures of the isomers. The experimentally determined momentum correlations and the isomer-resolved fragment-ion kinetic energies are matched closely by a classical Coulomb explosion model.

Identification of absolute geometries of cis and trans molecular isomers by Coulomb Explosion Imaging

PubMed Central

Ablikim, Utuq; Bomme, Cédric; Xiong, Hui; Savelyev, Evgeny; Obaid, Razib; Kaderiya, Balram; Augustin, Sven; Schnorr, Kirsten; Dumitriu, Ileana; Osipov, Timur; Bilodeau, René; Kilcoyne, David; Kumarappan, Vinod; Rudenko, Artem; Berrah, Nora; Rolles, Daniel

2016-01-01

An experimental route to identify and separate geometric isomers by means of coincident Coulomb explosion imaging is presented, allowing isomer-resolved photoionization studies on isomerically mixed samples. We demonstrate the technique on cis/trans 1,2-dibromoethene (C2H2Br2). The momentum correlation between the bromine ions in a three-body fragmentation process induced by bromine 3d inner-shell photoionization is used to identify the cis and trans structures of the isomers. The experimentally determined momentum correlations and the isomer-resolved fragment-ion kinetic energies are matched closely by a classical Coulomb explosion model. PMID:27910943

Identification of absolute geometries of cis and trans molecular isomers by Coulomb Explosion Imaging

DOE Office of Scientific and Technical Information (OSTI.GOV)

Ablikim, Utuq; Bomme, Cédric; Xiong, Hui

An experimental route to identify and separate geometric isomers by means of coincident Coulomb explosion imaging is presented, allowing isomer-resolved photoionization studies on isomerically mixed samples. We demonstrate the technique on cis/trans 1,2-dibromoethene (C 2H 2Br 2). The momentum correlation between the bromine ions in a three-body fragmentation process induced by bromine 3d inner-shell photoionization is used to identify the cis and trans structures of the isomers. Lastly, the experimentally determined momentum correlations and the isomer-resolved fragment-ion kinetic energies are matched closely by a classical Coulomb explosion model.

Identification of absolute geometries of cis and trans molecular isomers by Coulomb Explosion Imaging

DOE PAGES

Ablikim, Utuq; Bomme, Cédric; Xiong, Hui; ...

2016-12-02

An experimental route to identify and separate geometric isomers by means of coincident Coulomb explosion imaging is presented, allowing isomer-resolved photoionization studies on isomerically mixed samples. We demonstrate the technique on cis/trans 1,2-dibromoethene (C 2H 2Br 2). The momentum correlation between the bromine ions in a three-body fragmentation process induced by bromine 3d inner-shell photoionization is used to identify the cis and trans structures of the isomers. Lastly, the experimentally determined momentum correlations and the isomer-resolved fragment-ion kinetic energies are matched closely by a classical Coulomb explosion model.

Conformational analysis and vibrational spectroscopy of a paracetamol analogous: 2-Bromo-N-(2-hydroxy-5-methylphenyl)-2-methylpropanamide

NASA Astrophysics Data System (ADS)

Viana, Rommel B.; Quintero, David E.; Viana, Anderson B.; Moreno-Fuquen, Rodolfo

2017-11-01

We conducted an experimental and quantum chemical investigation of the electronic properties and vibrational mode couplings of a structure analogous to a paracetamol (acetaminophen): 2-Bromo-N-(2-hydroxy-5-methylphenyl)-2-methylpropanamide. The spectroscopic and electronic properties were carried out with the PBE1PBE functional, and G3MP2 was used to predict the heat of formation. Among the E/Z stereoisomers, we showed that the energy gap ranged from 3 to 10 kcal mol-1; the relative stability among the regioisomers (involving the different positions of the methyl and hydroxyl groups) exhibited energy differences lower than 5 kcal mol-1. A topological analysis using the Quantum Theory of Atoms in Molecules (QTAIM) was performed to determine the intramolecular hydrogen bonds that govern the configuration changes, and the Natural Bond Orbital method was used to estimate the interplay between the steric and electrostatic interactions that stabilized each isomer. It was also estimated the influence of the population methodology in to predict the atomic charge distribution for the title compound.

Nature of isomerism of solid isothiourea salts, inhibitors of nitric oxide synthases, as studied by 1H-14N nuclear quadrupole double resonance, X-ray, and density functional theory/quantum theory of atoms in molecules.

PubMed

Latosińska, J N; Latosińska, M; Seliger, J; Žagar, V; Maurin, J K; Kazimierczuk, Z

2012-02-09

Isothioureas, inhibitors of nitric oxide synthases, have been studied experimentally in solid state by nuclear quadrupole double resonance (NQDR) and X-ray methods and theoretically by the quantum theory of atoms in molecules/density functional theory. Resonance frequencies on (14)N have been detected and assigned to particular nitrogen sites in each molecule. The crystal packings of (S)-3,4-dichlorobenzyl-N-methylisothiouronium chloride with the disordered chlorine positions in benzene ring and (S)-butyloisothiouronium bromide have been resolved in X-ray diffraction studies. (14)N NQDR spectra have been found good indicators of isomer type and strength of intra- or intermolecular N-H···X (X = Cl, Br) interactions. From among all salts studied, only for (S)-2,3,4,5,6-pentabromobenzylisothiouronium chloride are both nitrogen sites equivalent, which has been explained by the slow exchange. This unique structural feature can be a key factor in the high biological activity of (S)-2,3,4,5,6-pentabromobenzylisothiouronium salts.

Naturally Occurring Structural Isomers in Serum IgA1 O-Glycosylation

PubMed Central

Takahashi, Kazuo; Smith, Archer D.; Poulsen, Knud; Kilian, Mogens; Julian, Bruce A.; Mestecky, Jiri; Novak, Jan; Renfrow, Matthew B.

2013-01-01

IgA is the most abundantly produced antibody and plays an important role in the mucosal immune system. Human IgA is represented by two isotypes, IgA1 and IgA2. The major structural difference between these two subclasses is the presence of nine potential sites of O-glycosylation in the hinge region between the first and second constant region domains of the heavy chain. Thr225, Thr228, Ser230, Ser232 and Thr236 have been identified as the predominant sites of O-glycan attachment. The range and distribution of O-glycan chains at each site within the context of adjacent sites in this clustered region create a complex heterogeneity of surface epitopes that is incompletely defined. We previously described the analysis of IgA1 O-glycan heterogeneity by use of high resolution LC/MS and electron capture dissociation tandem MS to unambiguously localize all amino acid attachment sites in IgA1 (Ale) myeloma protein. Here, we report the identification and elucidation of IgA1 O-glycopeptide structural isomers that occur based on amino acid position of the attached glycans (positional isomers) and the structure of the O-glycan chains at individual sites (glycan isomers). These isomers are present in a model IgA1 (Mce1) myeloma protein and occur naturally in normal human serum IgA1. Variable O-glycan chains attached to Ser230, Thr233 or Thr236 produce the predominant positional isomers, including O-glycans composed of a single GalNAc residue. These findings represent the first definitive identification of structural isomeric IgA1 O-glycoforms, define the single-site heterogeneity for all O-glycan sites in a single sample, and have implications for defining epitopes based on clustered O-glycan variability. PMID:22067045

Docking based design of diastereoisomeric MTCA as GPIIb/IIIa receptor inhibitor.

PubMed

Wang, Xiaozhen; Wang, Yuji; Wu, Jianhui; Gui, Lin; Zhang, Xiaoyi; Zheng, Meiqing; Wang, Yaonan; Zhao, Shurui; Li, Ze; Zhao, Ming; Peng, Shiqi

2017-12-01

In GPIIb/IIIa mediated arterial thrombosis platelet activation plays a central role. To discover platelet activation inhibitor the pharmacophores of GPIIb/IIIa receptor inhibitors and anti-thrombotic agents were analyzed. This led to the design of (1R,3S)- and (1S,3S)-1-methyl-1,2,3,4-tetrahydro-β-carboline-3-carboxylic acids as GPIIb/IIIa inhibitors. Comparing to (1S,3S)-isomer (1R,3S)-isomer had lower cdocker interaction energy. AFM image showed that the minimal effective concentration of (1S,3S)-isomer and (1R,3S)-isomer inhibiting platelet activation were 10 -5  M and 10 -6  M, respectively. In vivo 1 μmol/kg of oral (1S,3S)-isomer effectively inhibited the rats to form arterial thrombus and down regulated GPIIb/IIIa expression, but the activities were significantly lower than those of 1 μmol/kg of oral (1R,3S)-isomer. Both (1S,3S)-isomer and (1R,3S)-isomer can be safely used for structural modifications, but (1R,3S)-isomer should be superior to (1S,3S)-isomer. Copyright © 2017 Elsevier Ltd. All rights reserved.

Nuclear quantum effects on the structure and the dynamics of [H2O]8 at low temperatures.

PubMed

Videla, Pablo E; Rossky, Peter J; Laria, D

2013-11-07

We use ring-polymer-molecular-dynamics (RPMD) techniques and the semi-empirical q-TIP4P/F water model to investigate the relationship between hydrogen bond connectivity and the characteristics of nuclear position fluctuations, including explicit incorporation of quantum effects, for the energetically low lying isomers of the prototype cluster [H2O]8 at T = 50 K and at 150 K. Our results reveal that tunneling and zero-point energy effects lead to sensible increments in the magnitudes of the fluctuations of intra and intermolecular distances. The degree of proton spatial delocalization is found to map logically with the hydrogen-bond connectivity pattern of the cluster. Dangling hydrogen bonds exhibit the largest extent of spatial delocalization and participate in shorter intramolecular O-H bonds. Combined effects from quantum and polarization fluctuations on the resulting individual dipole moments are also examined. From the dynamical side, we analyze the characteristics of the infrared absorption spectrum. The incorporation of nuclear quantum fluctuations promotes red shifts and sensible broadening relative to the classical profile, bringing the simulation results in much more satisfactory agreement with direct experimental information in the mid and high frequency range of the stretching band. While RPMD predictions overestimate the peak position of the low frequency shoulder, the overall agreement with that reported using an accurate, parameterized, many-body potential is reasonable, and far superior to that one obtains by implementing a partially adiabatic centroid molecular dynamics approach. Quantum effects on the collective dynamics, as reported by instantaneous normal modes, are also discussed.

Structure, stability, and cluster-cage interactions in nitride clusterfullerenes M3N@C2n (M = Sc, Y; 2n = 68-98): a density functional theory study.

PubMed

Popov, Alexey A; Dunsch, Lothar

2007-09-26

Extensive semiempirical calculations of the hexaanions of IPR (isolated pentagon rule) and non-IPR isomers of C(68)-C(88) and IPR isomers of C(90)-C(98) followed by DFT calculations of the lowest energy structures were performed to find the carbon cages that can provide the most stable isomers of M(3)N@C(2n) clusterfullerenes (M = Sc, Y) with Y as a model for rare earth ions. DFT calculations of isomers of M(3)N@C(2n) (M = Sc, Y; 2n = 68-98) based on the most stable C(2n)(6-) cages were also performed. The lowest energy isomers found by this methodology for Sc(3)N@C(68), Sc(3)N@C(78), Sc(3)N@C(80), Y(3)N@C(78), Y(3)N@C(80), Y(3)N@C(84), Y(3)N@C(86), and Y(3)N@C(88) are those that have been shown to exist by single-crystal X-ray studies as Sc(3)N@C(2n) (2n = 68, 78, 80), Dy(3)N@C(80), and Tb(3)N@C(2n) (2n = 80, 84, 86, 88) clusterfullerenes. Reassignment of the carbon cage of Sc(2)@C(76) to the non-IPR Cs: 17490 isomer is also proposed. The stability of nitride clusterfullerenes was found to correlate well with the stability of the empty 6-fold charged cages. However, the dimensions of the cage in terms of its ability to encapsulate M(3)N clusters were also found to be an important factor, especially for the medium size cages and the large Y(3)N cluster. In some cases the most stable structures are based on the different cage isomers for Sc(3)N and Y(3)N clusters. Up to the cage size of C(84), non-IPR isomers of C(2n)(6-) and M(3)N@C(2n) were found to compete with or to be even more stable than IPR isomers. However, the number of adjacent pentagon pairs in the most stable non-IPR isomers decreases as cage size increases: the most stable M(3)N@C(2n) isomers have three such pairs for 2n = 68-72, two pairs for n = 74-80, and only one pair for n = 82, 84. For C(86) and C(88) the lowest energy IPR isomers are much more stable than any non-IPR isomer. The trends in the stability of the fullerene isomers and the cluster-cage binding energies are discussed, and general rules for stability of clusterfullerenes are established. Finally, the high yield of M(3)N@C(80) (Ih) clusterfullerenes for any metal is explained by the exceptional stability of the C(80)(6-) (Ih: 31924) cage, rationalized by the optimum distribution of the pentagons leading to the minimization of the steric strain, and structural similarities of C(80) (Ih: 31924) with the lowest energy non-IPR isomers of C(760(6-), C(78)(6-), C(82)(6-), and C(84)(6-) pointed out.

An ab initio study of the electronic structure and relative stability of the halogenated thiophosphorus compounds SPX (X = Cl, F, Br) and their isomers

NASA Astrophysics Data System (ADS)

Nowek, Andrzej; Richardson, Rhonda; Babinec, Peter; Leszczyński, Jerzy

1997-12-01

The electronic structure and relative stability of the halogenated thiophosphorus compounds SPCl, SPF, and SPBr and their isomers ClSP, FSP, and BrSP were investigated using ab initio post-Hartree-Fock methods. Molecular geometries of all these structures together with the transition states between isomers, have been optimized at the SCF, MP2, and CCSD levels. Single-point CCSD(T) and MP4 calculations have been performed at the optimal CCSD and MP2 geometries. All calculations have been done using the standard 6-311G(2d) basis set. Harmonic vibrational frequencies and IR intensities for all species were calculated at the correlated levels, and they are in good agreement with the available data from matrix-isolated IR spectroscopy. Because the isomers ClSP, FSP, and BrSP have not yet been experimentally observed, we extended our study by calculating of equilibrium constants of isomerization using Eyring transition state theory, and we have found that at sufficiently high temperatures (≈ 1000 K) the equilibrium constants are large enough for the possible detection of these isomers.

A Systematic Theoretical Study of UC6: Structure, Bonding Nature, and Spectroscopy.

PubMed

Du, Jiguang; Jiang, Gang

2017-11-20

The study of uranium carbides has received renewed attention in recent years due to the potential use of these compounds as fuels in new generations of nuclear reactors. The isomers of the UC 6 cluster were determined by DFT and ab initio methods. The structures obtained using SC-RECP for U were generally consistent with those obtained using an all-electron basis set (ZORA-SARC). The CCSD(T) calculations indicated that two isomers had similar energies and may coexist in laser evaporation experiments. The nature of the U-C bonds in the different isomers was examined via a topological analysis of the electron density, and the results indicated that the U-C bonds are predominantly closed-shell (ionic) interactions with a certain degree of covalent character in all cases, particularly in the linear species. The IR and UV-vis spectra of the isomers were theoretically simulated to provide information that can be used to identify the isomers of UC 6 in future experiments.

An application of artificial intelligence to the interpretation of mass spectra.

NASA Technical Reports Server (NTRS)

Buchanan, B. G.; Duffield, A. M.; Robertson, A. V.

1971-01-01

Description of the DENDRAL (Dendritic Algorithm) project, the objectives of which were to base the computer program on an alogorithm that generates an exhaustive, nonredundant list of all the structural isomers of a given chemical composition, and to devise a computer program that would perform an organic structure determination, given a molecular formula and a mass spectrum. This program is called 'Heuristic DENDRAL' and it operates by using the known structure/spectrum correlations to constrain the DENDRAL isomer generator to produce a single isomer for that composition. The collaboration of chemists and computer scientists has produced a tool of some practical utility from the chemical viewpoint, and an interesting program from the viewpoint of artificial intelligence.

Structural and electronic properties Te62+ and Te82+: A DFT study

NASA Astrophysics Data System (ADS)

Sharma, Tamanna; Tamboli, Rohit; Kanhere, D. G.; Sharma, Raman

2018-05-01

Structural and electronic properties of Tellurium cluster (Ten) and their cations (Ten2+) (n = 6, 8) have been studied theoretically using VASP within generalized gradient approximation. Ground state geometries and higher energy isomers of these clusters have been examined on the basis of total free energy calculations. Lowest energy isomers of neutral clusters are ring like structures whereas the lowest energy isomers of cations are polyhedral cages. HOMO-LUMO gap in cationic clusters is small compared to its neutral clusters. Removal of two electrons from the neutral cluster raises the free energy. Analysis of free energy, HOMO-LUMO gap and density of states (DOS) show that neutral cluster are more stable than their cations.

Atmospheric pressure chemical ionization studies of non-polar isomeric hydrocarbons using ion mobility spectrometry and mass spectrometry with different ionization techniques

NASA Technical Reports Server (NTRS)

Borsdorf, H.; Nazarov, E. G.; Eiceman, G. A.

2002-01-01

The ionization pathways were determined for sets of isomeric non-polar hydrocarbons (structural isomers, cis/trans isomers) using ion mobility spectrometry and mass spectrometry with different techniques of atmospheric pressure chemical ionization to assess the influence of structural features on ion formation. Depending on the structural features, different ions were observed using mass spectrometry. Unsaturated hydrocarbons formed mostly [M - 1]+ and [(M - 1)2H]+ ions while mainly [M - 3]+ and [(M - 3)H2O]+ ions were found for saturated cis/trans isomers using photoionization and 63Ni ionization. These ionization methods and corona discharge ionization were used for ion mobility measurements of these compounds. Different ions were detected for compounds with different structural features. 63Ni ionization and photoionization provide comparable ions for every set of isomers. The product ions formed can be clearly attributed to the structures identified. However, differences in relative abundance of product ions were found. Although corona discharge ionization permits the most sensitive detection of non-polar hydrocarbons, the spectra detected are complex and differ from those obtained with 63Ni ionization and photoionization. c. 2002 American Society for Mass Spectrometry.

Septipyridines as conformationally controlled substitutes for inaccessible bis(terpyridine)-derived oligopyridines in two-dimensional self-assembly

PubMed Central

Caterbow, Daniel; Künzel, Daniela; Mavros, Michael G; Groß, Axel; Landfester, Katharina

2011-01-01

Summary The position of the peripheral nitrogen atoms in bis(terpyridine)-derived oligopyridines (BTPs) has a strong impact on their self-assembly behavior at the liquid/HOPG (highly oriented pyrolytic graphite) interface. The intermolecular hydrogen bonding interactions in these peripheral pyridine units show specific 2D structures for each BTP isomer. From nine possible constitutional isomers only four have been described in the literature. The synthesis and self-assembling behavior of an additional isomer is presented here, but the remaining four members of the series are synthetically inaccessible. The self-assembling properties of three of the missing four BTP isomers can be mimicked by making use of the energetically preferred N–C–C–N transoid conformation between 2,2'-bipyridine subunits in a new class of so-called septipyridines. The structures are investigated by scanning tunneling microscopy (STM) and a combination of force-field and first-principles electronic structure calculations. PMID:22003448

The preferred conformation of dipeptides in the context of biosynthesis

NASA Astrophysics Data System (ADS)

Bywater, Robert P.; Veryazov, Valera

2013-09-01

Globular proteins are folded polypeptide structures comprising stretches of secondary structures (helical (α- or 310 helix type), polyproline helix or β-strands) interspersed by regions of less well-ordered structure ("random coil"). Protein fold prediction is a very active field impacting inte alia on protein engineering and misfolding studies. Apart from the many studies of protein refolding from the denatured state, there has been considerable interest in studying the initial formation of peptides during biosynthesis, when there are at the outset only a few residues in the emerging polypeptide. Although there have been many studies employing quantum chemical methods of the conformation of dipeptides, these have mostly been carried out in the gas phase or simulated water. None of these conditions really apply in the interior confines of the ribosome. In the present work, we are concerned with the conformation of dipeptides in this low dielectric environment. Furthermore, only the residue types glycine and alanine have been studied by previous authors, but we extend this repertoire to include leucine and isoleucine, position isomers which have very different structural propensities.

Strategy for designing stable and powerful nitrogen-rich high-energy materials by introducing boron atoms.

PubMed

Wu, Wen-Jie; Chi, Wei-Jie; Li, Quan-Song; Li, Ze-Sheng

2017-06-01

One of the most important aims in the development of high-energy materials is to improve their stability and thus ensure that they are safe to manufacture and transport. In this work, we theoretically investigated open-chain N 4 B 2 isomers using density functional theory in order to find the best way of stabilizing nitrogen-rich molecules. The results show that the boron atoms in these isomers are aligned linearly with their neighboring atoms, which facilitates close packing in the crystals of these materials. Upon comparing the energies of nine N 4 B 2 isomers, we found that the structure with alternating N and B atoms had the lowest energy. Structures with more than one nitrogen atom between two boron atoms had higher energies. The energy of N 4 B 2 increases by about 50 kcal/mol each time it is rearranged to include an extra nitrogen atom between the two boron atoms. More importantly, our results also show that boron atoms stabilize nitrogen-rich molecules more efficiently than carbon atoms do. Also, the combustion of any isomer of N 4 B 2 releases more heat than the corresponding isomer of N 4 C 2 does under well-oxygenated conditions. Our study suggests that the three most stable N 4 B 2 isomers (BN13, BN24, and BN34) are good candidates for high-energy molecules, and it outlines a new strategy for designing stable boron-containing high-energy materials. Graphical abstract The structural characteristics, thermodynamic stabilities, and exothermic properties of nitrogen-rich N 4 B 2 isomers were investigated by means of density functional theory.

Level Structure Above the T1/2 = 2 . 0 ×105 yr Isomer in 186Re

NASA Astrophysics Data System (ADS)

Matters, D. A.; McClory, J. W.; Kondev, F. G.; Carpenter, M. P.; Carroll, J. J.; Chiara, C. J.; Lane, G. J.; Kibédi, T.; Ideguchi, E.; Fang, Y.; Watanabe, H.; E435 Cagra Collaboration

2016-03-01

The level structure above the Kπ = (8+) , 149-keV isomer in 186Re is largely undeveloped. The isomer could play a role in the s-process nucleosynthesis of 187Os and 187Re and affect the accuracy of the Re-Os cosmochronometer. An experiment was conducted at the Research Center for Nuclear Physics (RCNP) at Osaka University, Japan, using the Clover Array Gamma-ray spectrometer at RCNP/RIBF for Advanced research (CAGRA) to measure γ-ray coincidences from (d , 2 n) reactions on an enriched 186W target. The γ - γ coincidence data obtained from the CAGRA array were analyzed along with data from a similar experiment performed in 2006 at the Australian National University. A preliminary analysis of the data reveals several new levels and transitions feeding the 186mRe isomer.

Characterization of solvated electrons in hydrogen cyanide clusters: (HCN)n- (n=3, 4)

NASA Astrophysics Data System (ADS)

Wu, Di; Li, Ying; Li, Zhuo; Chen, Wei; Li, Zhi-Ru; Sun, Chia-Chung

2006-02-01

Theoretical studies of the solvated electrons (HCN)n- (n =3, 4) reveal a variety of electron trapping possibilities in the (HCN)n (n =3, 4) clusters. Two isomers for (HCN)3- and four isomers for (HCN)4- are obtained at the MP2/aug -cc-pVDZ+dBF (diffusive bond functions) level of theory. In view of vertical electron detachment energies (VDEs) at the CCSD(T) level, the excess electron always "prefers" locating in the center of the system, i.e., the isomer with higher coordination number shows larger VDE value. However, the most stable isomers of the solvated electron state (HCN)3- and (HCN)4- are found to be the linear C∞ν and D∞h structures, respectively, but not the fullyl symmetric structures which have the largest VDE values.

Enumerating Substituted Benzene Isomers of Tree-Like Chemical Graphs.

PubMed

Li, Jinghui; Nagamochi, Hiroshi; Akutsu, Tatsuya

2018-01-01

Enumeration of chemical structures is useful for drug design, which is one of the main targets of computational biology and bioinformatics. A chemical graph with no other cycles than benzene rings is called tree-like, and becomes a tree possibly with multiple edges if we contract each benzene ring into a single virtual atom of valence 6. All tree-like chemical graphs with a given tree representation are called the substituted benzene isomers of . When we replace each virtual atom in with a benzene ring to obtain a substituted benzene isomer, distinct isomers of are caused by the difference in arrangements of atom groups around a benzene ring. In this paper, we propose an efficient algorithm that enumerates all substituted benzene isomers of a given tree representation . Our algorithm first counts the number of all the isomers of the tree representation by a dynamic programming method. To enumerate all the isomers, for each , our algorithm then generates the th isomer by backtracking the counting phase of the dynamic programming. We also implemented our algorithm for computational experiments.

Ortho-para spin isomers of the protons in the methylene group--possible implications for protein structure.

PubMed

Shinitzky, Meir; Elitzur, Avshalom C

2006-09-01

The two hydrogen atoms attached to the carbon in the methylene group are of two different spin configurations, similar to those in the case of water: ortho, where the two proton spins are parallel to each other, and para, where they are antiparallel. The ortho configuration has three degenerate states, while the para configuration is singular, leading to a statistical ratio of these isomers 3:1 ortho/para. Such spin isomers are present in glycine and most chiral amino acids where they may induce broadening of structural zones, a possibility which remains to be assessed. The implications of this neglected possibility could be far-reaching, in particular with respect to protein structure and the origins of biochirality.

Electronic and spectroscopic characterizations of SNP isomers

NASA Astrophysics Data System (ADS)

Trabelsi, Tarek; Al Mogren, Muneerah Mogren; Hochlaf, Majdi; Francisco, Joseph S.

2018-02-01

High-level ab initio electronic structure calculations were performed to characterize SNP isomers. In addition to the known linear SNP, cyc-PSN, and linear SPN isomers, we identified a fourth isomer, linear PSN, which is located ˜2.4 eV above the linear SNP isomer. The low-lying singlet and triplet electronic states of the linear SNP and SPN isomers were investigated using a multi-reference configuration interaction method and large basis set. Several bound electronic states were identified. However, their upper rovibrational levels were predicted to pre-dissociate, leading to S + PN, P + NS products, and multi-step pathways were discovered. For the ground states, a set of spectroscopic parameters were derived using standard and explicitly correlated coupled-cluster methods in conjunction with augmented correlation-consistent basis sets extrapolated to the complete basis set limit. We also considered scalar and core-valence effects. For linear isomers, the rovibrational spectra were deduced after generation of their 3D-potential energy surfaces along the stretching and bending coordinates and variational treatments of the nuclear motions.

Identification of Isomeric N-Glycan Structures by Mass Spectrometry with 157 nm Laser-Induced Photofragmentation

PubMed Central

Devakumar, Arugadoss; Mechref, Yehia; Kang, Pilsoo; Novotny, Milos V.; Reilly, James P.

2008-01-01

Characterization of structural isomers has become increasingly important and extremely challenging in glycobiology. This communication demonstrates the capability of ion-trap mass spectrometry in conjunction with 157 nm photofragmentation to identify different structural isomers of permethylated N-glycans derived from ovalbumin without chromatographic separation. The results are compared with CID experiments. Photodissociation generates extensive cross-ring fragment ions as well as diagnostic glycosidic product ions that are not usually observed in CID MS/MS experiments. The detection of these product ions aids in characterizing indigenous glycan isomers. The ion-trap facilitates MSn experiments on the diagnostic glycosidic fragments and cross-ring product ions generated through photofragmentation, thus allowing unambiguous assignment of all of the isomeric structures associated with the model glycoprotein utilized in this study. Photofragmentation is demonstrated to be a powerful technique for the structural characterization of glycans. PMID:18487060

Application of terahertz spectroscopy and theoretical calculation in dimethylurea isomers investigation

NASA Astrophysics Data System (ADS)

Zhao, Yonghong; Li, Zhi; Liu, Jianjun; Chen, Tao; Zhang, Huo; Qin, Binyi; Wu, Yifang

2018-03-01

The characteristic absorption spectra of two structural isomers of dimethylurea(DMU) in 0.6-1.8 THz region have been measured using terahertz time-domain spectroscopy (THZ-TDS) at room temperature. Significant differences have been found between their terahertz spectra and implied that the THZ-TDS is an effective means of identifying structural isomers. To simulate their spectra, calculations on single molecule and cluster of 1,1-DMU and 1,3-DMU were performed, and we found that the cluster calculations using DFT-D3 method are better to predict the experimental spectra. Using the normal mode as displacements in redundant internal coordinates and the GaussView program, most observed THz vibrational modes are assigned to bending and rocking modes related to the intermolecular hydrogen bonding interactions, and twisting mode of ethyl groups. The different spectral features of two isomers mainly arise from different intermolecular hydrogen bonds resulting from different atom arrangements in molecules and different molecule arrangements in crystals. Using the reduced-density-gradient (RDG) analysis, the positions and types of intermolecular hydrogen bonding interactions in 1,1-DMU and 1,3-DMU crystals are visualized. Therefore, we can confirm that THz-TDS can be used as an effective means for the recognition of structural isomers and detection of intermolecular hydrogen bonding interactions in these crystals.

Theoretical investigation of stabilities and optical properties of Si12C12 clusters

NASA Astrophysics Data System (ADS)

Duan, Xiaofeng F.; Burggraf, Larry W.

2015-01-01

By sorting through hundreds of globally stable Si12C12 isomers using a potential surface search and using simulated annealing, we have identified low-energy structures. Unlike isomers knit together by Si-C bonds, the lowest energy isomers have segregated carbon and silicon regions that maximize stronger C-C bonding. Positing that charge separation between the carbon and silicon regions would produce interesting optical absorption in these cluster molecules, we used time-dependent density functional theory to compare the calculated optical properties of four isomers representing structural classes having different types of silicon and carbon segregation regions. Absorptions involving charge transfer between segregated carbon and silicon regions produce lower excitation energies than do structures having alternating Si-C bonding for which frontier orbital charge transfer is exclusively from separated carbon atoms to silicon atoms. The most stable Si12C12 isomer at temperatures below 1100 K is unique as regards its high symmetry and large optical oscillator strength in the visible blue. Its high-energy and low-energy visible transitions (1.15 eV and 2.56 eV) are nearly pure one-electron silicon-to-carbon transitions, while an intermediate energy transition (1.28 eV) is a nearly pure carbon-to-silicon one-electron charge transfer.

How different is the borazine-acetylene dimer from the benzene-acetylene dimer? A matrix isolation infrared and ab initio quantum chemical study

NASA Astrophysics Data System (ADS)

Verma, Kanupriya; Viswanathan, K. S.; Majumder, Moumita; Sathyamurthy, N.

2017-11-01

The 1:1 dimer of borazine-acetylene has been studied for the first time, both experimentally and computationally. The borazine-acetylene dimer was trapped in Ar and N2 matrices, and studied using infrared spectroscopy. Our experiments clearly revealed two isomers of the borazine-acetylene complex, one in which the N-H of borazine interacted with the carbon of acetylene, and another in which the C-H of acetylene formed a hydrogen bond with a nitrogen atom of borazine. The formation of both isomers in the matrix was evidenced by shifts in the vibrational frequencies of the appropriate modes. Reassuringly, the experimental observations were corroborated by our computations using the second-order Møller-Plesset perturbation theoretic method and coupled-cluster singles, doubles and perturbative triples method in conjunction with different Dunning basis sets, which indicated both these isomers to be stable minima, with the N-HṡṡṡC complex being the global minimum. Atoms-in-molecules and energy decomposition analysis were also carried out for the different isomers of the dimer. These studies reveal that replacing the three C-C linkages in benzene with three B-N linkages in borazine modifies the interaction in the dimer sufficiently, to result in a different potential energy landscape for the borazine-acetylene system when compared with the benzene-acetylene system.

The Creation and Destruction of Hf-178m2 Isomer by Neutron Interaction

DOE Office of Scientific and Technical Information (OSTI.GOV)

Hsu, Hsiao-Hua; Talbert, Willard L.; Ward, Tom

The property of the isomer state in 178m2Hf was an interesting topic in nuclear structure studies during the time period 1970 to 1980. The state at 2.446 MeV with spin and parity K π = 16 +, has a half-life of 31 years. The isomer is described as a four-quasi-particle state. The K forbidden deexcitatiion by gamma emission is the reason for long half-life. During 1980, the isomer became a troublesome issue for radiation safety workers, because this isomer can also be produced in the first wall of a fussion reactor containing tungsten and also in a tungsten beam stopmore » of a high-energy accelerator.« less

Binding Energy Calculation of Patchouli Alcohol Isomer Cyclooxygenase Complexes Suggested as COX-1/COX-2 Selective Inhibitor

PubMed Central

Mahdi, Chanif; Nurdiana, Nurdiana; Kikuchi, Takheshi; Fatchiyah, Fatchiyah

2014-01-01

To understand the structural features that dictate the selectivity of the two isoforms of the prostaglandin H2 synthase (PGHS/COX), the three-dimensional (3D) structure of COX-1/COX-2 was assessed by means of binding energy calculation of virtual molecular dynamic with using ligand alpha-Patchouli alcohol isomers. Molecular interaction studies with COX-1 and COX-2 were done using the molecular docking tools by Hex 8.0. Interactions were further visualized by using Discovery Studio Client 3.5 software tool. The binding energy of molecular interaction was calculated by AMBER12 and Virtual Molecular Dynamic 1.9.1 software. The analysis of the alpha-Patchouli alcohol isomer compounds showed that all alpha-Patchouli alcohol isomers were suggested as inhibitor of COX-1 and COX-2. Collectively, the scoring binding energy calculation (with PBSA Model Solvent) of alpha-Patchouli alcohol isomer compounds (CID442384, CID6432585, CID3080622, CID10955174, and CID56928117) was suggested as candidate for a selective COX-1 inhibitor and CID521903 as nonselective COX-1/COX-2. PMID:25484897

A comparative study of the infrared and Raman spectra of aniline and o-, m-, p-phenylenediamine isomers.

PubMed

Badawi, Hassan M; Förner, Wolfgang; Ali, Shaikh A

2013-08-01

The structural stabilities of o-, m- and p-phenylenediamine (PDA) isomers were investigated by DFT-B3LYP and ab initio MP2 calculations with the 6-311G(**) basis set. From the calculations the three isomers were predicted to exist predominantly in an anti (transoid) structure. In the o-isomer, the syn (cisoid) form is calculated to turn to the anti (transoid) form with the two HNCC torsional angles of about 44 and 10° and the NH2 inversion barrier of 3-4 kcal/mol. The CCNH torsional angles in the m-PDA and p-PDA isomers were calculated to be about 25-26° as compared to 20° in aniline. A comparison of the Raman spectra of the three PDA-s with those of aniline shows the high sensitivity of the ring breathing mode to the nature of substituents in the aniline ring. The vibrational wavenumbers were computed at the DFT-B3LYP for aniline and the o-, m- and p-PDA isomers for the purpose of comparison. Complete vibrational assignments were made on the basis of normal coordinate analyses and potential energy distributions for aniline and the o-, m- and p-PDA molecules. Copyright © 2013 Elsevier B.V. All rights reserved.

Unraveling Unprecedented Charge Carrier Mobility through Structure Property Relationship of Four Isomers of Didodecyl[1]benzothieno[3,2-b][1]benzothiophene.

PubMed

Tsutsui, Yusuke; Schweicher, Guillaume; Chattopadhyay, Basab; Sakurai, Tsuneaki; Arlin, Jean-Baptiste; Ruzié, Christian; Aliev, Almaz; Ciesielski, Artur; Colella, Silvia; Kennedy, Alan R; Lemaur, Vincent; Olivier, Yoann; Hadji, Rachid; Sanguinet, Lionel; Castet, Frédéric; Osella, Silvio; Dudenko, Dmytro; Beljonne, David; Cornil, Jérôme; Samorì, Paolo; Seki, Shu; Geerts, Yves H

2016-09-01

The structural and electronic properties of four isomers of didodecyl[1]-benzothieno[3,2-b][1]benzothiophene (C12-BTBT) have been investigated. Results show the strong impact of the molecular packing on charge carrier transport and electronic polarization properties. Field-induced time-resolved microwave conductivity measurements unravel an unprecedented high average interfacial mobility of 170 cm(2) V(-1) s(-1) for the 2,7-isomer, holding great promise for the field of organic electronics. © 2016 The Authors. Published by WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Liquid chromatography fractionation with gas chromatography/mass spectrometry and preparative gas chromatography-nuclear magnetic resonance analysis of selected nonylphenol polyethoxylates.

PubMed

Wu, Ze-ying; Rühle, Christian P G; Marriott, Philip J

2011-07-01

Commercial nonylphenol polyethoxylates, designated as NPnEOs, where n is the number of ethoxy groups, comprise a range of ethoxylate groups. According to the starting material nonylphenol, they may also be composed of a complex mix of isomeric nonyl substituents. In order to study more fully the heterogeneity arising from both the ethoxylate and nonyl groups, a mixture of NPnEOs is first fractionated by normal phase liquid chromatography (NPLC) into separate fractions comprising individual ethoxymers, n. Preparative collection of each early elution ethoxymer fraction allows further separation of different isomeric nonyl group components by using analytical gas chromatography/mass spectrometry (GC/MS). The nonyl isomers are not resolved in the NPLC method. The distribution of the isomeric nonyl side chain of different ethoxymers bears close resemblance with each other, and also with the original nonylphenol starting material, although separation efficiency of the nonyl isomers for each ethoxymer decreases with increasing ethoxymer number. Mass spectrometry of the separated isomers display close similarity for presumed equivalent isomers in each fraction, based on elution order of the nonyl isomers. This suggests that each corresponding peak has the same isomer structure. Mass spectra are interpreted based on branching within the nonyl side chain. Preparative GC coupled with MS and nuclear magnetic resonance spectroscopy elucidated the molecular structure of one of the resolved isomers as 4-(1,3-dimethyl-1-propyl-butyl)-phenol diethoxylate. Copyright © 2011 Elsevier B.V. All rights reserved.

Intramolecular energy transfer and the driving mechanisms for large-amplitude collective motions of clusters

NASA Astrophysics Data System (ADS)

Yanao, Tomohiro; Koon, Wang Sang; Marsden, Jerrold E.

2009-04-01

This paper uncovers novel and specific dynamical mechanisms that initiate large-amplitude collective motions in polyatomic molecules. These mechanisms are understood in terms of intramolecular energy transfer between modes and driving forces. Structural transition dynamics of a six-atom cluster between a symmetric and an elongated isomer is highlighted as an illustrative example of what is a general message. First, we introduce a general method of hyperspherical mode analysis to analyze the energy transfer among internal modes of polyatomic molecules. In this method, the (3n-6) internal modes of an n-atom molecule are classified generally into three coarse level gyration-radius modes, three fine level twisting modes, and (3n-12) fine level shearing modes. We show that a large amount of kinetic energy flows into the gyration-radius modes when the cluster undergoes structural transitions by changing its mass distribution. Based on this fact, we construct a reactive mode as a linear combination of the three gyration-radius modes. It is shown that before the reactive mode acquires a large amount of kinetic energy, activation or inactivation of the twisting modes, depending on the geometry of the isomer, plays crucial roles for the onset of a structural transition. Specifically, in a symmetric isomer with a spherical mass distribution, activation of specific twisting modes drives the structural transition into an elongated isomer by inducing a strong internal centrifugal force, which has the effect of elongating the mass distribution of the system. On the other hand, in an elongated isomer, inactivation of specific twisting modes initiates the structural transition into a symmetric isomer with lower potential energy by suppressing the elongation effect of the internal centrifugal force and making the effects of the potential force dominant. This driving mechanism for reactions as well as the present method of hyperspherical mode analysis should be widely applicable to molecular reactions in which a system changes its overall mass distribution in a significant way.

Gaussian and linear deconvolution of LC-MS/MS chromatograms of the eight aminobutyric acid isomers

PubMed Central

Vemula, Harika; Kitase, Yukiko; Ayon, Navid J.; Bonewald, Lynda; Gutheil, William G.

2016-01-01

Isomeric molecules present a challenge for analytical resolution and quantification, even with MS-based detection. The eight-aminobutyric acid (ABA) isomers are of interest for their various biological activities, particularly γ-aminobutyric acid (GABA) and the d- and l-isomers of β-aminoisobutyric acid (β-AIBA; BAIBA). This study aimed to investigate LC-MS/MS-based resolution of these ABA isomers as their Marfey's (Mar) reagent derivatives. HPLC was able to separate three Mar-ABA isomers l-β-ABA (l-BABA), and l- and d-α-ABA (AABA) completely, with three isomers (GABA, and d/l-BAIBA) in one chromatographic cluster, and two isomers (α-AIBA (AAIBA) and d-BABA) in a second cluster. Partially separated cluster components were deconvoluted using Gaussian peak fitting except for GABA and d-BAIBA. MS/MS detection of Marfey's derivatized ABA isomers provided six MS/MS fragments, with substantially different intensity profiles between structural isomers. This allowed linear deconvolution of ABA isomer peaks. Combining HPLC separation with linear and Gaussian deconvolution allowed resolution of all eight ABA isomers. Application to human serum found a substantial level of l-AABA (13 μM), an intermediate level of l-BAIBA (0.8 μM), and low but detectable levels (<0.2 μM) of GABA, l-BABA, AAIBA, d-BAIBA, and d-AABA. This approach should be useful for LC-MS/MS deconvolution of other challenging groups of isomeric molecules. PMID:27771391

Synthesis, NMR, FT-IR, X-ray structural characterization, DFT analysis and isomerism aspects of 5-(2,6-dichlorobenzylidene)pyrimidine-2,4,6(1H,3H,5H)-trione.

PubMed

Barakat, Assem; Al-Najjar, Hany J; Al-Majid, Abdullah Mohammed; Soliman, Saied M; Mabkhot, Yahia Nasser; Shaik, Mohammed Rafi; Ghabbour, Hazem A; Fun, Hoong-Kun

2015-08-05

The synthesis and spectral characterization of the 5-(2,6-dichlorobenzylidene)pyrimidine-2,4,6(1H,3H,5H)-trione;3 was reported. The solid state molecular structure of 3 was studied using X-ray crystallography. The relative stabilities of the seven possible isomers of 3 were calculated by DFT/B3LYP method using 6-311 G(d,p) basis set. The calculated total energies and thermodynamic parameters were used to predict the relative stabilities of these isomers. The effect of solvent polarity on the relative stability of these isomers was studied at the same level of theory using PCM. It was found that the keto form, (T0), is the most stable isomer both in the gaseous state and solution. In solution, the calculated total energies of all isomers are decreased indicating that all isomers are stabilized by the solvent effect. The vibrational spectra of the most stable isomer, 3(T0) are calculated using the same level of theory and the results are compared with the experimentally measured FTIR spectra. Good correlation was obtained between the experimental and calculated vibrational frequencies (R(2)=0.9992). The electronic spectra of 3(T0) in gas phase as well as in solutions were calculated using the TD-DFT method. All the predicted electronic transitions showed very little spectral shifts and increase in the intensity of absorption due to solvent effect. Also the (1)H- and (13)C-NMR chemical shifts of the stable isomer were calculated and the results were correlated with the experimental data. Good correlations between the experimental and calculated chemical shifts were obtained. Copyright © 2015 Elsevier B.V. All rights reserved.

Computational Screening of Nanoporous Materials for Hexane and Heptane Isomer Separation

DOE PAGES

Chung, Yongchul G.; Bai, Peng; Haranczyk, Maciej; ...

2017-07-05

Computational high-throughput screening was carried out to assess a large number of experimentally reported metal–organic frameworks (MOFs) and zeolites for their utility in hexane isomer separation. Through the paper, we identified many MOFs and zeolites with high selectivity (S L+M > 10) for the group of n-hexane, 2-methylpentane, and 3-methylpentane (linear and monobranched isomers) versus 2,2-dimethylbutane and 2,3-dimethylbutane (dibranched isomers). This group of selective sorbents includes VICDOC (Fe 2(BDP) 3), a MOF with triangular pores that is known to exhibit high isomer selectivity and capacity. For three of these structures, the adsorption isotherms for a 10-component mixture of hexane andmore » heptane isomers were calculated. Subsequent simulations of column breakthrough curves showed that the DEYVUA MOF exhibits a longer process cycle time than VICDOC MOF or MRE zeolite, which are previously reported, high-performing materials, illustrating the importance of capacity in designing MOFs for practical applications. Among the identified candidates, we synthesized and characterized a MOF in a new copper form with high predicted adsorbent capacity (q L+M > 1.2 mol/L) and moderately high selectivity (S L+M ≈ 10). In conclusion, we examined the role of pore shape in hexane isomer separations, especially of triangular-shaped pores. We show through the potential energy surface and three-dimensional siting analyses that linear alkanes do not populate the corners of narrow triangular channels and that structures with nontriangular pores can efficiently separate hexane isomers. Detailed thermodynamic analysis illustrates how differences in the free energy of adsorption contribute to shape-selective separation in nanoporous materials.« less

Computational Screening of Nanoporous Materials for Hexane and Heptane Isomer Separation

DOE Office of Scientific and Technical Information (OSTI.GOV)

Chung, Yongchul G.; Bai, Peng; Haranczyk, Maciej

Computational high-throughput screening was carried out to assess a large number of experimentally reported metal–organic frameworks (MOFs) and zeolites for their utility in hexane isomer separation. Through the paper, we identified many MOFs and zeolites with high selectivity (S L+M > 10) for the group of n-hexane, 2-methylpentane, and 3-methylpentane (linear and monobranched isomers) versus 2,2-dimethylbutane and 2,3-dimethylbutane (dibranched isomers). This group of selective sorbents includes VICDOC (Fe 2(BDP) 3), a MOF with triangular pores that is known to exhibit high isomer selectivity and capacity. For three of these structures, the adsorption isotherms for a 10-component mixture of hexane andmore » heptane isomers were calculated. Subsequent simulations of column breakthrough curves showed that the DEYVUA MOF exhibits a longer process cycle time than VICDOC MOF or MRE zeolite, which are previously reported, high-performing materials, illustrating the importance of capacity in designing MOFs for practical applications. Among the identified candidates, we synthesized and characterized a MOF in a new copper form with high predicted adsorbent capacity (q L+M > 1.2 mol/L) and moderately high selectivity (S L+M ≈ 10). In conclusion, we examined the role of pore shape in hexane isomer separations, especially of triangular-shaped pores. We show through the potential energy surface and three-dimensional siting analyses that linear alkanes do not populate the corners of narrow triangular channels and that structures with nontriangular pores can efficiently separate hexane isomers. Detailed thermodynamic analysis illustrates how differences in the free energy of adsorption contribute to shape-selective separation in nanoporous materials.« less

The crystal structures of two isomers of 5-(phenyl-iso-thia-zol-yl)-1,3,4-oxa-thia-zol-2-one.

PubMed

Zhu, Shuguang; Schriver, Melbourne J; Hendsbee, Arthur D; Masuda, Jason D

2017-11-01

The syntheses and crystal structures of two isomers of phenyl iso-thia-zolyl oxa-thia-zolone, C 11 H 6 N 2 O 2 S 2 , are described [systematic names: 5-(3-phenyl-iso-thia-zol-5-yl)-1,3,4-oxa-thia-zol-2-one, (I), and 5-(3-phenyl-iso-thia-zol-4-yl)-1,3,4-oxa-thia-zol-2-one, (II)]. There are two almost planar (r.m.s. deviations = 0.032 and 0.063 Å) mol-ecules of isomer (I) in the asymmetric unit, which form centrosymmetric tetra-mers linked by strong S⋯N [3.072 (2) Å] and S⋯O contacts [3.089 (1) Å]. The tetra-mers are π-stacked parallel to the a -axis direction. The single mol-ecule in the asymmetric unit of isomer (II) is twisted into a non-planar conformation by steric repulsion [dihedral angles between the central iso-thia-zolyl ring and the pendant oxa-thia-zolone and phenyl rings are 13.27 (6) and 61.18 (7)°, respectively], which disrupts the π-conjugation between the heteroaromatic iso-thia-zoloyl ring and the non-aromatic oxa-thia-zolone heterocycle. In the crystal of isomer (II), the strong S⋯O [3.020 (1) Å] and S⋯C contacts [3.299 (2) Å] and the non-planar structure of the mol-ecule lead to a form of π-stacking not observed in isomer (I) or other oxa-thia-zolone derivatives.

Zwitterionic-hydrophilic interaction capillary liquid chromatography coupled to tandem mass spectrometry for the characterization of human alpha-acid-glycoprotein N-glycan isomers.

PubMed

Mancera-Arteu, Montserrat; Giménez, Estela; Barbosa, José; Peracaula, Rosa; Sanz-Nebot, Victòria

2017-10-23

In this work, a μZIC-HILIC-MS/MS methodology was established in negative ion mode for the characterization of glycan isomers. The possibility to separate the glycan isomers by the μZIC-HILIC strategy coupled to a high resolution tandem mass spectrometry detection permitted us to obtain valuable information about each glycan structure. The most important diagnostic ion fragments previously described to characterize structural features of glycans, were evaluated in this study using hAGP as model glycoprotein. The assignation of hAGP glycan isomers performed in our previous work using the GRIL strategy in combination with exoglycosidase digestion [1] was used in this paper to confirm or discard some ion fragments reported in the literature and delve into the structural characterization of glycan isomers. Sialic acid as well as fucose linkage-type glycan isomers were assigned using this approach and daughter ions with higher diagnostic value were determined. The location of α2-3/α2-6 sialic acids on antennas and a deeper characterization of several highly sialylated tri- and tetraantennary glycans was also possible using the established MS/MS method. Moreover, relying on the characterization performed in Ref. [1], core and antenna fucosylation were differentiated in this work using specific ion fragments obtained in the tandem mass spectra. This methodology was also applied to hAGP purified from control and pathological serum samples, which corroborated its robustness and its potential for finding novel glycan-based biomarkers in patho-glycomic studies. Copyright © 2017 Elsevier B.V. All rights reserved.

Fluorescence in complexes based on quinolines-derivatives: a search for better fluorescent probes.

PubMed

Mecca, Carolina Z P; Fonseca, Fernando L A; Bagatin, Izilda A

2016-11-05

Quinoline-derived fluorescent complexes were designed; synthesized by the reaction of 5-nitro-8-hydroxyquinoline and 5-chloro-8-hydroxyquinoline with Al(3+), Mg(2+), Zn(2+), and Cd(2+) salts (1-8); and characterized. The (1)H NMR spectra of complexes 1 and 5, containing Al(3+), were consistent with an octahedral structure having approximate D3 symmetry, and the results supported the favored facial isomer (fac). Data for complexes 2-4 and 6-8 supported the formation of tetrahedral structures. Intense luminescence was detected for complexes 5-8, even with the naked eye, as indicated by quantum yield values of 0.087, 0.094, 0.051, and 0.021, respectively. Furthermore, in contrast to 5-nitro-8-hydroxyquinoline, the 5-chloro-8-hydroxyquinoline ligand exhibited bands at different energies depending on the coordinated metal, which supported its potential application in ionic and biological probes, as well as in cell imaging. Copyright © 2016 Elsevier B.V. All rights reserved.

Atmospheric Chemistry of E- and Z-CF3CH═CHF (HFO-1234ze): OH Reaction Kinetics as a Function of Temperature and UV and IR Absorption Cross Sections.

PubMed

Antiñolo, María; Bravo, Iván; Jiménez, Elena; Ballesteros, Bernabé; Albaladejo, José

2017-11-02

We report here the rate coefficients for the OH reactions (k OH ) with E-CF 3 CH═CHF and Z-CF 3 CH═CHF, potential substitutes of HFC-134a, as a function of temperature (263-358 K) and pressure (45-300 Torr) by pulsed laser photolysis coupled to laser-induced fluorescence techniques. For the E-isomer, the existing discrepancy among previous results on the T dependence of k OH needs to be elucidated. For the Z-isomer, this work constitutes the first absolute determination of k OH . No pressure dependence of k OH was observed, while k OH exhibits a non-Arrhenius behavior: k OH (E) = [Formula: see text] and k OH (Z) = [Formula: see text] cm 3 molecule -1 s -1 , where uncertainties are 2σ. UV absorption cross sections, σ λ , are reported for the first time. From σ λ and considering a photolysis quantum yield of 1, an upper limit for the photolysis rate coefficients and lifetimes due to this process in the troposphere are estimated: 3 × 10 -8 s -1 and >1 year for the E-isomer and 2 × 10 -7 s -1 and >2 months for Z-CF 3 CH═CHF, respectively. Under these conditions, the overall estimated tropospheric lifetimes are 15 days (for the E-isomer) and 8 days (for the Z-isomer), the major degradation pathway being the OH reaction, with a contribution of the photolytic pathway of less than 3% (for E) and 13% (for Z). IR absorption cross sections were determined both experimentally (500-4000 cm -1 ) and theoretically (0-2000 cm -1 ). From the theoretical IR measurements, it is concluded that the contribution of the 0-500 cm -1 region to the total integrated cross sections is appreciable for the E-isomer (9%) but almost negligible for the Z-isomer (0.5%). Nevertheless, the impact on their radiative efficiency and global warming potential is negligible.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Yu, Chongqi; Harbich, Wolfgang; Sementa, Luca

Ligand-protected Au clusters are non-bleaching fluorescence markers in bio- and medical applications. We show that their fluorescence is an intrinsic property of the Au cluster itself. We find a very intense and sharp fluorescence peak located at λ =739.2 nm (1.68 eV) for Au20 clusters in a Ne matrix held at 6 K. The fluorescence reflects the HOMO-LUMO diabatic bandgap of the cluster. The cluster shows a very rich absorption fine structure reminiscent of well defined molecule-like quantum levels. These levels are resolved since Au20 has only one stable isomer (tetrahedral), therefore our sample is mono-disperse in cluster size andmore » conformation. Density-functional theory (DFT) and time-dependent DFT calculations clarify the nature of optical absorptionand predict both main absorption peaks and intrinsic fluorescence in good agreement with experiment.« less

The cluster Ir4 and its interaction with a hydrogen impurity. A density functional study.

PubMed

Bussai, Chuenchit; Krüger, Sven; Vayssilov, Georgi N; Rösch, Notker

2005-07-07

To contribute to the understanding of how iridium particles act as catalysts for hydrogenation and dehydrogenation of hydrocarbons, we have determined structures and binding energies of various isomers of Ir(4) as well as HIr(4) on the basis of relativistic density functional theory. The most stable isomer of Ir(4) showed a square planar structure with eight unpaired electrons. The tetrahedral structure, experimentally suggested for supported species, was calculated 49 kJ mol(-1) less stable. Hydrogen coordinates preferentially to a single Ir center of the planar cluster with a binding energy of up to 88 kJ mol(-1) with respect to the atom in the H(2) molecule. Terminal interaction of hydrogen with an Ir(4) tetrahedron causes the cluster to open to a butterfly structure. We calculated terminal binding of hydrogen at different Ir(4) isomers to be more stable than bridge coordination, at variance with earlier studies.

Phenyl-β-D-glucopyranoside and Phenyl-β-D-galactopyranoside dimers: Small Structural differences but Very Different Interactions

NASA Astrophysics Data System (ADS)

Usabiaga, Imanol; Camiruaga, Ander; Insausti, Aran; Çarçabal, Pierre; Cocinero, Emilio J.; León, Iker; Fernández, José A.

2018-02-01

We report a combination of laser spectroscopy in molecular jets and quantum mechanical calculations to characterize the aggregation preferences of phenyl-β-D-glucopyranoside (β-PhGlc) and phenyl-β-D-galactopyranoside (β-PhGal) homodimers. At least two structures of β-PhGlc dimer were found maintaining the same intramolecular interactions of the monomers, but with additional intermolecular interactions between the hydroxyl groups. Several isomers were also found for the dimer of β-PhGal forming extensive hydrogen bond networks between the interacting molecules, of very different shape. All the species found present several CH•••Pi and OH•••Pi interactions that add stability to the aggregates. The results show how even the smallest change in a substituent, from axial to equatorial position, plays a decisive role in the formation of the dimers. These conclusions reinforce the idea that the small structural changes between sugar units are amplified by formation of intra and intermolecular hydrogen bond networks, helping other molecules (proteins, receptors) to easily read the sugar code of glycans.

Isolation and spectral characterization of thermally generated multi-Z-isomers of lycopene and the theoretically preferred pathway to di-Z-isomers.

PubMed

Honda, Masaki; Kudo, Tatsuya; Kuwa, Takahiro; Higashiura, Takuma; Fukaya, Tetsuya; Inoue, Yoshinori; Kitamura, Chitoshi; Takehara, Munenori

2017-02-01

Lycopene has a large number of geometric isomers caused by E/Z isomerization at arbitrary sites within the 11 conjugated double bonds, offering varying characteristics related to features such as antioxidant capacity and bioavailability. However, the geometric structures of only a few lycopene Z-isomers have been thoroughly identified from natural sources. In this study, seven multi-Z-isomers of lycopene, (9Z,13'Z)-, (5Z,13Z,9'Z)-, (9Z,9'Z)-, (5Z,13'Z)-, (5Z,9'Z)-, (5Z,9Z,5'Z)-, and (5Z,9Z)-lycopene, were obtained from tomato samples by thermal isomerization, and then isolated by elaborate chromatography, and fully assigned using proton nuclear magnetic resonance. Moreover, the theoretically preferred pathway from (all-E)-lycopene to di-Z-isomers was examined with a computational approach using a Gaussian program. Fine-tuning of the HPLC separation conditions led to the discovery of novel multi-Z-isomers, and whose formation was supported by advanced theoretical calculations.

Active sites of the cytochrome p450cam (CYP101) F87W and F87A mutants. Evidence for significant structural reorganization without alteration of catalytic regiospecificity.

PubMed

Tuck, S F; Graham-Lorence, S; Peterson, J A; Ortiz de Montellano, P R

1993-01-05

Ferricyanide oxidation of the aryl-iron complexes formed by the reaction of cytochrome P450 enzymes with arylhydrazines causes in situ migration of the aryl group from the iron to the porphyrin nitrogen atoms. The regiochemistry of this migration, defined by the ratio of the four possible N-arylprotoporphyrin IX isomers, provides a method for mapping the topologies of cytochrome P450 active sites. The method has been validated by using it to examine the active site of cytochrome P450cam (CYP101), for which a crystal structure is available. In agreement with the crystal structure, reaction with phenylhydrazine gives a 5:25:70 ratio of the NA:NC:ND (subscript indicates pyrrole ring) N-phenylprotoporphyrin IX isomers. Naphthylhydrazine, however, yields exclusively the NC regioisomer and 4-(phenyl)phenylhydrazine the NA:NC:ND isomers in a 14:40:46 ratio. These isomer ratio differences are readily explained by topological differences between the upper and lower reaches of the active site. Having validated the aryl-iron shift as a topological probe, we used it to investigate the structural changes caused by mutation of Phe-87, a residue that provides the ceiling over pyrrole ring D in the crystal structure of cytochrome P450cam. Mutation of Phe-87 to a tryptophan causes no detectable change in the regiochemistry of camphor hydroxylation and only minor changes in the N-aryl isomer ratios. However, mutation of Phe-87 to an alanine, which was expected to open up the region above pyrrole ring D, severely decreased the proportion of the ND in favor of the NA isomer. Less rather than more space is therefore available over pyrrole ring D in the F87A mutant despite the fact that the regiochemistry of camphor hydroxylation remains unchanged. These results provide evidence for significant structural reorganization in the upper regions of the substrate binding site without alteration of the camphor hydroxylation regiospecificity in the F87A mutant.

Characterization of an alternative low energy fold for bovine α-lactalbumin formed by disulfide bond shuffling.

PubMed

Lewney, Sarah; Smith, Lorna J

2012-03-01

Bovine α-lactalbumin (αLA) forms a misfolded disulfide bond shuffled isomer, X-αLA. This X-αLA isomer contains two native disulfide bridges (Cys 6-Cys 120 and Cys 28-Cys 111) and two non-native disulfide bridges (Cys 61-Cys 73 and Cys 77-Cys 91). MD simulations have been used to characterize the X-αLA isomer and its formation via disulfide bond shuffling and to compare it with the native fold of αLA. In the simulations of the X-αLA isomer the structure of the α-domain of native αLA is largely retained in agreement with experimental data. However, there are significant rearrangements in the β-domain, including the loss of the native β-sheet and calcium binding site. Interestingly, the energies of X-αLA and native αLA in simulations in the absence of calcium are closely similar. Thus, the X-αLA isomer represents a different low energy fold for the protein. Calcium binding to native αLA is shown to help preserve the structure of the β-domain of the protein limiting possibilities for disulfide bond shuffling. Hence, binding calcium plays an important role in both maintaining the native structure of αLA and providing a mechanism for distinguishing between folded and misfolded species. Copyright © 2011 Wiley Periodicals, Inc.

Machine Learning of Parameters for Accurate Semiempirical Quantum Chemical Calculations

DOE Office of Scientific and Technical Information (OSTI.GOV)

Dral, Pavlo O.; von Lilienfeld, O. Anatole; Thiel, Walter

2015-05-12

We investigate possible improvements in the accuracy of semiempirical quantum chemistry (SQC) methods through the use of machine learning (ML) models for the parameters. For a given class of compounds, ML techniques require sufficiently large training sets to develop ML models that can be used for adapting SQC parameters to reflect changes in molecular composition and geometry. The ML-SQC approach allows the automatic tuning of SQC parameters for individual molecules, thereby improving the accuracy without deteriorating transferability to molecules with molecular descriptors very different from those in the training set. The performance of this approach is demonstrated for the semiempiricalmore » OM2 method using a set of 6095 constitutional isomers C7H10O2, for which accurate ab initio atomization enthalpies are available. The ML-OM2 results show improved average accuracy and a much reduced error range compared with those of standard OM2 results, with mean absolute errors in atomization enthalpies dropping from 6.3 to 1.7 kcal/mol. They are also found to be superior to the results from specific OM2 reparameterizations (rOM2) for the same set of isomers. The ML-SQC approach thus holds promise for fast and reasonably accurate high-throughput screening of materials and molecules.« less

Combined Quantum Chemical/Raman Spectroscopic Analyses of Li+ Cation Solvation: Cyclic Carbonate Solvents - Ethylene Carbonate and Propylene Earbonate

DOE Office of Scientific and Technical Information (OSTI.GOV)

Allen, Joshua L.; Borodin, Oleg; Seo, D. M.

2014-12-01

Combined computational/Raman spectroscopic analyses of ethylene carbonate (EC) and propylene carbonate (PC) solvation interactions with lithium salts are reported. It is proposed that previously reported Raman analyses of (EC)n-LiX mixtures have utilized faulty assumptions. In the present studies, density functional theory (DFT) calculations have provided corrections in terms of both the scaling factors for the solvent's Raman band intensity variations and information about band overlap. By accounting for these factors, the solvation numbers obtained from two different EC solvent bands are in excellent agreement with one another. The same analysis for PC, however, was found to be quite challenging. Commerciallymore » available PC is a racemic mixture of (S)- and (R)-PC isomers. Based upon the quantum chemistry calculations, each of these solvent isomers may exist as multiple conformers due to a low energy barrier for ring inversion, making deconvolution of the Raman bands daunting and inherently prone to significant error. Thus, Raman spectroscopy is able to accurately determine the extent of the EC...Li+ cation solvation interactions using the provided methodology, but a similar analysis of PC...Li+ cation solvation results in a significant underestimation of the actual solvation numbers.« less

Machine learning of parameters for accurate semiempirical quantum chemical calculations

DOE PAGES

Dral, Pavlo O.; von Lilienfeld, O. Anatole; Thiel, Walter

2015-04-14

We investigate possible improvements in the accuracy of semiempirical quantum chemistry (SQC) methods through the use of machine learning (ML) models for the parameters. For a given class of compounds, ML techniques require sufficiently large training sets to develop ML models that can be used for adapting SQC parameters to reflect changes in molecular composition and geometry. The ML-SQC approach allows the automatic tuning of SQC parameters for individual molecules, thereby improving the accuracy without deteriorating transferability to molecules with molecular descriptors very different from those in the training set. The performance of this approach is demonstrated for the semiempiricalmore » OM2 method using a set of 6095 constitutional isomers C 7H 10O 2, for which accurate ab initio atomization enthalpies are available. The ML-OM2 results show improved average accuracy and a much reduced error range compared with those of standard OM2 results, with mean absolute errors in atomization enthalpies dropping from 6.3 to 1.7 kcal/mol. They are also found to be superior to the results from specific OM2 reparameterizations (rOM2) for the same set of isomers. The ML-SQC approach thus holds promise for fast and reasonably accurate high-throughput screening of materials and molecules.« less

Variations of structures and solid-state conductivity of isomeric silver(I) coordination polymers having linear and V-shaped thiophene-centered ditriazole ligands

DOE Office of Scientific and Technical Information (OSTI.GOV)

Hu, Bin; School of Environmental and Chemical Engineering, Nanchang Hangkong University, Nanchang, 330063; Geng, Jiao

2014-07-01

A pair of new linear and V-shaped acceptor–donor–acceptor (A−D−A) thiophene-centered ditriazole structural isomers, i.e., 2,5-di(1H-1,2,4-triazol-1-yl)thiophene (L{sup 1}) and 3,4-di(1H-1,2,4-triazol-1-yl)thiophene (L{sup 2}), has been synthesized and characterized. They are used as μ{sub 2}-bridging ligands to prepare a pair of silver(I) coordination polymers formulated as [Ag(L{sup 1})(NO{sub 3})]{sub n} (1) and [Ag(L{sup 2})(NO{sub 3})]{sub n} (2), which are also structural isomers at the supramolecular level. X-ray single-crystal diffraction analyses for 1 and 2 reveal that they exhibit the same one-dimensional (1D) coordination polymers but different structural architectures because of the distinguishable shape and configuration of isomeric ligands (L{sup 1} and L{sup 2})more » and the alterations of the coordination numbers. More interestingly, compared with the free ligands, 1D silver(I) polymeric isomers 1 and 2 show significant enhancement of solid-state conductivity to different extents (1.42×10{sup 4} and 2.17×10{sup 3} times), where 6.96 times' enhancement of solid-state conductivity from 1 to 2 has been observed. The formation of Ag–N coordinative bonds and the configurational discrepancy of L{sup 1} and L{sup 2} are believed to play important roles in facilitating the electron transport between molecules, which can also be supported by Density Function Theory calculations of their band gaps. - Graphical abstract: A pair of linear and V-shaped isomeric thiophene-centered ditriazole ligands (L{sup 1}) and L{sup 2} are used to prepare a pair of silver(I) polymeric isomers (1 and 2), where significant enhancement of solid-state conductivity to different extents are observed originating from the distinguishable shape and configuration of isomeric ligands. - Highlights: • A pair of linear and V-shaped thiophene-centered ditriazole structural isomers is prepared. • They are used as µ{sub 2}-bridging ligands to prepare a pair of silver(I) polymeric isomers. • Significant enhancement of solid-state conductivity is observed for each polymeric isomer.« less

Identification and characterization of isomeric N-glycans of human alfa-acid-glycoprotein by stable isotope labelling and ZIC-HILIC-MS in combination with exoglycosidase digestion.

PubMed

Mancera-Arteu, Montserrat; Giménez, Estela; Barbosa, José; Sanz-Nebot, Victòria

2016-10-12

In this study, a ZIC-HILIC-MS methodology for the analysis of N-glycan isomers was optimized to obtain greater detection sensitivity and thus identify more glycan structures in hAGP. In a second step, this method was combined with glycan reductive isotope labelling (GRIL) through [(12)C6]/[(13)C6]-aniline and exoglycosidase digestion to characterize the different glycan isomers. The GRIL method allows the peak areas resulting from two different labelled samples to be compared, since neither retention time shifts nor variations in the ionization of glycans between these samples are obtained. First, sialic acid linkage assignations were performed for most hAGP glycan isomers with α2-3 sialidase digestion. Bi-, tri- and tetraantennary glycan isomers with different terminal sialic acid linkages to galactose (α2-3 or α2-6) were assigned, and the potential of this technique for the structural characterization of isobaric isomers was therefore demonstrated. Furthermore, fucose linkage isomers of hAGP glycans were also characterized using this isotope-labelling approach in combination with α1-3,4 fucosidase and β1-4 galactosidase digestion. α1-3 antennary fucoses and α1-6 core fucosylation were detected in hAGP fucosylated glycans. These established methodologies can be extremely useful for patho-glycomic studies to characterize glycoproteins of biomedical interest and find novel glycan isomers that could be used as biomarkers in cancer research. Copyright © 2016 Elsevier B.V. All rights reserved.

Linear and branched perfluorooctane sulfonate (PFOS) isomer patterns differ among several tissues and blood of polar bears.

PubMed

Greaves, Alana K; Letcher, Robert J

2013-09-01

Perfluorooctane sulfonate (PFOS) is a globally distributed persistent organic pollutant that has been found to bioaccumulate and biomagnify in aquatic food webs. Although principally in its linear isomeric configuration, 21-35% of the PFOS manufactured via electrochemical fluorination is produced as a branched structural isomer. PFOS isomer patterns were investigated in multiple tissues of polar bears (Ursus maritimus) from East Greenland. The liver (n = 9), blood (n = 19), brain (n = 16), muscle (n = 5), and adipose (n = 5) were analyzed for linear PFOS (n-PFOS), as well as multiple mono- and di-trifluoromethyl-substituted branched isomers. n-PFOS accounted for 93.0 ± 0.5% of Σ-PFOS isomer concentrations in the liver, whereas the proportion was significantly lower (p<0.05) in the blood (85.4 ± 0.5%). Branched isomers were quantifiable in the liver and blood, but not in the brain, muscle, or adipose. In both the liver and blood, 6-perfluoromethylheptane sulfonate (P6MHpS) was the dominant branched isomer (2.61 ± 0.10%, and 3.26 ± 0.13% of Σ-PFOS concentrations, respectively). No di-trifluoromethyl-substituted isomers were detectable in any of the tissues analyzed. These tissue-specific isomer patterns suggest isomer-specific pharmacokinetics, perhaps due to differences in protein affinities, and thus differences in protein interactions, as well transport, absorption, and/or metabolism in the body. Crown Copyright © 2013. Published by Elsevier Ltd. All rights reserved.

Travelling-wave ion mobility and negative ion fragmentation of high mannose N-glycans

PubMed Central

Harvey, David J.; Scarff, Charlotte A.; Edgeworth, Matthew; Struwe, Weston B.; Pagel, Kevin; Thalassinos, Konstantinos; Crispin, Max; Scrivens, Jim

2016-01-01

The isomeric structure of high-mannose N-glycans can significantly impact biological recognition events. Here, the utility of travelling-wave ion mobility-mass spectrometry (TW IM-MS)for isomer separation of high-mannose N-glycans is investigated. Negative ion fragmentation using collision-induced dissociation (CID) gave more informative spectra than positive ion spectra with mass-different fragment ions characterizing many of the isomers. Isomer separation by ion mobility in both ionization modes was generally limited, with the arrival time distributions (ATD) often showing little sign of isomers. However, isomers could be partially resolved by plotting extracted fragment ATDs of the diagnostic fragment ions from the negative ion spectra and the fragmentation spectra of the isomers could be extracted by using ions from limited areas of the ATD peak. In some cases, asymmetric ATDs were observed but no isomers could be detected by fragmentation. In these cases, it was assumed that conformers were being separated. Collision cross sections (CCSs) of the isomers in positive and negative fragmentation mode were estimated from TW IM-MS data using dextran glycans as calibrant. More complete CCS data were achieved in negative ion mode by utilizing the diagnostic fragment ions. Examples of isomer separations are shown for N-glycans released from the well-characterized glycoproteins chicken ovalbumin, porcine thyroglobulin and gp120 from the human immunodeficiency virus. In addition to the cross sectional data, details of the negative ion collision-induced dissociation (CID) spectra of all resolved isomers are discussed. PMID:26956389

On the upper bound of the thermodynamic stability of fullerenes from small to giant

NASA Astrophysics Data System (ADS)

Pankratyev, Evgeniy Yu; Khatymov, Rustem V.; Sabirov, Denis Sh; Yuldashev, Arthur V.

2018-07-01

From the large variety of C20sbnd C720 fullerenes, the energetically most stable isomers were chosen and studied within the PBE/3ζ quantum-chemical approximation. A phenomenological model of the dependence of the standard enthalpy of formation and entropy of the selected isomers on the number of the carbon atoms is developed. From the analysis of the constants of the phenomenological model, it follows that the C60, C70, C180, and C1500 molecules hold a prominent position among the hypothetical and/or experimentally discovered fullerenes. For the selected energy-stable isomers, the values of the singlet-triplet splitting were calculated. The ground state of the C260sbnd C3, C320sbnd D3d and C500sbnd D3d molecules were found to be of triplet multiplicity that may indicate their low kinetic stability and/or possibility of existence in the derivatized forms. In view of the lack of relevant experimental thermodynamic data on fullerenes, the obtained in this work approximation dependences, expressed in a simple analytical form, may provide useful tool for fast assessing the energetic characteristics of fullerenes, as well as for prediction of those undiscovered yet.

Structures, energetics, vibrational spectra of NH4+ (H2O)(n=4,6) clusters: Ab initio calculations and first principles molecular dynamics simulations.

PubMed

Karthikeyan, S; Singh, Jiten N; Park, Mina; Kumar, Rajesh; Kim, Kwang S

2008-06-28

Important structural isomers of NH(4) (+)(H(2)O)(n=4,6) have been studied by using density functional theory, Moller-Plesset second order perturbation theory, and coupled-cluster theory with single, double, and perturbative triple excitations [CCSD(T)]. The zero-point energy (ZPE) correction to the complete basis set limit of the CCSD(T) binding energies and free energies is necessary to identify the low energy structures for NH(4) (+)(H(2)O)(n=4,6) because otherwise wrong structures could be assigned for the most probable structures. For NH(4) (+)(H(2)O)(6), the cage-type structure, which is more stable than the previously reported open structure before the ZPE correction, turns out to be less stable after the ZPE correction. In first principles Car-Parrinello molecular dynamics simulations around 100 K, the combined power spectrum of three lowest energy isomers of NH(4) (+)(H(2)O)(4) and two lowest energy isomers of NH(4) (+)(H(2)O)(6) explains each experimental IR spectrum.

Structures, energetics, vibrational spectra of NH4+(H2O)n=4,6 clusters: Ab initio calculations and first principles molecular dynamics simulations

NASA Astrophysics Data System (ADS)

Karthikeyan, S.; Singh, Jiten N.; Park, Mina; Kumar, Rajesh; Kim, Kwang S.

2008-06-01

Important structural isomers of NH4+(H2O)n=4,6 have been studied by using density functional theory, Møller-Plesset second order perturbation theory, and coupled-cluster theory with single, double, and perturbative triple excitations [CCSD(T)]. The zero-point energy (ZPE) correction to the complete basis set limit of the CCSD(T) binding energies and free energies is necessary to identify the low energy structures for NH4+(H2O)n=4,6 because otherwise wrong structures could be assigned for the most probable structures. For NH4+(H2O)6, the cage-type structure, which is more stable than the previously reported open structure before the ZPE correction, turns out to be less stable after the ZPE correction. In first principles Car-Parrinello molecular dynamics simulations around 100 K, the combined power spectrum of three lowest energy isomers of NH4+(H2O)4 and two lowest energy isomers of NH4+(H2O)6 explains each experimental IR spectrum.

Big Data Meets Quantum Chemistry Approximations: The Δ-Machine Learning Approach.

PubMed

Ramakrishnan, Raghunathan; Dral, Pavlo O; Rupp, Matthias; von Lilienfeld, O Anatole

2015-05-12

Chemically accurate and comprehensive studies of the virtual space of all possible molecules are severely limited by the computational cost of quantum chemistry. We introduce a composite strategy that adds machine learning corrections to computationally inexpensive approximate legacy quantum methods. After training, highly accurate predictions of enthalpies, free energies, entropies, and electron correlation energies are possible, for significantly larger molecular sets than used for training. For thermochemical properties of up to 16k isomers of C7H10O2 we present numerical evidence that chemical accuracy can be reached. We also predict electron correlation energy in post Hartree-Fock methods, at the computational cost of Hartree-Fock, and we establish a qualitative relationship between molecular entropy and electron correlation. The transferability of our approach is demonstrated, using semiempirical quantum chemistry and machine learning models trained on 1 and 10% of 134k organic molecules, to reproduce enthalpies of all remaining molecules at density functional theory level of accuracy.

An isomer-specific study of solid nitromethane decomposition pathways - Detection of aci-nitromethane (H2CNO(OH)) and nitrosomethanol (HOCH2NO) intermediates

NASA Astrophysics Data System (ADS)

Maksyutenko, Pavlo; Förstel, Marko; Crandall, Parker; Sun, Bing-Jian; Wu, Mei-Hung; Chang, Agnes H. H.; Kaiser, Ralf I.

2016-08-01

An isomer specific study of energetic electron exposed nitromethane ices was performed via photoionization - reflectron time of flight mass spectrometry (PI-ReTOF-MS) of the subliming products employing tunable vacuum ultraviolet light for ionization. Supported by electronic structure calculations, nitromethane (CH3NO2) was found to isomerize to methyl nitrite (CH3ONO) and also via hydrogen migration to the hitherto elusive aci-nitromethane isomer (H2CNO(OH)). The latter isomerizes to nitrosomethanol (HOCH2NO) through hydroxyl group (OH) migration, and, probably, ring closure to the cyclic 2-hydroxy-oxaziridine isomer (c-H2CON(OH)) as well. The importance of hydrogen migrations was also verified via the nitrosomethane (CH3NO) - formaldehyde oxime isomer (CH2NOH) pair.

A density functional theory computational study of adsorption of Di-Meta-Cyano Azobenzene molecules on Si (111) surfaces

NASA Astrophysics Data System (ADS)

Motevalli, Benyamin; Taherifar, Neda; Wu, Bisheng; Tang, Wenxin; Liu, Jefferson Zhe

2017-11-01

The adsorption of di-meta-cyano azobenzene (DMC) cis and trans isomers on non-passivated and passivated Si (111) (7 × 7) surfaces is studied using density functional theory (DFT) calculations. Our results reveal that on the non-passivated surface the 12 Si adatoms are accessible to form chemical bonds with DMC molecules. Interestingly, the trans isomer forms two chemical bonds near the corner hole atom in Si (111) (7 × 7) surface, which is not observed in the widely studied metallic surfaces. The DMC isomers show significant structural distortion in the chemisorption case. The strong chemical bonds (and high bonding energy) could be detrimental to conformation switching between these two isomers under external stimuli. The physisorption case is also examined. Monte Carlo (MC) simulations with empirical force fields were employed to search about 106 different adsorption positions and DMC molecule orientations to identify the stable adsorption sites (up to six). The DFT-PBE and DFT-D2 calculations were then carried out to obtain the relaxed atomistic structures and accurate adsorption energy. We find that it is imperative to take van der Waals (vdW) interaction into account in DFT calculations. Our results show that the adsorption sites generally are encompassed by either the Si adatoms or the passivated H atoms, which could enhance the long-range dispersion interaction between DMC molecules and Si surfaces. The molecular structures of both isomers remain unchanged compared with gas phase. The obtained adsorption energy results ΔEads are moderate (0.2-0.8 eV). At some adsorption sites on the passivated surface, both isomers have similar moderate ΔEads (0.4-0.6 eV), implying promises of molecular switching that should be examined in experiments.

Resolving the HONO formation mechanism in the ionosphere via ab initio molecular dynamic simulations

PubMed Central

He, Rongxing; Li, Lei; Zhong, Jie; Zhu, Chongqin; Francisco, Joseph S.; Zeng, Xiao Cheng

2016-01-01

Solar emission produces copious nitrosonium ions (NO+) in the D layer of the ionosphere, 60 to 90 km above the Earth’s surface. NO+ is believed to transfer its charge to water clusters in that region, leading to the formation of gaseous nitrous acid (HONO) and protonated water cluster. The dynamics of this reaction at the ionospheric temperature (200–220 K) and the associated mechanistic details are largely unknown. Using ab initio molecular dynamics (AIMD) simulations and transition-state search, key structures of the water hydrates—tetrahydrate NO+(H2O)4 and pentahydrate NO+(H2O)5—are identified and shown to be responsible for HONO formation in the ionosphere. The critical tetrahydrate NO+(H2O)4 exhibits a chain-like structure through which all of the lowest-energy isomers must go. However, most lowest-energy isomers of pentahydrate NO+(H2O)5 can be converted to the HONO-containing product, encountering very low barriers, via a chain-like or a three-armed, star-like structure. Although these structures are not the global minima, at 220 K, most lowest-energy NO+(H2O)4 and NO+(H2O)5 isomers tend to channel through these highly populated isomers toward HONO formation. PMID:27071120

Resolving the HONO formation mechanism in the ionosphere via ab initio molecular dynamic simulations.

PubMed

He, Rongxing; Li, Lei; Zhong, Jie; Zhu, Chongqin; Francisco, Joseph S; Zeng, Xiao Cheng

2016-04-26

Solar emission produces copious nitrosonium ions (NO(+)) in the D layer of the ionosphere, 60 to 90 km above the Earth's surface. NO(+) is believed to transfer its charge to water clusters in that region, leading to the formation of gaseous nitrous acid (HONO) and protonated water cluster. The dynamics of this reaction at the ionospheric temperature (200-220 K) and the associated mechanistic details are largely unknown. Using ab initio molecular dynamics (AIMD) simulations and transition-state search, key structures of the water hydrates-tetrahydrate NO(+)(H2O)4 and pentahydrate NO(+)(H2O)5-are identified and shown to be responsible for HONO formation in the ionosphere. The critical tetrahydrate NO(+)(H2O)4 exhibits a chain-like structure through which all of the lowest-energy isomers must go. However, most lowest-energy isomers of pentahydrate NO(+)(H2O)5 can be converted to the HONO-containing product, encountering very low barriers, via a chain-like or a three-armed, star-like structure. Although these structures are not the global minima, at 220 K, most lowest-energy NO(+)(H2O)4 and NO(+)(H2O)5 isomers tend to channel through these highly populated isomers toward HONO formation.

The influence of isomer purity on trap states and performance of organic thin-film transistors.

PubMed

Diemer, Peter J; Hayes, Jacori; Welchman, Evan; Hallani, Rawad; Pookpanratana, Sujitra J; Hacker, Christina A; Richter, Curt A; Anthony, John E; Thonhauser, Timo; Jurchescu, Oana D

2017-01-01

Organic field-effect transistor (OFET) performance is dictated by its composition and geometry, as well as the quality of the organic semiconductor (OSC) film, which strongly depends on purity and microstructure. When present, impurities and defects give rise to trap states in the bandgap of the OSC, lowering device performance. Here, 2,8-difluoro-5,11-bis(triethylsilylethynyl)-anthradithiophene is used as a model system to study the mechanism responsible for performance degradation in OFETs due to isomer coexistence. The density of trapping states is evaluated through temperature dependent current-voltage measurements, and it is discovered that OFETs containing a mixture of syn - and anti -isomers exhibit a discrete trapping state detected as a peak located at ~ 0.4 eV above the valence-band edge, which is absent in the samples fabricated on single-isomer films. Ultraviolet photoelectron spectroscopy measurements and density functional theory calculations do not point to a significant difference in electronic band structure between individual isomers. Instead, it is proposed that the dipole moment of the syn -isomer present in the host crystal of the anti -isomer locally polarizes the neighboring molecules, inducing energetic disorder. The isomers can be separated by applying gentle mechanical vibrations during film crystallization, as confirmed by the suppression of the peak and improvement in device performance.

Structural analysis of conjugated linoleic acid produced by Lactobacillus plantarum, and factors affecting isomer production.

PubMed

Kishino, Shigenobu; Ogawa, Jun; Ando, Akinori; Iwashita, Takashi; Fujita, Tsuyoshi; Kawashima, Hiroshi; Shimizu, Sakayu

2003-01-01

An isomer of the conjugated linoleic acid (CLA) produced from linoleic acid by Lactobacillus plantarum was identified as cis-9,trans-11-octadecadienoic acid by proton nuclear magnetic resonance spectroscopy. Together with earlier results, we concluded that the bacterium produces two CLA isomers, cis-9,trans-11- and trans-9,trans-11-octadecadienoic acid from linoleic acid. The addition of L-serine, glucose, AgNO3, or NaCl to the reaction mixture reduced production of the latter.

Metabolism, Mass Spectral Analysis and Mode of Action of Trichothecene Mycotoxins.

DTIC Science & Technology

1987-09-15

per billion. An isomer of HT-2 was detected. The mass spectra of H-i (parent and daughter ions) were obtained. Toxic Fusarium isolates were identified...and T-2-tetraol as well as their daughter ion sepctra have been obtained. An isomer of HT-2 ýC-4 acetate) was discovered in a Fusarium culture using...the daughter ions of HT-2 as a probe. Its structure wasdetermined using parent-daughter mass spectra. The detection of the isomer in the Fusarium

Isomer Information from Ion Mobility Separation of High-Mannose Glycan Fragments.

PubMed

Harvey, David J; Seabright, Gemma E; Vasiljevic, Snezana; Crispin, Max; Struwe, Weston B

2018-05-01

Extracted arrival time distributions of negative ion CID-derived fragments produced prior to traveling-wave ion mobility separation were evaluated for their ability to provide structural information on N-linked glycans. Fragmentation of high-mannose glycans released from several glycoproteins, including those from viral sources, provided over 50 fragments, many of which gave unique collisional cross-sections and provided additional information used to assign structural isomers. For example, cross-ring fragments arising from cleavage of the reducing terminal GlcNAc residue on Man 8 GlcNAc 2 isomers have unique collision cross-sections enabling isomers to be differentiated in mixtures. Specific fragment collision cross-sections enabled identification of glycans, the antennae of which terminated in the antigenic α-galactose residue, and ions defining the composition of the 6-antenna of several of the glycans were also found to have different cross-sections from isomeric ions produced in the same spectra. Potential mechanisms for the formation of the various ions are discussed and the estimated collisional cross-sections are tabulated. Graphical Abstract ᅟ.

A molecular heterojunction of zinc phthalocyanine and peanut-shaped fullerene polymer: A density functional study

NASA Astrophysics Data System (ADS)

Tanikawa, Kousei; Ohno, Kaoru; Noda, Yusuke; Ono, Shota; Kuwahara, Riichi; Takashima, Akito; Nakaya, Masato; Onoe, Jun

2017-10-01

We have performed first-principles density functional calculations of a molecular heterojunction of a zinc phthalocyanine (ZnPc) molecule and a peanut-shaped fullerene polymer (PSFP) made from several coalesced cross-linked C60 molecules. The PSFP has many isomers and all have both spatially localized (near ZnPc) and metallic conducting levels. Here we consider four typical isomers. From the resulting electronic structure, we discuss the applicability of these isomers to organic photovoltaics (OPV), electrodes, and light harvesting materials. If one of the isomers called T3, which has the largest energy gap, is used together with ZnPc for OPV, this system shows more than 20% energy conversion efficiency.

Stereochemistry and solvent role in protein folding: nuclear magnetic resonance and molecular dynamics studies of poly-L and alternating-L,D homopolypeptides in dimethyl sulfoxide.

PubMed

Srivastava, Kinshuk Raj; Kumar, Anil; Goyal, Bhupesh; Durani, Susheel

2011-05-26

The competing interactions folding and unfolding protein structure remain obscure. Using homopolypeptides, we ask if poly-L structure may have a role. We mutate the structure to alternating-L,D stereochemistry and substitute water as the fold-promoting solvent with methanol and dimethyl sulfoxide (DMSO) as the fold-denaturing solvents. Circular dichroism and molecular dynamics established previously that, while both isomers were folded in water, the poly-L isomer was unfolded and alternating-L,D isomer folded in methanol. Nuclear magnetic resonance and molecular dynamics establish now that both isomers are unfolded in DMSO. We calculated energetics of folding-unfolding equilibrium with water and methanol as solvents. We have now calculated interactions of unfolded polypeptide structures with DMSO as solvent. Methanol was found to unfold and water fold poly-L structure as a dielectric. DMSO has now been found to unfold both poly-L and alternating-L,D structures by strong solvation of peptides to disrupt their hydrogen bonds. Accordingly, we propose that while linked peptides fold protein structure with hydrogen bonds they unfold the structure electrostatically due to the stereochemical effect of the poly-L structure. Protein folding to ordering of peptide hydrogen bonds with water as canonical solvent may thus involve two specific and independent solvent effects-one, strong screening of electrostatics of poly-L linked peptides, and two, weak dipolar solvation of peptides. Correspondingly, protein denaturation may involve two independent solvent effects-one, weak dielectric to unfold poly-L structure electrostatically, and two, strong polarity to disrupt peptide hydrogen bonds by solvation of peptides.

Quantum chemical modeling of enzymatic reactions: the case of 4-oxalocrotonate tautomerase.

PubMed

Sevastik, Robin; Himo, Fahmi

2007-12-01

The reaction mechanism of 4-oxalocrotonate tautomerase (4-OT) is studied using the density functional theory method B3LYP. This enzyme catalyzes the isomerisation of unconjugated alpha-keto acids to their conjugated isomers. Two different quantum chemical models of the active site are devised and the potential energy curves for the reaction are computed. The calculations support the proposed reaction mechanism in which Pro-1 acts as a base to shuttle a proton from the C3 to the C5 position of the substrate. The first step (proton transfer from C3 to proline) is shown to be the rate-limiting step. The energy of the charge-separated intermediate (protonated proline-deprotonated substrate) is calculated to be quite low, in accordance with measured pKa values. The results of the two models are used to evaluate the methodology employed in modeling enzyme active sites using quantum chemical cluster models.

The Demonstration of the Feasibility of the Tuning and Stimulation of Nuclear Radiation.

DTIC Science & Technology

1988-10-31

line, or the center of a resonance pattern, is called the isomer shift. It is due to the electrostatic interaction of the nucleus with the electron ...magnetic moment due to the presence of unpaired electrons , the material is either paramagnetic or ferromagnetic. In paramagnetic materials these moments...capture and fission.4,5,8 A very fertile interdisciplinary area of nuclear quantum electronics 7 appeared to be developing, encouraged by the

Ab initio correlated study of the Al13H- anion: Isomers, their kinetic stability and vertical detachment energies

NASA Astrophysics Data System (ADS)

Moc, Jerzy

2012-01-01

We report correlated ab initio calculations for the Al13H- cluster anion isomers, their kinetic stability and vertical detachment energies (VDEs). Of the two most energetically favored anion structures involving H atom in terminal and threefold bridged sites of the icosahedral Al13-, the higher energy ‘threefold bridged' isomer is shown to be of low kinetic stability. Our results are consistent with the recent photoelectron spectroscopy (PE) study of Grubisic et al. who observed two distinct Al13H- isomers, one of them identified as ‘metastable'. The VDE energies computed at the CCSD(T)/aug-cc-pVTZ//MP2/aug-cc-pVDZ level for the ‘terminal' and ‘threefold bridged' Al13H- isomers of 3.21 and 2.32 eV are in good agreement with those determined in the PE study.

Quantum chemistry and excited states: First investigations on pyrene-like molecules

NASA Technical Reports Server (NTRS)

Parisel, Olivier; Ellinger, Y.

1994-01-01

Although the calculations are expected to be accurate within 10%, it follows then that there cannot be proposed unquestionable one-to-one attribution due to the density of the DIB's (Diffuse Interstellar Bands). Nevertheless, it has been shown that if one is interested in the experimental study of methyl-pyrene cations, for example, then, the most promising candidate is the 1-methyl isomer: this isomer has been investigated by d'Hendecourt and Leger (1993,1994) and their spectrum shows very striking features in very good agreement with both our calculations and a few DIB's. However, 1-methyl-pyrene cation is not the only product susceptible of being formed in this experiment, and further investigations are in progress to give a complete interpretations of the results. This preliminary report on pyrene-like molecules illustrates the role that theoretical calculations can ply in both the design and the interpretation of experiments.

On the competition between weak O-H···F and C-H···F hydrogen bonds, in cooperation with C-H···O contacts, in the difluoromethane – tert-butyl alcohol cluster

PubMed Central

Spada, Lorenzo; Tasinato, Nicola; Bosi, Giulio; Vazart, Fanny; Barone, Vincenzo; Puzzarini, Cristina

2017-01-01

The 1:1 complex of tert-butyl alcohol with difluoromethane has been characterized by means of a joint experimental-computational investigation. Its rotational spectrum has been recorded by using a pulsed-jet Fourier-Transform microwave spectrometer. The experimental work has been guided and supported by accurate quantum-chemical calculations. In particular, the computed potential energy landscape pointed out the formation of three stable isomers. However, the very low interconversion barriers explain why only one isomer, showing one O-H···F and two C-H···O weak hydrogen bonds, has been experimentally characterized. The effect of the H → tert-butyl- group substitution has been analyzed from the comparison to the difluoromethane-water adduct. PMID:28919646

Progress in Electromagnetic Alteration of Nuclear Decay Properties

NASA Astrophysics Data System (ADS)

Casperson, R. J.; Hughes, R. O.; Burke, J. T.; Scielzo, N. D.; Soufli, R.

2014-03-01

Significant alteration of nuclear decay properties would have important consequences, ranging from novel approaches to nuclear batteries and gamma-ray lasers, to improved viability for physics experiments with short-lived targets. Quantum systems that decay by photon emission must couple to the electromagnetic modes of the local environment, and by modifying these modes, one can manipulate the rate of spontaneous emission. The nuclear isomer 235mU is low-energy, long-lived, and is easily populated through 239Pu α-decay, which makes it an excellent benchmark for this effect. The decay rate of this isomer in a variety of environments is currently under investigation. Implications of this work will be discussed, and first results will be presented. This work performed under the auspices of the U.S. Department of Energy by Lawrence Livermore National Laboratory under Contract DE-AC52-07NA27344.

Progress in Electromagnetic Alteration of Nuclear Decay Properties

NASA Astrophysics Data System (ADS)

Casperson, R. J.; Burke, J. T.; Hughes, R. O.; Scielzo, N. D.; Soufli, R.

2013-10-01

Significant alteration of nuclear decay properties would have important consequences, ranging from novel approaches to nuclear batteries and gamma-ray lasers, to improved viability for physics experiments with short-lived targets. Quantum systems that decay by photon emission must couple to the electromagnetic modes of the local environment, and by modifying these modes, one can manipulate the rate of spontaneous emission. The nuclear isomer 235mU is low-energy, long-lived, and is easily populated through 239Pu α-decay, which makes it an excellent benchmark for this effect. The decay rate of this isomer in a variety of environments is currently under investigation. Implications of this work will be discussed, and first results will be presented. This work performed under the auspices of the U.S. Department of Energy by Lawrence Livermore National Laboratory under Contract DE-AC52-07NA27344.

Cyanomethanimine Isomers in Cold Interstellar Clouds: Insights from Electronic Structure and Kinetic Calculations

NASA Astrophysics Data System (ADS)

Vazart, Fanny; Latouche, Camille; Skouteris, Dimitrios; Balucani, Nadia; Barone, Vincenzo

2015-09-01

New insights into the formation of interstellar cyanomethanimine, a species of great relevance in prebiotic chemistry, are provided by electronic structure and kinetic calculations for the reaction CN + CH2 = NH. This reaction is a facile formation route of Z,E-C-cyanomethanimine, even under the extreme conditions of density and temperature typical of cold interstellar clouds. E-C-cyanomethanimine has been recently identified in Sgr B2(N) in the Green Bank Telescope (GBT) PRIMOS survey by P. Zaleski et al. and no efficient formation routes have been envisaged so far. The rate coefficient expression for the reaction channel leading to the observed isomer E-C-cyanomethanimine is 3.15 × 10-10 × (T/300)0.152 × e(-0.0948/T). According to the present study, the more stable Z-C-cyanomethanimine isomer is formed with a slightly larger yield (4.59 × 10-10 × (T/300)0.153 × e(-0.0871/T). As the detection of E-isomer is favored due to its larger dipole moment, the missing detection of the Z-isomer can be due to the sensitivity limit of the GBT PRIMOS survey and the detection of the Z-isomer should be attempted with more sensitive instrumentation. The CN + CH2 = NH reaction can also play a role in the chemistry of the upper atmosphere of Titan where the cyanomethanimine products can contribute to the buildup of the observed nitrogen-rich organic aerosols that cover the moon.

Isomer-specific determination of 4-nonylphenols using comprehensive two-dimensional gas chromatography/time-of-flight mass spectrometry.

PubMed

Eganhouse, Robert P; Pontolillo, James; Gaines, Richard B; Frysinger, Glenn S; Gabriel, Frédéric L P; Kohler, Hans-Peter E; Giger, Walter; Barber, Larry B

2009-12-15

Technical nonylphenol (tNP), used for industrial production of nonylphenol polyethoxylate surfactants, is a complex mixture of C(3-10)-phenols. The major components, 4-nonylphenols, are weak endocrine disruptors whose estrogenicities vary according to the structure of the branched nonyl group. Thus, accurate risk assessment requires isomer-specific determination of 4-NPs. Comprehensive two-dimensional gas chromatography/time-of-flight mass spectrometry (GC x GC/ToFMS) was used to characterize tNP samples obtained from seven commercial suppliers. Under optimal chromatographic conditions, 153-204 alkylphenol peaks, 59-66 of which were identified as 4-NPs, were detected. The 4-NPs comprised approximately 86-94% of tNP, with 2-NPs and decylphenols making up approximately 2-9% and approximately 2-5%, respectively. The tNP products were analyzed for eight synthetic 4-NP isomers, and results were compared with published data based on GC/MS analysis. Significant differences were found among the products and between two samples from a single supplier. The enhanced resolution of GC x GC coupled with fast mass spectral data acquisition by ToFMS facilitated identification of all major 4-NP isomers and a number of previously unrecognized components. Analysis of tNP altered by the bacterium, Sphingobium xenophagum Bayram, revealed several persistent 4-NPs whose structures and estrogenicities are presently unknown. The potential of this technology for isomer-specific determination of 4-NP isomers in environmental matrices is demonstrated using samples of wastewater-contaminated groundwater and municipal wastewater.

Isomer-specific determination of 4-nonylphenols using comprehensive two-dimensional gas chromatography/time-of-flight mass spectrometry

USGS Publications Warehouse

Eganhouse, R.P.; Pontolillo, J.; Gaines, R.B.; Frysinger, G.S.; Gabriel, F.L.P.; Kohler, H.-P.E.; Giger, W.; Barber, L.B.

2009-01-01

Technical nonylphenol (tNP), used for industrial production of nonylphenol polyethoxylate surfactants, is a complex mixture of C3-10-phenols. The major components, 4-nonylphenols, are weak endocrine disruptors whose estrogenicities vary according to the structure of the branched nonyl group. Thus, accurate risk assessment requires isomer-specific determination of 4-NPs. Comprehensive two-dimensional gas chromatography/time-of-flight mass spectrometry (GC x GC/ ToFMS) was used to characterize tNP samples obtained from seven commercial suppliers. Under optimal chromatographic conditions, 153-204 alkylphenol peaks, 59-66 of which were identified as 4-NPs, were detected. The 4-NPs comprised ???86-94% of tNP, with 2-NPs and decylphenols making up???2-9%and???2-5%, respectively. The tNP products were analyzed for eight synthetic 4-NP isomers, and results were compared with published data based on GC/ MS analysis. Significant differences were found among the products and between two samples from a single supplier. The enhanced resolution of GC x GC coupled with fast mass spectral data acquisition by ToFMS facilitated identification of all major 4-NP isomers and a number of previously unrecognized components. Analysis of tNP altered by the bacterium, Sphingobium xenophagum Bayram, revealed several persistent 4-NPs whose structures and estrogenicities are presently unknown. The potential of this technology for isomer-specific determination of 4-NP isomers in environmental matrices is demonstrated using samples of wastewatercontaminated groundwater and municipal wastewater. ?? 2009 American Chemical Society.

Oxidation of cinnamic acid derivatives: A pulse radiolysis and theoretical study

NASA Astrophysics Data System (ADS)

Yadav, Pooja; Mohan, Hari; Maity, Dilip Kumar; Suresh, Cherumuttathu H.; Rao, B. S. Madhav

2008-07-01

Second order rate constants in the range of ( k = 1.6-4.5) × 10 9 dm 3 mol -1 s -1 were obtained for the rad OH induced oxidation of nitro- and methoxycinnamic acid derivatives in neutral solutions using pulse radiolysis. The transient absorption spectra exhibited a broad peak around 360-410 nm in o-methoxy, o- and p-nitrocinnamates or two peaks around 310-330 and 370-410 nm in other isomers. Quantum chemical calculations revealed that addition of rad OH to olefinic moiety yielded considerably more stable structures than ring addition products and the para system among the latter is the most stable. Spin density analysis suggested that olefinic adducts retained the aromaticity in contrast to its loss in ring rad OH adducts. An excellent linear correlation between the relative stabilities of the rad OH adducts (after accounting for the aromatic stabilization in olefinic adducts) and the maximum Sd values is also obtained.

Mass spectrometry of analytical derivatives. 2. "Ortho" and "Para" effects in electron ionization mass spectra of derivatives of hydroxy, mercapto and amino benzoic acids.

PubMed

Todua, Nino G; Mikaia, Anzor I

2016-01-01

Derivatives requiring either anhydrous or aqueous reaction conditions were prepared for robust and reliable gas chromatography/mass spectrometry (GC/MS) characterization of hydroxyl, mercapto, and amino benzoic acids Methylation and trialkylsilytation are employed for blocking the acidic function. Alkyl, trimethylsilyl, acetyl, perfluoroacyl and alkoxycarbonyl derivatization groups are introduced to hydroxyl, mercapto and amino functions. The electron ionization induced fragmentation characteristics of corresponding derivatives are explained by comparing the MS 1 spectra of unlabeled compounds to their 2 H and 13 C labeled analogs, and analysis of collision-induced dissociation data from MS 2 spectra. Competing fragmentation alternatives are identified and specific decomposition processes are detailed that characterize (a) ortho isomers due to interaction or vicinal functional substituents and (b) para isomers prone to forming para quinoid type structures. Skeletal and hydrogen rearrangements typical for methyl benzoates and the blocking groups are considered when discussing diagnostically important ions. Characteristic ions produced as a result of rearrangements in ortho isomers are classified, and skeletal rearrangements required to produce para quinoid type ions specific for para isomers are noted. Key ions for structure elucidation and differentiation of isomers for derivatives of substituted benzoic acids by GC/MS are suggested.

Mass spectrometry of analytical derivatives. 2. “Ortho” and “Para” effects in electron ionization mass spectra of derivatives of hydroxy, mercapto and amino benzoic acids1

PubMed Central

Todua, Nino G.; Mikaia, Anzor I.

2016-01-01

Derivatives requiring either anhydrous or aqueous reaction conditions were prepared for robust and reliable gas chromatography/mass spectrometry (GC/MS) characterization of hydroxyl, mercapto, and amino benzoic acids Methylation and trialkylsilytation are employed for blocking the acidic function. Alkyl, trimethylsilyl, acetyl, perfluoroacyl and alkoxycarbonyl derivatization groups are introduced to hydroxyl, mercapto and amino functions. The electron ionization induced fragmentation characteristics of corresponding derivatives are explained by comparing the MS1 spectra of unlabeled compounds to their 2H and 13C labeled analogs, and analysis of collision-induced dissociation data from MS2 spectra. Competing fragmentation alternatives are identified and specific decomposition processes are detailed that characterize (a) ortho isomers due to interaction or vicinal functional substituents and (b) para isomers prone to forming para quinoid type structures. Skeletal and hydrogen rearrangements typical for methyl benzoates and the blocking groups are considered when discussing diagnostically important ions. Characteristic ions produced as a result of rearrangements in ortho isomers are classified, and skeletal rearrangements required to produce para quinoid type ions specific for para isomers are noted. Key ions for structure elucidation and differentiation of isomers for derivatives of substituted benzoic acids by GC/MS are suggested. PMID:27891187

Physical chemistry and membrane properties of two phosphatidylinositol bisphosphate isomers.

PubMed

Slochower, David R; Wang, Yu-Hsiu; Radhakrishnan, Ravi; Janmey, Paul A

2015-05-21

The most highly charged phospholipids, polyphosphoinositides, are often involved in signaling pathways that originate at cell-cell and cell-matrix contacts, and different isomers of polyphosphoinositides have distinct biological functions that cannot be explained by separate highly specific protein ligand binding sites [Lemmon, Nat. Rev. Mol. Cell Biol., 2008, 9, 99-111]. PtdIns(3,5)P2 is a low abundance phosphoinositide localized to cytoplasmic-facing membrane surfaces, with relatively few known ligands, yet PtdIns(3,5)P2 plays a key role in controlling membrane trafficking events and cellular stress responses that cannot be duplicated by other phosphoinositides [Dove et al., Nature, 1997, 390, 187-192; Michell, FEBS J., 2013, 280, 6281-6294]. Here we show that PtdIns(3,5)P2 is structurally distinct from PtdIns(4,5)P2 and other more common phospholipids, with unique physical chemistry. Using multiscale molecular dynamics techniques on the quantum level, single molecule, and in bilayer settings, we found that the negative charge of PtdIns(3,5)P2 is spread over a larger area, compared to PtdIns(4,5)P2, leading to a decreased ability to bind divalent ions. Additionally, our results match well with experimental data characterizing the cluster forming potential of these isomers in the presence of Ca(2+) [Wang et al., J. Am. Chem. Soc., 2012, 134, 3387-3395; van den Bogaart et al., Nature, 2011, 479, 552-555]. Our results demonstrate that the different cellular roles of PtdIns(4,5)P2 and PtdIns(3,5)P2in vivo are not simply determined by their localization by enzymes that produce or degrade them, but also by their molecular size, ability to chelate ions, and the partial dehydration of those ions, which might affect the ability of PtdIns(3,5)P2 and PtdIns(4,5)P2 to form phosphoinositide-rich clusters in vitro and in vivo.

Conformational Preferences of β– and γ–Aminated Proline Analogues

PubMed Central

Flores-Ortega, Alejandra; Casanovas, Jordi; Nussinov, Ruth; Alemán, Carlos

2010-01-01

Quantum mechanical calculations have been used to investigate how the incorporation of an amino group to the Cβ- or Cγ-positions of the pyrrolidine ring affects the intrinsic conformational properties of the proline. Specifically, a conformational study of the N-acetyl-N′-methylamide derivatives of four isomers of aminoproline, which differ not only in the β- or γ-position of the substituent but also in its cis or trans relative disposition, has been performed. In order to further understand the role of the intramolecular hydrogen bonds between the backbone carbonyl groups and the amino side group, a conformational study was also performed on the corresponding four analogues of dimethylaminoproline. In addition, the effects of solvation on aminoproline and dimethylaminoproline dipeptides have been evaluated using a Self Consistent Reaction Field model, and considering four different solvents (carbon tetrachloride, chloroform, methanol and water). Results indicate that the incorporation of the amino substituent into the pyrrolidine ring affects the conformational properties, with backbone⋯side chain intramolecular hydrogen bonds detected when it is incorporated in a cis relative disposition. In general, the incorporation of the amino side group tends to stabilize those structures where the peptide bond involving the pyrrolidine nitrogen is arranged in cis. The aminoproline isomer with the substituent attached to the Cγ-position with a cis relative disposition is the most stable in the gas-phase and in chloroform, methanol and water solutions. Replacement of the amino side group by the dimethylamino substituent produces significant changes in the potential energy surfaces of the four investigated dimethylaminoproline-containing dipeptides. Thus, these changes affect not only the number of minima, which increases considerably, but also the backbone and pseudorotational preferences. In spite of these effects, comparison of the conformational preferences, i.e. the more favored conformers, calculated for different isomers of aminoproline and dimethylaminoproline dipeptides showed a high degree of consistency for the two families of compounds. PMID:18842022

Differentiating Positional Isomers of Nucleoside Modifications by Higher-Energy Collisional Dissociation Mass Spectrometry (HCD MS)

NASA Astrophysics Data System (ADS)

Jora, Manasses; Burns, Andrew P.; Ross, Robert L.; Lobue, Peter A.; Zhao, Ruoxia; Palumbo, Cody M.; Beal, Peter A.; Addepalli, Balasubrahmanyam; Limbach, Patrick A.

2018-06-01

The analytical identification of positional isomers (e.g., 3-, N 4-, 5-methylcytidine) within the > 160 different post-transcriptional modifications found in RNA can be challenging. Conventional liquid chromatography coupled with tandem mass spectrometry (LC-MS/MS) approaches rely on chromatographic separation for accurate identification because the collision-induced dissociation (CID) mass spectra of these isomers nearly exclusively yield identical nucleobase ions (BH2 +) from the same molecular ion (MH+). Here, we have explored higher-energy collisional dissociation (HCD) as an alternative fragmentation technique to generate more informative product ions that can be used to differentiate positional isomers. LC-MS/MS of modified nucleosides characterized using HCD led to the creation of structure- and HCD energy-specific fragmentation patterns that generated unique fingerprints, which can be used to identify individual positional isomers even when they cannot be separated chromatographically. While particularly useful for identifying positional isomers, the fingerprinting capabilities enabled by HCD also offer the potential to generate HPLC-independent spectral libraries for the rapid analysis of modified ribonucleosides. [Figure not available: see fulltext.

Two New Isomers of Palmityl-4-hydroxycinnamate from Flowers of Taraxacum Species.

PubMed

Dudáš, Matej; Vilková, Mária; Béres, Tibor; Repcák, Miroslav; Mártonfi, Pavol

2016-06-01

Two isomers, (Z)- and (E)-palmityl 4-hydroxycinnamate [hexadecyl(2Z)-3-(4-hydroxyphenyl)prop-2-enoate and hexadecyl(2E)-3-(4-hydroxyphenyl)prop-2-enoate] were isolated for the first time from ligulate flowers of Taraxacum linearisquameum Soest (sect. Taraxacum). The highest amount of these compounds was detected in pollen grains; 0.26 mg/100 mg DW of the (E)-isomer and 0.096 mg/100 mg DW of the (Z)-isomer. The structures of these compounds were elucidated by a combination of HPLC-ESI-Qtof-MS and 1D and 2D NMR spectroscopy. Their presence was confirmed in other species of Taraxacum, but they were not found in the male - sterile triploid agamospermous taxon T. parnassicum.

Density functional study on structure and stability of bimetallic AuNZn (N<=6) clusters and their cations

NASA Astrophysics Data System (ADS)

Tanaka, Hiromasa; Neukermans, Sven; Janssens, Ewald; Silverans, Roger E.; Lievens, Peter

2003-10-01

A systematic study on the structure and stability of zinc doped gold clusters has been performed by density functional theory calculations. All the lowest-energy isomers found have a planar structure and resemble pure gold clusters in shape. Stable isomers tend to equally delocalize valence s electrons of the constituent atoms over the entire structure and maximize the number of Au-Zn bonds in the structure. This is because the Au-Zn bond is stronger than the Au-Au bond and gives an extra σ-bonding interaction by the overlap between vacant Zn 4p and valence Au 6s(5d) orbitals. No three-dimensional isomers were found for Au5Zn+ and Au4Zn clusters containing six delocalized valence electrons. This result reflects that these clusters have a magic number of delocalized electrons for two-dimensional systems. Calculated vertical ionization energies and dissociation energies as a function of the cluster size show odd-even behavior, in agreement with recent mass spectrometric observations [Tanaka et al., J. Am. Chem. Soc. 125, 2862 (2003)].

Structural Mimics of the [Fe]-Hydrogenase: A Complete Set for Group VIII Metals.

PubMed

Barik, Chandan Kr; Ganguly, Rakesh; Li, Yongxin; Leong, Weng Kee

2018-06-18

A set of structural mimics of the [Fe]-hydrogenase active site comprising all the group VIII metals, viz., [M(2-NHC(O)C 5 H 4 N)(CO) 2 (2-S-C 5 H 4 N)], has been synthesized. They exist as a mixture of isomers in solution, and the relative stability of the isomers depends on the nature of the metal and the substituent at the 6-position of the pyridine ligand.

A theoretical study on the geometry and spectroscopic properties of ground-state and local minima isomers of (CuS)n=2-6 clusters

NASA Astrophysics Data System (ADS)

Luque-Ceballos, Jonathan C.; Posada-Borbón, Alvaro; Herrera-Urbina, Ronaldo; Aceves, R.; Juárez-Sánchez, J. Octavio; Posada-Amarillas, Alvaro

2018-03-01

Spectroscopic properties of gas-phase copper sulfide clusters (CuS)n (n = 2-6) are calculated using Density Functional Theory (DFT) and time-dependent (TD) DFT approaches. The energy landscape of the potential energy surface is explored through a basin-hopping DFT methodology. Ground-state and low-lying isomer structures are obtained. The global search was performed at the B3PW91/SDD level of theory. Normal modes are calculated to validate the existence of optimal cluster structures. Energetic properties are obtained for the ground-state and isomer clusters and their relative energies are evaluated for probing isomerization. This is a few tenths of an eV, except for (CuS)2 cluster, which presents energy differences of ∼1 eV. Notable differences in the infrared spectra exist between the ground-state and first isomer structures, even for the (CuS)5 cluster, which has in both configurations a core copper pyramid. TDDFT provides the simulated absorption spectrum, presenting a theoretical description of optical absorption bands in terms of electronic excitations in the UV and visible regions. Results exhibit a significant dependence of the calculated UV/vis spectra on clusters size and shape regarding the ground state structures. Optical absorption is strong in the UV region, and weak or forbidden in the visible region of the spectrum.

Synthesis, spectroscopic and TD-DFT quantum mechanical study of azo-azomethine dyes. A laser induced trans-cis-trans photoisomerization cycle

NASA Astrophysics Data System (ADS)

Georgiev, Anton; Kostadinov, Anton; Ivanov, Deyan; Dimov, Deyan; Stoyanov, Simeon; Nedelchev, Lian; Nazarova, Dimana; Yancheva, Denitsa

2018-03-01

This paper describes the synthesis, spectroscopic characterization and quantum mechanical calculations of three azo-azomethine dyes. The dyes were synthesized via condensation reaction between 4-(dimethylamino)benzaldehyde and three different 4-aminobenzene azo dyes. Quantum chemical calculations on the optimized molecular geometry and electron densities of the trans (E) and cis (Z) isomers and their vibrational frequencies have been computed by using DFT/B3LYP density-functional theory with 6-311 ++G(d,p) basis set in vacuo. The thermodynamic parameters such as total electronic energy E (RB3LYP), enthalpy H298 (sum of electronic and thermal enthalpies), free Gibbs energy G298 (sum of electronic and thermal free Gibbs energies) and dipole moment μ were computed for trans (E) and cis (Z) isomers in order to estimate the ΔEtrans → cis, Δμtrans → cis,ΔHtrans → cis, ΔGtrans → cis and ΔStrans → cis values. After molecular geometry optimization the electronic spectra have been obtained by TD-DFT calculations at same basis set and correlated with the spectra of vapour deposited nanosized films of the dyes. The NBO analysis was performed in order to understand the intramolecular charge transfer and energy of resonance stabilization. Solvatochromism was investigated by UV-VIS spectroscopy in five different organic solvents with increasing polarity. The dynamic photoisomerization experiments have been performed in DMF by pump lasers λ = 355 nm (mostly E → Z) and λ = 491 nm (mostly Z → E) in spectral region 300 nm - 800 nm at equal concentrations and times of illumination in order to investigate the photodynamical trans-cis-trans properties of the sbnd CHdbnd Nsbnd and sbnd Ndbnd Nsbnd chromophore groups of the dyes.

Nuclear spectroscopy with Geant4: Proton and neutron emission & radioactivity

NASA Astrophysics Data System (ADS)

Sarmiento, L. G.; Rudolph, D.

2016-07-01

With the aid of a novel combination of existing equipment - JYFLTRAP and the TASISpec decay station - it is possible to perform very clean quantum-state selective, high-resolution particle-γ decay spectroscopy. We intend to study the determination of the branching ratio of the ℓ = 9 proton emission from the Iπ = 19/2-, 3174-keV isomer in the N = Z - 1 nucleus 53Co. The study aims to initiate a series of similar experiments along the proton dripline, thereby providing unique insights into "open quantum systems". The technique has been pioneered in case studies using SHIPTRAP and TASISpec at GSI. Newly available radioactive decay modes in Geant4 simulations are going to corroborate the anticipated experimental results.

Rapid In Situ Profiling of Lipid C═C Location Isomers in Tissue Using Ambient Mass Spectrometry with Photochemical Reactions.

PubMed

Tang, Fei; Guo, Chengan; Ma, Xiaoxiao; Zhang, Jian; Su, Yuan; Tian, Ran; Shi, Riyi; Xia, Yu; Wang, Xiaohao; Ouyang, Zheng

2018-05-01

Rapid and in situ profiling of lipids using ambient mass spectrometry (AMS) techniques has great potential for clinical diagnosis, biological studies, and biomarker discovery. In this study, the online photochemical reaction involving carbon-carbon double bonds was coupled with a surface sampling technique to develop a direct tissue-analysis method with specificity to lipid C═C isomers. This method enabled the in situ analysis of lipids from the surface of various tissues or tissue sections, which allowed the structural characterization of lipid isomers within 2 min. Under optimized reaction conditions, we have established a method for the relative quantitation of lipid C═C location isomers by comparing the abundances of the diagnostic ions arising from each isomer, which has been proven effective through the established linear relationship ( R 2 = 0.999) between molar ratio and diagnostic ion ratio of the FA 18:1 C═C location isomers. This method was then used for the rapid profiling of unsaturated lipid C═C isomers in the sections of rat brain, lung, liver, spleen, and kidney, as well as in normal and diseased rat tissues. Quantitative information on FA 18:1 and PC 16:0-18:1 C═C isomers was obtained, and significant differences were observed between different samples. To the best of our knowledge, this is the first study to report the direct analysis of lipid C═C isomers in tissues using AMS. Our results demonstrated that this method can serve as a rapid analytical approach for the profiling of unsaturated lipid C═C isomers in biological tissues and should contribute to functional lipidomics and clinical diagnosis.

Photosensitization by iodinated DNA minor groove binding ligands: Evaluation of DNA double-strand break induction and repair.

PubMed

Briggs, Benjamin; Ververis, Katherine; Rodd, Annabelle L; Foong, Laura J L; Silva, Fernando M Da; Karagiannis, Tom C

2011-05-03

Iodinated DNA minor groove binding bibenzimidazoles represent a unique class of UVA photosensitizer and their extreme photopotency has been previously characterized. Earlier studies have included a comparison of three isomers, referred to as ortho-, meta- and para-iodoHoechst, which differ only in the location of the iodine substituent in the phenyl ring of the bibenzimidazole. DNA breakage and clonogenic survival studies in human erythroleukemic K562 cells have highlighted the higher photo-efficiency of the ortho-isomer (subsequently designated UV(A)Sens) compared to the meta- and para-isomers. In this study, the aim was to compare the induction and repair of DNA double-strand breaks induced by the three isomers in K562 cells. Further, we examined the effects of the prototypical broad-spectrum histone deacetylase inhibitor, Trichostatin A, on ortho-iodoHoechst/UVA-induced double-strand breaks in K562 cells. Using γH2AX as a molecular marker of the DNA lesions, our findings indicate a disparity in the induction and particularly, in the repair kinetics of double-strand breaks for the three isomers. The accumulation of γH2AX foci induced by the meta- and para-isomers returned to background levels within 24 and 48 h, respectively; the number of γH2AX foci induced by ortho-iodoHoechst remained elevated even after incubation for 96 h post-irradiation. These findings provide further evidence that the extreme photopotency of ortho-iodoHoechst is due to not only to the high quantum yield of dehalogenation, but also to the severity of the DNA lesions which are not readily repaired. Finally, our findings which indicate that Trichostatin A has a remarkable potentiating effect on ortho-iodoHoechst/UVA-induced DNA lesions are encouraging, particularly in the context of cutaneous T-cell lymphoma, for which a histone deacetylase inhibitor is already approved for therapy. This finding prompts further evaluation of the potential of combination therapies. Copyright © 2011 Elsevier B.V. All rights reserved.

Isomers and shell evolution in neutron-rich nuclei below the doubly magic nucleus 132Sn

NASA Astrophysics Data System (ADS)

Watanabe, Hiroshi

2018-05-01

The level structures of the very neutron-rich nuclei 128Pd82 and 126Pd80 have been investigated for the first time. A new isomer with a half-life of 5.8(8) μs in 128Pd is proposed to have a spin and parity of 8+ and is associated with a maximally aligned configuration arising from the g9/2Pd proton subshell with seniority υ = 2. The level sequence below the 8+ isomer is similar to that in the N = 82 isotone 130Cd, but the electric quadrupole transition that depopulates the 8+ isomer is more hindered in 128Pd than in 130Cd, as expected in the seniority scheme for a semi-magic, spherical nucleus. For 126Pd, three new isomers with Jπ = (5-), (7-), and (10+) have been identified with half-lives of 0.33(4) μs, 0.44(3) μs, and 23.0(8) ms, respectively. The smaller energy difference between the 10+ and 7- isomers in 126Pd than in the heavier N = 80 isotones can be interpreted as being ascribed to the monopole shift of the h11/2 neutron orbit. The nature of the N = 82 shell closure scrutinized with these characteristic isomers is discussed.

Nucleoside adducts from the in vitro reaction of benzo[a]pyrene-7,8-dihydrodiol 9,10-oxide or benzo[a]pyrene 4,5-oxide with nucleic acids.

PubMed

Jennette, K W; Jeffrey, A M; Blobstein, S H; Beland, F A; Harvey, R G; Weinstein, I B

1977-03-08

The covalent binding of benzo[a]pyrene 4,5-oxide and benzo[a]pyrene-7,8-dihydrodiol 9,10-oxide isomer I and isomer II to nucleic acids in aqueous acetone solution has been investigated. Benzo[a]pyrene 4,5-oxide reacted preferentially with guanosine residues. On the other hand, benzo[a]pyrene-7,8-dihydrodiol 9,10-oxide isomer I and II reacted extensively with guanosine, adenosine, and cytidine residues. Time course studies showed that the reactivity of isomer I or isomer II with homopolyribonucleotides followed the order poly(G) greater than poly(A) greater than poly(C). Alkaline or enzymatic hydrolysis of the modified nucleic acids and subsequent chromatography on Sephadex LH-20 columns yielded benzo[a]pyrene-nucleotide adducts. These were enzymatically converted to the corresponding nucleosides which were resolved into several distinct components by high-pressure liquid chromatography. Evidence was obtained for the presence of multiple nucleoside adducts of guanosine, adenosine, cytidine, deoxyguanosine, deoxyadenosine, and deoxycytidine. The HPLC profiles of adducts formed with isomer I were different from the corresponding profiles of adducts formed with isomer II. Structural aspects of these nucleoside adducts are discussed.

Isomer Shift and Magnetic Moment of the Long-Lived 1/2^{+} Isomer in _{30}^{79}Zn_{49}: Signature of Shape Coexistence near ^{78}Ni.

PubMed

Yang, X F; Wraith, C; Xie, L; Babcock, C; Billowes, J; Bissell, M L; Blaum, K; Cheal, B; Flanagan, K T; Garcia Ruiz, R F; Gins, W; Gorges, C; Grob, L K; Heylen, H; Kaufmann, S; Kowalska, M; Kraemer, J; Malbrunot-Ettenauer, S; Neugart, R; Neyens, G; Nörtershäuser, W; Papuga, J; Sánchez, R; Yordanov, D T

2016-05-06

Collinear laser spectroscopy is performed on the _{30}^{79}Zn_{49} isotope at ISOLDE-CERN. The existence of a long-lived isomer with a few hundred milliseconds half-life is confirmed, and the nuclear spins and moments of the ground and isomeric states in ^{79}Zn as well as the isomer shift are measured. From the observed hyperfine structures, spins I=9/2 and I=1/2 are firmly assigned to the ground and isomeric states. The magnetic moment μ (^{79}Zn)=-1.1866(10)μ_{N}, confirms the spin-parity 9/2^{+} with a νg_{9/2}^{-1} shell-model configuration, in excellent agreement with the prediction from large scale shell-model theories. The magnetic moment μ (^{79m}Zn)=-1.0180(12)μ_{N} supports a positive parity for the isomer, with a wave function dominated by a 2h-1p neutron excitation across the N=50 shell gap. The large isomer shift reveals an increase of the intruder isomer mean square charge radius with respect to that of the ground state, δ⟨r_{c}^{2}⟩^{79,79m}=+0.204(6)  fm^{2}, providing first evidence of shape coexistence.

Influence of N-Oxide Introduction on the Stability of Nitrogen-Rich Heteroaromatic Rings: A Quantum Chemical Study.

PubMed

Yuan, Jia; Long, Xinping; Zhang, Chaoyang

2016-12-01

N-Oxidization is an important strategy for enhancing the density and energy of energetic materials. Nevertheless, the influence of N + -O - introduction on molecular stability remains relatively unknown. Thus, the present work comprehensively studied 102 basic N-rich ring structures, including azoles, furazans, and azines, as well as their N-oxides by quantum chemical calculations. The introduction of N + -O - weakens molecular stability in most cases because the process elongates chemical bonds, decreases ring aromaticity, narrows the gaps between the highest occupied and lowest unoccupied molecular orbitals, and increases the photochemical reactivity. Besides, the easy H transfer to the neighboring O atom, which forms a N-OH isomer in azoles, renders the stabilization by N-oxide introduction ineffective. However, N-oxide introduction can enhance the molecular stability of 1,2,3,4-tetrazine-1,3-dioxide and tetrazino-tetrazine 1,3,6,8-tetraoxide by promoting σ-π separation and relieving lone-pair repulsion. Moreover, the alternate arrangement of positive and negative charges is another factor stabilizing the 1,2,3,4-tetrazine ring by 1,3-dioxidation. Finally, we assess the accessibility of N-oxidized azoles and azines by regarding N 2 O and H 2 O 2 as oxidizers. We find that all the oxidations were exothermic, thermodynamically spontaneous, and kinetically feasible. After an overall evaluation, we propose 19 N-oxides as basic structures for high-energy materials with considerable stability.

Quantum chemical calculations and experimental investigations on 2-aminobenzoic acid-cyclodiphosph(V)azane derivative and its homo-binuclear Cu(II) complex

NASA Astrophysics Data System (ADS)

El-Gogary, Tarek M.; Alaghaz, Abdel-Nasser M. A.; Ammar, Reda A. A.

2012-03-01

A novel 2-aminobenzoic acid-cyclodiphosph(V)azane ligand H4L and its homo-binuclear Cu(II) complex of the type [Cu2L(H2O)2].2.5 H2O in which L is 1,3-di(-o-pyridyl)-2,4-(dioxo)-2',4'-bis-(2-iminobenzoic acid) cyclodiphosph(V)azane, were synthesized and characterized by different physical techniques. Infrared spectra of the complex indicate deprotonation and coordination of the imine NH and carboxyl COOH groups. It also confirms that nitrogen atom of the pyridine ring contribute to the complexation. Electronic spectra and magnetic susceptibility measurements reveal square-planar geometry for the Cu(II) complex. The elemental analyses and thermogravimetric results have justified the [Cu2L(H2O)2]·2.5H2O composition of the complex. Quantum chemical calculations were utilized to explore the electronic structure and stability of the H4L as well as the binuclear Cu(II) complex. Computational studies have been carried out at the DFT-B3LYP/6-31G(d) level of theory on the structural and spectroscopic properties of H4L and its binuclear Cu(II) complex. Different tautomers and geometrical isomers of the ligand were optimized at the ab initio DFT level. Simulated IR frequencies were scaled and compared with that experimentally measured. TD-DFT method was used to compute the UV-VIS spectra which show good agreement with measured electronic spectra.

Separation of cis and trans geometric isomers by Coulomb explosion imaging

NASA Astrophysics Data System (ADS)

Ablikim, Utuq; Kaderiya, B.; Kumarapan, V.; Rudenko, A.; Rolles, D.; Bomme, C.; Savelyev, E.; Xiong, H.; Berrah, N.; Kilcoyne, D.

2016-05-01

Isomers, i.e. molecules with the same chemical formula but different chemical structure, play an important role in many biological processes. Recently, it was shown that it is possible to identify different isomers of a chiral molecule by Coulomb explosion imaging. Here, we show that by imaging the Coulomb explosion of C2 H2 Br2 molecules after inner-shell photoionization, we are able to separate a mixture of cis and trans structures using the momentum correlation between ionic fragments measured in coincidence. Furthermore, we used this capability to investigate the isomer-selective photoionization and fragmentation dynamics of C2 H2 Br2 after Br (3d) ionization. Coulomb explosion simulation results for momentum correlation as well as kinetic energies match closely the experimental results. This project is supported by the DOE, Office of Science, BES, Division of Chemical, Geological and Biological Sciences under Award Number DE-FG02-86ER13491 (U.A., B.K., V.K., A.R., D.R.) and Award Number DE-SC0012376 (H.X., N.B.).

Isomer Information from Ion Mobility Separation of High-Mannose Glycan Fragments

NASA Astrophysics Data System (ADS)

Harvey, David J.; Seabright, Gemma E.; Vasiljevic, Snezana; Crispin, Max; Struwe, Weston B.

2018-05-01

Extracted arrival time distributions of negative ion CID-derived fragments produced prior to traveling-wave ion mobility separation were evaluated for their ability to provide structural information on N-linked glycans. Fragmentation of high-mannose glycans released from several glycoproteins, including those from viral sources, provided over 50 fragments, many of which gave unique collisional cross-sections and provided additional information used to assign structural isomers. For example, cross-ring fragments arising from cleavage of the reducing terminal GlcNAc residue on Man8GlcNAc2 isomers have unique collision cross-sections enabling isomers to be differentiated in mixtures. Specific fragment collision cross-sections enabled identification of glycans, the antennae of which terminated in the antigenic α-galactose residue, and ions defining the composition of the 6-antenna of several of the glycans were also found to have different cross-sections from isomeric ions produced in the same spectra. Potential mechanisms for the formation of the various ions are discussed and the estimated collisional cross-sections are tabulated. [Figure not available: see fulltext.

Accurate thermochemistry and spectroscopy of the oxygen-protonated sulfur dioxide isomers.

PubMed

Puzzarini, Cristina

2011-12-28

Despite the promising relevance of protonated sulfur dioxide in astrophysical and atmospheric fields, its thermochemical and spectroscopic characterization is very limited. High-level quantum-chemical calculations have shown that the most stable isomer is the cis oxygen-protonated sulfur dioxide, HOSO(+), while the trans form is about 2 kcal mol(-1) less stable; even less stable (by about 42 kcal mol(-1)) is the S-protonated isomer [V. Lattanzi et al., J. Chem. Phys., 2010, 133, 194305]. The enthalpy of formation for the cis- and trans-HOSO(+) is presented, based on the well tested HEAT protocol [A. Tajti et al., J. Chem. Phys., 2004, 121, 11599]. Systematically extrapolated ab initio energies, accounting for electron correlation through coupled cluster theory, including up to single, double, triple and quadruple excitations, have been corrected for core-electron correlation, anharmonic zero-point vibrational energy, diagonal Born-Oppenheimer and scalar relativistic effects. As a byproduct, proton affinity of sulfur dioxide and atomization energies have also been obtained at the same levels of theory. Vibrational and rotational spectroscopic properties have been investigated by means of composite schemes that allow us to account for truncation of basis set as well as core correlation. Where available, for both thermochemistry and spectroscopy, very good agreement with experimental data has been observed.

The origin of exo-selectivity in methyl cyanoformate addition onto the C=C bond of norbornene in Pd-catalyzed cyanoesterification.

PubMed

Okuda, Yasuhiro; Szilagyi, Robert K; Mori, Seiji; Nishihara, Yasushi

2014-07-07

A computational investigation has been carried out to elucidate the origin of the exclusive exo-selectivity in the Pd-catalyzed cyanoesterification of strained cyclic olefins, norbornene and norbornadiene. A hybrid density functional was selected for the level of theory with a triple-ζ quality basis set, which was proposed in an earlier study to provide an experimentally sound ground state electronic structure description for palladium(ii) and palladium(iv) complexes from multi-edge X-ray absorption spectroscopic measurements. Given that the product of oxidative addition can be isolated, we focused on the olefin coordination as the earliest possible origin of exo-selectivity. The calculated geometric structure for the trans-Pd(CN)(COOR)(PPh3)2 complex at the BHandHLYP/def2TZVP/PCM(toluene) level is in an excellent agreement with its experimental structure from crystallographic measurements. Upon dissociation of one of its phosphane ligands, the coordinatively unsaturated trans-isomer is only 17 kJ mol(-1) away from the isomerization transition state, leading to the 14-electron cis-isomers that are 17 to 37 kJ mol(-1) lower in energy than the trans-isomers. Regardless of the initial complex for olefin coordination, the exo-isomer for the norbornene complex is at least 8 kJ mol(-1) lower than the corresponding endo-isomer. The origin of this considerable difference in Gibbs free energy can be attributed to the remarkably different steric and agostic hydrogen interactions between the methylene and the ethylene bridges of the norbornene and the adjacent cis-ligands at the Pd(II) center.

Two-photon absorption spectra of carotenoids compounds

NASA Astrophysics Data System (ADS)

Vivas, Marcelo Gonçalves; Silva, Daniel Luiz; Boni, Leonardo de; Zalesny, Robert; Bartkowiak, Wojciech; Mendonca, Cleber Renato

2011-05-01

Carotenoids are biosynthetic organic pigments that constitute an important class of one-dimensional π-conjugated organic molecules with enormous potential for application in biophotonic devices. In this context, we studied the degenerate two-photon absorption (2PA) cross-section spectra of two carotenoid compounds (β-carotene and β-apo-8'-carotenal) employing the conventional and white-light-continuum Z-scan techniques and quantum chemistry calculations. Because carotenoids coexist at room temperature as a mixture of isomers, the 2PA spectra reported here are due to samples containing a distribution of isomers, presenting distinct conjugation length and conformation. We show that these compounds present a defined structure on the 2PA spectra, that peaks at 650 nm with an absorption cross-section of approximately 5000 GM, for both compounds. In addition, we observed a 2PA band at 990 nm for β-apo-8'-carotenal, which was attributed to a overlapping of 11Bu+-like and 21Ag--like states, which are strongly one- and two-photon allowed, respectively. Spectroscopic parameters of the electronic transitions to singlet-excited states, which are directly related to photophysical properties of these compounds, were obtained by fitting the 2PA spectra using the sum-over-states approach. The analysis and interpretations of the 2PA spectra of the investigated carotenoids were supported by theoretical predictions of one- and two-photon transitions carried out using the response functions formalism within the density functional theory framework, using the long-range corrected CAM-B3LYP functional.

Towards solar energy storage in the photochromic dihydroazulene-vinylheptafulvene system.

PubMed

Cacciarini, Martina; Skov, Anders B; Jevric, Martyn; Hansen, Anne S; Elm, Jonas; Kjaergaard, Henrik G; Mikkelsen, Kurt V; Brøndsted Nielsen, Mogens

2015-05-11

One key challenge in the field of exploitation of solar energy is to store the energy and make it available on demand. One possibility is to use photochromic molecules that undergo light-induced isomerization to metastable isomers. Here we present efforts to develop solar thermal energy storage systems based on the dihydroazulene (DHA)/vinylheptafulvene (VHF) photo/thermoswitch. New DHA derivatives with one electron-withdrawing cyano group at position 1 and one or two phenyl substituents in the five-membered ring were prepared by using different synthetic routes. In particular, a diastereoselective reductive removal of one cyano group from DHAs incorporating two cyano groups at position 1 turned out to be most effective. Quantum chemical calculations reveal that the structural modifications provide two benefits relative to DHAs with two cyano groups at position 1: 1) The DHA-VHF energy difference is increased (i.e., higher energy capacity of metastable VHF isomer); 2) the Gibbs free energy of activation is increased for the energy-releasing VHF to DHA back-reaction. In fact, experimentally, these new derivatives were so reluctant to undergo the back-reaction at room temperature that they practically behaved as DHA to VHF one-way switches. Although lifetimes of years are at first attractive, which offers the ultimate control of energy release, for a real device it must of course be possible to trigger the back-reaction, which calls for further iterations in the future. © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

New Insights into Structure and Luminescence of Eu III and Sm III Complexes of the 3,4,3-LI(1,2-HOPO) Ligand

DOE PAGES

Daumann, Lena J.; Tatum, David S.; Snyder, Benjamin E. R.; ...

2015-01-21

We report the preparation and new insight into photophysical properties of luminescent hydroxypyridonate complexes [M IIIL] - (M = Eu or Sm) of the versatile 3,4,3-LI(1,2-HOPO) ligand (L). We report the crystal structure of this ligand with EuIII as well as insights into the coordination behavior and geometry in solution by using magnetic circular dichroism. In addition TD-DFT calculations were used to examine the excited states of the two different chromophores present in the 3,4,3-LI(1,2-HOPO) ligand. We find that the Eu III and Sm III complexes of this ligand undergo a transformation after in situ preparation to yield complexes withmore » higher quantum yield (QY) over time. We propose that the lower QY in the in situ complexes is not only due to water quenching but could also be due to a lower degree of f-orbital overlap (in a kinetic isomer) as indicated by magnetic circular dichroism measurements.« less

Theoretical Study of the Metal-Controlled Dehydrogenation Mechanism of MN2H3BH3 (M = Li, Na, K): A New Family of Hydrogen Storage Material.

PubMed

Li, Tong; Zhang, Jian-Guo

2018-02-08

Metal hydrazineboranes (MHBs), as a kind of new hydrogen storage materials, show excellent hydrogen storage performance and dehydrogenation properties. Herein, we designed multiple dehydrogenation pathways to compare the metal-controlled effect. Quantum chemistry theory is used to calculate the crystal structure for determining the molecular structure. With an increase of the metal radius, the energy difference of the isomers also increases. The dehydrogenation pathways of lithium hydrazineborane (path A) and sodium hydrazineborane (path B) appear totally similar to each other in the dehydrogenation process despite the energy barrier, as well as the comparison paths A' (for LiHB) and B' (for NaHB). In contrast with LiHB and NaHB, the tautomeric reaction occurs in the potassium hydrazineborane (KHB) first, and the following dehydrogenation path is similar to that of the LiHB and NaHB. It explores the hydrogen-release properties of the different metal hydrazineboranes and also indcates the affection of the metal in the metal hydrazineboranes hydrogen-storage system.

Ab Initio Modeling of the Electronic Absorption Spectrum of Previtamin D in Solution

NASA Astrophysics Data System (ADS)

Zhu, Tianyang

To study the solvent effects of water on the previtamin D absorption spectrum, we use the quantum mechanics (QM)/molecular mechanics (MM) method combined with replica-exchange molecular dynamics (REMD). The QM method is applied for the previtamin D molecule and the MM method is used for the water molecules. To enhance conformational sampling of the flexible previtamin D molecule we apply REMD. Based on the REMD structures, we calculate the macroscopic ensemble of the absorption spectrum in solution by time-dependent density functional theory (TDDFT). Comparison between the calculated spectrum in the gas phase and in the solution reveals minor influences of the solvent on the absorption spectrum. In the conventional molecule dynamics simulation, the previtamin D molecule can be trapped by local minimum and cannot overcome energetics barriers when it is calculated at the room temperature. In addition, the higher temperature calculation for the molecule in REMD allows to overcome energetics barriers and to change the structure to other rotational isomers, then switch to the lower temperature and gives a more complete result in the configuration space for the lower temperature.

The water hexamer: three-body interactions, structures, energetics, and OH-stretch spectroscopy at finite temperature.

PubMed

Tainter, C J; Skinner, J L

2012-09-14

Using a newly developed and recently parameterized classical empirical simulation model for water that involves explicit three-body interactions, we determine the eleven most stable isomers of the water hexamer. We find that the lowest energy isomer is one of the cage structures, in agreement with far-IR and microwave experiments. The energy ordering for the binding energies is cage > glove > book > bag > chair > boat > chaise, and energies relative to the cage are in good agreement with CCSD(T) calculations. The three-body contributions to the cage, book, and chair are also in reasonable agreement with CCSD(T) results. The energy of each isomer results from a delicate balance involving the number of hydrogen bonds, the strain of these hydrogen bonds, and cooperative and anti-cooperative three-body interactions, whose contribution we can understand simply from the form of the three-body interactions in the simulation model. Oxygen-oxygen distances in the cage and book isomers are in good agreement with microwave experiments. Hydrogen-bond distances depend on both donor and acceptor, which can again be understood from the three-body model. Fully anharmonic OH-stretch spectra are calculated for these low-energy structures, and compared with shifted harmonic results from ab initio and density functional theory calculations. Replica-exchange molecular dynamics simulations were performed from 40 to 194 K, which show that the cage isomer has the lowest free energy from 0 to 70 K, and the book isomer has the lowest free energy from 70 to 194 K. OH-stretch spectra were calculated between 40 and 194 K, and results at 40, 63, and 79 K were compared to recent experiments, leading to re-assignment of the peaks in the experimental spectra. We calculate local OH-stretch cumulative spectral densities for different donor-acceptor types and compare to analogous results for liquid water.

Shells, orbit bifurcations, and symmetry restorations in Fermi systems

DOE Office of Scientific and Technical Information (OSTI.GOV)

Magner, A. G., E-mail: magner@kinr.kiev.ua; Koliesnik, M. V.; Arita, K.

The periodic-orbit theory based on the improved stationary-phase method within the phase-space path integral approach is presented for the semiclassical description of the nuclear shell structure, concerning themain topics of the fruitful activity ofV.G. Soloviev. We apply this theory to study bifurcations and symmetry breaking phenomena in a radial power-law potential which is close to the realistic Woods–Saxon one up to about the Fermi energy. Using the realistic parametrization of nuclear shapes we explain the origin of the double-humped fission barrier and the asymmetry in the fission isomer shapes by the bifurcations of periodic orbits. The semiclassical origin of themore » oblate–prolate shape asymmetry and tetrahedral shapes is also suggested within the improved periodic-orbit approach. The enhancement of shell structures at some surface diffuseness and deformation parameters of such shapes are explained by existence of the simple local bifurcations and new non-local bridge-orbit bifurcations in integrable and partially integrable Fermi-systems. We obtained good agreement between the semiclassical and quantum shell-structure components of the level density and energy for several surface diffuseness and deformation parameters of the potentials, including their symmetry breaking and bifurcation values.« less

Density functional theoretical study on enantiomerization of 2,2'-biphenol.

PubMed

Sahnoun, Riadh; Koseki, Shiro; Fujimura, Yuichi

2006-02-23

The S-R enantiomerization processes of 2,2'-biphenol (biphenol) have been investigated using density functional theory (DFT). Five isomers for biphenol were identified: I0, which is the most stable isomer; I1a and I1b, which are formed by a restricted rotation of one OH group; and I2a and I2b, which are formed by a restricted rotation of the two OH groups where a and b denote cis and trans configurations, respectively. Each isomer has R- and S-enantiomers. The energies relative to the most stable isomer I0 are 1.6, 3.3, 5.3, and 5.5 kcal mol(-1) for I1a, I1b, I2a, and I2b, respectively. The direct enantiomerization of I0, in which the phenol-ring rotation is considered to be the reaction coordinate while the OH rotations are frozen, is forbidden because of the repulsion between the two OH groups. The transition states for isomerizations of I0 to other isomers (I1a, I1b, I2a, or I2b) were calculated as well as those for the other direct enantiomerizations except for that of I0. From the viewpoint of the least number of the transition states and their low energy levels, the probable S-R enantiomerization of I0 is expressed as a sequential process of isomerization: I0,S --> I1a,S, a direct enantiomerization induced by one of the two OH rotations, I1a,S --> I1a,R, and another isomerization, I1a,R --> I0,R, that is, I0,S --> I1a,S --> I1a,R --> I0,R as the whole process. This process is effective in quantum control of the enantiomerization of biphenol and can be carried out by a sequence of a pump-dump IR laser-pulse scheme.

Multifunctional Octamethyltetrasila[2.2]cyclophanes: Conformational Variations, Circularly Polarized Luminescence, and Organic Electroluminescence.

PubMed

Shimada, Masaki; Yamanoi, Yoshinori; Ohto, Tatsuhiko; Pham, Song-Toan; Yamada, Ryo; Tada, Hirokazu; Omoto, Kenichiro; Tashiro, Shohei; Shionoya, Mitsuhiko; Hattori, Mineyuki; Jimura, Keiko; Hayashi, Shigenobu; Koike, Hikaru; Iwamura, Munetaka; Nozaki, Koichi; Nishihara, Hiroshi

2017-08-16

Both symmetrical and unsymmetrical cyclophanes containing disilane units, tetrasila[2.2]cyclophanes 1-9, were synthesized. The syn and anti conformations and the kinetics of inversion between two anti-isomers were investigated by X-ray diffraction and variable-temperature NMR analysis, respectively. The flipping motion of two aromatic rings was affected by the bulkiness of the aromatic moiety (1 vs 6), the phase (solid vs solution), and the inclusion by host molecules (1 vs 1⊂[Ag 2 L] 2+ ). The photophysical, electrochemical, and structural properties of the compounds were thoroughly investigated. Unsymmetrical tetrasila[2.2]cyclophanes 5-8 displayed blue-green emission arising from intramolecular charge transfer. Compound 6 emitted a brilliant green light in the solid state under 365 nm irradiation and showed a higher fluorescence quantum yield in the solid state (Φ = 0.49) than in solution (Φ = 0.05). We also obtained planar chiral tetrasila[2.2]cyclophane 9, which showed interesting chiroptical properties, such as a circularly polarized luminescence (CPL) with a dissymmetry factor of |g lum | = ca. 2 × 10 -3 at 500 nm. Moreover, an organic green light-emitting diode that showed a maximum external quantum efficiency (η ext ) of ca. 0.4% was fabricated by doping 4,4'-bis(2,2'-diphenylvinyl)-1,1'-biphenyl with 6.

Weak hydrogen bond topology in 1,1-difluoroethane dimer: A rotational study

NASA Astrophysics Data System (ADS)

Chen, Junhua; Zheng, Yang; Wang, Juan; Feng, Gang; Xia, Zhining; Gou, Qian

2017-09-01

The rotational spectrum of the 1,1-difluoroethane dimer has been investigated by pulsed-jet Fourier transform microwave spectroscopy. Two most stable isomers have been detected, which are both stabilized by a network of three C—H⋯F—C weak hydrogen bonds: in the most stable isomer, two difluoromethyl C—H groups and one methyl C—H group act as the weak proton donors whilst in the second isomer, two methyl C—H groups and one difluoromethyl C—H group act as the weak proton donors. For the global minimum, the measurements have also been extended to its four 13C isotopologues in natural abundance, allowing a precise, although partial, structural determination. Relative intensity measurements on a set of μa-type transitions allowed estimating the relative population ratio of the two isomers as NI/NII ˜ 6/1 in the pulsed jet, indicating a much larger energy gap between these two isomers than that expected from ab initio calculation, consistent with the result from pseudo-diatomic dissociation energies estimation.

High-spin yrast structure of 204Hg from the decay of a four-hole, 22+ isomer

NASA Astrophysics Data System (ADS)

Wrzesiński, J.; Lane, G. J.; Maier, K. H.; Janssens, R. V. F.; Dracoulis, G. D.; Broda, R.; Byrne, A. P.; Carpenter, M. P.; Clark, R. M.; Cromaz, M.; Fornal, B.; Lauritsen, T.; Macchiavelli, A. O.; Rejmund, M.; Szpak, B.; Vetter, K.; Zhu, S.

2015-10-01

A high-spin isomer with τ >700 ns has been found in 204Hg , populated in reactions of 1360-MeV 208Pb and 330-MeV 48Ca beams with a thick 238U target and a 1450-MeV 208Pb beam on a thick 208Pb target. The observed γ -ray decay of the isomer has established the yrast states below it, including another isomer with τ =33 (3 ) ns. The experimental results are compared with shell-model calculations that include four holes in the configuration space between 132Sn and 208Pb . The available spectroscopic information, including transition strengths, total conversion, and angular correlation coefficients, together with the observed agreement with the calculations, allows spin, parity, and configuration assignments to be proposed for the experimental states. The τ >700 ns isomer is the 22+ state of maximum spin available from the alignment of the four valence holes with the configuration π h11/2 -2ν i13/2 -2 .

Enantioselective separation of defined endocrine-disrupting nonylphenol isomers.

PubMed

Acir, Ismail-Hakki; Wüst, Matthias; Guenther, Klaus

2016-08-01

Nonylphenol is in the focus of worldwide endocrine-disrupter research and accounted for as a priority hazardous substance of the Water Framework Directive of the European Union. Technical nonylphenol consists of a very complex mixture of isomers and enantiomers. As estrogenic effect and degradation behavior in environmental processes of single nonylphenols are heavily dependent on the structure of the nonyl side chain, it is absolutely necessary to consider the nonylphenol problem from an isomer and enantiomer-specific viewpoint. In this study, an enantiomer-specific separation of eight defined synthesized nonylphenol isomers by five different special chiral cyclodextrin columns was performed underivatized and after methylation, silylation, and acylation. This work demonstrates that three columns out of the investigated five show an excellent separation behavior for the studied different nonylphenol isomers and can be used for the enantiomer-specific determination of nonylphenols in food, other biological matrices, and environmental samples in the future. Graphical abstract Enantiomeric pair of 4-NP170 (4-[1-ethyl-1,3,3-trimethylbutyl]phenol).

ATR-FTIR spectroscopic investigation of the cis- and trans-bis-(α-amino acids) copper(II) complexes

NASA Astrophysics Data System (ADS)

Berestova, Tatyana V.; Kuzina, Lyudmila G.; Amineva, Natalya A.; Faizrakhmanov, Ilshat S.; Massalimov, Ismail A.; Mustafin, Akhat G.

2017-06-01

The crystalline phases of the trans-(a) and cis-(b)-isomers of bis-(α-amino acids) copper(II) complexes [Cu(bL)2] 1-5 (bL - bidentate ligand: gly (1), S-ala (2), R,S-val (3), (±)-thr (4), R,S-phe (5)) were studied by ATR-FTIR spectroscopy in the mid region IR spectrum. It was established that asymmetric νas(COO) and symmetric νs(COO) stretching vibrations of carboxylic groups of 1-5 are sensitive to change of the geometric structure and have a different maxima for the trans(a)- and cis(b)-isomers. It found that νas(COO) and νs(COO) stretching vibrations of cis-isomers are broadened and shifted to longer wavelengths (b) as compared with trans-isomers (a). Shown that peculiarities of crystal packing molecules of geometric isomers may affect on carboxylate stretching vibration bis-α-amino acids complexes copper(II) 1-5 a,b.

Basic medium oxidation of aromatic α-hydroxy-ketones: A free radical mechanism

NASA Astrophysics Data System (ADS)

Gómez-Vidales, Virginia; Vargas, Marina; Meléndez, Iván; Salmón, Manuel; Sansón-O, Carmen; Zaragoza, I. P.; Zolotukhin, Mikhail; Salcedo, Roberto

2010-01-01

A systematic study was undertaken of the EPR of sodium hydroxide solutions of Benzoin, Anisoin and Thenoin in both ethanol and DMSO as well as their corresponding ionised species of varying colours. In all cases, the EPR consist of symmetric spectra, resulting from the generation of a free radical-anion. Furthermore, theoretical DFT methods were applied in order to study the radical anions, revealing the reason for the colour change in the solutions and in the case of benzoin, found to be related to the interaction between the cis and trans-isomers with the molecules in the two solvents. We have defined the structure of the cis-isomer and for the first time we have described how the adduct between the cis-isomer and the solvent molecule, results in a stable conformer. This corresponds with the EPR results which indicated a significant difference between the cis and trans-isomers. Both the theoretical and experimental results inspired similar descriptions of the significant differences between the cis and trans-isomers in solution.

Theoretical studies on the structural and spectra properties of two C74 fullerenes and the chlorinated species C74Cl10

NASA Astrophysics Data System (ADS)

Zheng, Mei; Song, Xitong; Li, Xiaoqi; Qi, Jiayuan

2018-07-01

The geometrical/electronic structures, X-ray photoelectron spectroscopy (XPS) and near-edge X-ray absorption fine structure spectroscopy of two especially C74 fullerenes (D3h-C74 and C1-C74) and the chlorinated species C1-C74Cl10, which are newly isolated in the experiment, have been calculated by means of the density functional theory (DFT) method. Effective changes in the electronic structure and simulated X-ray spectra have been observed after chlorination. Strong isomer dependence has been found in both spectra, thus the 'fingerprints' in the spectra can be employed as a tool to identify the isomers. The ultraviolet-visible (UV-vis) absorption spectrum of C1-C74Cl10 has been performed by using the time-dependent DFT method. The generated UV-vis spectrum coincides with the previous experimental counterpart. The results of this work can provide useful information especially for isomer identification and further study on fullerenes by means of the aforementioned spectroscopy techniques.

IR + VUV double resonance spectroscopy and extended density functional theory studies of ketone solvation by alcohol: 2-butanone·(methanol)n, n = 1-4 clusters.

PubMed

Shin, Joong-Won; Bernstein, Elliot R

2017-09-28

Infrared plus vacuum ultraviolet (IR + VUV) photoionization vibrational spectroscopy of 2-butanone/methanol clusters [MEK·(MeOH) n , n = 1-4] is performed to explore structures associated with hydrogen bonding of MeOH molecules to the carbonyl functional group of the ketone. IR spectra and X3LYP/6-31++G(d,p) calculations show that multiple isomers of MEK·(MeOH) n are generated in the molecular beam as a result of several hydrogen bonding sites available to the clusters throughout the size range investigated. Isomer interconversion involving solvating MeOH rearrangement should probably occur for n = 1 and 2. The mode energy for a hydrogen bonded OH stretching transition gradually redshifts as the cluster size increases. Calculations suggest that the n = 3 cluster isomers adopt structures in which the MEK molecule is inserted into the cyclic MeOH hydrogen bond network. In larger structures, the cyclic network may be preserved.

Using One's Hands for Naming Optical Isomers and Other Stereochemical Positions.

ERIC Educational Resources Information Center

Mezl, Vasek A.

1996-01-01

Presents a method that allows students to use their hands to obtain the stereochemistry of chiral centers without redrawing the structure. Discusses the use of the model in: determining the configurations of amino acids, determining if sugars are D or L isomers, the sequence rule procedure, prochirality, naming the sides of trigonal carbons, and…

Fac and mer isomers of Ru(II) tris(pyrazolyl-pyridine) complexes as models for the vertices of coordination cages: structural characterisation and hydrogen-bonding characteristics.

PubMed

Metherell, Alexander J; Cullen, William; Stephenson, Andrew; Hunter, Christopher A; Ward, Michael D

2014-01-07

We have prepared a series of mononuclear fac and mer isomers of Ru(II) complexes containing chelating pyrazolyl-pyridine ligands, to examine their differing ability to act as hydrogen-bond donors in MeCN. This was prompted by our earlier observation that octanuclear cube-like coordination cages that contain these types of metal vertex can bind guests such as isoquinoline-N-oxide (K = 2100 M(-1) in MeCN), with a significant contribution to binding being a hydrogen-bonding interaction between the electron-rich atom of the guest and a hydrogen-bond donor site on the internal surface of the cage formed by a convergent set of CH2 protons close to a 2+ metal centre. Starting with [Ru(L(H))3](2+) [L(H) = 3-(2-pyridyl)-1H-pyrazole] the geometric isomers were separated by virtue of the fact that the fac isomer forms a Cu(I) adduct which the mer isomer does not. Alkylation of the pyrazolyl NH group with methyl iodide or benzyl bromide afforded [Ru(L(Me))3](2+) and [Ru(L(bz))3](2+) respectively, each as their fac and mer isomers; all were structurally characterised. In the fac isomers the convergent group of pendant -CH2R or -CH3 protons defines a hydrogen-bond donor pocket; in the mer isomer these protons do not converge and any hydrogen-bonding involving these protons is expected to be weaker. For both [Ru(L(Me))3](2+) and [Ru(L(bz))3](2+), NMR titrations with isoquinoline-N-oxide in MeCN revealed weak 1 : 1 binding (K ≈ 1 M(-1)) between the guest and the fac isomer of the complex that was absent with the mer isomer, confirming a difference in the hydrogen-bond donor capabilities of these complexes associated with their differing geometries. The weak binding compared to the cage however occurs because of competition from the anions, which are free to form ion-pairs with the mononuclear complex cations in a way that does not happen in the cage complexes. We conclude that (i) the presence of fac tris-chelate sites in the cage to act as hydrogen-bond donors, and (ii) exclusion of counter-ions from the central cavity leaving these hydrogen-bonding sites free to interact with guests, are both important design criteria for future coordination cage hosts.

Mechanism for odd-electron anion generation of dihydroxybenzoic acid isomers in matrix-assisted laser desorption/ionization mass spectrometry with density functional theory calculations.

PubMed

Yamagaki, Tohru; Takeuchi, Michika; Watanabe, Takehiro; Sugahara, Kohtaro; Takeuchi, Takae

2016-12-30

Proton and radical are transferred between matrices and matrix and analyte in matrix-assisted laser desorption/ionization (MALDI) and these transfers drive ionization of analytes. The odd-electron anion [M-2H] •- was generated in dihydroxybenzoic acids (DHBs) and the ion abundance of the 2,5-DHB was the highest among six DHB isomers. We were interested in the mechanism of the ion generation of the odd-electron anion. The observed [M-2H] •- and [M-3H] - ions, which were generated with the hydrogen radical removed from the phenolic hydroxyl groups (OH) in DHB isomers, were analyzed using negative-ion MALDI-MS. The enthalpy for ion generation and their stable structures were calculated using the density functional theory (DFT) calculation program Gaussian 09 with the B3LYP functional and the 6-31+G(d) basis set. The number of observed [M-2H] •- and [M-3H] - ions of the DHB isomers was dependent on the positions of the phenolic OH groups in the DHB isomers because the carboxy group interacts with the ortho OH group due to neighboring group participation, as confirmed from the stable structures of the [M-2H] •- anions calculated with the Gaussian 09 program. The DHB isomers were placed into three categories according to the number of the ions. Odd-electron anions ([M-2H] •- ) and [M-2H • -H] - ([M-3H] - ) ions were generated from DHB isomers due to removal of the hydrogen radical from the phenolic groups. The enthalpy for ion generation revealed that ion formation proceeds via a two-step pathway through the [M-M] - ion as an intermediate. © 2016 The Authors. Rapid Communications in Mass Spectrometry Published by John Wiley & Sons Ltd. © 2016 The Authors. Rapid Communications in Mass Spectrometry Published by John Wiley & Sons Ltd.

Quantum rotation of ortho and para-water encapsulated in a fullerene cage

PubMed Central

Beduz, Carlo; Carravetta, Marina; Chen, Judy Y.-C.; Concistrè, Maria; Denning, Mark; Frunzi, Michael; Horsewill, Anthony J.; Johannessen, Ole G.; Lawler, Ronald; Lei, Xuegong; Levitt, Malcolm H.; Li, Yongjun; Mamone, Salvatore; Murata, Yasujiro; Nagel, Urmas; Nishida, Tomoko; Ollivier, Jacques; Rols, Stéphane; Rõõm, Toomas; Sarkar, Riddhiman; Turro, Nicholas J.; Yang, Yifeng

2012-01-01

Inelastic neutron scattering, far-infrared spectroscopy, and cryogenic nuclear magnetic resonance are used to investigate the quantized rotation and ortho–para conversion of single water molecules trapped inside closed fullerene cages. The existence of metastable ortho-water molecules is demonstrated, and the interconversion of ortho-and para-water spin isomers is tracked in real time. Our investigation reveals that the ground state of encapsulated ortho water has a lifted degeneracy, associated with symmetry-breaking of the water environment. PMID:22837402

Experimental and theoretical investigation of three-dimensional nitrogen-doped aluminum clusters AI 8N - and AI 8N

DOE Office of Scientific and Technical Information (OSTI.GOV)

Wang, Leiming; Huang, Wei; Wang, Lai S.

The structure and electronic properties of the Al 8N - and Al 8N clusters were investigated by combined photoelectron spectroscopy and ab initio studies. Congested photoelectron spectra were observed and experimental evidence was obtained for the presence of multiple isomers for Al 8N - Global minimum searches revealed several structures for Al 8N - with close energies. The calculated vertical detachment energies of the two lowest-lying isomers, which are of C 2v and C s symmetry, respectively, were shown to agree well with the experimental data. Unlike the three-dimensional structures of Al 6N - and Al 7N -, in whichmore » the dopant N atom has a high coordination number of 6,the dopant N atom in the two low-lying isomers of Al 8N - has a lower coordination number of 4 and 5, respectively. The competition between the Al–Al and Al–N interactions are shown to determine the global minimum structures of the doped aluminum clusters and results in the structural diversity for both Al 8N - and Al8N. © 2009 American Institute of Physics« less

Anti-Cancer Efficacy of Silybin Derivatives - A Structure-Activity Relationship

PubMed Central

Agarwal, Chapla; Wadhwa, Ritambhara; Deep, Gagan; Biedermann, David; Gažák, Radek; Křen, Vladimír; Agarwal, Rajesh

2013-01-01

Silybin or silibinin, a flavonolignan isolated from Milk thistle seeds, is one of the popular dietary supplements and has been extensively studied for its antioxidant, hepatoprotective and anti-cancer properties. We have envisioned that potency of silybin could be further enhanced through suitable modification/s in its chemical structure. Accordingly, here, we synthesized and characterized a series of silybin derivatives namely 2,3-dehydrosilybin (DHS), 7-O-methylsilybin (7OM), 7-O-galloylsilybin (7OG), 7,23-disulphatesilybin (DSS), 7-O-palmitoylsilybin (7OP), and 23-O-palmitoylsilybin (23OP); and compared their anti-cancer efficacy using human bladder cancer HTB9, colon cancer HCT116 and prostate carcinoma PC3 cells. In all the 3 cell lines, DHS, 7OM and 7OG demonstrated better growth inhibitory effects and compared to silybin, while other silybin derivatives showed lesser or no efficacy. Next, we prepared the optical isomers (A and B) of silybin, DHS, 7OM and 7OG, and compared their anti-cancer efficacy. Isomers of these three silybin derivatives also showed better efficacy compared with respective silybin isomers, but in each, there was no clear cut silybin A versus B isomer activity preference. Further studies in HTB cells found that DHS, 7OM and 7OG exert better apoptotic activity than silibinin. Clonogenic assays in HTB9 cells further confirmed that both the racemic mixtures as well as pure optical isomers of DHS, 7OM and 7OG were more effective than silybin. Overall, these results clearly suggest that the anti-cancer efficacy of silybin could be significantly enhanced through structural modifications, and identify strong anti-cancer efficacy of silybin derivatives, namely DHS, 7OM, and 7OG, signifying that their efficacy and toxicity should be evaluated in relevant pre-clinical cancer models in rodents. PMID:23555889

Predictive coupled-cluster isomer orderings for some Si{sub n}C{sub m} (m, n ≤ 12) clusters: A pragmatic comparison between DFT and complete basis limit coupled-cluster benchmarks

DOE Office of Scientific and Technical Information (OSTI.GOV)

Byrd, Jason N., E-mail: byrd.jason@ensco.com; ENSCO, Inc., 4849 North Wickham Road, Melbourne, Florida 32940; Lutz, Jesse J., E-mail: jesse.lutz.ctr@afit.edu

The accurate determination of the preferred Si{sub 12}C{sub 12} isomer is important to guide experimental efforts directed towards synthesizing SiC nano-wires and related polymer structures which are anticipated to be highly efficient exciton materials for the opto-electronic devices. In order to definitively identify preferred isomeric structures for silicon carbon nano-clusters, highly accurate geometries, energies, and harmonic zero point energies have been computed using coupled-cluster theory with systematic extrapolation to the complete basis limit for set of silicon carbon clusters ranging in size from SiC{sub 3} to Si{sub 12}C{sub 12}. It is found that post-MBPT(2) correlation energy plays a significant rolemore » in obtaining converged relative isomer energies, suggesting that predictions using low rung density functional methods will not have adequate accuracy. Utilizing the best composite coupled-cluster energy that is still computationally feasible, entailing a 3-4 SCF and coupled-cluster theory with singles and doubles extrapolation with triple-ζ (T) correlation, the closo Si{sub 12}C{sub 12} isomer is identified to be the preferred isomer in the support of previous calculations [X. F. Duan and L. W. Burggraf, J. Chem. Phys. 142, 034303 (2015)]. Additionally we have investigated more pragmatic approaches to obtaining accurate silicon carbide isomer energies, including the use of frozen natural orbital coupled-cluster theory and several rungs of standard and double-hybrid density functional theory. Frozen natural orbitals as a way to compute post-MBPT(2) correlation energy are found to be an excellent balance between efficiency and accuracy.« less

Hazard identification of cis/trans-zearalenone through the looking-glass.

PubMed

Dellafiora, Luca; Galaverna, Gianni; Dall'Asta, Chiara; Cozzini, Pietro

2015-12-01

Among the food-related health issues, the presence of contaminants has a prominent role, due to the wide range of exogenous compounds that can occur in food commodities and to their large differences in structure and biological activity. A comprehensive assessment of the related risk is thus actually demanding in terms of time and facilities involved. In this context, the use of computational strategies can be an effective choice for supporting the hazard identification procedure at the early stage. In this work, we focused on the food contaminant zearalenone by comparing the trans and cis isomers, respectively the well-known mycoestrogen and its still largely understudied isomer. We estimated the possible effects exerted by human metabolism on the xenoestrogenicity of cis-ZEN by using a validated in silico strategy based on docking simulations and rescoring procedures. Similarly, the exploitation of the most promising enzymatic detoxifying routes designed for trans-ZEN - which relies on the enzyme lactono hydrolase from Clonostachys rosea - has been assessed for the cis-isomer as well. Our results showed that both isomers can act as functional analogues with respect to xenoestrogenic activity, and several cis-ZEN metabolites with high biological potential have been identified. On the contrary, in spite of the high degree of structural analogy, the cis isomer showed a pattern of interaction with the degrading enzyme in stark contrast with that observed for trans-ZEN. For these reasons, the outcomes presented herein strongly support the inclusion of cis-ZEN in further studies of occurrence, metabolism and bioactivity assessment, and suggest the need for a dedicated handling for the cis isomer in risk assessment studies. Copyright © 2015 Elsevier Ltd. All rights reserved.

A multi-method approach toward de novo glycan characterization: a Man-5 case study.

PubMed

Prien, Justin M; Prater, Bradley D; Cockrill, Steven L

2010-05-01

Regulatory agencies' expectations for biotherapeutic approval are becoming more stringent with regard to product characterization, where minor species as low as 0.1% of a given profile are typically identified. The mission of this manuscript is to demonstrate a multi-method approach toward de novo glycan characterization and quantitation, including minor species at or approaching the 0.1% benchmark. Recently, unexpected isomers of the Man(5)GlcNAc(2) (M(5)) were reported (Prien JM, Ashline DJ, Lapadula AJ, Zhang H, Reinhold VN. 2009. The high mannose glycans from bovine ribonuclease B isomer characterization by ion trap mass spectrometry (MS). J Am Soc Mass Spectrom. 20:539-556). In the current study, quantitative analysis of these isomers found in commercial M(5) standard demonstrated that they are in low abundance (<1% of the total) and therefore an exemplary "litmus test" for minor species characterization. A simple workflow devised around three core well-established analytical procedures: (1) fluorescence derivatization; (2) online rapid resolution reversed-phase separation coupled with negative-mode sequential mass spectrometry (RRRP-(-)-MS(n)); and (3) permethylation derivatization with nanospray sequential mass spectrometry (NSI-MS(n)) provides comprehensive glycan structural determination. All methods have limitations; however, a multi-method workflow is an at-line stopgap/solution which mitigates each method's individual shortcoming(s) providing greater opportunity for more comprehensive characterization. This manuscript is the first to demonstrate quantitative chromatographic separation of the M(5) isomers and the use of a commercially available stable isotope variant of 2-aminobenzoic acid to detect and chromatographically resolve multiple M(5) isomers in bovine ribonuclease B. With this multi-method approach, we have the capabilities to comprehensively characterize a biotherapeutic's glycan array in a de novo manner, including structural isomers at >/=0.1% of the total chromatographic peak area.

Laser desorption single-conformation UV and IR spectroscopy of the sulfonamide drug sulfanilamide, the sulfanilamide-water complex, and the sulfanilamide dimer.

PubMed

Uhlemann, Thomas; Seidel, Sebastian; Müller, Christian W

2017-06-07

We have studied the conformational preferences of the sulfonamide drug sulfanilamide, its dimer, and its monohydrated complex through laser desorption single-conformation UV and IR spectroscopy in a molecular beam. Based on potential energy curves for the inversion of the anilinic and the sulfonamide NH 2 groups calculated at DFT level, we suggest that the zero-point level wave function of the sulfanilamide monomer is appreciably delocalized over all four conformer wells. The sulfanilamide dimer, and the monohydrated complex each exhibit a single isomer in the molecular beam. The isomeric structures of the sulfanilamide dimer and the monohydrated sulfanilamide complex were assigned based on their conformer-specific IR spectra in the NH and OH stretch region. Quantum Theory of Atoms in Molecules (QTAIM) analysis of the calculated electron density in the water complex suggests that the water molecule is bound side-on in a hydrogen bonding pocket, donating one O-HO[double bond, length as m-dash]S hydrogen bond and accepting two hydrogen bonds, a NHO and a CHO hydrogen bond. QTAIM analysis of the dimer electron density suggests that the C i symmetry dimer structure exhibits two dominating N-HO[double bond, length as m-dash]S hydrogen bonds, and three weaker types of interactions: two CHO bonds, two CHN bonds, and a chalcogen OO interaction. Most interestingly, the molecular beam dimer structure closely resembles the R dimer unit - the dimer unit with the greatest interaction energy - of the α, γ, and δ crystal polymorphs. Interacting Quantum Atoms analysis provides evidence that the total intermolecular interaction in the dimer is dominated by the short-range exchange-correlation contribution.

Chlorination pattern effect on thermodynamic parameters and environmental degradability for C₁₀-SCCPs: Quantum chemical calculation based on virtual combinational library.

PubMed

Sun, Yuzhen; Pan, Wenxiao; Lin, Yuan; Fu, Jianjie; Zhang, Aiqian

2016-01-01

Short-chain chlorinated paraffins (SCCPs) are still controversial candidates for inclusion in the Stockholm Convention. The inherent mixture nature of SCCPs makes it rather difficult to explore their environmental behaviors. A virtual molecule library of 42,720 C10-SCCP congeners covering the full structure spectrum was constructed. We explored the structural effects on the thermodynamic parameters and environmental degradability of C10-SCCPs through semi-empirical quantum chemical calculations. The thermodynamic properties were acquired using the AM1 method, and frontier molecular orbital analysis was carried out to obtain the E(HOMO), E(LUMO) and E(LUMO)-E(HOMO) for degradability exploration at the same level. The influence of the chlorination degree (N(Cl)) on the relative stability and environmental degradation was elucidated. A novel structural descriptor, μ, was proposed to measure the dispersion of the chlorine atoms within a molecule. There were significant correlations between thermodynamic values and N(Cl), while the reported N(Cl)-dependent pollution profile of C10-SCCPs in environmental samples was basically consistent with the predicted order of formation stability of C10-SCCP congeners. In addition, isomers with large μ showed higher relative stability than those with small μ. This could be further verified by the relationship between μ and the reactivity of nucleophilic substitution and OH attack respectively. The C10-SCCP congeners with less Cl substitution and lower dispersion degree are susceptible to environmental degradation via nucleophilic substitution and hydroxyl radical attack, while direct photolysis of C10-SCCP congeners cannot readily occur due to the large E(LUMO)-E(HOMO) values. The chlorination effect and the conclusions were further checked with appropriate density functional theory (DFT) calculations. Copyright © 2015. Published by Elsevier B.V.

Structure-Odor Relationship Study on Geraniol, Nerol, and Their Synthesized Oxygenated Derivatives.

PubMed

Elsharif, Shaimaa Awadain; Buettner, Andrea

2018-03-14

Despite being isomers having the same citrus-like, floral odor, geraniol, 1, and nerol, 3, show different odor thresholds. To date, no systematic studies are at hand elucidating the structural features required for their specific odor properties. Therefore, starting from these two basic structures and their corresponding esters, namely, geranyl acetate, 2, and neryl acetate, 4, a total of 12 oxygenated compounds were synthesized and characterized regarding retention indices (RI), mass spectrometric (MS), and nuclear magnetic resonance (NMR) data. All compounds were individually tested for their odor qualities and odor thresholds in air (OT). Geraniol, the Z-isomer, with an OT of 14 ng/L, was found to be more potent than its E-isomer, nerol, which has an OT of 60 ng/L. However, 8-oxoneryl acetate was the most potent derivative within this study, exhibiting an OT of 8.8 ng/L, whereas 8-oxonerol was the least potent with an OT of 493 ng/L. Interestingly, the 8-oxo derivatives smell musty and fatty, whereas the 8-hydroxy derivatives show odor impressions similar to those of 1 and 3. 8-Carboxygeraniol was found to be odorless, whereas its E-isomer, 8-carboxynerol, showed fatty, waxy, and greasy impressions. Overall, we observed that oxygenation on C-8 affects mainly the odor quality, whereas the E/ Z position of the functional group on C-1 affects the odor potency.

Enhancing glycan isomer separations with metal ions and positive and negative polarity ion mobility spectrometry-mass spectrometry analyses

DOE Office of Scientific and Technical Information (OSTI.GOV)

Zheng, Xueyun; Zhang, Xing; Schocker, Nathaniel S.

Glycomics has become an increasingly important field of research since glycans play critical roles in biology processes ranging from molecular recognition and signaling to cellular communication. Glycans often conjugate with other biomolecules such as proteins and lipids, and alter their properties and functions, so understanding the effect glycans have on cellular systems is essential. However the analysis of glycans is extremely difficult due to their complexity and structural diversity (i.e., the number and identity of monomer units, and configuration of their glycosidic linkages and connectivities). In this work, we coupled ion mobility spectrometry with mass spectrometry (IMS-MS) to characterize glycanmore » standards and biologically important isomers of synthetic αGal-containing O-glycans including glycotopes of the protozoan parasite Trypanosoma cruzi, which is the causative agent of Chagas disease. IMS-MS results showed significant differences for the glycan structural isomers when analyzed in positive and negative polarity and complexed with different metal cations. These results suggest specific metal ions or ion polarities could be used to target and baseline separate glycan isomers of interest with IMS-MS.« less

Endohedral fullerenes contaning transition-metal clusters

NASA Astrophysics Data System (ADS)

Bhusal, Shusil; Basurto, Luis; Zope, Rajendra; Baruah, Tunna

We report detailed investigation of structural, electronic, and spectroscopic properties of VSc2N-containing fullerenes in the size range C68 - C96. First, the candidate structures of the ground state are obtained using a systematic approach in which a large number of isomers of endohedral fullerenes were screened for their energetic stability. Stability of some of the most promising isomers were further studied using density functional theory at the all-electron level using large polarized Gaussian basis sets. The effect of the V doping is examined on the structure, spin states and the magnetic properties of the endohedral fullerenes. De-SC0002168, NSF-DMR 125302, DE-SC0006818.

Theoretical prediction of a new stable structure of Au28(SR)20 cluster

NASA Astrophysics Data System (ADS)

Sun, Xiangxiang; Wang, Pu; Xiong, Lin; Pei, Yong

2018-07-01

A new stable structure of Au28(SR)20 cluster is predicted, which has the same gold core as two known structures but different Au-S framework. The new Au28(SR)20 cluster is proposed to be a key link in the evolution of Au22(SR)18, Au34(SR)22 and Au40(SR)24 clusters. The four clusters belong to a homogenous Au16+6N(SR)16+2N series (N = 1-4). The relative stabilities of the new Au28 isomer structure were confirmed by density functional theory calculations including dispersion corrections (DFT-D). It is found that upon protection of certain SR ligands, the new isomer structure has lower or comparable energies to two known cluster structures.

Tuning zinc coordination architectures by benzenedicarboxylate position isomers and bis(triazole)

NASA Astrophysics Data System (ADS)

Peng, Yan-fen; Li, Ke; Zhao, Shan; Han, Shan-shan; Li, Bao-long; Li, Hai-Yan

2015-08-01

Three position isomers 1,2-, 1,3-, 1,4-benzenedicarboxylate and 1,4-bis(1,2,4-triazol-4-yl)benzene were used to assembly zinc(II) coordination polymers {[Zn2(btx)0.5(1,2-bdc)2(H2O)]·H2O}n (1), {[Zn(btx)(1,3-bdc)]·2H2O·(DMF)}n (2) and {[Zn(btx)(1,4-bdc)]·3H2O}n (3). 1 is a (3,4,4,4)-connected two-dimensional network with point symbol (42·6)(44·62)(43·62·8)(42·6·103). 2 shows a two-dimensional (4,4) network. 3 exhibits a 5-fold interpenetrated three-dimensional diamondoid network. The structural versatility shows that the structures of coordination polymers can be tuned by the position isomers ligands. The luminescence and thermal stability were investigated.

Tautomeric transformation of temozolomide, their proton affinities and chemical reactivities: A theoretical approach.

PubMed

Sang-Aroon, Wichien; Ruangpornvisuti, Vithaya; Amornkitbamrung, Vittaya

2016-05-01

The gas-phase geometry optimizations of bare, mono- and dihydrated complexes of temozolomide isomers were carried out using density functional calculation at the M06-2X/6-31+G(d,p) level of the theory. The structures and protonation energies of protonated species of temozolomide are reported. Chemical indices of all isomers and protonated species are also reported. Energies, thermodynamic quantities, rate constants and equilibrium constants of tautomeric and rotameric transformations of all isomers I1↔TZM↔HIa↔HIb↔I2↔I3 in bare and hydrated systems were obtained. Copyright © 2016 Elsevier Inc. All rights reserved.

Structural characterization of two novel potential anticholinesterasic agents

NASA Astrophysics Data System (ADS)

Oliveira, Paulo R.; Wiectzycosky, Franciele; Basso, Ernani A.; Gonçalves, Regina A. C.; Pontes, Rodrigo M.

2003-09-01

Two novel compounds with possible anticholinesterase activity have been synthesized containing a carbamate and a dimethylamine group in 1,2-positions of a cyclohexane ring ( cis and trans isomers). Conformer populations were established by a combination of NMR 1H coupling constant analysis and DFT (B3LYP/6-311+G(d,p)) calculations. 13C chemical shifts were calculated in order to confirm signal attributions. The cis isomer adopts a conformation in which the carbamate group lies at the axial position (>99%), whereas the trans isomer adopts a diequatorial arrangement (98%). These preferences have been explained in terms of syn-1,3-diaxial interactions of the individual groups.

Novel synthesis and characterization of five isomers of (C(70))(2) fullerene dimers.

PubMed

Forman, Grant S; Tagmatarchis, Nikos; Shinohara, Hisanori

2002-01-16

The synthesis and characterization of dimers and polymers, wherein two or more cages are linked, represent an important frontier in the chemistry of fullerene derivatives. A simple and novel method that requires no special apparatus has been developed for the dimerization of [70]fullerene to (C70)2. Upon grinding [70]fullerene in a mortar and pestle in the presence of K2CO3, five structural isomers of (C70)2 have been produced. These isomers are separated from one another via high performance liquid chromatography and are characterized by 13C NMR, UV-vis-NIR absorption and mass spectroscopy.

Mapping and quantifying isomer sets of hydrocarbons (≥ C12) in diesel exhaust, lubricating oil and diesel fuel samples using GC × GC-ToF-MS

NASA Astrophysics Data System (ADS)

Alam, Mohammed S.; Zeraati-Rezaei, Soheil; Liang, Zhirong; Stark, Christopher; Xu, Hongming; MacKenzie, A. Rob; Harrison, Roy M.

2018-05-01

Airborne particles and vapours, like many other environmental samples including water, soils and sediments, contain complex mixtures of hydrocarbons, often deriving from crude oil either before or after fractionation into fuels, lubricants and feedstocks. Comprehensive 2D gas chromatography time-of-flight mass spectrometry (GC × GC-ToF-MS), offers a very powerful technique that separates and identifies many compounds in complicated hydrocarbon mixtures. However, quantification and identification of individual constituents at high ionization energies would require hundreds of expensive (when available) standards for calibration. Although the precise chemical structure of hydrocarbons does matter for their environmental impact and fate, strong similarities can be expected for compounds having very similar chemical structures and carbon numbers. There is, therefore, a clear benefit in an analytical technique which is specific enough to separate different classes of compounds and to distinguish homologous series while avoiding the need to handle each isomer individually. Varying EI (electron impact) ionization mass spectrometry significantly enhances the identification of individual isomers and homologous compound groups, which we refer to as isomer sets. Advances are reported in mapping and quantifying isomer sets of hydrocarbons (≥ C12) in diesel fuel, lubricating oil and diesel exhaust emissions. By using this analysis we report mass closures of ca. 90 and 75 % for diesel fuel and lubricating oil, and identify 85 and 75 % of the total ion current for gas- and particulate-phase diesel exhaust emissions.

Weak hydrogen bond topology in 1,1-difluoroethane dimer: A rotational study.

PubMed

Chen, Junhua; Zheng, Yang; Wang, Juan; Feng, Gang; Xia, Zhining; Gou, Qian

2017-09-07

The rotational spectrum of the 1,1-difluoroethane dimer has been investigated by pulsed-jet Fourier transform microwave spectroscopy. Two most stable isomers have been detected, which are both stabilized by a network of three C-H⋯F-C weak hydrogen bonds: in the most stable isomer, two difluoromethyl C-H groups and one methyl C-H group act as the weak proton donors whilst in the second isomer, two methyl C-H groups and one difluoromethyl C-H group act as the weak proton donors. For the global minimum, the measurements have also been extended to its four 13 C isotopologues in natural abundance, allowing a precise, although partial, structural determination. Relative intensity measurements on a set of μ a -type transitions allowed estimating the relative population ratio of the two isomers as N I /N II ∼ 6/1 in the pulsed jet, indicating a much larger energy gap between these two isomers than that expected from ab initio calculation, consistent with the result from pseudo-diatomic dissociation energies estimation.

The origin of light hydrocarbons

DOE Office of Scientific and Technical Information (OSTI.GOV)

Mango, F.D.

2000-04-01

The light hydrocarbons (LHs) are probably intermediates in the catalytic decomposition of oil to gas. Two lines of evidence support this possibility. First, the reaction was duplicated experimentally under moderate conditions. Second, natural LHs exhibit the characteristics of catalytic products, in particular a proportionality between isomers: (xy{sub i})/(x{sub i}y) = {alpha} (where x and x{sub i} are isomers; y and y{sub i} are isomers that are structurally similar to x and x{sub i}; and {alpha} is a constant). All oils exhibit this relationship with coefficients of correlation reaching 0.99. Isomer ratios change systematically with concentrations, some approaching thermodynamic equilibrium, othersmore » not. The correlations reported are the strongest yet disclosed for the LHs. Isomers are related in triads (e.g., n-hexane {leftrightarrow} 2-methylpentane {leftrightarrow} 3-methylpentane), consistent with cyclopropane precursors. The LHs obtained experimentally are indistinguishable from natural LHs in (xy{sub i})/(x{sub i}y). These relationships are not explained by physical fractionations, equilibrium control, or noncatalytic modes of origin. A catalytic origin, on the other hand, has precedence, economy and experimental support.« less

[Influence of conjugated linoleic acids on metabolic processes in cells and tissues].

PubMed

Siwiec, Ewa; Stachowska, Ewa

2017-01-01

Conjugated linoleic acids (CLA) are constitutional and geometric isomers of this acid. The most commonly consumed geometric isomers are cis-9,trans-11 (c9, t11) CLA and trans-10, cis-12 (t10,c12) CLA. These isomers together with trans-9,trans-11 CLA and trans-10,trans-12 CLA constitute about 90% of all CLA in natural products. Different structure of the isomers affects their functions in the body. Differences in the effects on organs and tissues are sometimes small and sometimes opposed, sometimes the isomers work synergistically. Diverse influence has been shown mainly in neoplastic processes and lipid metabolism. For example, differences in inhibition of proliferation of prostate cancer cells are explained by different pathways: t10,c12 CLA acts on apoptosis and cell cycle control genes, while c9,t11 CLA regulates genes involved in metabolism of arachidonic acid with subsequent impairment of eicosanoids synthesis. Other studies have shown that t10,c12 CLA, but not c9,t11 CLA, can induce fat reduction in adipose tissue and apoptosis of adipocytes in mice.

Quantum optimal control of isomerization dynamics of a one-dimensional reaction-path model dominated by a competing dissociation channel

NASA Astrophysics Data System (ADS)

Kurosaki, Yuzuru; Artamonov, Maxim; Ho, Tak-San; Rabitz, Herschel

2009-07-01

Quantum wave packet optimal control simulations with intense laser pulses have been carried out for studying molecular isomerization dynamics of a one-dimensional (1D) reaction-path model involving a dominant competing dissociation channel. The 1D intrinsic reaction coordinate model mimics the ozone open→cyclic ring isomerization along the minimum energy path that successively connects the ozone cyclic ring minimum, the transition state (TS), the open (global) minimum, and the dissociative O2+O asymptote on the O3 ground-state A1' potential energy surface. Energetically, the cyclic ring isomer, the TS barrier, and the O2+O dissociation channel lie at ˜0.05, ˜0.086, and ˜0.037 hartree above the open isomer, respectively. The molecular orientation of the modeled ozone is held constant with respect to the laser-field polarization and several optimal fields are found that all produce nearly perfect isomerization. The optimal control fields are characterized by distinctive high temporal peaks as well as low frequency components, thereby enabling abrupt transfer of the time-dependent wave packet over the TS from the open minimum to the targeted ring minimum. The quick transition of the ozone wave packet avoids detrimental leakage into the competing O2+O channel. It is possible to obtain weaker optimal laser fields, resulting in slower transfer of the wave packets over the TS, when a reduced level of isomerization is satisfactory.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Aguado, Alfredo; Roncero, Octavio; Zanchet, Alexandre

The impact of the photodissociation of HCN and HNC isomers is analyzed in different astrophysical environments. For this purpose, the individual photodissociation cross sections of HCN and HNC isomers have been calculated in the 7–13.6 eV photon energy range for a temperature of 10 K. These calculations are based on the ab initio calculation of three-dimensional adiabatic potential energy surfaces of the 21 lower electronic states. The cross sections are then obtained using a quantum wave packet calculation of the rotational transitions needed to simulate a rotational temperature of 10 K. The cross section calculated for HCN shows significant differencesmore » with respect to the experimental one, and this is attributed to the need to consider non-adiabatic transitions. Ratios between the photodissociation rates of HCN and HNC under different ultraviolet radiation fields have been computed by renormalizing the rates to the experimental value. It is found that HNC is photodissociated faster than HCN by a factor of 2.2 for the local interstellar radiation field and 9.2 for the solar radiation field, at 1 au. We conclude that to properly describe the HNC/HCN abundance ratio in astronomical environments illuminated by an intense ultraviolet radiation field, it is necessary to use different photodissociation rates for each of the two isomers, which are obtained by integrating the product of the photodissociation cross sections and ultraviolet radiation field over the relevant wavelength range.« less

Transient isomers in the photodissociation of bromoiodomethane

NASA Astrophysics Data System (ADS)

Marcellini, Moreno; Nasedkin, Alexandr; Zietz, Burkhard; Petersson, Jonas; Vincent, Jonathan; Palazzetti, Federico; Malmerberg, Erik; Kong, Qingyu; Wulff, Michael; van der Spoel, David; Neutze, Richard; Davidsson, Jan

2018-04-01

The photochemistry of halomethanes is fascinating for the complex cascade reactions toward either the parent or newly synthesized molecules. Here, we address the structural rearrangement of photodissociated CH2IBr in methanol and cyclohexane, probed by time-resolved X-ray scattering in liquid solution. Upon selective laser cleavage of the C-I bond, we follow the reaction cascade of the two geminate geometrical isomers, CH2I-Br and CH2Br-I. Both meta-stable isomers decay on different time scales, mediated by solvent interaction, toward the original parent molecule. We observe the internal rearrangement of CH2Br-I to CH2I-Br in cyclohexane by extending the time window up to 3 μs. We track the photoproduct kinetics of CH2Br-I in methanol solution where only one isomer is observed. The effect of the polarity of solvent on the geminate recombination pathways is discussed.

UV-induced bond modifications in thymine and thymine dideoxynucleotide: structural elucidation of isomers by differential mobility mass spectrometry.

PubMed

St-Jacques, Antony; Anichina, Janna; Schneider, Bradley B; Covey, Thomas R; Bohme, Diethard K

2010-07-15

Differential mobility spectrometry has been applied to reveal the occurrence of isomerization of thymine nucleobase and of thymine dideoxynucleotide d(5'-TT-3') due to bond redisposition induced by UV irradiation at 254 nm of frozen aqueous solutions of these molecules. Collision-induced dissociation (CID) spectra of electrosprayed photoproducts of the thymine solution suggest the presence of two isomers (the so-called cyclobutane and 6,4-photoproducts) in addition to the proton-bound thymine dimer, and these were separated using differential mobility spectrometry/mass spectrometry (DMS/MS) techniques with water as the modifier. Similar experiments with d(5'-TT-3') revealed the formation of a new isomer of deprotonated thymine dideoxynucleotide upon UV irradiation that was easily distinguished using DMS/MS with isopropanol as the modifier. The results reinforce the usefulness of DMS/MS in isomer separation.

Pronounced photosensitivity of molecular [Ru(bpy)2(OSO)]+ solutions based on two photoinduced linkage isomers.

PubMed

Dieckmann, Volker; Eicke, Sebastian; Rack, Jeffrey J; Woike, Theo; Imlau, Mirco

2009-08-17

Photosensitive properties of [Ru(bpy)(2)(OSO)] PF(6) dissolved in propylene carbonate originating from photoinduced linkage isomerism have been studied by temperature and exposure dependent transmission and UV/Vis absorption spectroscopy. An exceeding photochromic photosensitivity of S = (63 +/- 10) x 10(3) cm l J(-1) mol(-1) is determined. It is attributed to a maximum population of 100% molecules in the photoinduced isomers, a unique absorption cross section per molecule and a very low light exposure of Q(0) = (0.25 +/- 0.03) Ws cm(-2) for isomerism. Relaxation studies of O-bonded to S-bonded isomers at different temperatures verify the existence of two distinct structures of linkage isomers determined by the activation energies of E(A,1) = (0.76 +/- 0.08) eV and E(A,2) = (1.00 +/- 0.14) eV.

Synthesis and isolation of one isomer of C{sub 60}H{sub 6}

DOE Office of Scientific and Technical Information (OSTI.GOV)

Meier, M.S.; Weedon, B.R.; Spielmann, H.P.

1996-11-20

A reaction is reported that produces C{sub 60}H{sub 6} with essentially no contamination by adjacent oxidation states. The compound is formed as one dominant isomer and one minor isomer, and the assignment is reported of the structure of the major isomer through a comparison of its C-H coupled {sup 13}C NMR spectrum with that of 1, 2-C{sub 60}H{sub 2}. Isolation of the major C{sub 60}H{sub 6} band was accomplished by HPLC using a preparative Buckyclutcher column and an automated injector/fraction collector. Analysis of the fraction containing 1 (a cranberry-colored solution when concentrated) by Buckyclutcher and C{sub 18} HPCL in severalmore » different solvent systems has failed to produce evidence of more than one component. The typical isolated yield is 35%. 15 refs., 3 figs.« less

Activation of Reactive MALDI Adduct Ions Enables Differentiation of Dihydroxylated Vitamin D Isomers

NASA Astrophysics Data System (ADS)

Qi, Yulin; Müller, Miriam J.; Volmer, Dietrich A.

2017-12-01

Vitamin D compounds are secosteroids, which are best known for their role in bone health. More recent studies have shown that vitamin D metabolites and catabolites such as dihydroxylated species (e.g., 1,25- and 24,25-dihydroxyvitamin D3) play key roles in the pathologies of various diseases. Identification of these isomers by mass spectrometry is challenging and currently relies on liquid chromatography, as the isomers exhibit virtually identical product ion spectra under collision induced dissociation conditions. Here, we developed a simple MALDI-CID method that utilizes ion activation of reactive analyte/matrix adducts to distinguish isomeric dihydroxyvitamin D3 species, without the need for chromatography separation or chemical derivatization techniques. Specifically, reactive 1,5-diaminonaphthalene adducts of dihydroxyvitamin D3 compounds formed during MADI were activated and specific cleavages in the secosteroid's backbone structure were achieved that produced isomer-diagnostic fragment ions. [Figure not available: see fulltext.

X2Y2 isomers: tuning structure and relative stability through electronegativity differences (X = H, Li, Na, F, Cl, Br, I; Y = O, S, Se, Te).

PubMed

El-Hamdi, Majid; Poater, Jordi; Bickelhaupt, F Matthias; Solà, Miquel

2013-03-04

We have studied the XYYX and X2YY isomers of the X2Y2 species (X = H, Li, Na, F, Cl, Br, I; Y = O, S, Se, Te) using density functional theory at the ZORA-BP86/QZ4P level. Our computations show that, over the entire range of our model systems, the XYYX isomers are more stable than the X2YY forms except for X = F and Y = S and Te, for which the F2SS and F2TeTe isomers are slightly more stable. Our results also point out that the Y-Y bond length can be tuned quite generally through the X-Y electronegativity difference. The mechanism behind this electronic tuning is the population or depopulation of the π* in the YY fragment.

Differentiation of closely related isomers: application of data mining techniques in conjunction with variable wavelength infrared multiple photon dissociation mass spectrometry for identification of glucose-containing disaccharide ions.

PubMed

Stefan, Sarah E; Ehsan, Mohammad; Pearson, Wright L; Aksenov, Alexander; Boginski, Vladimir; Bendiak, Brad; Eyler, John R

2011-11-15

Data mining algorithms have been used to analyze the infrared multiple photon dissociation (IRMPD) patterns of gas-phase lithiated disaccharide isomers irradiated with either a line-tunable CO(2) laser or a free electron laser (FEL). The IR fragmentation patterns over the wavelength range of 9.2-10.6 μm have been shown in earlier work to correlate uniquely with the asymmetry at the anomeric carbon in each disaccharide. Application of data mining approaches for data analysis allowed unambiguous determination of the anomeric carbon configurations for each disaccharide isomer pair using fragmentation data at a single wavelength. In addition, the linkage positions were easily assigned. This combination of wavelength-selective IRMPD and data mining offers a powerful and convenient tool for differentiation of structurally closely related isomers, including those of gas-phase carbohydrate complexes.

Isomeric effects on the self-assembly of a plausible prebiotic nucleoside analogue: A theoretical study

DOE Office of Scientific and Technical Information (OSTI.GOV)

Vallejo, Emmanuel; Fuentes-Cabrera, Miguel; Sumpter, Bobby G.

For this study, the self-assembly properties of N(9)-(2,3-dihydroxypropyl adenine) (DHPA), a plausible prebiotic nucleoside analogue of adenosine, were investigated using density functional theory. Two different isomers were considered, and it is found that while both isomers can form a variety of structures, including chains, one of them is also able to form cages and helixes. When these results were put in the context of substrate supported molecular self-assembly, it is concluded that gas-phase self-assembly studies that consider isomer identity and composition not only can aid interpreting the experimental results, but also reveal structures that might be overlooked otherwise. In particular,more » this study suggest that a double-helical structure made of DHPA molecules which could have implications in prebiotic chemistry and nanotechnology, is stable even at room temperature. For example electrical properties (energy gap of 4.52eV) and a giant permanent electrical dipole moment (49.22 Debye) were found in our larger double-helical structure (3.7 nm) formed by 14 DHPA molecules. Lastly, the former properties could be convenient for construction of organic dielectric-based devices.« less

Isomeric effects on the self-assembly of a plausible prebiotic nucleoside analogue: A theoretical study

DOE PAGES

Vallejo, Emmanuel; Fuentes-Cabrera, Miguel; Sumpter, Bobby G.; ...

2016-10-22

For this study, the self-assembly properties of N(9)-(2,3-dihydroxypropyl adenine) (DHPA), a plausible prebiotic nucleoside analogue of adenosine, were investigated using density functional theory. Two different isomers were considered, and it is found that while both isomers can form a variety of structures, including chains, one of them is also able to form cages and helixes. When these results were put in the context of substrate supported molecular self-assembly, it is concluded that gas-phase self-assembly studies that consider isomer identity and composition not only can aid interpreting the experimental results, but also reveal structures that might be overlooked otherwise. In particular,more » this study suggest that a double-helical structure made of DHPA molecules which could have implications in prebiotic chemistry and nanotechnology, is stable even at room temperature. For example electrical properties (energy gap of 4.52eV) and a giant permanent electrical dipole moment (49.22 Debye) were found in our larger double-helical structure (3.7 nm) formed by 14 DHPA molecules. Lastly, the former properties could be convenient for construction of organic dielectric-based devices.« less

Shape coexistence in the odd-odd nucleus Y 98 : The role of the g 9 / 2 neutron extruder

DOE Office of Scientific and Technical Information (OSTI.GOV)

Urban, W.; Czerwiński, M.; Kurpeta, J.

Excited states in Y-98, populated in neutron-induced fission of U-235 and in spontaneous fission of Cm-248 and Cf-252, have been studied by means of gamma spectroscopy using the Lohengrin fission-fragment separator at ILL Grenoble and the EXILL, Eurogam2, and Gammasphere Ge arrays. Two new isomers have been found in Y-98: a deformed one with T-1/2 = 180(7) ns and a rotational band on top of it, and a spherical one with T-1/2 = 0.45(15) mu s, analogous to the 8(+) isomer in Y-96, corresponding to the (nu g(7/2), pi g(9/2))(8+) spherical configuration. Using the JYFLTRAP Penning trap, an accurate excitationmore » energy of 465.7(7) keV has been determined for the 2.36-s isomer in Y-98. This result and the studies of excited levels in Zr-98, populated in beta-decay of the isomer, indicate a new spin-parity, I-pi = (7)(+) for the isomer. The high spin and the decay properties of this isomer suggest the presence of the 9/2(+)[ 404] neutron extruder orbital in its structure. This is consistent with the large deformation of the isomer, reported recently. The present work does not provide arguments to support the special role of the nu g(7/2)-pi g(9/2) interaction (the spin-orbit-partner, or SOP, mechanism).« less

Biochemistry of Microbial Degradation of Hexachlorocyclohexane and Prospects for Bioremediation

PubMed Central

Lal, Rup; Pandey, Gunjan; Sharma, Pooja; Kumari, Kirti; Malhotra, Shweta; Pandey, Rinku; Raina, Vishakha; Kohler, Hans-Peter E.; Holliger, Christof; Jackson, Colin; Oakeshott, John G.

2010-01-01

Summary: Lindane, the γ-isomer of hexachlorocyclohexane (HCH), is a potent insecticide. Purified lindane or unpurified mixtures of this and α-, β-, and δ-isomers of HCH were widely used as commercial insecticides in the last half of the 20th century. Large dumps of unused HCH isomers now constitute a major hazard because of their long residence times in soil and high nontarget toxicities. The major pathway for the aerobic degradation of HCH isomers in soil is the Lin pathway, and variants of this pathway will degrade all four of the HCH isomers although only slowly. Sequence differences in the primary LinA and LinB enzymes in the pathway play a key role in determining their ability to degrade the different isomers. LinA is a dehydrochlorinase, but little is known of its biochemistry. LinB is a hydrolytic dechlorinase that has been heterologously expressed and crystallized, and there is some understanding of the sequence-structure-function relationships underlying its substrate specificity and kinetics, although there are also some significant anomalies. The kinetics of some LinB variants are reported to be slow even for their preferred isomers. It is important to develop a better understanding of the biochemistries of the LinA and LinB variants and to use that knowledge to build better variants, because field trials of some bioremediation strategies based on the Lin pathway have yielded promising results but would not yet achieve economic levels of remediation. PMID:20197499

Low-symmetry structures of Au32Z (Z = +1, 0, -1) clusters.

PubMed

Jalbout, Abraham F; Contreras-Torres, Flavio F; Pérez, Luis A; Garzón, Ignacio L

2008-01-24

In this work, we have explored new stable structures of the Au32Z (Z = +1, 0, -1) clusters. Theoretical calculations using density functional theory within the generalized-gradient approximation were performed. Our results show that, in the anion state (Au32-), low-symmetry (disordered) structures are preferred over the caged fullerene-like isomer. In addition, the cationic cluster (Au32+) also exhibits a disordered low-symmetry structure as its lowest energy configuration, but it is much closer in energy to the fullerene-like isomer. These results, obtained at T = 0 K, indicate that disordered structures for the Au32- and Au32+ clusters may be detected not only at room temperature, as was experimentally verified for the Au32- one, but also at much lower temperatures.

First-principles energetics of water clusters and ice: A many-body analysis

NASA Astrophysics Data System (ADS)

Gillan, M. J.; Alfè, D.; Bartók, A. P.; Csányi, G.

2013-12-01

Standard forms of density-functional theory (DFT) have good predictive power for many materials, but are not yet fully satisfactory for cluster, solid, and liquid forms of water. Recent work has stressed the importance of DFT errors in describing dispersion, but we note that errors in other parts of the energy may also contribute. We obtain information about the nature of DFT errors by using a many-body separation of the total energy into its 1-body, 2-body, and beyond-2-body components to analyze the deficiencies of the popular PBE and BLYP approximations for the energetics of water clusters and ice structures. The errors of these approximations are computed by using accurate benchmark energies from the coupled-cluster technique of molecular quantum chemistry and from quantum Monte Carlo calculations. The systems studied are isomers of the water hexamer cluster, the crystal structures Ih, II, XV, and VIII of ice, and two clusters extracted from ice VIII. For the binding energies of these systems, we use the machine-learning technique of Gaussian Approximation Potentials to correct successively for 1-body and 2-body errors of the DFT approximations. We find that even after correction for these errors, substantial beyond-2-body errors remain. The characteristics of the 2-body and beyond-2-body errors of PBE are completely different from those of BLYP, but the errors of both approximations disfavor the close approach of non-hydrogen-bonded monomers. We note the possible relevance of our findings to the understanding of liquid water.

Distinguishing between protein dynamics and dye photophysics in single-molecule FRET experiments.

PubMed

Chung, Hoi Sung; Louis, John M; Eaton, William A

2010-02-17

Förster resonance energy transfer (FRET) efficiency distributions in single-molecule experiments contain both structural and dynamical information. Extraction of this information from these distributions requires a careful analysis of contributions from dye photophysics. To investigate how mechanisms other than FRET affect the distributions obtained by counting donor and acceptor photons, we have measured single-molecule fluorescence trajectories of a small alpha/beta protein, i.e., protein GB1, undergoing two-state, folding/unfolding transitions. Alexa 488 donor and Alexa 594 acceptor dyes were attached to cysteines at positions 10 and 57 to yield two isomers-donor(10)/acceptor(57) and donor(57)/acceptor(10)-which could not be separated in the purification. The protein was immobilized via binding of a histidine tag added to a linker sequence at the N-terminus to cupric ions embedded in a polyethylene-glycol-coated glass surface. The distribution of FRET efficiencies assembled from the trajectories is complex with widths for the individual peaks in large excess of that caused by shot noise. Most of this complexity can be explained by two interfering photophysical effects-a photoinduced red shift of the donor dye and differences in the quantum yield of the acceptor dye for the two isomers resulting from differences in quenching rate by the cupric ion. Measurements of steady-state polarization, calculation of the donor-acceptor cross-correlation function from photon trajectories, and comparison of the single molecule and ensemble kinetics all indicate that conformational distributions and dynamics do not contribute to the complexity. Copyright 2010 Biophysical Society. Published by Elsevier Inc. All rights reserved.

227 Views of RNA: Is RNA Unique in Its Chemical Isomer Space?

PubMed Central

Meringer, Markus; Goodwin, Jay

2015-01-01

Abstract Ribonucleic acid (RNA) is one of the two nucleic acids used by extant biochemistry and plays a central role as the intermediary carrier of genetic information in transcription and translation. If RNA was involved in the origin of life, it should have a facile prebiotic synthesis. A wide variety of such syntheses have been explored. However, to date no one-pot reaction has been shown capable of yielding RNA monomers from likely prebiotically abundant starting materials, though this does not rule out the possibility that simpler, more easily prebiotically accessible nucleic acids may have preceded RNA. Given structural constraints, such as the ability to form complementary base pairs and a linear covalent polymer, a variety of structural isomers of RNA could potentially function as genetic platforms. By using structure-generation software, all the potential structural isomers of the ribosides (BC5H9O4, where B is nucleobase), as well as a set of simpler minimal analogues derived from them, that can potentially serve as monomeric building blocks of nucleic acid–like molecules are enumerated. Molecules are selected based on their likely stability under biochemically relevant conditions (e.g., moderate pH and temperature) and the presence of at least two functional groups allowing the monomers to be incorporated into linear polymers. The resulting structures are then evaluated by using molecular descriptors typically applied in quantitative structure–property relationship (QSPR) studies and predicted physicochemical properties. Several databases have been queried to determine whether any of the computed isomers had been synthesized previously. Very few of the molecules that emerge from this structure set have been previously described. We conclude that ribonucleosides may have competed with a multitude of alternative structures whose potential proto-biochemical roles and abiotic syntheses remain to be explored. Key Words: Evolution—Chemical evolution—Exobiology—Prebiotic chemistry—RNA world. Astrobiology 15, 538–558. PMID:26200431

Mass Spectrometry Based Identification of Geometric Isomers during Metabolic Stability Study of a New Cytotoxic Sulfonamide Derivatives Supported by Quantitative Structure-Retention Relationships

PubMed Central

Belka, Mariusz; Hewelt-Belka, Weronika; Sławiński, Jarosław; Bączek, Tomasz

2014-01-01

A set of 15 new sulphonamide derivatives, presenting antitumor activity have been subjected to a metabolic stability study. The results showed that besides products of biotransformation, some additional peaks occurred in chromatograms. Tandem mass spectrometry revealed the same mass and fragmentation pathway, suggesting that geometric isomerization occurred. Thus, to support this hypothesis, quantitative structure-retention relationships were applied. Human liver microsomes were used as an in vitro model of metabolism. The biotransformation reactions were tracked by liquid chromatography assay and additionally, fragmentation mass spectra were recorded. In silico molecular modeling at a semi-empirical level was conducted as a starting point for molecular descriptor calculations. A quantitative structure-retention relationship model was built applying multiple linear regression based on selected three-dimensional descriptors. The studied compounds revealed high metabolic stability, with a tendency to form hydroxylated biotransformation products. However, significant chemical instability in conditions simulating human body fluids was noticed. According to literature and MS data geometrical isomerization was suggested. The developed in sillico model was able to describe the relationship between the geometry of isomer pairs and their chromatographic retention properties, thus it supported the hypothesis that the observed pairs of peaks are most likely geometric isomers. However, extensive structural investigations are needed to fully identify isomers’ geometry. An effort to describe MS fragmentation pathways of novel chemical structures is often not enough to propose structures of potent metabolites and products of other chemical reactions that can be observed in compound solutions at early drug discovery studies. The results indicate that the relatively non-expensive and not time- and labor-consuming in sillico approach could be a good supportive tool assisting the identification of cis-trans isomers based on retention data. This methodology can be helpful during the structural identification of biotransformation and degradation products of new chemical entities - potential new drugs. PMID:24893169

Pentalysine β-Carbonylphthalocyanine Zinc: An Effective Tumor-Targeting Photosensitizer for Photodynamic Therapy

PubMed Central

Chen, Zhuo; Zhou, Shanyong; Chen, Jincan; Deng, Yicai; Luo, Zhipu; Chen, Hongwei; Hamblin, Michael R.

2010-01-01

Unsymmetrical phthalocyanine derivatives have been widely studied as photosensitizers for photodynamic therapy (PDT), targeting various tumor types. However, the preparation of unsymmetrical phthalocyanines is always a challenge due to the presence of many possible structural isomers. Herein we report a new unsymmetrical zinc phthalocyanine, pentalysine β-carbonylphthalocyanine zinc (ZnPc-(Lys)5), that was prepared in large quantity and high purity. This is a water-soluble cationic photosensitizer and maintains a high quantum yield of singlet oxygen generation similar to that of unsubstituted zinc phthalocyanine (ZnPc). Compared with anionic ZnPc counterparts, ZnPc-(Lys)5 shows a higher level cellular uptake and 20-fold higher phototoxicity toward tumor cells. Pharmacokinetics and PDT studies of ZnPc-(Lys)5 in S180 tumor-bearing mice showed a high ratio of tumor versus skin retention and significant tumor inhibition. This new molecular framework will allow synthetic diversity in the number of lysine residues incorporated and will facilitate future QSAR studies. PMID:20458713

Theoretical study of ethylbenzenium ions: the mechanism for splitting off ethene, and the formation of a pi complex of ethene and the benzenium ion.

PubMed

Kolboe, Stein; Svelle, Stian; Arstad, Bjørnar

2009-02-05

Structures and energies of protonated ethylbenzene and 2,6-dimethylethylbenzene have been studied by quantum chemical calculations. The main goal is to study the mechanism for splitting off ethene from protonated ethylbenzene. Data are reported for the four ethylbenzenium isomers arising depending on the position of the proton on the benzene ring: a pi complex where ethene is weakly bonded to a benzenium ion and two transition states connected with the cleavage of the ethylbenzenium ion. The larger part of the data that are reported has been obtained at the B3LYP/cc-pVTZ level of theory. Energies obtained by the Gaussian-3 G3B3 composite method are also given. Computations have also been carried out at the MP2/6-311++G(d,p) level of theory. The calculated results can be reconciled with published experimental observations, and they give information about the reaction system that is not obtained by experimental techniques.

Molecular solar thermal energy storage in photoswitch oligomers increases energy densities and storage times.

PubMed

Mansø, Mads; Petersen, Anne Ugleholdt; Wang, Zhihang; Erhart, Paul; Nielsen, Mogens Brøndsted; Moth-Poulsen, Kasper

2018-05-16

Molecular photoswitches can be used for solar thermal energy storage by photoisomerization into high-energy, meta-stable isomers; we present a molecular design strategy leading to photoswitches with high energy densities and long storage times. High measured energy densities of up to 559 kJ kg -1 (155 Wh kg -1 ), long storage lifetimes up to 48.5 days, and high quantum yields of conversion of up to 94% per subunit are demonstrated in norbornadiene/quadricyclane (NBD/QC) photo-/thermoswitch couples incorporated into dimeric and trimeric structures. By changing the linker unit between the NBD units, we can at the same time fine-tune light-harvesting and energy densities of the dimers and trimers so that they exceed those of their monomeric analogs. These new oligomers thereby meet several of the criteria to be met for an optimum molecule to ultimately enter actual devices being able to undergo closed cycles of solar light-harvesting, energy storage, and heat release.

Nuclear magnetic resonance spectroscopy in the structure elucidation and biosynthesis of natural products

DOE Office of Scientific and Technical Information (OSTI.GOV)

Meksuriyen, D.

1988-01-01

Examination of a chloroform extract of Dracaena loureiri Gagnep (Agavaceae), a Thia medicinal plant possessing antibacterial activity, has led to the isolation of fifteen flavenoids. The biogenic relationships among these flavenoids isolated were briefly discussed. Definition of the skeleton and the unambiguous assignment of all of the protons of the isolates was achieved through extensive 2D-homonuclear chemical shift correlation, nuclear Overhauser effect (NOE) difference spectroscopy and 2D-NOE experiments. The {sup 1}H and {sup 13}C NMR spectra of staurosporine, a potent biologically active agent from Streptomyces staurosporeus, were unambiguously assigned by using 2D homonuclear chemical shift correlation, NOE, {sup 1}H-detected heteronuclearmore » multiple-quantum coherence via direct coupling and via multiple-bond coupling for resonance assignments of protonated and nonprotonated carbons, respectively. S. Staurosporeus was found to utilize endogenous and exogenous D- and L-isomers of trytophan in the production of staurosporine. The biosynthesis of staurosporine was examined by employing carbon-14, tritium, and carbon-13 labeled precursors.« less

Interactions in the ionic liquid [EMIM][FAP]: a coupled experimental and computational analysis.

PubMed

Voroshylova, Iuliia V; Teixeira, Filipe; Costa, Renata; Pereira, Carlos M; Cordeiro, M Natália D S

2016-01-28

Gas-phase electronic and structural properties of the room temperature ionic liquid 1-ethyl-3-methylimidazolium tris(perfluoroethyl)trifluorophosphate ([EMIM][FAP]) were studied using density functional theory, and confirmed with results from infrared spectroscopy. A conformational analysis allowed the identification of several plausible conformers of the ion pairs. For the detected conformers, the infrared spectra were predicted and their thermodynamic properties were evaluated. The topology of the electronic density of the most stable conformers of [EMIM][FAP] ion pairs were characterised using the quantum theory of atoms in molecules. A number of possible hydrogen bonds between the cations and anions of the ionic liquid were identified. Excellent correspondence was found between the predicted spectra of gas-phase [EMIM][FAP] conformers and the experimental infrared spectrum, which in turn allowed a clear attribution of the vibration modes of [EMIM][FAP]. Finally, the contribution of the various conformers of both isomers of the [FAP](-) anion to the ionic liquid macro-properties is shown.

UV-induced solvent free synthesis of truxillic acid-bile acid conjugates

NASA Astrophysics Data System (ADS)

Koivukorpi, Juha; Kolehmainen, Erkki

2009-07-01

The solvent free UV-induced [2 + 2] intermolecular cycloaddition of two molecules of 3α-cinnamic acid ester of methyl lithocholate produced in 99% yield of α- and ɛ-truxillic acid-bis(methyl lithocholate) isomers, which possess two structurally different potential binding sites. A prerequisite for this effective solid state reaction is a proper self-assembled crystal structure of the starting conjugate crystallized from acetonitrile. The crystallization of cinnamic acid ester of methyl lithocholate from acetonitrile produces two different crystalline forms (polymorphs), which is the reason for the solid state formation of two isomers of truxillic acid-bis(methyl lithocholate).

Profiling of the molecular weight and structural isomer abundance of macroalgae-derived phlorotannins.

PubMed

Heffernan, Natalie; Brunton, Nigel P; FitzGerald, Richard J; Smyth, Thomas J

2015-01-16

Phlorotannins are a group of complex polymers of phloroglucinol (1,3,5-trihydroxybenzene) unique to macroalgae. These phenolic compounds are integral structural components of the cell wall in brown algae, but also play many secondary ecological roles such as protection from UV radiation and defense against grazing. This study employed Ultra Performance Liquid Chromatography (UPLC) with tandem mass spectrometry to investigate isomeric complexity and observed differences in phlorotannins derived from macroalgae harvested off the Irish coast (Fucus serratus, Fucus vesiculosus, Himanthalia elongata and Cystoseira nodicaulis). Antioxidant activity and total phenolic content assays were used as an index for producing phlorotannin fractions, enriched using molecular weight cut-off dialysis with subsequent flash chromatography to profile phlorotannin isomers in these macroalgae. These fractions were profiled using UPLC-MS with multiple reaction monitoring (MRM) and the level of isomerization for specific molecular weight phlorotannins between 3 and 16 monomers were determined. The majority of the low molecular weight (LMW) phlorotannins were found to have a molecular weight range equivalent to 4-12 monomers of phloroglucinol. The level of isomerization within the individual macroalgal species differed, resulting in substantially different numbers of phlorotannin isomers for particular molecular weights. F. vesiculosus had the highest number of isomers of 61 at one specific molecular mass, corresponding to 12 phloroglucinol units (PGUs). These results highlight the complex nature of these extracts and emphasize the challenges involved in structural elucidation of these compounds.

Profiling of the Molecular Weight and Structural Isomer Abundance of Macroalgae-Derived Phlorotannins

PubMed Central

Heffernan, Natalie; Brunton, Nigel P.; FitzGerald, Richard J.; Smyth, Thomas J.

2015-01-01

Phlorotannins are a group of complex polymers of phloroglucinol (1,3,5-trihydroxybenzene) unique to macroalgae. These phenolic compounds are integral structural components of the cell wall in brown algae, but also play many secondary ecological roles such as protection from UV radiation and defense against grazing. This study employed Ultra Performance Liquid Chromatography (UPLC) with tandem mass spectrometry to investigate isomeric complexity and observed differences in phlorotannins derived from macroalgae harvested off the Irish coast (Fucus serratus, Fucus vesiculosus, Himanthalia elongata and Cystoseira nodicaulis). Antioxidant activity and total phenolic content assays were used as an index for producing phlorotannin fractions, enriched using molecular weight cut-off dialysis with subsequent flash chromatography to profile phlorotannin isomers in these macroalgae. These fractions were profiled using UPLC-MS with multiple reaction monitoring (MRM) and the level of isomerization for specific molecular weight phlorotannins between 3 and 16 monomers were determined. The majority of the low molecular weight (LMW) phlorotannins were found to have a molecular weight range equivalent to 4–12 monomers of phloroglucinol. The level of isomerization within the individual macroalgal species differed, resulting in substantially different numbers of phlorotannin isomers for particular molecular weights. F. vesiculosus had the highest number of isomers of 61 at one specific molecular mass, corresponding to 12 phloroglucinol units (PGUs). These results highlight the complex nature of these extracts and emphasize the challenges involved in structural elucidation of these compounds. PMID:25603345

Structural isomers of polyfluorinated di- and tri-alkylated phosphate ester surfactants present in industrial blends and in microwave popcorn bags.

PubMed

Trier, Xenia; Nielsen, Nikoline Juul; Christensen, Jan H

2011-09-01

In this study, we provide strategies for detecting and quantifying the structural isomers of polyfluorinated di- and tri-alkyl surfactants (PFAS) by mass spectrometry (MS). We specifically investigate polyfluorinated dialkylated phosphate ester surfactants (x:2/y:2 diPAPS, (F(CF(2))( x )CH(2)CH(2)O-P(O)(O)(-)-OCH(2)CH(2)(CF(2))( y )F)) and their thioether analogues (x:2/y:2 S-diPAPS, F(CF(2))( x )CH(2)CH(2)SCH(2)-C[CH(2)O)(2)P(O)(O)(-)]-CH(2)SCH(2)CH(2)(CF(2))( y )F), which are used for industrial applications, such as oil- and water-repellent coatings on paper and board. DiPAPS have been found in human blood and are metabolised to the persistent perfluoroalkyl carboxylic acids (PFCA) in rats. A microwave popcorn bag extract was analysed by ultrahigh-pressure liquid chromatography coupled to a negative electrospray ionisation-quadrupole time-of-flight MS. The extract contained S-diPAPS, diPAPS and trialkylated (triPAPS) impurities. TriPAPS were also present in industrial and synthetic diPAPS standards, and were verified with an 8:2/8:2/8:2 triPAPS standard. The eight elemental compositions (m/z's) of diPAPS in the extract represent 19 precursor ion structures, and the six S-diPAPS m/z's represent at least 13 structures. The diPAPS had [M-H](-) precursor ions of m/z 789, 889,…1,489 and the S-diPAPS of m/z 921, 1,021,…1,421, corresponding to fluorinated chains from C(6-18). Each m/z appeared as one to three chromatographic peaks of structural isomers, where, e.g. m/z 1,189 was present as 10:2/10:2, 8:2/12:2 and 6:2/14:2 diPAPS. The isomers formed different products ions, thus only half of the m/z 1,189 diPAPS concentration was measured with one precursor ion > product ion transition. In general, knowledge about structural isomers of poly-alkylated PFAS is needed for the estimation of types and amounts of perfluorinated degradation products, such as PFCA from diPAPS.

Characterization of Isomeric Glycans by Reversed Phase Liquid Chromatography-Electronic Excitation Dissociation Tandem Mass Spectrometry

NASA Astrophysics Data System (ADS)

Tang, Yang; Wei, Juan; Costello, Catherine E.; Lin, Cheng

2018-04-01

The occurrence of numerous structural isomers in glycans from biological sources presents a severe challenge for structural glycomics. The subtle differences among isomeric structures demand analytical methods that can provide structural details while working efficiently with on-line glycan separation methods. Although liquid chromatography-tandem mass spectrometry (LC-MS/MS) is a powerful tool for mixture analysis, the commonly utilized collision-induced dissociation (CID) method often does not generate a sufficient number of fragments at the MS2 level for comprehensive structural characterization. Here, we studied the electronic excitation dissociation (EED) behaviors of metal-adducted, permethylated glycans, and identified key spectral features that could facilitate both topology and linkage determinations. We developed an EED-based, nanoscale, reversed phase (RP)LC-MS/MS platform, and demonstrated its ability to achieve complete structural elucidation of up to five structural isomers in a single LC-MS/MS analysis. [Figure not available: see fulltext.

Quantum mechanical characterization of the He4ICl weakly bound complex.

PubMed

Valdés, Álvaro; Prosmiti, Rita

2013-08-15

Vibrational calculations are performed for the 12-dimensional He4ICl van der Waals complex using the multiconfiguration time-dependent Hartree (MCTDH) method. The potential energy surface of the cluster is represented as a sum of the triatomic He-ICl ab initio parametrized terms plus the He-He interactions. The topology of the potential presents higher anisotropy compared to the one with a homonuclear dopant, and this is clearly reflected in the structure and energetics of the low-lying conformers of the system. In order to take advantage of the MCTDH method, natural potential fits are employed for the potential energy operator, and also, a mode combination scheme is introduced in order to speed up the computations. Zero-point energy, binding energies, and vibrationally averaged structures of different isomers of the He4ICl cluster are obtained. The present results predict that the (3,1,0) structure, involving three He atoms in the near T-shaped and one He atom in the linear configurations, to be the most stable one in accord with recent experimental findings. Comparisons with previous theoretical and experimental data are presented, and the stability of the high-order conformers is discussed in connection with the multiple minima (global and local) of the underlying potential surface.

Ultrafast Relaxation Dynamics of Au 38 (SC 2 H 4 Ph) 24 Nanoclusters and Effects of Structural Isomerism

DOE Office of Scientific and Technical Information (OSTI.GOV)

Zhou, Meng; Tian, Shubo; Zeng, Chenjie

Structural isomerism in nanoparticles has recently emerged as a new topic and stimulated research interest because the atomic structures of ultrasmall nanoparticles may have great impact on their fundamental properties and applications. We report the correlation between ultrafast relaxation dynamics and atomic structures of two isomers of thiolate-protected Au 38(SC 2H 4Ph) 24. The bi-icosahedral Au 38 (denoted as Au 38Q) with a Au 23 inner core in its atomic structure shows rapid decay (1.5 ps) followed by nanosecond relaxation to the ground state, whereas its structural isomer (Au 38T) exhibits similar relaxation processes, but the rapid decay is acceleratedmore » by ~50% (1.0 ps). The picosecond relaxations in both cases can be assigned to core–shell charge transfer or electronic rearrangement within the metal core. The acceleration of the fast decay in Au38T is ascribed to its unique core structure, which is made up of a mono-icosahedral Au 13 capped by a Au 12 tri-tetrahedron by sharing two atoms. Interestingly, coherent phonon emissions (25 cm –1 for Au 38Q, 27 and 60 cm –1 for Au 38T) are observed in both isomers with pumping in the NIR region. These results illustrate for the first time the importance of atomic structures in the photophysics of same sized gold nanoclusters.« less

Ultrafast Relaxation Dynamics of Au 38 (SC 2 H 4 Ph) 24 Nanoclusters and Effects of Structural Isomerism

DOE PAGES

Zhou, Meng; Tian, Shubo; Zeng, Chenjie; ...

2016-12-22

Structural isomerism in nanoparticles has recently emerged as a new topic and stimulated research interest because the atomic structures of ultrasmall nanoparticles may have great impact on their fundamental properties and applications. We report the correlation between ultrafast relaxation dynamics and atomic structures of two isomers of thiolate-protected Au 38(SC 2H 4Ph) 24. The bi-icosahedral Au 38 (denoted as Au 38Q) with a Au 23 inner core in its atomic structure shows rapid decay (1.5 ps) followed by nanosecond relaxation to the ground state, whereas its structural isomer (Au 38T) exhibits similar relaxation processes, but the rapid decay is acceleratedmore » by ~50% (1.0 ps). The picosecond relaxations in both cases can be assigned to core–shell charge transfer or electronic rearrangement within the metal core. The acceleration of the fast decay in Au38T is ascribed to its unique core structure, which is made up of a mono-icosahedral Au 13 capped by a Au 12 tri-tetrahedron by sharing two atoms. Interestingly, coherent phonon emissions (25 cm –1 for Au 38Q, 27 and 60 cm –1 for Au 38T) are observed in both isomers with pumping in the NIR region. These results illustrate for the first time the importance of atomic structures in the photophysics of same sized gold nanoclusters.« less

Rotational Spectroscopy of the Low Energy Conformer of 2-METHYLBUTYRONITRILE and Search for it Toward Sagittarius B2(N2)

NASA Astrophysics Data System (ADS)

Müller, Holger S. P.; Wehres, Nadine; Zingsheim, Oliver; Lewen, Frank; Schlemmer, Stephan; Grabow, Jens-Uwe; Garrod, Robin T.; Belloche, Arnaud; Menten, Karl M.

2017-06-01

Quite recently, some of us detected iso-propyl cyanide as the first branched alkyl molecule in space. The identification was made in an ALMA Cycle 0 and 1 molecular line survey of Sagittarius B2(N) at 3 mm. The branched isomer was only slightly less abundant than its straight-chain isomer with a ratio of about 2:5. While initial chemical models favored the branched isomer somewhat, more recent models are able to reproduce the observed ratio. Moreover, the models predicted that among the next longer butyl cyanides (BuCNs) 2-methylbutyronitrile (2-MBN) should be more abundant than both n-BuCN and 3-MBN by factors of around 2, with t-BuCN being almost negligible. With the rotational spectra of t- and n-BuCN studied, we investigated those of 2-MBN and 3-MBN betwen ˜40 and ˜400 GHz by conventional absorption spectroscopy and by chirped-pulse and resonator Fourier transform microwave (FTMW) spectroscopy. The analyses were guided by quantum-chemical calculations. A. Belloche, R. T. Garrod, H. S. P. Müller, and K. M. Menten, Science 345 1584. R. T. Garrod, A. Belloche, H. S. P. Müller, and K. M. Menten, Astron. Astrophys., in press; doi: 10.1051/0004-6361/201630254. With the rotational spectra of t- and n-BuCN studied, we investigated those of 2-MBN and 3-MBN betwen ˜40 and ˜400 GHz by conventional absorption spectroscopy and by chirped-pulse and resonator Fourier transform microwave (FTMW) spectroscopy. The analyses were guided by quantum-chemical calculations. Here we report the analysis of the low-energy conformer of 2-MBN and a search for it in our current ALMA data. Two additional conformers are higher by ˜250 and ˜280 cm^{-1}. The low-energy conformer displays a very rich rotational spectrum because of its great asymmetry (κ ≈ 0.14) and large a- and b-dipole moment components. Accurate ^{14}N quadrupole coupling parameters were obtained from the FTMW spectral recordings.

Normal-phase liquid chromatography retention behavior of polycyclic aromatic hydrocarbon and their methyl-substituted derivatives on an aminopropyl stationary phase.

PubMed

Wilson, Walter B; Hayes, Hugh V; Sander, Lane C; Campiglia, Andres D; Wise, Stephen A

2017-09-01

Retention indices for 124 polycyclic aromatic hydrocarbons (PAHs) and 62 methyl-substituted (Me-) PAHs were determined using normal-phase liquid chromatography (NPLC) on a aminopropyl (NH 2 ) stationary phase. PAH retention behavior on the NH 2 phase is correlated to the total number of aromatic carbons in the PAH structure. Within an isomer group, non-planar isomers generally elute earlier than planar isomers. MePAHs generally elute slightly later but in the same region as the parent PAHs. Correlations between PAH retention behavior on the NH 2 phase and PAH thickness (T) values were investigated to determine the influence of non-planarity for isomeric PAHs with four to seven aromatic rings. Correlation coefficients ranged from r = 0.19 (five-ring peri-condensed molecular mass (MM) 252 Da) to r = -0.99 (five-ring cata-condensed MM 278 Da). In the case of the smaller PAHs (MM ≤ 252 Da), most of the PAHs had a planar structure and provided a low correlation. In the case of larger PAHs (MM ≥ 278 Da), nonplanarity had a significant influence on the retention behavior and good correlation between retention and T was obtained for the MM 278 Da, MM 302 Da, MM 328 Da, and MM 378 Da isomer sets. Graphical abstract NPLC separation of the three-, four-, five-, and six-ring PAH isomers with different number of aromatic carbon atoms and degrees of non-planarity (Thickness, T). The inserted figure plots the number of aromatic carbon atoms vs. the log I value for the 124 parent PAHs.

Determination of fucoxanthin isomers in microalgae (Isochrysis sp.) by high-performance liquid chromatography coupled with diode-array detector multistage mass spectrometry coupled with positive electrospray ionization.

PubMed

Crupi, Pasquale; Toci, Aline Theodore; Mangini, Silvio; Wrubl, Federico; Rodolfi, Liliana; Tredici, Mario R; Coletta, Antonio; Antonacci, Donato

2013-05-15

Due to their health benefits, there is growing interest in the production and use of carotenoids from natural sources, e.g. microalgae. To date, only Haematococcus pluvialis and Dunaliella, that accumulate, respectively, astaxanthin and β-carotene in large quantities, are grown commercially. However, interest is also being focused on other xanthophylls, such as (all-E)-fucoxanthin characterized by anti-obesity and anti-carcinogenic effects. In this regard, rigorous chemical and analytical techniques following preparative isolation of components are needed to unequivocally identify individual carotenoids in microalgae. The carotenoid profile of Isochrysis sp. biomass, produced in closed photobioreactors, was determined by reversed-phase C30 (RP-30) high-performance liquid chromatography coupled with diode-array detector mass spectrometry using positive electrospray ionization (HPLC/DAD-MS/ESI(+) ) analysis. Additionally, multistage mass spectrometry (MS(n) ) analyses, together with fine structures of the UV-vis spectra, were used to differentiate structural and geometrical isomers. This technique allowed the simultaneous determination of geometrical, isomers of fucoxanthin (all-E-fucoxanthin, 13Z-, 13'Z- and 9'Z-fucoxanthin), diatoxanthin and 5,8-epoxydiadinoxanthin diasteroisomers (R/S). The analyzed extracts contained fucoxanthin isomers as the major carotenoids and, in particular, (all-E)-fucoxanthin was the main geometrical isomer (~85%) found at a concentration of 17 mg/g of the lyophilized biomass. Considering the high content of fucoxanthin in Isochrysis sp. biomass, the microalga could be proposed as a source of this compound for nutraceutical and pharmaceutical applications. Copyright © 2013 John Wiley & Sons, Ltd.

CYANOMETHANIMINE ISOMERS IN COLD INTERSTELLAR CLOUDS: INSIGHTS FROM ELECTRONIC STRUCTURE AND KINETIC CALCULATIONS

DOE Office of Scientific and Technical Information (OSTI.GOV)

Vazart, Fanny; Latouche, Camille; Skouteris, Dimitrios

2015-09-10

New insights into the formation of interstellar cyanomethanimine, a species of great relevance in prebiotic chemistry, are provided by electronic structure and kinetic calculations for the reaction CN + CH{sub 2} = NH. This reaction is a facile formation route of Z,E-C-cyanomethanimine, even under the extreme conditions of density and temperature typical of cold interstellar clouds. E-C-cyanomethanimine has been recently identified in Sgr B2(N) in the Green Bank Telescope (GBT) PRIMOS survey by P. Zaleski et al. and no efficient formation routes have been envisaged so far. The rate coefficient expression for the reaction channel leading to the observed isomermore » E-C-cyanomethanimine is 3.15 × 10-10 × (T/300){sup 0.152} × e{sup (−0.0948/T)}. According to the present study, the more stable Z-C-cyanomethanimine isomer is formed with a slightly larger yield (4.59 × 10{sup −10} × (T/300){sup 0.153} × e{sup (−0.0871/T)}. As the detection of E-isomer is favored due to its larger dipole moment, the missing detection of the Z-isomer can be due to the sensitivity limit of the GBT PRIMOS survey and the detection of the Z-isomer should be attempted with more sensitive instrumentation. The CN + CH{sub 2} = NH reaction can also play a role in the chemistry of the upper atmosphere of Titan where the cyanomethanimine products can contribute to the buildup of the observed nitrogen-rich organic aerosols that cover the moon.« less

Structure and dynamics of [3.3]paracyclophane as studied by nuclear magnetic resonance and density functional theory calculations.

PubMed

Dodziuk, Helena; Szymański, Sławomir; Jaźwiński, Jarosław; Marchwiany, Maciej E; Hopf, Henning

2010-09-30

Strained cyclophanes with small (-CH(2)-)(n) bridges connecting two benzene rings are interesting objects of basic research, mostly because of the nonplanarity of the rings and of interference of π-electrons of the latter. For title [3.3]paracyclophane, in solutions occurring in two interconverting cis and trans conformers, the published nuclear magnetic resonance (NMR) data are incomplete and involve its partially deuterated isotopomers. In this paper, variable-temperature NMR studies of its perprotio isotopomer combined with DFT quantum chemical calculations provide a complete characterization of the solution structure, NMR parameters, and interconversion of the cis and trans isomers of the title compound. Using advanced methods of spectral analysis, total quantitative interpretation of its proton NMR spectra in both the static and dynamic regimes is conducted. In particular, not only the geminal but also all of the vicinal J(HH) values for the bridge protons are determined, and for the first time, complete Arrhenius data for the interconversion process are reported. The experimental proton and carbon chemical shifts and the (n)J(HH), (1)J(CH), and (1)J(CC) coupling constants are satisfactorily reproduced theoretically by the values obtained from the density functional theory calculations.

New K isomers in the neutron-rich N =100 isotones 162Sm, 163Eu, and 164Gd

NASA Astrophysics Data System (ADS)

Yokoyama, R.; Go, S.; Kameda, D.; Kubo, T.; Inabe, N.; Fukuda, N.; Takeda, H.; Suzuki, H.; Yoshida, K.; Kusaka, K.; Tanaka, K.; Yanagisawa, Y.; Ohtake, M.; Sato, H.; Shimizu, Y.; Baba, H.; Kurokawa, M.; Nishimura, D.; Ohnishi, T.; Iwasa, N.; Chiba, A.; Yamada, T.; Ideguchi, E.; Fujii, T.; Nishibata, H.; Ieki, K.; Murai, D.; Momota, S.; Sato, Y.; Hwang, J. W.; Kim, S.; Tarasov, O. B.; Morrissey, D. J.; Sherrill, B. M.; Simpson, G.; Praharaj, C. R.

2017-03-01

Very neutron-rich Z ˜60 isotopes produced by in-flight fission of a 345 MeV/nucleon 238U beam at the RI Beam Factory, RIKEN Nishina Center, have been studied by delayed γ -ray spectroscopy. New isomers were discovered in the neutron-rich N =100 isotones 162Sm, 163Eu, and 164Gd. Half-lives, γ -ray energies, and relative intensities of these isomers were obtained. Level schemes were proposed for these nuclei and the first 2+ and 4+ states were assigned for the even-even nuclei. The first 2+ and 4+ state energies decrease as the proton numbers get smaller. The energies and the half-lives of the new isomers are very similar to those of 4- isomers known in less neutron-rich N =100 isotones 168Er and 170Yb. A deformed Hartree-Fock with angular momentum projection model suggests Kπ=4- two-quasiparticle states with ν 7 /2 [633 ]⊗ν 1 /2 [521 ] configurations with similar excitation energy. The results suggest that neutron-rich N =100 nuclei are well deformed and the deformation gets larger as Z decreases to 62. The onset of K isomers with the same configuration at almost the same energy in N =100 isotones indicates that the neutron single-particle structures of neutron-rich isotones down to Z =62 do not change significantly from those of the Z =70 stable nuclei. Systematics of the excitation energies of new isomers can be explained without the predicted N =100 shell gap.

Intramolecular mobility of η(5)-ligands in chiral zirconocene complexes and the enantioselectivity of alkene functionalization by organoaluminum compounds.

PubMed

Parfenova, Lyudmila V; Zakirova, Irina V; Kovyazin, Pavel V; Karchevsky, Stanislav G; Istomina, Galina P; Khalilov, Leonard M; Dzhemilev, Usein M

2016-08-09

The effect of solvent nature (CD2Cl2, d8-toluene, d8-THF) on the conformational behavior of neomenthyl-substituted zirconocenes CpInd*ZrCl2 (Cp = η(5)-C5H5, Ind* = η(5)-neomenthylindenyl), CpCp'ZrCl2 (Cp = η(5)-C5H5, Cp' = η(5)-neomenthyl-4,5,6,7-tetrahydroindenyl), and Ind*2ZrCl2 (Ind* = η(5)-neomenthylindenyl) was shown by means of dynamic NMR spectroscopy, and the constants and thermodynamic parameters of conformer exchange were determined. The experimental conformational composition of the complexes was compared with structures obtained by quantum chemical modeling using the DFT methods PBE/3ζ and M06-2X/cc-pVDZ(H, C, Cl)/cc-pVDZ-PP(Zr), which predicted three rotamers in the case of both CpInd*ZrCl2 and CpCp'ZrCl2, and seven rotational isomers for Ind*2ZrCl2, three of these being C2-symmetric and the others being asymmetric. The enantioselectivity of the conformationally mobile complex Ind*2ZrCl2 in the reactions of terminal alkenes with AlR3 (R = Me, Et) was compared with that of rigid ansa-complexes, rac-p-S, p-S-[Y(η(5)-C9H10)2]ZrX2 (Y = SiMe2, C2H4; X = S-binaphtholate). Faster exchange between the conformers of Ind*2ZrCl2 in a chlorinated solvent gives the structural isomer of catalytically active sites, which affords higher substrate conversion and reaction enantioselectivity. Binding of the ligands to ansa-zirconocenes prevents the rotational isomerism of the complexes, providing the same configuration of the β-stereogenic center in the methyl- and ethylalumination products (unlike the conformationally mobile complex Ind*2ZrCl2) with an enantiomeric purity of 50-65%.

The Synthesis and X-ray Structural Characterization of mer and fac isomers of the Technetium(I) Nitrosyl Complex [TcCl(2)(NO)(PNPpr)].

PubMed

Nicholson, T L; Mahmood, A; Refosco, F; Tisato, F; Müller, P; Jones, A G

2009-08-01

The nitrosyl complex H[TcNOCl(4)] reacts with the tridentate ligand bis[(2-diphenylphosphino)propyl]amine (PNPpr) to yield a mixture of the mer or fac isomers of [TcCl(2)(NO)(PNPpr)]. In acetonitrile, where the ligand is freely soluble, reaction occurs at room temperature to yield mostly the mer isomer with the linear nitrosyl ligand cis to the amine ligand; and the phosphine ligands arranged in a mutually trans orientation. The reaction in methanol requires reflux to dissolve the lipophilic ligand and generates the fac isomer of [TcCl2(NO)(PNPpr)] as the major product, with the tridentate ligand in a facial arrangement, leaving the chlorides and nitrosyl ligand in the remaining facial sites. The steric bulk of the tridentate ligand's diphenylphophino- moieties results in a significant distortion from octahedral geometry, with the P-Tc-P bond angle expanded to 99.48(4)°. The infrared spectra display absorptions from these nitrosyl ligands in the 1700 and 1800 cm(-1) regions for the fac and mer isomers respectively. The ESI(+) mass spectra each display the parent ion at 647 m/z.

Homochiral Asymmetric Triacylglycerol Isomers in Egg Yolk.

PubMed

Nagai, Toshiharu; Ishikawa, Keiko; Yoshinaga, Kazuaki; Yoshida, Akihiko; Beppu, Fumiaki; Gotoh, Naohiro

2017-12-01

The composition of triacylglycerol (TAG) positional isomer (-PI) and enantiomer (-E) in immature chicken egg yolk, mature chicken yolk, and chicken meat was examined. POO (consisting of one palmitic acid (P) and two oleic acids (Os)), PPO (consisting of two Ps and one O), and PPL (consisting of two Ps and one linoleic acid (L)) were treated as representative TAG molecular species in all the analytical samples because P, O, and L were the major fatty acids comprising egg and chicken meat. sn-POO (binding P at sn-1 position) was predominant in egg yolks, while sn-OOP and sn-OPO were present in chicken meat. This difference was ascribed to the different roles of these isomers as nutrients, because TAG in egg yolk is important for new born organisms and TAG in chicken meat is used for fat accumulation. The compositions of the TAG isomers in PPO and PPL in egg yolk were similar, and O and L did not bind at the sn-1 position. In contrast, all the isomers of PPO and PPL were found in chicken meat. These results imply that the TAG structure could be modified so that the nutrient requirement is fulfilled in egg yolk and chicken meat.

Inositol Pentakisphosphate Isomers Bind PH Domains with Varying Specificity and Inhibit Phosphoinositide Interactions

DOE Office of Scientific and Technical Information (OSTI.GOV)

S Jackson; S Al-Saigh; C Schultz

2011-12-31

PH domains represent one of the most common domains in the human proteome. These domains are recognized as important mediators of protein-phosphoinositide and protein-protein interactions. Phosphoinositides are lipid components of the membrane that function as signaling molecules by targeting proteins to their sites of action. Phosphoinositide based signaling pathways govern a diverse range of important cellular processes including membrane remodeling, differentiation, proliferation and survival. Myo-Inositol phosphates are soluble signaling molecules that are structurally similar to the head groups of phosphoinositides. These molecules have been proposed to function, at least in part, by regulating PH domain-phosphoinositide interactions. Given the structural similaritymore » of inositol phosphates we were interested in examining the specificity of PH domains towards the family of myo-inositol pentakisphosphate isomers. In work reported here we demonstrate that the C-terminal PH domain of pleckstrin possesses the specificity required to discriminate between different myo-inositol pentakisphosphate isomers. The structural basis for this specificity was determined using high-resolution crystal structures. Moreover, we show that while the PH domain of Grp1 does not possess this high degree of specificity, the PH domain of protein kinase B does. These results demonstrate that some PH domains possess enough specificity to discriminate between myo-inositol pentakisphosphate isomers allowing for these molecules to differentially regulate interactions with phosphoinositides. Furthermore, this work contributes to the growing body of evidence supporting myo-inositol phosphates as regulators of important PH domain-phosphoinositide interactions. Finally, in addition to expanding our knowledge of cellular signaling, these results provide a basis for developing tools to probe biological pathway.« less

Design of liquid crystals with 'de Vries-like' properties: structural variants of carbosilane-terminated 5-phenylpyrimidine mesogens.

PubMed

Schubert, Christopher P J; Müller, Carsten; Bogner, Andreas; Giesselmann, Frank; Lemieux, Robert P

2017-05-14

Structural variants of the 'de Vries-like' mesogen 5-[4-(12,12,14,14,16,16-hexamethyl-12,14,16-trisilaheptadecyloxy)phenyl]-2-hexyloxypyrimidine (QL16-6), including two isomers with branched iso-tricarbosilane end-groups, were synthesized and their mesomorphic and 'de Vries-like' properties were characterized by polarized optical microscopy, differential scanning calorimetry, small angle and 2D X-ray scattering techniques. A comparative analysis of isomers with linear and branched tricarbosilane end-groups shows that they exhibit comparable mesomorphic and 'de Vries-like' properties. Furthermore, the difference in effective molecular length L eff between the linear and branched isomers in the SmA and SmC phases (ca. 4-5 Å), which was derived from 2D X-ray scattering experiments, suggests that the linear tricarbosilane end-group is hemispherical in shape on the time-average, as predicted by a DFT conformational analysis at the B3LYP/6-31G* level.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Gobrecht, David; Cristallo, Sergio; Piersanti, Luciano

Silicon carbide (SiC) grains are a major dust component in carbon-rich asymptotic giant branch stars. However, the formation pathways of these grains are not fully understood. We calculate ground states and energetically low-lying structures of (SiC){sub n}, n = 1, 16 clusters by means of simulated annealing and Monte Carlo simulations of seed structures and subsequent quantum-mechanical calculations on the density functional level of theory. We derive the infrared (IR) spectra of these clusters and compare the IR signatures to observational and laboratory data. According to energetic considerations, we evaluate the viability of SiC cluster growth at several densities andmore » temperatures, characterizing various locations and evolutionary states in circumstellar envelopes. We discover new, energetically low-lying structures for Si{sub 4}C{sub 4}, Si{sub 5}C{sub 5}, Si{sub 15}C{sub 15}, and Si{sub 16}C{sub 16} and new ground states for Si{sub 10}C{sub 10} and Si{sub 15}C{sub 15}. The clusters with carbon-segregated substructures tend to be more stable by 4–9 eV than their bulk-like isomers with alternating Si–C bonds. However, we find ground states with cage geometries resembling buckminsterfullerens (“bucky-like”) for Si{sub 12}C{sub 12} and Si{sub 16}C{sub 16} and low-lying stable cage structures for n ≥ 12. The latter findings thus indicate a regime of cluster sizes that differ from small clusters as well as from large-scale crystals. Thus—and owing to their stability and geometry—the latter clusters may mark a transition from a quantum-confined cluster regime to a crystalline, solid bulk-material. The calculated vibrational IR spectra of the ground-state SiC clusters show significant emission. They include the 10–13 μ m wavelength range and the 11.3 μm feature inferred from laboratory measurements and observations, respectively, although the overall intensities are rather low.« less

CuCl2 for the isolation of a broad array of endohedral fullerenes containing metallic, metallic carbide, metallic nitride, and metallic oxide clusters, and separation of their structural isomers.

PubMed

Stevenson, Steven; Rottinger, Khristina A

2013-08-19

A typical arc-synthesis generates many types of fullerenes and endohedrals. Resulting soot extracts contain a complex mixture of >50 types of fullerenes, metallofullerenes, and their structural isomers. Prior to application development, novel separation methods are required to fractionate this rich array of metallic, metallic carbide, metallic nitride, and metallic oxide endohedrals, all of which can be present in a single, soot extract. Herein, we report the discovery of CuCl2 as a Lewis acid that will selectively precipitate only the more reactive members of each of these endohedral families. The more reactive Sc4O2@Ih-C80, Sc3C2@Ih-C80, and Sc3N@D3h-C78 endohedrals are quickly removed from extracts to greatly decrease the number of endohedrals present in a sample. Experiments indicate that enrichment factors of several orders of magnitude can be achieved within minutes of reaction time. CuCl2 also has sufficient selectivity to resolve and separate structural isomers, as demonstrated with Er2@C82 (isomer I, Cs(6)-C82 versus isomer III). The selective complexation of CuCl2 with fullerenes can be correlated to their first oxidation potential. We estimate a significantly lower threshold of precipitation for CuCl2 (<0.19 V) compared to stronger Lewis acids. Fullerenes and metallofullerenes having first oxidation potentials above 0.19 V tend to remain unreacted in solution. In contrast, species with first oxidation potentials below 0.19 V (vs Fc/Fc(+)) precipitate via complexation, and are easily decomplexed. CuCl2 is compared to Lewis acids having higher precipitation thresholds (e.g., FeCl3) in our goal to predict a priori which endohedrals would remain in solution versus which endohedral species would complex and precipitate. The ability to predict endohedral precipitation a priori is beneficial to the design of purification strategies for metallofullerenes.

Isomer-Specific Spectroscopy of Benzene-(H2O)n, n = 6,7: Benzene's Role in Reshaping Water's Three-Dimensional Networks.

PubMed

Tabor, Daniel P; Kusaka, Ryoji; Walsh, Patrick S; Sibert, Edwin L; Zwier, Timothy S

2015-05-21

The water hexamer and heptamer are the smallest sized water clusters that support three-dimensional hydrogen-bonded networks, with several competing structures that could be altered by interactions with a solute. Using infrared-ultraviolet double resonance spectroscopy, we record isomer-specific OH stretch infrared spectra of gas-phase benzene-(H2O)(6,7) clusters that demonstrate benzene's surprising role in reshaping (H2O)(6,7). The single observed isomer of benzene-(H2O)6 incorporates an inverted book structure rather than the cage or prism. The main conformer of benzene-(H2O)7 is an inserted-cubic structure in which benzene replaces one water molecule in the S4-symmetry cube of the water octamer, inserting itself into the water cluster by engaging as a π H-bond acceptor with one water and via C-H···O donor interactions with two others. The corresponding D(2d)-symmetry inserted-cube structure is not observed, consistent with the calculated energetic preference for the S4 over the D(2d) inserted cube. A reduced-dimension model that incorporates stretch-bend Fermi resonance accounts for the spectra in detail and sheds light on the hydrogen-bonding networks themselves and on the perturbations imposed on them by benzene.

Hyperfine structure in 229gTh3+ as a probe of the 229gTh→ 229mTh nuclear excitation energy.

PubMed

Beloy, K

2014-02-14

We identify a potential means to extract the 229gTh→ 229mTh nuclear excitation energy from precision microwave spectroscopy of the 5F(5/2,7/2) hyperfine manifolds in the ion 229gTh3+. The hyperfine interaction mixes this ground fine structure doublet with states of the nuclear isomer, introducing small but observable shifts to the hyperfine sublevels. We demonstrate how accurate atomic structure calculations may be combined with the measurement of the hyperfine intervals to quantify the effects of this mixing. Further knowledge of the magnetic dipole decay rate of the isomer, as recently reported, allows an indirect determination of the nuclear excitation energy.

Infrared detection of (H 2O) 20 isomers of exceptional stability: A drop-like and a face-sharing pentagonal prism cluster

DOE PAGES

Pradzynski, Christoph C.; Dierking, Christoph W.; Zurheide, Florian; ...

2014-09-01

Water clusters containing fully coordinated water molecules are model systems that mimic the local environment of the condensed phase. Present knowledge about the water cluster size regime in which the transition from the allsurface to the fully solvated water molecules occurs is mainly based on theoretical predictions in lieu of the absence of precisely size resolved experimental measurements. Here, we report size and isomer selective infrared (IR) spectra of (H 2O) 20 clusters tagged with a sodium atom by employing IR excitation modulated photoionization spectroscopy. The observed absorption patterns in the OH stretching ”fingerprint” region are consistent with the theoreticallymore » predicted spectra of two structurally distinct isomers: A drop-like cluster with a fully coordinated (interior) water and an edge-sharing pentagonal prism cluster in which all atoms are on the surface. The observed isomers show exceptional stability and are predicted to be nearly isoenergetic.« less

Facial and meridional isomers of holmium-nitrate N-tert-butylacetamide complexes

NASA Astrophysics Data System (ADS)

Chang, Ye-Di; Xue, Jun-Hui; Kang, Xiao-Yan; Yang, Li-Min; Li, Wei-Hong; Xu, Yi-Zhuang; Zhao, Guo-Zhong; Zhang, Gao-Hui; Liu, Ke-Xin; Chen, Jia-Er; Wu, Jin-Guang

2018-06-01

Two Ho(C6H13NO)3(NO3)3 complexes formed by holmium nitrate and N-tert-butylacetamide (NtBA) (Ho-NtBA(I) in a Cc space group, and Ho-NtBA(II) in a P21/c space group) are reported here to investigate the coordination of lanthanide ions with amide groups. Using X-ray single crystal diffraction, FTIR, Raman, FIR and THz methods the structures of the two complexes were identified, in which Ho3+ is 9-coordinated to three carbonyl oxygen atoms provided by three NtBA ligands and three bidentate nitrate ions to form the "facial" and "meridional" isomers. Their FTIR and Raman spectra indicate the formation of two holmium complexes, the variations of NtBA after holmium coordination and the spectra are similar for the isomers in some extent. Their FIR and THz spectroscopic results show the coordination of holmium ions and THz maybe more sensitive to isomers. The results demonstrate the coordination behaviors of holmium ions and NtBA ligand.

Separation of Opiate Isomers Using Electrospray Ionization and Paper Spray Coupled to High-Field Asymmetric Waveform Ion Mobility Spectrometry

NASA Astrophysics Data System (ADS)

Manicke, Nicholas E.; Belford, Michael

2015-05-01

One limitation in the growing field of ambient or direct analysis methods is reduced selectivity caused by the elimination of chromatographic separations prior to mass spectrometric analysis. We explored the use of high-field asymmetric waveform ion mobility spectrometry (FAIMS), an ambient pressure ion mobility technique, to separate the closely related opiate isomers of morphine, hydromorphone, and norcodeine. These isomers cannot be distinguished by tandem mass spectrometry. Separation prior to MS analysis is, therefore, required to distinguish these compounds, which are important in clinical chemistry and toxicology. FAIMS was coupled to a triple quadrupole mass spectrometer, and ionization was performed using either a pneumatically assisted heated electrospray ionization source (H-ESI) or paper spray, a direct analysis method that has been applied to the direct analysis of dried blood spots and other complex samples. We found that FAIMS was capable of separating the three opiate structural isomers using both H-ESI and paper spray as the ionization source.

Shedding light into the detailed excited-state relaxation pathways and reaction mechanisms of thionaphthol isomers.

PubMed

Riyad, Yasser M; Naumov, Sergej; Hermann, Ralf; Abel, Bernd

2011-02-10

Nanosecond laser flash photolysis employing transient detection of emission and absorption in combination with pulse radiolysis and quantum theory has been employed to shed light into the kinetics, quantum yields, and mechanisms of the deactivation of the first excited singlet state of 1- and 2-thionaphthols (NpSH(S(1))). In contrast to thiophenols (ArSH(S(1))), the results revealed that the decay of the first excited singlet state of 1- and 2-thionaphthols (NpSH(S(1))) is governed by radiationless internal conversion (Φ(IC) = 0.29-0.46; 0.016-0.190) and intersystem crossing (Φ(ISC) = 0.14-0.15; 0.4-0.6), respectively, with pronounced S-H photodissociation (Φ(D) = 0.40-0.55; 0.35-0.40). Fluorescence as a deactivation channel plays a minor role (Φ(F) = 0.001-0.010; 0.010-0.034). Quantum chemical calculations helped in understanding the formation of naphthylthiyl radicals and rationalizing the differences in the efficiency of intersystem crossing of the 1- and 2-thionaphthol systems.

A photoelectron spectroscopy and quantum chemical study on ternary Al-B-O clusters: AlnBO2- and AlnBO2 (n = 2, 3).

PubMed

Ou, Ting; Feng, Yuan; Tian, Wen-Juan; Zhao, Li-Juan; Kong, Xiang-Yu; Xu, Hong-Guang; Zheng, Wei-Jun; Zhai, Hua-Jin

2018-02-14

Both B and Al have high oxygen affinity and their oxidation processes are highly exothermic, hinting at intriguing physical chemistry in ternary Al-B-O clusters. We report a combined photoelectron spectroscopy and density-functional study on the structural, electronic, and bonding properties of Al n BO 2 - and Al n BO 2 (n = 2, 3) clusters. Ground-state vertical detachment energies (VDEs) are measured to be 2.83 and 2.24 eV for Al 2 BO 2 - and Al 3 BO 2 - , respectively. A weak isomer is also observed for Al 3 BO 2 - with a VDE of 1.31 eV. Coalescence-kick global searches allow the identification of candidate structures, confirmed via comparisons with experiment. The Al 2 BO 2 - anion is V-shaped in geometry, C s ( 1 A'), with an Al center connecting to OB and OAl terminals. It can be viewed alternatively as the fusion of BOAl and AlOAl by sharing an Al atom. Al 3 BO 2 - has a C s ( 2 A'') global minimum in which an Al 2 dimer interacts with bridging boronyl (BO) and an OAl unit, as well as a low-lying C 2v ( 2 B 2 ) isomer consisting of boronyl and OAl that are doubly bridged by two Al atoms. The BO 2 block (linear O[double bond, length as m-dash]B[double bond, length as m-dash]O chain) is nonexistent in any of the anion and neutral species. Chemical bonding in these Al-B-O clusters is elucidated via canonical molecular orbitals and adaptive natural density partitioning. The cluster structures are also rationalized using the concept of sequential and competitive oxidation of B versus Al centers in Al n B. The first O atom prefers to oxidize B and form BO, whereas the second O atom has options to interact with a fresh Al/Al n /Al n B unit or a BO group. The former route wins thermodynamically, leading to the observed geometries.

The Photodissociation of HCN and HNC: Effects on the HNC/HCN Abundance Ratio in the Interstellar Medium

NASA Astrophysics Data System (ADS)

Aguado, Alfredo; Roncero, Octavio; Zanchet, Alexandre; Agúndez, Marcelino; Cernicharo, José

2017-03-01

The impact of the photodissociation of HCN and HNC isomers is analyzed in different astrophysical environments. For this purpose, the individual photodissociation cross sections of HCN and HNC isomers have been calculated in the 7-13.6 eV photon energy range for a temperature of 10 K. These calculations are based on the ab initio calculation of three-dimensional adiabatic potential energy surfaces of the 21 lower electronic states. The cross sections are then obtained using a quantum wave packet calculation of the rotational transitions needed to simulate a rotational temperature of 10 K. The cross section calculated for HCN shows significant differences with respect to the experimental one, and this is attributed to the need to consider non-adiabatic transitions. Ratios between the photodissociation rates of HCN and HNC under different ultraviolet radiation fields have been computed by renormalizing the rates to the experimental value. It is found that HNC is photodissociated faster than HCN by a factor of 2.2 for the local interstellar radiation field and 9.2 for the solar radiation field, at 1 au. We conclude that to properly describe the HNC/HCN abundance ratio in astronomical environments illuminated by an intense ultraviolet radiation field, it is necessary to use different photodissociation rates for each of the two isomers, which are obtained by integrating the product of the photodissociation cross sections and ultraviolet radiation field over the relevant wavelength range.

Rotational Spectrum and Large Amplitude Motions of 3,4-, 2,5- and 3,5-DIMETHYL-BENZALDEHYDE

NASA Astrophysics Data System (ADS)

Kleiner, I.; Tudorie, M.; Jahn, M.; Grabow, J.-U.; Goubet, M.

2012-06-01

The microwave spectra of the 3,4-, 2,5- and 3,5-Dimethyl-Benzaldehyde (DMBA) molecules have been recorded for the first time in the 2-26.5 GHz frequency range, using the COBRA-FTMW spectrometer in Hannover, with an instrumental uncertainty of 0.5 kHz for unblended lines. The experimental assignments and fits are supplemented by ab initio quantum chemical calculations,conformational energy landscape, and dipole moment components. The analysis of the spectra for the three isomers are in progress. The latest results, including spectroscopic constants and large amplitude motion parameters, will be presented. This investigation follows the study of the spectra of the 4-Methyl-Benzaldehyde molecule. The DMBA isomers belong to a similar series of molecules formally obtained by adding a second methyl group at the aromatic ring. These molecules serve as prototype systems for the development of the theoretical model of asymmetric top molecules having Cs symmetry while containing two inequivalent methyl tops (C3v), exhibiting different barrier heights and coupling terms to methyl internal rotation. Thus, the DMBA isomers represent benchmark species for testing the two-top internal rotors BELGI program written recently. Supported by the ANR-08-BLAN-0054 contract (France), the Deutsche Forschungsgemeinschaft, and the Land Niedersachsen (Germany). H. Saal, W. Caminati, I. Kleiner, A. R. Hight-Walker, J. T. Hougen, J.-U. Grabow, to be published. M. Tudorie, I. Kleiner, J. T. Hougen, S. Melandri, L. W. Sutikdja, W. Stahl, J. Mol. Spectrosc., 269 (2011), 211-225

Normal-phase liquid chromatography retention behavior of polycyclic aromatic sulfur heterocycles and alkyl-substituted polycyclic aromatic sulfur heterocycle isomers on an aminopropyl stationary phase.

PubMed

Wilson, Walter B; Hayes, Hugh V; Sander, Lane C; Campiglia, Andres D; Wise, Stephen A

2018-02-01

Retention indices for 67 polycyclic aromatic sulfur heterocycles (PASHs) and 80 alkyl-substituted PASHs were determined using normal-phase liquid chromatography (NPLC) on an aminopropyl (NH 2 ) stationary phase. The retention behavior of PASH on the NH 2 phase is correlated with the number of aromatic carbon atoms and two structural characteristics have a significant influence on their retention: non-planarity (thickness, T) and the position of the sulfur atom in the bay-region of the structure. Correlations between solute retention on the NH 2 phase and T of PASHs were investigated for three cata-condensed (cata-) PASH isomer groups: (a) 13 four-ring molecular mass (MM) 234 Da cata-PASHs, (b) 20 five-ring MM 284 Da cata-PASHs, and (c) 12 six-ring MM 334 Da cata-PASHs. Correlation coefficients ranged from r = -0.49 (MM 234 Da) to r = -0.65 (MM 334 Da), which were significantly lower than structurally similar PAH isomer groups (r = -0.70 to r = -0.99). The NPLC retention behavior of the PASHs are compared to similar results for PAHs.

Fine tuning and orientation control of surface Cu complexes on TiO2(110) premodified with mercapto compounds: the effect of different mercapto group positions.

PubMed

Takakusagi, Satoru; Nojima, Hirotaka; Ariga, Hiroko; Uehara, Hiromitsu; Miyazaki, Kotaro; Chun, Wang-Jae; Iwasawa, Yasuhiro; Asakura, Kiyotaka

2013-09-07

Three-dimensional structures of vacuum-deposited Cu species formed on TiO2(110) surfaces premodified with three mercaptobenzoic acid (MBA) isomers were studied using polarization-dependent total reflection fluorescence X-ray absorption fine structure (PTRF-XAFS). We explored the possibility of fine tuning and orientation control of the surface Cu structures, including their coordination and configuration against the surface, according to the different mercapto group positions of the three MBA isomers (o-, m-, and p-MBA). Almost linear S-Cu-O (lattice O of TiO2) surface compounds were formed on the three MBA-modified TiO2(110) surfaces; however, the orientation of the Cu species on the o- and m-MBA-modified TiO2(110) surfaces (40-45° inclined from the surface normal) was different from that on the p-MBA-modified TiO2(110) surface (60° from the surface normal). This work suggests that the selection of a different MBA isomer for premodification of a single crystal TiO2(110) surface enables fine tuning and orientation control of surface Cu complexes.

CP/MAS 13C NMR characterization of the isomeric states and intermolecular packing in tris(8-hydroxyquinoline) aluminum(III) (Alq3).

PubMed

Kaji, Hironori; Kusaka, Yasunari; Onoyama, Goro; Horii, Fumitaka

2006-04-05

The isomeric states and intermolecular packing of tris(8-hydroxyquinoline) aluminum(III) (Alq(3)) in the alpha-, gamma-, and delta-crystalline forms and in the amorphous state, which are important for understanding the light-emitting and electron-transport properties, have been analyzed by CP/MAS (13)C NMR. This simple NMR experiment shows that the isomeric state of alpha- and amorphous Alq(3) is meridional, whereas that of gamma- and delta-Alq(3) is facial. In the amorphous Alq(3), the inclusion of facial isomers has been under debate. Our experiments show that meridional isomers are dominant in the amorphous Alq(3), although the existence of facial isomers cannot be completely denied. The local structure of amorphous Alq(3) is similar to that of alpha-Alq(3) and is significantly different from those of gamma- and delta-Alq(3). Among these Alq(3) samples, the effect of intermolecular interaction is not found only for gamma-Alq(3). This finding can explain the good solvent solubility of gamma-Alq(3), compared with the other crystalline forms. It is also shown that the structures are locally disordered not only for amorphous Alq(3) but also for alpha-Alq(3), although clear X-ray diffraction peaks are observed for alpha-Alq(3). In contrast, the local structures of gamma- and delta-Alq(3) are well defined. A clear relation is found between the spectral patterns of CP/MAS (13)C NMR and the fluorescence wavelengths; the samples, which consist of facial isomers, show blue-shifted fluorescence compared with those of meridionals.

A theoretical DFT study on the structural parameters and azide-tetrazole equilibrium in substituted azidothiazole systems.

PubMed

Abu-Eittah, Rafie H; El-Kelany, Khaled E

2012-12-01

Azido-tetrazole equilibrium is sensitive to: substitution, solvent, temperature and phase. In this work, the effects of the type and position of substitution on the thiazole ring of azidothiazoles on its structural parameters and on the azido-tetrazole equilibrium have been theoretically investigated using the density functional procedures at the B3LYP/6-311G(∗∗) level of theory. This study includes the investigation of the equilibrium geometry, the transformation of the trans-conformer to the cis one then the ring closure to the tetrazole isomer. The transition states of the two steps were located, confirmed and the structural parameters were calculated. In all the steps of calculations, geometry optimization was considered. The results obtained indicate that substitution by: -NO(2) and -CN group shifts the equilibrium to the azide side and in some cases the tetrazole isomer is not obtained. On the other hand, substitution by: -NH(2) and -OH groups shifts the equilibrium to the tetrazole side and in some cases the azide isomer is not obtained and if formed changes spontaneously to the tetrazole isomer. The decisive parameters which determine the position of the equilibrium are: charge density on atoms N3 and N8, rearrangement of bond length and bond angles during the process of cyclization and variation of dipole moment as a result of cyclization. Results of this work indicate that substitution on C5 is more efficient than substitution on C4 of the thiazole ring. Copyright © 2012 Elsevier B.V. All rights reserved.

Photochemical and Photophysical Properties of Phthalocyanines Modified with Optically Active Alcohols.

PubMed

Ramos, Aline A; Nascimento, Francisco B; de Souza, Thaiza F M; Omori, Alvaro T; Manieri, Tânia M; Cerchiaro, Giselle; Ribeiro, Anderson O

2015-07-24

Three phthalocyanine derivatives were synthesized and characterized: one modified with a racemic mixture of 1-(4-bromophenyl)ethanol and two other macrocycles modified with each one of the enantioenriched isomers (R)-1-(4-bromophenyl)ethanol and (S)-1-(4-bromophenyl)ethanol. The compounds were characterized by 1H-NMR spectroscopy, mass spectrometry, UV-Vis absorption, and excitation and emission spectra. Additionally, partition coefficient values and the quantum yield of the generation of oxygen reactive species were determined. Interestingly, the phthalocyanine containing a (R)-1-(4-bromophenyl)ethoxy moiety showed higher quantum yield of reactive oxygen species generation than other compounds under the same conditions. In addition, the obtained fluorescence microscopy and cell viability results have shown that these phthalocyanines have different interactions with mammary MCF-7 cells. Therefore, our results indicate that the photochemical and biological properties of phthalocyanines with chiral ligands should be evaluated separately for each enantiomeric species.

Heme Distortions in Sperm-Whale Carbonmonoxy Myoglobin: Correlations between Rotational Strengths and Heme Distortions in MD-Generated Structures

DOE Office of Scientific and Technical Information (OSTI.GOV)

KIEFL,CHRISTOPH; SCREERAMA,NARASIMHA; LU,YI

2000-07-13

The authors have investigated the effects of heme rotational isomerism in sperm-whale carbonmonoxy myoglobin using computational techniques. Several molecular dynamics simulations have been performed for the two rotational isomers A and B, which are related by a 180{degree} rotation around the {alpha}-{gamma} axis of the heme, of sperm-whale carbonmonoxy myoglobin in water. Both neutron diffraction and NMR structures were used as starting structures. In the absence of an experimental structure, the structure of isomer B was generated by rotating the heme in the structure of isomer A. Distortions of the heme from planarity were characterized by normal coordinate structural decompositionmore » and by the angle of twist of the pyrrole rings from the heme plane. The heme distortions of the neutron diffraction structure were conserved in the MD trajectories, but in the NMR-based trajectories, where the heme distortions are less well defined, they differ from the original heme deformations. The protein matrix induced similar distortions on the heroes in orientations A and B. The results suggest that the binding site prefers a particular macrocycle conformation, and a 180{degree} rotation of the heme does not significantly alter the protein's preference for this conformation. The intrinsic rotational strengths of the two Soret transitions, separated according to their polarization in the heme plane, show strong correlations with the ruf-deformation and the average twist angle of the pyrrole rings. The total rotational strength, which includes contributions from the chromophores in the protein, shows a weaker correlation with heme distortions.« less

Structural, kinetic, and thermodynamic characterization of the interconverting isomers of MS-325, a gadolinium(III)-based magnetic resonance angiography contrast agent.

PubMed

Tyeklar, Zoltan; Dunham, Stephen U; Midelfort, Katarina; Scott, Daniel M; Sajiki, Hirano; Ong, Karen; Lauffer, Randall B; Caravan, Peter; McMurry, Thomas J

2007-08-06

The amphiphilic gadolinium complex MS-325 ((trisodium-{(2-(R)-[(4,4-diphenylcyclohexyl) phosphonooxymethyl] diethylenetriaminepentaacetato) (aquo)gadolinium(III)}) is a contrast agent for magnetic resonance angiography (MRA). MS-325 comprises a GdDTPA core with an appended phosphodiester moiety linked to a diphenylcyclohexyl group to facilitate noncovalent binding to serum albumin and extension of the plasma half-life in vivo. The chiral DTPA ligand (R) was derived from L-serine, and upon complexation with gadolinium, forms two interconvertible diastereomers, denoted herein as isomers A and B. X-ray crystallography of the tris(ethylenediamine)cobalt(III) salt derivative of isomer A revealed a structure in the polar acentric space group P32. The structure consisted of three independent molecules of the gadolinium complex in the asymmetric unit along with three Delta-[Co(en)3]3+ cations, and it represents an unusual example of spontaneous Pasteur resolution of the cobalt cation. The geometry of the coordination core was best described as a distorted trigonal prism, and the final R factor was 5.6%. The configuration of the chiral central nitrogen of the DTPA core was S. The Gd-water (2.47-2.48 A), the Gd-acetate oxygens (2.34-2.42 A), and the Gd-N bond distances (central N, 2.59-2.63 A; terminal N, 2.74-2.80 A) were similar to other reported GdDTPA structures. The structurally characterized single crystal was one of two interconvertable diastereomers (isomers A and B) that equilibrated to a ratio of 1.81 to 1 at pH 7.4 and were separable at elevated pH by ion-exchange chromatography. The rate of isomerization was highly pH dependent: k1 = (1.45 +/- 0.08) x 102[H+] + (4.16 +/- 0.30) x 105[H+]2; k-1 = (2.57 +/- 0.17) x 102[H+] + (7.54 +/- 0.60) x 105[H+]2.

Temperature effects on prevalent structures of hydrated Fe{sup +} complexes: Infrared spectroscopy and DFT calculations of Fe{sup +}(H{sub 2}O){sub n} (n = 3–8)

DOE Office of Scientific and Technical Information (OSTI.GOV)

Ohashi, Kazuhiko, E-mail: kazu@chem.kyushu-univ.jp; Sekiya, Hiroshi; Sasaki, Jun

2014-12-07

Hydrated Fe{sup +} ions are produced in a laser-vaporization cluster source of a triple quadrupole mass spectrometer. The Fe{sup +}(H{sub 2}O){sub n} (n = 3–8) complexes are mass-selected and probed with infrared (IR) photodissociation spectroscopy in the OH-stretch region. Density functional theory (DFT) calculations are also carried out for analyzing the experimental IR spectra and for evaluating thermodynamic quantities of low-lying isomers. Solvation through H-bonding instead of direct coordination to Fe{sup +} is observed already at n = 3, indicating the completion of the first hydration shell with two H{sub 2}O molecules. Size dependent variations in the spectra for nmore » = 5–7 provide evidence for the second-shell completion at n = 6, where a linearly coordinated Fe{sup +}(H{sub 2}O){sub 2} subunit is solvated with four H{sub 2}O molecules. Overall spectral features for n = 3–8 agree well with those predicted for 2-coordinated structures. DFT calculations predict that such 2-coordinated structures are lowest in energy for smaller n. However, 4-coordinated isomers are predicted to be more stable for n = 7 and 8; the energy ordering is in conflict with the IR spectroscopic observation. Examination of free energy as a function of temperature suggests that the ordering of the isomers at warmer temperatures can be different from the ordering near 0 K. For n = 7 and 8, the 4-coordinated isomers should be observed at low temperatures because they are lowest in enthalpy. Meanwhile, outer-shell waters in the 2-coordinated structures are bound less rigidly; their contribution to entropy is rather large. The 2-coordinated structures become abundant at warmer temperatures, owing to the entropy effect.« less

Density functional theory study of structural and electronic properties of trans and cis structures of thiothixene as a nano-drug.

PubMed

Noori Tahneh, Akram; Bagheri Novir, Samaneh; Balali, Ebrahim

2017-11-25

The geometrical structure, electronic and optical properties, electronic absorption spectra, vibrational frequencies, natural charge distribution, MEP analysis and thermodynamic properties of the trans and cis structures of the drug thiothixene were investigated using density functional theory (DFT) and time-dependent DFT (TDDFT) methods with the B3LYP hybrid functional and 6-311 + G(d,p) basis set. The results of the calculations demonstrate that the cis structure of thiothixene has appropriate quantum properties that can act as an active medicine. The relative energies of trans and cis structures of thiothixene shows that the cis structure is more stable than the trans structure, with a small energy difference. TDDFT calculations show that the cis structure of thiothixene has the best absorption properties. The calculated NLO properties show that the NLO properties of the cis structure of thiothixene are higher than the trans structure, and the fact that the chemical hardness of the cis structure is lower than that of the trans structure that indicates that the reactivity and charge transfer of the cis isomer of thiothixene is higher than that of trans thiothixene. The molecular electrostatic potential (MEP) maps of both structures of thiothixene demonstrate that the oxygen atoms of the molecule are appropriate areas for electrophilic reactions. The vibrational frequencies of the two conformations of thiothixene demonstrate that both structures of thiothixene have almost similar modes of vibrations. The calculated thermodynamic parameters show that these quantities increase with enhancing temperature due to the enhancement of molecular vibrational intensities with temperature. Graphical abstract Trans/Cis isomerization of thiothixene drug.

Ab initio structures and polarizabilities of sodium clusters

NASA Astrophysics Data System (ADS)

Kronik, Leeor; Vasiliev, Igor; Jain, Manish; Chelikowsky, James R.

2001-09-01

We present quantitative ab initio calculations for Na cluster structures and polarizabilities, for all cluster sizes up to 20 atoms. Our calculations are performed by combining an ab initio core-corrected pseudopotential and a gradient-corrected density functional within a real space approach. We find the cluster bonding to be very floppy and catalog a host of low-energy quasi-degenerate isomers for all second-decade clusters. The existence of these isomers results in a band of polarizability values for each cluster size even at zero temperature. This eliminates any finer structure in the polarizability curve. We further show that the experimental polarizability values are consistently underestimated by calculations at zero temperature. By computing the effects of structure expansion and distortion due to a finite temperature we arrive at a quantitative agreement between theory and experiment.

Separation and identification of structural isomers by quadrupole collision-induced dissociation-hydrogen/deuterium exchange-infrared multiphoton dissociation (QCID-HDX-IRMPD).

PubMed

Gucinski, Ashley C; Somogyi, Arpád; Chamot-Rooke, Julia; Wysocki, Vicki H

2010-08-01

A new approach that uses a hybrid Q-FTICR instrument and combines quadrupole collision-induced dissociation, hydrogen-deuterium exchange, and infrared multiphoton dissociation (QCID-HDX-IRMPD) has been shown to effectively separate and differentiate isomeric fragment ion structures present at the same m/z. This method was used to study protonated YAGFL-OH (free acid), YAGFL-NH(2) (amide), cyclic YAGFL, and YAGFL-OCH(3) (methyl ester). QCID-HDX of m/z 552.28 (C(29)H(38)N(5)O(6)) from YAGFL-OH reveals at least two distributions of ions corresponding to the b(5) ion and a non-C-terminal water loss ion structure. Subsequent IRMPD fragmentation of each population shows distinct fragmentation patterns, reflecting the different structures from which they arise. This contrasts with data for YAGFL-NH(2) and YAGFL-OCH(3), which do not show two distinct H/D exchange populations for the C(29)H(38)N(5)O(6) structure formed by NH(3) and HOCH(3) loss, respectively. Relative extents of exchange for C(29)H(38)N(5)O(6) ions from six sequence isomers (YAGFL, AGFLY, GFLYA, FLYAG, LYAGF, and LFGAY) show a sequence dependence of relative isomer abundance. Supporting action IRMPD spectroscopy data are also presented herein and also show that multiple structures are present for the C(29)H(38)N(5)O(6) species from YAGFL-OH. Copyright 2010. Published by Elsevier Inc.

Accurate ab initio Quartic Force Fields of Cyclic and Bent HC2N Isomers

NASA Technical Reports Server (NTRS)

Inostroza, Natalia; Huang, Xinchuan; Lee, Timothy J.

2012-01-01

Highly correlated ab initio quartic force field (QFFs) are used to calculate the equilibrium structures and predict the spectroscopic parameters of three HC2N isomers. Specifically, the ground state quasilinear triplet and the lowest cyclic and bent singlet isomers are included in the present study. Extensive treatment of correlation effects were included using the singles and doubles coupled-cluster method that includes a perturbational estimate of the effects of connected triple excitations, denoted CCSD(T). Dunning s correlation-consistent basis sets cc-pVXZ, X=3,4,5, were used, and a three-point formula for extrapolation to the one-particle basis set limit was used. Core-correlation and scalar relativistic corrections were also included to yield highly accurate QFFs. The QFFs were used together with second-order perturbation theory (with proper treatment of Fermi resonances) and variational methods to solve the nuclear Schr dinger equation. The quasilinear nature of the triplet isomer is problematic, and it is concluded that a QFF is not adequate to describe properly all of the fundamental vibrational frequencies and spectroscopic constants (though some constants not dependent on the bending motion are well reproduced by perturbation theory). On the other hand, this procedure (a QFF together with either perturbation theory or variational methods) leads to highly accurate fundamental vibrational frequencies and spectroscopic constants for the cyclic and bent singlet isomers of HC2N. All three isomers possess significant dipole moments, 3.05D, 3.06D, and 1.71D, for the quasilinear triplet, the cyclic singlet, and the bent singlet isomers, respectively. It is concluded that the spectroscopic constants determined for the cyclic and bent singlet isomers are the most accurate available, and it is hoped that these will be useful in the interpretation of high-resolution astronomical observations or laboratory experiments.

Experimental and density functional theoretical investigations of linkage isomerism in six-coordinate FeNO(6) iron porphyrins with axial nitrosyl and nitro ligands.

PubMed

Novozhilova, Irina V; Coppens, Philip; Lee, Jonghyuk; Richter-Addo, George B; Bagley, Kimberly A

2006-02-15

A critical component of the biological activity of NO and nitrite involves their coordination to the iron center in heme proteins. Irradiation (330 < lambda < 500 nm) of the nitrosyl-nitro compound (TPP)Fe(NO)(NO(2)) (TPP = tetraphenylporphyrinato dianion) at 11 K results in changes in the IR spectrum associated with both nitro-to-nitrito and nitrosyl-to-isonitrosyl linkage isomerism. Only the nitro-to-nitrito linkage isomer is obtained at 200 K, indicating that the isonitrosyl linkage isomer is less stable than the nitrito linkage isomer. DFT calculations reveal two ground-state conformations of (porphine)Fe(NO)(NO(2)) that differ in the relative axial ligand orientations (i.e., GS parallel and GS perpendicular). In both conformations, the FeNO group is bent (156.4 degrees for GS parallel, 159.8 degrees for GS perpendicular) for this formally {FeNO}(6) compound. Three conformations of the nitrosyl-nitrito isomer (porphine)Fe(NO)(ONO) (MSa parallel, MSa perpendicular, and MSa(L)) and two conformations of the isonitrosyl-nitro isomer (porphine)Fe(ON)(NO(2)) (MSb parallel and MSb perpendicular) are identified, as are three conformations of the double-linkage isomer (porphine)Fe(ON)(ONO) (MSc parallel, MSc perpendicular, MSc(L)). Only 2 of the 10 optimized geometries contain near-linear FeNO (MSa(L)) and FeON (MSc(L)) bonds. The energies of the ground-state and isomeric structures increase in the order GS < MSa < MSb < MSc. Vibrational frequencies for all of the linkage isomers have been calculated, and the theoretical gas-phase absorption spectrum of (porphine)Fe(NO)(NO(2)) has been analyzed to obtain information on the electronic transitions responsible for the linkage isomerization. Comparison of the experimental and theoretical IR spectra does not provide evidence for the existence of a double linkage isomer of (TPP)Fe(NO)(NO(2)).

Effects of side-chain orientation on the backbone conformation of the dehydrophenylalanine residue. Theoretical and X-ray study.

PubMed

Buczek, Aneta; Siodłak, Dawid; Bujak, Maciej; Broda, Małgorzata A

2011-04-21

Two E isomers of α,β-dehydro-phenylalanine, Ac-(E)-ΔPhe-NHMe (1a) and Ac-(E)-ΔPhe-NMe(2) (2a), have been synthesized and their low temperature structures determined by single-crystal X-ray diffraction. A systematic theoretical analysis was performed on these molecules and their Z isomers (1b and 2b). The ϕ,ψ potential energy surfaces were calculated at the MP2/6-31+G(d,p) and B3LYP/6-31+G(d,p) levels in the gas phase and at the B3LYP/6-31+G(d,p) level in the chloroform and water solutions with the SCRF-PCM method. All minima were fully optimized by the MP2 and DFT methods, and their relative stabilities were analyzed in terms of π-conjugation, internal H-bonds, and dipole-dipole interactions between carbonyl groups. The results indicate that all the studied compounds can adopt the conformation H (ϕ, ψ ≈ ±40°, ∓120°) which is atypical for standard amino acids residues. A different arrangement of the side chain in the E and Z isomers causes them to have different conformational preferences. In the presence of a polar solvent both Z isomers of ΔPhe (1b and 2b) are found to adopt the 3(10)-helical conformation (left- and right-handed are equally likely). On the other hand, this conformation is not accessible or highly energetic for E isomers of ΔPhe (1a and 2a). Those isomers have an intrinsic inclination to have an extended conformation. The conformational space of the Z isomers is much more restricted than that of the E derivative both in the gas phase and in solution. In the gas phase the E isomers of ΔPhe have lower energies than the Z ones, but in the aqueous solution the energy order is reversed.

Mutual diffusion coefficients of heptane isomers in nitrogen: A molecular dynamics study

NASA Astrophysics Data System (ADS)

Chae, Kyungchan; Violi, Angela

2011-01-01

The accurate knowledge of transport properties of pure and mixture fluids is essential for the design of various chemical and mechanical systems that include fluxes of mass, momentum, and energy. In this study we determine the mutual diffusion coefficients of mixtures composed of heptane isomers and nitrogen using molecular dynamics (MD) simulations with fully atomistic intermolecular potential parameters, in conjunction with the Green-Kubo formula. The computed results were compared with the values obtained using the Chapman-Enskog (C-E) equation with Lennard-Jones (LJ) potential parameters derived from the correlations of state values: MD simulations predict a maximum difference of 6% among isomers while the C-E equation presents that of 3% in the mutual diffusion coefficients in the temperature range 500-1000 K. The comparison of two approaches implies that the corresponding state principle can be applied to the models, which are only weakly affected by the anisotropy of the interaction potentials and the large uncertainty will be included in its application for complex polyatomic molecules. The MD simulations successfully address the pure effects of molecular structure among isomers on mutual diffusion coefficients by revealing that the differences of the total mutual diffusion coefficients for the six mixtures are caused mainly by heptane isomers. The cross interaction potential parameters, collision diameter σ _{12}, and potential energy well depth \\varepsilon _{12} of heptane isomers and nitrogen mixtures were also computed from the mutual diffusion coefficients.

Nuclear States with Abnormally Large Radii (size Isomers)

NASA Astrophysics Data System (ADS)

Ogloblin, A. A.; Demyanova, A. S.; Danilov, A. N.; Belyaeva, T. L.; Goncharov, S. A.

2015-06-01

Application of the methods of measuring the radii of the short-lived excited states (Modified diffraction model MDM, Inelastic nuclear rainbow scattering method INRS, Asymptotic normalization coefficients method ANC) to the analysis of some nuclear reactions provide evidence of existing in 9Be, 11B, 12C, 13C the excited states whose radii exceed those of the corresponding ground states by ~ 30%. Two types of structure of these "size isomers" were identified: neutron halo an α-clusters.

g-factor measurements of isomeric states in 174W

NASA Astrophysics Data System (ADS)

Rocchini, M.; Nannini, A.; Benzoni, G.; Melon, B.; John, P. R.; Ur, C. A.; Avigo, R.; Bazzacco, D.; Blasi, N.; Bocchi, G.; Bottoni, S.; Bracco, A.; Camera, F.; Ceruti, S.; Crespi, F. C. L.; Georgiev, G.; Giaz, A.; Gottardo, A.; Leoni, S.; Menegazzo, R.; Mengoni, D.; Michelagnoli, C.; Million, B.; Modamio, V.; Morales, A. I.; Napoli, D. R.; Ottanelli, M.; Pellegri, L.; Perego, A.; Valiente-Dobon, J. J.; Wieland, O.

2016-05-01

The experimental setup GAMIPE used for gyro magnetic factor measurements at Laboratori Nazionali di Legnaro and a recent experimental work regarding K-isomers in 174W are described. Aim of the experiment is to study the detailed structure of the isomeric states wave functions, by the measurement of the magnetic dipole moments. This piece of information can provide interesting hints for theoretical models. Preliminary results concerning the population of the isomers of interest and half-lives are presented.

IR and Raman spectra of nitroanthracene isomers: substitional effects based on density functional theory study.

PubMed

Alparone, Andrea; Librando, Vito

2012-04-01

Structure, IR and Raman spectra of 1-, 2- and 9-nitroanthracene isomers (1-NA, 2-NA and 9-NA) were calculated and analyzed through density functional theory computations using the B3LYP functional with the 6-311+G** basis set. Steric and π-conjugative effects determine the characteristic ONCC dihedral angles, which vary from 0° (2-NA) to 28-29° (1-NA) and 59° (9-NA), influencing the relative order of stability along the series 9-NA<1-NA<2-NA. The spectral regions at wavenumber values>3000 cm(-1) and <1000 cm(-1) little depend on the substituent position. The Raman and IR intensity values of the characteristic symmetric nitro group stretching transition, appearing between 1310 and 1345 cm(-1), are rather sensitive to the position of the substituent, decreasing regularly on passing from the planar to the NO2-rotated isomers (9-NA<1-NA<2-NA). In the medium-energy spectral region (1000-1700 cm(-1)), the number and the relative position of the strongest Raman bands are of potential utility to discriminate the NA isomers. Structural and spectroscopic results suggest that the unknown mutagenic activity of 1-NA is expected to be between that of 9-NA and 2-NA. Copyright © 2011 Elsevier B.V. All rights reserved.

Nonadiabatic dynamics simulation of photoisomerization mechanism of the second stablest isomer of N-salicilydenemethylfurylamine

NASA Astrophysics Data System (ADS)

Gao, Aihua; Li, Jianpeng; Wang, Dehua; Ma, Xiaoguang; Wang, Meishan

2018-02-01

The photoisomerization processes of the second stablest isomer in the aromatic Schiff base, N-salicilydenemethylfurylamine, in the gas phase have been studied by static electronic structure calculations and surface-hopping dynamics simulations based on the Zhu-Nakamura theory. Various stable structures are obtained in the optimization because of different orientations of methyl-furyl part with respect to the salicylaldimine part and different orientations of hydroxy group with respect to the benzene ring. Upon photoexcitation into the first excited state, bond isomerization in the salicylaldimine part is completely suppressed until the strong excited-state hydrogen bond is broken. The decay pathway involves two excited-state minima, one in cis-enol form and the other in cis-keto form. After the excited-state proton transfer, twists of bonds lead to a conical intersection between the ground and excited states. After internal conversion around a conical intersection, the molecule is stabilized in cis- or trans-keto form. If the reverse hydrogen transfer process occurs in the ground state, the molecule will finally end up in the cis-enol region. The cis-keto and trans-keto isomers are observed as photoproducts. According to our full-dimensional nonadiabatic dynamics simulations, we find the excited-state intramolecular proton transfer and torsions of three single bonds in the chain to be responsible for photoisomerization of the second stablest isomer of N-salicilydenemethylfurylamine.

Loss of benzene to generate an enolate anion by a site-specific double-hydrogen transfer during CID fragmentation of o-alkyl ethers of ortho-hydroxybenzoic acids.

PubMed

Attygalle, Athula B; Bialecki, Jason B; Nishshanka, Upul; Weisbecker, Carl S; Ruzicka, Josef

2008-09-01

Collision-induced dissociation of anions derived from ortho-alkyloxybenzoic acids provides a facile way of producing gaseous enolate anions. The alkyloxyphenyl anion produced after an initial loss of CO(2) undergoes elimination of a benzene molecule by a double-hydrogen transfer mechanism, unique to the ortho isomer, to form an enolate anion. Deuterium labeling studies confirmed that the two hydrogen atoms transferred in the benzene loss originate from positions 1 and 2 of the alkyl chain. An initial transfer of a hydrogen atom from the C-1 position forms a phenyl anion and a carbonyl compound, both of which remain closely associated as an ion/neutral complex. The complex breaks either directly to give the phenyl anion by eliminating the neutral carbonyl compound, or to form an enolate anion by transferring a hydrogen atom from the C-2 position and eliminating a benzene molecule in the process. The pronounced primary kinetic isotope effect observed when a deuterium atom is transferred from the C-1 position, compared to the weak effect seen for the transfer from the C-2 position, indicates that the first transfer is the rate determining step. Quantum mechanical calculations showed that the neutral loss of benzene is a thermodynamically favorable process. Under the conditions used, only the spectra from ortho isomers showed peaks at m/z 77 for the phenyl anion and m/z 93 for the phenoxyl anion, in addition to that for the ortho-specific enolate anion. Under high collision energy, the ortho isomers also produce a peak at m/z 137 for an alkene loss. The spectra of meta and para compounds show a peak at m/z 92 for the distonic anion produced by the homolysis of the O-C bond. Moreover, a small peak at m/z 136 for a distonic anion originating from an alkyl radical loss allows the differentiation of para compounds from meta isomers.

Lanthanum-mediated dehydrogenation of butenes: Spectroscopy and formation of La(C4H6) isomers

NASA Astrophysics Data System (ADS)

Cao, Wenjin; Hewage, Dilrukshi; Yang, Dong-Sheng

2018-01-01

La atom reactions with 1-butene, 2-butene, and isobutene are carried out in a laser-vaporization molecular beam source. The three reactions yield the same La-hydrocarbon products from the dehydrogenation and carbon-carbon bond cleavage and coupling of the butenes. The dehydrogenated species La(C4H6) is the major product, which is characterized with mass-analyzed threshold ionization (MATI) spectroscopy and quantum chemical computations. The MATI spectrum of La(C4H6) produced from the La+1-butene reaction exhibits two band systems, whereas the MATI spectra produced from the La+2-butene and isobutene reactions display only a single band system. Each of these spectra shows a strong origin band and several vibrational progressions. The two band systems from the spectrum of the 1-butene reaction are assigned to the ionization of two isomers: La[C(CH2)3] (Iso A) and La(CH2CHCHCH2) (Iso B), and the single band system from the spectra of the 2-butene and isobutene reactions is attributed to Iso B and Iso A, respectively. The ground electronic states are 2A1 (C3v) for Iso A and 2A' (Cs) for Iso B. The ionization of the doublet state of each isomer removes a La 6s-based electron and leads to the 1A1 ion of Iso A and the 1A' ion of Iso B. The formation of both isomers consists of La addition to the C=C double bond, La insertion into two C(sp3)—H bonds, and H2 elimination. In addition to these steps, the formation of Iso A from the La+1-butene reaction may involve the isomerization of 1-butene to isobutene prior to the C—H bond activation, whereas the formation of Iso B from the La+trans-2-butene reaction may include the trans- to cis-butene isomerization after the C—H bond activation.

Probing the Methyl Torsional Barriers of the E and Z Isomers of Butadienyl Acetate by Microwave Spectroscopy

NASA Astrophysics Data System (ADS)

Jabri, Atef; Nguyen, Ha Vinh Lam; Kleiner, Isabelle; Van, Vinh; Stahl, Wolfgang

2016-06-01

The Fourier transform microwave spectra of the E and the Z isomer of butadienyl acetate have been measured in the frequency range from 2 to 26.5 GHz under molecular beam conditions. The most stable conformer of each isomer, in which all heavy atoms are located in a symmetry plane, was identified after analyzing the spectrum by comparison with results from quantum chemical calculations. The barrier to internal rotation of the acetyl methyl group was found to be 149.1822(20) cm-1 and 150.2128(48) cm-1 for the E and the Z isomer, respectively, which are similar to that of vinyl acetate. A comparison between two theoretical approaches treating internal rotations, the rho axis method (using the program BELGI-Cs) and combined axis method (using the program XIAM), is also performed. Since several years we study the barriers to internal rotation of the acetyl methyl group in acetates, CH3-COOR. Currently, we assume that all acetates can be divided into three classes. Class I contains α,β saturated acetates, where the torsional barrier is always close to 100 cm-1. Examples are a series of alkyl acetates such as methyl acetate and ethyl acetate. Class II contains α,β-unsaturated acetates where the C=C double bond is located in the COO plane. This is the case of vinyl acetate and butadienyl acetate. Finally, in class III with isopropenyl acetate and phenyl acetate as two representatives, α,β-unsaturated acetates, in which the double bond is not located in the COO plane, are collected. There, we observed a barrier height around 135 cm-1. This observation will be discussed in details. B. Velino, A. Maris, S. Melandri, W. Caminati, J. Mol. Spectrosc. 2009, 256, 228 H. V. L. Nguyen, A. Jabri, V. Van, and W. Stahl, J. Phys. Chem. A, 2014, 118, 12130.

Theoretical characterization of stable eta1-N2O-, eta2-N2O-, eta1-N2-, and eta2-N2-bound species: intermediates in the addition reactions of nitrogen hydrides with the pentacyanonitrosylferrate(II) ion.

PubMed

Olabe, José A; Estiú, Guillermina L

2003-08-11

The addition of nitrogen hydrides (hydrazine, hydroxylamine, ammonia, azide) to the pentacyanonitrosylferrate(II) ion has been analyzed by means of density functional calculations, focusing on the identification of stable intermediates along the reaction paths. Initial reversible adduct formation and further decomposition lead to the eta(1)- and eta(2)-linkage isomers of N(2)O and N(2), depending on the nucleophile. The intermediates (adducts and gas-releasing precursors) have been characterized at the B3LYP/6-31G level of theory through the calculation of their structural and spectroscopic properties, modeling the solvent by means of a continuous approach. The eta(2)-N(2)O isomer is formed at an initial stage of adduct decompositions with the hydrazine and azide adducts. Further conversion to the eta(1)-N(2)O isomer is followed by Fe-N(2)O dissociation. Only the eta(1)-N(2)O isomer is predicted for the reaction with hydroxylamine, revealing a kinetically controlled N(2)O formation. eta(1)-N(2) and eta(2)-N(2) isomers are also predicted as stable species.

Identification, Tissue Distribution, and Bioaccumulation Potential of Cyclic Perfluorinated Sulfonic Acids Isomers in an Airport Impacted Ecosystem.

PubMed

Wang, Yuan; Vestergren, Robin; Shi, Yali; Cao, Dong; Xu, Lin; Cai, Yaqi; Zhao, Xiaoli; Wu, Fengchang

2016-10-18

The use of cyclic perfluoroalkyl acids as anticorrosive agents in hydraulic fluids remains a poorly characterized source of organofluorine compounds to the environment. Here, we investigated the presence of perfluoroethylenecyclohexanesulfonate (PFECHS) isomers in environmental samples for the first time using a combination of high resolution and tandem mass spectrometry. Five distinct peaks attributed to different isomers of PFECHS and perfluoropropylcyclopentanesulfonate (PFPCPeS) were identified in environmental samples. The sum of PFECHS and PFPCPeS isomers displayed logarithmically decreasing spatial trends in water (1.04-324 ng/L) and sediment samples (

Isolation and characterization of (15Z)-lycopene thermally generated from a natural source

DOE Office of Scientific and Technical Information (OSTI.GOV)

Takehara, Munenori, E-mail: takehara@mat.usp.ac.jp; Kuwa, Takahiro; Inoue, Yoshinori

(15Z)-Lycopene was prepared by thermal isomerization of (all-E)-lycopene derived from tomatoes, and isolated by using a series of chromatographies. The fine red crystalline powder of (15Z)-lycopene was obtained from 556 mg of (all-E)-lycopene with a yield of 0.6 mg (purity: reversed-phase HPLC, 97.2%; normal-phase HPLC, ≥99.9%), and {sup 1}H and {sup 13}C NMR spectra of the isomer were fully assigned. More refined computational analyses that considered differences in the energy levels of the conformers involved in isomerization have also determined the stabilities of (15Z)-lycopene and other geometric isomers, along with the activation energies during isomerization from the all-E form. The fine controlmore » of conditions for HPLC separation and an advanced theoretical insight into geometric isomerization have led to the discovery of the 15Z-isomer generated from a natural source. - Highlights: • (15Z)-lycopene, isomerized from the all-E form of a natural source, was purified. • The obtained (15Z)-lycopene was structurally identified by an NMR analysis. • A modified theoretical study accounted for the generation of the 15Z-isomer. • This study demonstrated the occurrence of the isomer from a natural origin.« less

The impact of electron correlations on the energetics and stability of silicon nanoclusters

DOE Office of Scientific and Technical Information (OSTI.GOV)

Matsko, N. L.; Baturin, V. S.; Lepeshkin, S. V.

2016-08-21

The first-principles prediction of stable nanocluster structure is often hampered by the existence of many isomer configurations with energies close to the ground state. This fact attaches additional importance to many-electron effects beyond density functional theory (DFT), because their contributions can change a subtle energy order of competitive structures. To analyze this problem, we consider, as an example, the energetics of silicon nanoclusters passivated by hydrogen Si{sub 10}H{sub 2n} (0 ≤ n ≤ 11), where passivation changes the structure from compact to loosely packed and branched. Our calculations performed with DFT, hybrid functionals, and Hartree-Fock methods, as well as bymore » the GW approximation, confirm a considerable sensitivity of isomer energy ordering to many-electron effects.« less

A quantum chemical study for the multichannel reaction PH 2 + PH 2

NASA Astrophysics Data System (ADS)

Pimentel, André S.; Viana, Rommel B.

2007-04-01

The PH 2 + PH 2 multichannel reaction path was proposed in this study. The transition state that connects the reactants to cis-P 2H 2 isomer was found for the first time ever. This process is not allowed to occur at ordinary conditions because of its high energy barrier, 70 kcal mol -1. The PH 2 + PH 2 disproportionation to form the triplet PH 3 radical is an exothermic and spontaneous reaction. The PH 2 + PH 2 reaction may also form the P 2H 4 molecule in the absence of surfaces.

Stability and structure in [alpha]- and [beta]-keggin heteropolytungstates, [Xn+W12O40](8-n)-, X = p-block cation

Treesearch

Wade A. Neiwert; Jennifer J. Cowan; Kenneth I. Hardcastle; Craig L. Hill; Ira A. Weinstock

2002-01-01

[Beta]-[SiW12O40]4- (C3v symmetry) is sufficiently higher in energy than its [alpha]-isomer analogue that effectively complete conversion to [alpha]-[SiW12O40]4- (Td) is observed. By contrast, [beta]- and [alpha]-[AlW12O40]5- ([beta]- and [alpha]-1; C3v and Td, respectively) are sufficiently close in energy that both isomers are readily seen in 27Al NMR spectra of...

Synthesis and Electronic Properties of Fluoreno[2,1-a]fluorenedione and Fluoreno[1,2-a]fluorenedione.

PubMed

Hacker, Allison S; Pavano, Mauricio; Wood, James E; Immoos, Chad E; Hashimoto, Hannah; Genis, Sam P; Frantz, Derik K

2018-01-05

The [2,1-a]- and [1,2-a]-isomers of fluorenofluorenedione have been synthesized via intramolecular Friedel-Crafts acylations. DFT calculations indicate that the [1,2-a]-isomer adopts a twisted, helical C 2 -symmetric structure and that its protonated form is the thermodynamic product of the Friedel-Crafts acylation in hot sulfuric acid. Absorption spectroscopy and cyclic voltammetry measurements provide experimental estimations of frontier molecular orbital energy levels, which are reported and discussed.

A DFT/HF study of the potential energy surface of protonated ethane C2H7+

NASA Astrophysics Data System (ADS)

Hrusak, Jan; Zabka, Jan; Dolejsek, Zdenek; Herman, Zdenek

1997-11-01

Structures and energies of several isomers of the C2H7+ cation have been calculated using the parametrized B3LYP HF/DFT method. The B3LYP/6-31G** geometries of the individual isomers are of at least the same quality as the MP2/6-31G** results. The zero-point-energy corrected relative stabilities of the individual C2H7+ isomers are in excellent agreement with the much more costly MP4SDTQ/6-31G** MO calculations. A structure with a linear C---H---C skeleton and a CC distance of about 2.5 A was found to be a higher order saddle point on the PES resulting from curve crossing between the reactant and product channels CH3+ + CH4; this finding is of importance in interpreting the experimental results on the hydride ion transfer between CH3+ and CH4. The calculations are also consistent with the earlier experimental results on the formation of the products C2H5+ + H2.

Isomeric Detergent Comparison for Membrane Protein Stability: Importance of Inter-Alkyl-Chain Distance and Alkyl Chain Length

PubMed Central

Cho, Kyung Ho; Hariharan, Parameswaran; Mortensen, Jonas S.; Du, Yang; Nielsen, Anne K.; Byrne, Bernadette; Kobilka, Brian K.; Loland, Claus J.; Guan, Lan

2017-01-01

Membrane proteins encapsulated by detergent micelles are widely used for structural study. Because of their amphipathic property, detergents have the ability to maintain protein solubility and stability in an aqueous medium. However, conventional detergents have serious limitations in their scope and utility, particularly for eukaryotic membrane proteins and membrane protein complexes. Thus, a number of new agents have been devised; some have made significant contributions to membrane protein structural studies. However, few detergent design principles are available. In this study, we prepared meta and ortho isomers of the previously reported para-substituted xylene-linked maltoside amphiphiles (XMAs), along with alkyl chain-length variation. The isomeric XMAs were assessed with three membrane proteins, and the meta isomer with a C12 alkyl chain was most effective at maintaining solubility/stability of the membrane proteins. We propose that interplay between the hydrophile–lipophile balance (HLB) and alkyl chain length is of central importance for high detergent efficacy. In addition, differences in inter-alkyl-chain distance between the isomers influence the ability of the detergents to stabilise membrane proteins. PMID:27981750

A combined photoelectron spectroscopy and ab initio study of the quasi-planar B24(-) cluster.

PubMed

Popov, Ivan A; Piazza, Zachary A; Li, Wei-Li; Wang, Lai-Sheng; Boldyrev, Alexander I

2013-10-14

The structure and chemical bonding of the 24-atom boron cluster are investigated using photoelectron spectroscopy and ab initio calculations. The joint experimental and theoretical investigation shows that B24(-) possesses a quasi-planar structure containing fifteen outer and nine inner atoms with six of the inner atoms forming a filled pentagonal moiety. The central atom of the pentagonal moiety is puckered out of plane by 0.9 Å, reminiscent of the six-atom pentagonal caps of the well-known B12 icosahedral unit. The next closest isomer at the ROCCSD(T) level of theory has a tubular double-ring structure. Comparison of the simulated spectra with the experimental data shows that the global minimum quasi-planar B24(-) isomer is the major contributor to the observed photoelectron spectrum, while the tubular isomer has no contribution to the experiment. Chemical bonding analyses reveal that the periphery of the quasi-planar B24 constitutes 15 classical 2c-2e B-B σ-bonds, whereas delocalized σ- and π-bonds are found in the interior of the cluster with one unique 6c-2e π-bond responsible for bonding in the B-centered pentagon. The current work suggests that the 24-atom boron cluster continues to be quasi-2D, albeit the tendency to form filled pentagonal units, characteristic of 3D cage-like structures of bulk boron, is observed.

Structural characterization of a D-isomer specific 2-hydroxyacid dehydrogenase from Lactobacillus delbrueckii ssp. bulgaricus.

PubMed

Holton, Simon J; Anandhakrishnan, Madhankumar; Geerlof, Arie; Wilmanns, Matthias

2013-02-01

Hydroxyacid dehydrogenases, responsible for the stereospecific conversion of 2-keto acids to 2-hydroxyacids in lactic acid producing bacteria, have a range of biotechnology applications including antibiotic synthesis, flavor development in dairy products and the production of valuable synthons. The genome of Lactobacillus delbrueckii ssp. bulgaricus, a member of the heterogeneous group of lactic acid bacteria, encodes multiple hydroxyacid dehydrogenases whose structural and functional properties remain poorly characterized. Here, we report the apo and coenzyme NAD⁺ complexed crystal structures of the L. bulgaricusD-isomer specific 2-hydroxyacid dehydrogenase, D2-HDH. Comparison with closely related members of the NAD-dependent dehydrogenase family reveals that whilst the D2-HDH core fold is structurally conserved, the substrate-binding site has a number of non-canonical features that may influence substrate selection and thus dictate the physiological function of the enzyme. Copyright © 2012 Elsevier Inc. All rights reserved.

A Mechanistic and Structural Analysis of the Inhibition of the 90-kDa Heat Shock Protein by the Benzoquinone and Hydroquinone AnsamycinsS⃞

PubMed Central

Reigan, Philip; Siegel, David; Guo, Wenchang

2011-01-01

The benzoquinone ansamycins inhibit the ATPase activity of the 90-kDa heat shock protein (Hsp90), disrupting the function of numerous client proteins involved in oncogenesis. In this study, we examine the role of NAD(P)H:quinone oxidoreductase 1 (NQO1) in the metabolism of trans- and cis-amide isomers of the benzoquinone ansamycins and their mechanism of Hsp90 inhibition. Inhibition of purified human Hsp90 by a series of benzoquinone ansamycins was examined in the presence and absence of NQO1, and their relative rate of NQO1-mediated reduction was determined. Computational-based molecular docking simulations indicated that the trans- but not the cis-amide isomers of the benzoquinone ansamycins could be accommodated by the NQO1 active site, and the ranking order of binding energies correlated with the relative reduction rate using purified human NQO1. The trans-cis isomerization of the benzoquinone ansamycins in Hsp90 inhibition has been disputed in recent reports. Previous computational studies have used the closed or cocrystallized Hsp90 structures in an attempt to explore this isomerization step; however, we have successfully docked both the trans- and cis-amide isomers of the benzoquinone ansamycins into the open Hsp90 structure. The results of these studies indicate that both trans- and cis-amide isomers of the hydroquinone ansamycins exhibited increased binding affinity for Hsp90 relative to their parent quinones. Our data support a mechanism in which trans- rather than cis-amide forms of benzoquinone ansamycins are metabolized by NQO1 to hydroquinone ansamycins and that Hsp90-mediated trans-cis isomerization via tautomerization plays an important role in subsequent Hsp90 inhibition. PMID:21285336

Characterization and Determination of Interesterification Markers (Triacylglycerol Regioisomers) in Confectionery Oils by Liquid Chromatography-Mass Spectrometry

PubMed Central

Santoro, Valentina; Aigotti, Riccardo; Gastaldi, Daniela; Romaniello, Francesco; Forte, Emanuele; Magni, Martina; Baiocchi, Claudio

2018-01-01

Interesterification is an industrial transformation process aiming to change the physico-chemical properties of vegetable oils by redistributing fatty acid position within the original constituent of the triglycerides. In the confectionery industry, controlling formation degree of positional isomers is important in order to obtain fats with the desired properties. Silver ion HPLC (High Performance Liquid Chromatography) is the analytical technique usually adopted to separate triglycerides (TAGs) having different unsaturation degrees. However, separation of TAG positional isomers is a challenge when the number of double bonds is the same and the only difference is in their position within the triglyceride molecule. The TAG positional isomers involved in the present work have a structural specificity that require a separation method tailored to the needs of confectionery industry. The aim of this work was to obtain a chromatographic resolution that might allow reliable qualitative and quantitative evaluation of TAG positional isomers within reasonably rapid retention times and robust in respect of repeatability and reproducibility. The resulting analytical procedure was applied both to confectionery raw materials and final products. PMID:29462917

The role of core excitations in the structure and decay of the 16 + spin-gap isomer in 96Cd

DOE PAGES

Davies, Paul John; Grawe, H.; Moschner, K.; ...

2017-02-14

The first evidence for β -delayed proton emission from the 16 + spin gap isomer in 96Cd is presented. The data were obtained from the Rare Isotope Beam Factory, at the RIKEN Nishina Center, using the BigRIPS spectrometer and the EURICA decay station. βp branching ratios for the ground state and 16 + isomer have been extracted along with more precise lifetimes for these states and the lifetime for the ground state decay of 95Cd. Large scale shell model (LSSM) calculations have been performed and WKB estimates made for ℓ=0,2,4 proton emission from three resonance-like states in 96Ag, that aremore » populated by the β decay of the isomer, and the results compared to the new data. The calculations suggest that ℓ=2 proton emission from the resonance states, which reside ~5 MeV above the proton separation energy, dominates the proton decay. Finally, the results highlight the importance of core-excited wavefunction components for the 16 + state.« less

The Influence of Interfaces on Properties of Thin-Film Inorganic Structural Isomers Containing SnSe-NbSe2 Subunits.

PubMed

Alemayehu, Matti B; Falmbigl, Matthias; Ta, Kim; Johnson, David C

2015-04-28

Inorganic isomers ([SnSe]1+δ)m(NbSe2)n([SnSe]1+δ)p(NbSe2)q([SnSe]1+δ)r(NbSe2)s where m, n, p, q, r, and s are integers and m + p + r = n + q + s = 4 were prepared using the modulated elemental reactant technique. This series of all six possible isomers provides an opportunity to study the influence of interface density on properties while maintaining the same unit cell size and composition. As expected, all six compounds were observed to have the same atomic compositions and an almost constant c-axis lattice parameter of ≈4.90(5) nm, with a slight trend in the c-axis lattice parameter correlated with the different number of interfaces in the isomers: two, four and six. The structures of the constituents in the ab-plane were independent of one another, confirming the nonepitaxial relationship between them. The temperature dependent electrical resistivities revealed metallic behavior for all the six compounds. Surprisingly, the electrical resistivity at room temperature decreases with increasing number of interfaces. Hall measurements suggest this results from changes in carrier concentration, which increases with increasing thickness of the thickest SnSe block in the isomer. Carrier mobility scales with the thickness of the thickest NbSe2 block due to increased interfacial scattering as the NbSe2 blocks become thinner. The observed behavior suggests that the two constituents serve different purposes with respect to electrical transport. SnSe acts as a charge donor and NbSe2 acts as the charge transport layer. This separation of function suggests that such heterostructures can be designed to optimize performance through choice of constituent, layer thickness, and layer sequence. A simplistic model, which predicts the properties of the complex isomers from a weighted sum of the properties of building blocks, was developed. A theoretical model is needed to predict the optimal compound for specific properties among the many potential compounds that can be prepared.

Initiating Molecular Growth in the Interstellar Medium via Dimeric Complexes of Observed Ions and Molecules

NASA Technical Reports Server (NTRS)

Bera, Partha P.; Head-Gordon, Martin; Lee, Timothy J.

2011-01-01

A feasible initiation step for particle growth in the interstellar medium (ISM) is simulated by means of ab quantum chemistry methods. The systems studied are dimer ions formed by pairing nitrogen containing small molecules known to exist in the ISM with ions of unsaturated hydrocarbons or vice versa. Complexation energies, structures of ensuing complexes and electronic excitation spectra of the encounter complexes are estimated using various quantum chemistry methods. Moller-Plesset perturbation theory (MP2, Z-averaged perturbation theory (ZAP2), coupled cluster singles and doubles with perturbative triples corrections (CCSD(T)), and density functional theory (DFT) methods (B3LYP) were employed along with the correlation consistent cc-pVTZ and aug-cc-pVTZ basis sets. Two types of complexes are predicted. One type of complex has electrostatic binding with moderate (7-20 kcal per mol) binding energies, that are nonetheless significantly stronger than typical van der Waals interactions between molecules of this size. The other type of complex develops strong covalent bonds between the fragments. Cyclic isomers of the nitrogen containing complexes are produced very easily by ion-molecule reactions. Some of these complexes show intense ultraviolet visible spectra for electronic transitions with large oscillator strengths at the B3LYP, omegaB97, and equations of motion coupled cluster (EOM-CCSD) levels. The open shell nitrogen containing carbonaceous complexes especially exhibit a large oscillator strength electronic transition in the visible region of the electromagnetic spectrum.

Quantum and Statistical Mechanics Applied to Singlet Carbenes, Pericyclic Reactions, and Condensed Phase Phenomena

NASA Astrophysics Data System (ADS)

Evanseck, Jeffrey Donald

The completed research covers a broad range of theoretical applications in organic chemistry. It is divided into three chapters which covers the chemistry of singlet carbenes (Chapter 1), substituent effects in pericyclic rearrangements (Chapter 2), and the effects of solvent on the reactivity of organic reactions (Chapter 3). The selectivity between 1,2- and 1,4-intramolecular additions to restricted diene systems has been investigated. A decrease in activation energy for the intramolecular cycloaddition is noted for systems which approach the idealized geometry found with intermolecular addition of carbenes to olefins. Direct substitution at the carbene site dramatically effects the predicted activation barriers for 1,2-hydrogen shifts. An excellent correlation between the activation energy and a substituents sigma_sp {rm R}{rm o} parameters has been demonstrated. The long standing problem of orbital alignment influences on the selectivity of 1,2-hydrogen arrangements shows significant geometric distortions, yet has little influence on the rates of singlet alkylcarbene rearrangements. The exo-selectivities observed for 1,2-shifts in rigid systems are explained by torsional and steric interactions which develop in the transition structures. Substituent effects on pericyclic reactions have been computed for several conrotatory and disrotatory electrocyclizations. The six-electron disrotatory electrocyclization of 1-substituted hexatrienes displays a strong electronic component in determining stereoselectivity, despite incredible steric interference. The eight-electron conrotatory electrocyclization transition structure of 1-substituted octatetraene has an unusual helical transition structure which does not differentiate between substituent position. The effects of solvents on the acidity differences between E and Z esters has supplemented earlier ab initio quantum mechanical results on the enhanced acidity of Meldrum's acid. Monte Carlo simulations predict a preferential stabilization of the E isomer in both acetonitrile and aqueous solutions. The rates of intramolecular Diels-Alder reactions are compared to recent experimental work and predictions of different solvent systems are made.

The crystal structure of red fluorescent protein TagRFP-T reveals the mechanism of its superior photostability

DOE Office of Scientific and Technical Information (OSTI.GOV)

Liu, Rui; Liang, Qing-Nan; Du, Shu-Qi

2016-08-19

The red fluorescent protein variant TagRFP-T has greatly improved photostability over its parent molecule, TagRFP, but the underlying mechanism leading to this improvement is to date unknown. The 1.95 Å resolution crystallographic structure of TagRFP-T showed that its chromophore exists as a mixture of cis and trans coplanar isomers in roughly equal proportions. Interestingly, both isomers are able to fluoresce, a property that has never been observed in any other fluorescent protein. We propose a “circular restoration model” for TagRFP-T to explain its superior photostability: There are four co-existing chromophore states (cis/trans protonated/ionized state) that can be driven by light tomore » transform from one state into another. This model also explains how TagRPF-T essentially eliminates the temporary dark state (reversible photobleaching). - Highlights: • The 1.95 Å resolution crystal structure of TagRFP-T was determined. • The chromophore of TagRFP-T contains a mixture of cis and trans coplanar isomers. • A “circular restoration model” was proposed to explain the superior photostability. • The chromophore can reversibly convert between cis/trans protonated/ionized states. • The light-driven conversion reduce the dark state (reversible photobleaching).« less

Geometry optimization and excited state properties of the new symmetric (E)-Stilbene derivative for application in thermostable polarizing PVA-films: A combined experimental and DFT approach

NASA Astrophysics Data System (ADS)

Shahab, Siyamak; Almodarresiyeh, Hora Alhosseini; Filippovich, Liudmila; Hajikolaee, Fatemeh Haji; Kumar, Rakesh; Darroudi, Mahdieh; Mashayekhi, Mahsa

2016-09-01

In the present work, quantum-chemical calculations used for the structural analysis of the new symmetric (E)-Stilbene derivative: (Potassium 2,2‧-((ethane-1,2-diylbis(4,1-phenylene))bis(azanediyl))diacetate) (P) (Trans isomer) using DFT/B3LYP/LanL2MB level of theory. The FT-IR and 1H NMR spectra of the compound P are presented. The electronic absorption spectrum of the P in aqueous medium was calculated using TDB3LYP/LanL2MB method. The excitation energies, electronic transitions and oscillator strengths for studied structure have also been calculated. The experimental, calculated UV/Vis and emission spectra of the P are presented and discussed. The geometry optimization of the molecule P in excited state and its electronic spectrum was carried out by the same method. In excited state the molecule P loses its symmetry and becomes unstable form. First time on the basis of polyvinyl alcohol (PVA) and the new designed structure P thermostable polarizing film absorbing at λmax = 410 nm was created. Polarizing Efficiency (PE) of obtained film is 96% at Stretching Degree (Rs) 3.0. In oriented PVA-films is the phenomenon of anisotropy of thermal conductivity (λ||/λ⊥) which is very important for development of thermostable polarizing films.

Flexibility of "polyunsaturated fatty acid chains" and peptide backbones: A comparative ab initio study.

PubMed

Law, Jacqueline M S; Setiadi, David H; Chass, Gregory A; Csizmadia, Imre G; Viskolcz, Béla

2005-01-27

The conformational properties of omega-3 type of polyunsaturated fatty acid (PUFA) chains and their fragments were studied using Hartree-Fock (RHF/3-21G) and DFT (B3LYP/6-31G(d)) methods. Comparisons between a unit (U) fragment of the PUFA chain and a mono N-Ac-glycine-NHMe residue show that both structures have the same sequence of sp2-sp3-sp2 atoms. The flexibility of PUFA originates in the internal rotation about the above pairs of sigma bonds. Therefore, potential energy surfaces (PESs) were generated by a scan around the terminal dihedral angles (phi t1 and phi t2) as well as the phi 1 and psi 1 dihedrals of both 1U congeners (Me-CHCH-CH2-CHCHMe and MeCONH-CH2-CONHMe) at the RHF/3-21G level of theory. An interesting similarity was found in the flexibility between the cis allylic structure and the trans peptide models. A flat landscape can be seen in the cis 1U (hepta-2,5-diene) surface, implying that several conformations are expected to be found in this (PES). An exhaustive search carried out on the 1U and 2U models revealed that straight chain structures such as trans and cis beta (phi 1 approximately psi 1 approximately 120 degrees; phi 2 approximately psi 2 approximately -120 degrees) or trans and cis extended (phi 1 approximately psi 1 approximately phi 2 approximately psi 2 approximately 120 degrees) can be formed at the lowest energy of both isomers. However, forming helical structures, such as trans helix (phi 1 approximately -120 degrees, psi 1 approximately 12 degrees; phi 2 approximately -120 degrees, psi 2 approximately 12 degrees) or cis helix (phi 1 approximately -130 degrees, psi 1 approximately 90 degrees; phi 2 approximately -145 degrees, psi 2 approximately 90 degrees) will require more energy. These six conformations, found in 2U, were selected to construct longer chains such as 3U, 4U, 5U, and 6U to obtain the thermochemistry of secondary structures. The variation in the extension or compression of the chain length turned out to be a factor of 2 between the helical and nonhelical structures. The inside diameter of the "tube" of cis helix turned out to be 3.5 A after discounting the internal H atoms. Thermodynamic functions were computed at the B3LYP/6-311+G(2d,p)//B3LYP/6-31G(d). The cis-trans isomerization energy of 1.7 +/- 0.2 kcal mol(-1) unit(-1) for all structure pairs indicates that the conformer selection was consistent. A folding energy of 0.5 +/- 0.1 kcal mol(-1) unit(-1) has been extracted from the energy comparison of the helices and most extended nonhelical structures. The entropy change associated with the folding (Delta S(folding)) is decreases faster with the degree of polymerization (n) for the cis than for the trans isomer. As a consequence, the linear relationships between (Delta G(folding)) and n for the cis and trans isomer crossed at about n = 3. This suggested that the naturally occurring cis isomer less ready to fold than the trans isomer since a greater degree of organization is exhibited by the cis isomer during the folding process. The result of this work leads to the question within the group additivity rule: could the method applied in our study of the folding of polyallylic hydrocarbons be useful in investigating the thermochemistry of protein folding?

Glass transition dynamics and boiling temperatures of molecular liquids and their isomers.

PubMed

Wang, Li-Min; Richert, Ranko

2007-03-29

The relation between a dynamic and a thermodynamic temperature, glass transition Tg and boiling point Tb, is investigated for various glass-forming liquids, with emphasis on monohydroxy alcohols. As is well known, Tb and Tg are positively correlated across a large variety of liquids. However, we found that the same quantities show a negative correlation within an isomeric series, i.e., Tb decreases with increasing Tg for different isomers of the same chemical formula. For the alcohol series, CnH2n+1OH with 3 < or = n < or = 10, a master curve of the negative Tg - Tb correlation is obtained if the temperatures are normalized to the respective values of the n-alkanols. This Tg - Tb dependence of isomeric liquids is linked to entropic effects and responsible for much of the scatter of the correlation observed for a large number of molecular organic glass-formers with 45 < Tg < 250 K. Dielectric relaxation is measured for three groups of isomers: (a) 3-methoxyl-1-butanol and 2-iso-propoxyethanol, (b) 1,4-, 1,2-, and 2,4-pentanediol, and (c) di-n- and di-iso-butyl phthalate. Two key parameters of the dynamics, fragility m and stretching exponent beta, are found to be indistinguishable within isomers of moderately different Tgs. Larger fragility differences are readily expected with pronounced structural change, but no systematic trend is observed within an isomer series. The results provide a useful tool for assessing Tg, m, and beta for marginal glass formers on the basis of their isomers.

Ion mobility and clustering of sodium hydroxybenzoates in aqueous solutions: a molecular dynamics simulation study.

PubMed

Gujt, Jure; Podlipnik, Črtomir; Bešter-Rogač, Marija; Spohr, Eckhard

2014-09-28

The relative position of the hydroxylic and the carboxylic group in the isomeric hydroxybenzoate (HB) anions is known to have a large impact on transport properties of this species. It also influences crucially the self-organisation of cationic surfactants. In this article a systematic investigation of aqueous solutions of the ortho, meta, and para isomers of the HB anion is presented. Molecular dynamics simulations of all three HB isomers were conducted for two different concentrations at 298.15 K and using two separate water models. From the resulting trajectories we calculated the self-diffusion coefficient of each isomer. According to the calculated self-diffusion coefficients, isomers were ranked in the order o-HB > m-HB > p-HB at both concentrations for both the used SPC and SPC/E water models, which agrees very well with the experiment. The structural analysis revealed that at lower concentration, where the tendency for dimerisation or cluster formation is low, hydrogen bonding with water determines the mobility of the HB anion. o-HB forms the least hydrogen bonds and is therefore the most mobile, and p-HB, which forms the most hydrogen bonds with water, is the least mobile isomer. At higher concentration the formation of clusters also needs to be considered. The ortho isomer predominantly forms dimers with 2 hydrogen bonds per dimer between one OH and one carboxylate group of each anion. m-HB mostly forms clusters of sizes around 5 and p-HB forms clusters of sizes even larger than 10, which can be either rings or chains.

Spherical harmonics based descriptor for neural network potentials: Structure and dynamics of Au147 nanocluster.

PubMed

Jindal, Shweta; Chiriki, Siva; Bulusu, Satya S

2017-05-28

We propose a highly efficient method for fitting the potential energy surface of a nanocluster using a spherical harmonics based descriptor integrated with an artificial neural network. Our method achieves the accuracy of quantum mechanics and speed of empirical potentials. For large sized gold clusters (Au 147 ), the computational time for accurate calculation of energy and forces is about 1.7 s, which is faster by several orders of magnitude compared to density functional theory (DFT). This method is used to perform the global minimum optimizations and molecular dynamics simulations for Au 147 , and it is found that its global minimum is not an icosahedron. The isomer that can be regarded as the global minimum is found to be 4 eV lower in energy than the icosahedron and is confirmed from DFT. The geometry of the obtained global minimum contains 105 atoms on the surface and 42 atoms in the core. A brief study on the fluxionality in Au 147 is performed, and it is concluded that Au 147 has a dynamic surface, thus opening a new window for studying its reaction dynamics.

Computational prediction of the spectroscopic parameters of methanediol, an elusive molecule for interstellar detection

DOE Office of Scientific and Technical Information (OSTI.GOV)

Barrientos, Carmen; Redondo, Pilar; Largo, Antonio

2014-04-01

The molecular structure of methanediol has been investigated by means of quantum chemical calculations. Two conformers, corresponding to C{sub 2} and C {sub s} symmetries, respectively, were considered. The C{sub 2} conformer is found to lie about 1.7 (at 298 K) or 2.3 (at 0 K) kcal mol{sup –1} below the C {sub s} conformer. Predictions for their rotational constants, vibrational frequencies, IR intensities, and dipole moments have been provided. The lowest-lying isomer has a very low dipole moment, around 0.03 D, whereas the C {sub s} conformer has a relatively high dipole moment, namely, 2.7 D. The barrier formore » the C {sub s} →C{sub 2} process is predicted to be around 0.7-1 kcal mol{sup –1}. Based on the energetic results the proportion of the C{sub s} conformer is likely to be negligible under low temperature conditions, such as in the interstellar medium. Therefore, it is predicted that detection by radioastronomy of methanediol would be rather unlikely.« less

Spherical harmonics based descriptor for neural network potentials: Structure and dynamics of Au147 nanocluster

NASA Astrophysics Data System (ADS)

Jindal, Shweta; Chiriki, Siva; Bulusu, Satya S.

2017-05-01

We propose a highly efficient method for fitting the potential energy surface of a nanocluster using a spherical harmonics based descriptor integrated with an artificial neural network. Our method achieves the accuracy of quantum mechanics and speed of empirical potentials. For large sized gold clusters (Au147), the computational time for accurate calculation of energy and forces is about 1.7 s, which is faster by several orders of magnitude compared to density functional theory (DFT). This method is used to perform the global minimum optimizations and molecular dynamics simulations for Au147, and it is found that its global minimum is not an icosahedron. The isomer that can be regarded as the global minimum is found to be 4 eV lower in energy than the icosahedron and is confirmed from DFT. The geometry of the obtained global minimum contains 105 atoms on the surface and 42 atoms in the core. A brief study on the fluxionality in Au147 is performed, and it is concluded that Au147 has a dynamic surface, thus opening a new window for studying its reaction dynamics.

IR photodissociation spectroscopy of (OCS){sub n}{sup +} and (OCS){sub n}{sup −} cluster ions: Similarity and dissimilarity in the structure of CO{sub 2}, OCS, and CS{sub 2} cluster ions

DOE Office of Scientific and Technical Information (OSTI.GOV)

Inokuchi, Yoshiya, E-mail: y-inokuchi@hiroshima-u.ac.jp; Ebata, Takayuki

2015-06-07

Infrared photodissociation (IRPD) spectra of (OCS){sub n}{sup +} and (OCS){sub n}{sup −} (n = 2–6) cluster ions are measured in the 1000–2300 cm{sup −1} region; these clusters show strong CO stretching vibrations in this region. For (OCS){sub 2}{sup +} and (OCS){sub 2}{sup −}, we utilize the messenger technique by attaching an Ar atom to measure their IR spectra. The IRPD spectrum of (OCS){sub 2}{sup +}Ar shows two bands at 2095 and 2120 cm{sup −1}. On the basis of quantum chemical calculations, these bands are assigned to a C{sub 2} isomer of (OCS){sub 2}{sup +}, in which an intermolecular semi-covalent bondmore » is formed between the sulfur ends of the two OCS components by the charge resonance interaction, and the positive charge is delocalized over the dimer. The (OCS){sub n}{sup +} (n = 3–6) cluster ions show a few bands assignable to “solvent” OCS molecules in the 2000–2080 cm{sup −1} region, in addition to the bands due to the (OCS){sub 2}{sup +} ion core at ∼2090 and ∼2120 cm{sup −1}, suggesting that the dimer ion core is kept in (OCS){sub 3–6}{sup +}. For the (OCS){sub n}{sup −} cluster anions, the IRPD spectra indicate the coexistence of a few isomers with an OCS{sup −} or (OCS){sub 2}{sup −} anion core over the cluster range of n = 2–6. The (OCS){sub 2}{sup −}Ar anion displays two strong bands at 1674 and 1994 cm{sup −1}. These bands can be assigned to a C{sub s} isomer with an OCS{sup −} anion core. For the n = 2–4 anions, this OCS{sup −} anion core form is dominant. In addition to the bands of the OCS{sup −} core isomer, we found another band at ∼1740 cm{sup −1}, which can be assigned to isomers having an (OCS){sub 2}{sup −} ion core; this dimer core has C{sub 2} symmetry and {sup 2}A electronic state. The IRPD spectra of the n = 3–6 anions show two IR bands at ∼1660 and ∼2020 cm{sup −1}. The intensity of the latter component relative to that of the former one becomes stronger and stronger with increasing the size from n = 2 to 4, which corresponds to the increase of “solvent” OCS molecules attached to the OCS{sup −} ion core, but it suddenly decreases at n = 5 and 6. These IR spectral features of the n = 5 and 6 anions are ascribed to the formation of another (OCS){sub 2}{sup −} ion core having C{sub 2v} symmetry with {sup 2}B{sub 2} electronic state.« less

Doubly magic 208Pb: High-spin states, isomers, and E 3 collectivity in the yrast decay

NASA Astrophysics Data System (ADS)

Broda, R.; Janssens, R. V. F.; Iskra, Ł. W.; Wrzesinski, J.; Fornal, B.; Carpenter, M. P.; Chiara, C. J.; Cieplicka-Oryńczak, N.; Hoffman, C. R.; Kondev, F. G.; Królas, W.; Lauritsen, T.; Podolyak, Zs.; Seweryniak, D.; Shand, C. M.; Szpak, B.; Walters, W. B.; Zhu, S.; Brown, B. A.

2017-06-01

Yrast and near-yrast levels up to spin values in excess of I =30 ℏ have been delineated in the doubly magic 208Pb nucleus following deep-inelastic reactions involving 208Pb targets and, mostly, 430-MeV 48Ca and 1440-MeV 208Pb beams. The level scheme was established up to an excitation energy of 16.4 MeV, based on multifold γ-ray coincidence relationships measured with the Gammasphere array. Below the well-known, 0.5-μs 10+ isomer, ten new transitions were added to earlier work. The delineation of the higher parts of the level sequence benefited from analyses involving a number of prompt- and delayed-coincidence conditions. Three new isomeric states were established along the yrast line with Iπ=20- (10 342 keV), 23+ (11 361 keV), and 28- (13 675 keV), and respective half-lives of 22(3), 12.7(2), and 60(6) ns. Gamma transitions were also identified preceding in time the 28- isomer; however, only a few could be placed in the level scheme and no firm spin-parity quantum numbers could be proposed. In contrast, for most states below this 28- isomer, firm spin-parity values were assigned, based on total electron-conversion coefficients, deduced for low-energy (<500 keV ) transitions from γ-intensity balances, and on measured γ-ray angular distributions. The latter also enabled the quantitative determination of mixing ratios. The transition probabilities extracted for all isomeric transitions in 208Pb have been reviewed and discussed in terms of the intrinsic structure of the initial and final levels involved. Particular emphasis was placed on the many observed E 3 transitions as they often exhibit significant enhancements in strength [of the order of tens of Weisskopf units (W.u.)] comparable to the one seen for the neutron j15 /2→g9 /2 E 3 transition in 209Pb. In this context, the enhancement of the 725-keV E 3 transition (56 W.u.) associated with the decay of the highest-lying 28- isomer observed in this work remains particularly challenging to explain. Large-scale shell-model calculations were performed with two approaches, a first one where the 1, 2, and 3 particle-hole excitations do not mix with one another, and another more complex one, in which such mixing takes place. The calculated levels were compared with the data and a general agreement is observed for most of the 208Pb level scheme. At the highest spins and energies, however, the correspondence between theory and experiment is less satisfactory and the experimental yrast line appears to be more regular than the calculated one. This regularity is notable when the level energies are plotted versus the I (I +1 ) product and the observed, nearly linear, behavior was considered within a simple "rotational" interpretation. Within this approximate picture, the extracted moment of inertia suggests that only the 76 valence nucleons participate in the "rotation" and that the 132Sn spherical core remains inert.

Doubly magic Pb 208 : High-spin states, isomers, and E 3 collectivity in the yrast decay

DOE PAGES

Broda, R.; Janssens, R. V. F.; Iskra, Ł. W.; ...

2017-06-12

Yrast and near-yrast levels up to spin values in excess of I = 30h have been delineated in the doubly-magic 208Pb nucleus following deep-inelastic reactions involving 208Pb targets and, mostly, 430-MeV 48Ca and 1440-MeV 208Pb beams. The level scheme was established up to an excitation energy of 16.4 MeV, based on multi-fold γ-ray coincidence relationships measured with the Gammasphere array. Below the well-known, 0.5-μs 10 + isomer, ten new transitions were added to earlier work. The delineation of the higher parts of the level sequence benefited from analyses involving a number of prompt- and delayed-coincidence conditions. Three new isomeric statesmore » were established along the yrast line with I π = 20 - (10342 keV), 23 + (11361 keV), and 28 - (13675 keV), and respective half-lives of 22(3), 12.7(2), and 60(6) ns. Gamma transitions were also identified preceding in time the 28 - isomer, however, only a few could be placed in the level scheme and no firm spin-parity quantum numbers could be proposed. In contrast, for most states below this 28 - isomer, firm spin-parity values were assigned, based on total electron-conversion coefficients, deduced for low-energy (<500 keV) transitions from γ-intensity balances, and on measured γ-ray angular distributions. The latter also enabled the quantitative determination of mixing ratios. The transition probabilities extracted for all isomeric transitions in 208Pb have been reviewed and discussed in terms of the intrinsic structure of the initial and final levels involved. Particular emphasis was placed on the many observed E3 transitions as they often exhibit significant enhancements in strength (of the order of tens of W.u.) comparable to the one seen for the neutron j 15/2→g 9/2 E3 transition in 209Pb. In this context, the enhancement of the 725-keV E3 transition (56 W.u.) associated with the decay of the highest-lying 28 - isomer observed in this work remains particularly challenging to explain. Large-scale shell-model calculations were performed with two approaches, a first one where the 1, 2, and 3 particle-hole excitations do not mix with one another, and another more complex one, in which such mixing takes place. We compared the calculated levels with the data and a general agreement is observed for most of the 208Pb level scheme. At the highest spins and energies, however, the 2 correspondence between theory and experiment is less satisfactory and the experimental yrast line appears to be more regular than the calculated one. This regularity is notable when the level energies are plotted versus the I(I+1) product and the observed, nearly linear, behavior was considered within a simple “rotational” interpretation. Furthermore, within this approximate picture, the extracted moment of inertia suggests that only the 76 valence nucleons participate in the “rotation” and that the 132Sn spherical core remains inert.« less

Bridged HPSi and Linear HSiP as Probes of the SiP Radical in Astrophysical/Interstellar Media

NASA Astrophysics Data System (ADS)

Fortenberry, Ryan C.; Francisco, Joseph S.

2017-07-01

The SiP radical has a \\tilde{X}{}2{{\\Pi }} ground state and a low-lying A{}2{{{Σ }}}+ state with a transition wavelength of greater than 20 μm. However, this transition has a near-zero oscillator strength making it all but unobservable. Addition of a hydrogen atom to the system creates the strangely bent HPSi molecule and also the linear HSiP isomer, lying 0.50 eV above the bent. The electron-deficient P-Si π cloud in \\tilde{X}{}2{{\\Pi }} SiP is stabilized by the addition of the hydrogen atom, making this isomer the preferred form of HPSi. The HSiP linear isomer can be formed from A{}2{{{Σ }}}+ SiP. As a result, the [HPSi]/[HSiP] ratio could serve as tracer of the otherwise unobservable but low-lying A{}2{{{Σ }}}+≤ftarrow \\tilde{X}{}2{{\\Pi }} electronic transition of SiP. The high-level quantum chemical computations employed here imply that the rotational lines of HPSi and HSiP will overlap extensively, but the vibrational frequencies, especially the hydride stretch, are significantly separated. The hydride stretches are in the 5 μm range, making them excellent candidates for mid-IR observations with the Stratsopheric Observatory for Infrared Astronomy or with the James Webb Space Telescope. Furthermore, the rotational constants and vibrational frequencies of \\tilde{X}{}2{{\\Pi }} SiP, A{}2{{{Σ }}}+ SiP, and \\tilde{X}{}1{{{Σ }}}+ SiP- are also provided in addition to the relative energies of all five species.

Spectroscopy and high-spin structure of 210Fr: Isomerism and potential evidence for configuration mixing

NASA Astrophysics Data System (ADS)

Margerin, V.; Lane, G. J.; Dracoulis, G. D.; Palalani, N.; Smith, M. L.; Stuchbery, A. E.

2016-06-01

The structure of 210Fr has been established up to an excitation energy of ˜5.5 MeV and spins of ˜25 ℏ , via time-correlated γ -ray spectroscopy and using the 197Au(18O,5 n )210Fr reaction with pulsed beams at an energy of 97 MeV. A significantly different level scheme has been obtained compared to previous publications. Several isomers are reported here, including a Jπ=(23) +,τ =686 (9 ) -ns state at 4417 keV and a 10-, 29.8(11)-ns state at 1113 keV. The former isomer has been associated with the π (h9/2 3i13/2 2) ν (p1/2 -2f5/2 -1) configuration and decays via proposed E 3 transitions with strengths of 8.4(3) and 21.2(8) W.u. There are only very few known cases of a high-spin isomer decaying via two parallel E 3 transitions. Indeed, this is not seen in other Fr nuclei, and consequently these strengths differ from related decays in the neighboring isotopes. However, by examining the systematics of E 3 transitions in trans-lead nuclei, we suggest that the weaker of the two transitions decays to a mixed 20- state. Systematics of the 10- isomer are also discussed. Comparisons are made between the observed spectrum of states and those predicted from semiempirical shell-model calculations.

Evidence for two interconverting protein isomers in the methotrexate complex of dihydrofolate reductase from Escherichia coli

DOE Office of Scientific and Technical Information (OSTI.GOV)

Falzone, C.J.; Benkovic, S.J.; Wright, P.E.

1991-02-26

Two-dimensional {sup 1}H NMR methods and a knowledge of the X-ray crystal structure have been used to make resonance assignments for the amino acid side chains of dihydrofolate reductase from Escherichia coli complexed with methotrexate. The H7 proton on the pteridine ring of methotrexate was found to have NOEs to the methyl protons of Leu-28 which were assigned by using the L28F mutant. These NOEs indicated that the orientation of the methotrexate pteridine ring is similar in both solution and crystal structures. During the initial assignment process, it became evident that many of the resonances in this complex, unlike thosemore » of the folate complex, are severally broadened or doubled. The observation of two distinct sets of resonances in a ratio of approximately 2:1 was attributed to the presence of two protein isomers. Many of the side chains with clearly doubled resonances were located in the {beta}-sheet and the active site. Preliminary studies on the apoprotein also revealed doubled resonances in the absence of the inhibitor, indicating the existence of the protein isomers prior to methotrexate binding. In contrast to the methotrexate complex, the binary complex with folate and the ternary MTX-NADPH-DHFR complex presented a single enzyme form. These results are proposed to reflect the ability of folate and NADPH to bind predominantly to one protein isomer.« less

Photochemistry of the Stilbenes in Methanol. Trapping the Common Phantom Singlet State.

PubMed

Saltiel, Jack; Gupta, Shipra

2018-06-21

A comparative study of the photochemistry of cis- and trans-stilbene in methanol shows that both isomers undergo methanol photoaddition giving similar yields of α-methoxybibenzyl in competition with cis-trans photoisomerization. Methanol addition occurs primarily following torsional relaxation of the lowest excited singlet states of each isomer, 1 c* and 1 t*, to a common twisted singlet excited state intermediate, 1 p*, initially called the phantom singlet state. The addition is consistent with the zwitterionic character of 1 p*. Ether forms by direct 1,2-addition of CH 3 OH to the central carbon atoms and by 1,1-addition following rearrangement to 1-benzyl-1-phenylcarbene. Use of CD 3 OD and GC/MS (gas chromatographic/mass spectroscopic) analysis of the ether products revealed that the ratio of carbene/direct addition pathways is higher starting from cis-stilbene. We conclude that 1 p* formed from 1 c* is hotter than 1 p* formed from 1 t*. Surprisingly, except for favoring the carbene pathway, the use of higher energy photons (254 vs 313 nm) does not affect the overall ether quantum yield starting from cis-stilbene, but significantly enhances both pathways starting from trans-stilbene. It appears that carbene formation and direct methanol addition to higher trans-stilbene excited state(s) compete with relaxation to S 1 . Substitution of D for the vinyl Hs of stilbene enhances the direct addition pathway more than two-fold and strongly suppresses the carbene insertion pathway, revealing a large, k pc d0 / k pc d2 = 6.3, primary deuterium isotope effect in the carbene rearrangement. The two-fold increase in the ether quantum yield is due primarily to a 2.75-fold increase in the lifetime of 1 p* on deuterium substitution of the vinyl hydrogens.

[Derivatives of lupinin and epilupinin as ligands of various cholinesterases].

PubMed

Basova, N E; Kormilitsyn, B N; Rozengart, E V; Saakov, V S; Suvorov, A A

2012-01-01

Literature data have been summarized on interaction of cholinesterases of some mammals and arthropods with a group of isomer derivatives of alkaloid lupini and its epimer epilupinin. As substrates of cholinesterases of several mammals there are studied 8 acetates containing in their molecules the chinolysidin bicycle with different structure of N-alkyl radical, which showed certain elements of specificity of action. For 2 isomer esters that are derivatives of the protonated base of the lupinin and epilupinin structures, differences in their substrate characteristics were revealed. The polyenzyme analysis if anticholinesterase efficiency was performed for 30 organophosphorus inhibitors that are dialkoxyphosphorus derivatives of lupinin and epilupinin; as a result, quite a few peculiarities of their action depending on their structure were revealed. Several tested compounds turned out to act as specific inhibitors of cholinesterases of some mammals and arthropods.

Sc2O@Cs(126339)-C92: Di-scandium oxide cluster encapsulated into a large fullerene cage

NASA Astrophysics Data System (ADS)

Gu, Yong-Xin; Li, Qiao-Zhi; Li, De-Huai; Zhao, Rui-Sheng; Zhao, Xiang

2018-04-01

The geometric, electronic structure and thermodynamic stability of Sc2O@C92 has been characterized by using hybrid density functional theory calculations combined with statistical thermodynamic analyses. Results indicate that the isolated pentagon rule (IPR) isomers Sc2O@Cs(126339)-C92, Sc2O@C1(126367)-C92 and Sc2O@C1(126390)-C92 are favorable. Noteworthy, it is the first time to declare that fullerene isomer Cs(126339)-C92 could be considered as the suitable cage to encapsulate metallic cluster. The electronic properties of these three isomers were performed with frontier molecular orbital (HOMO and LUMO) analyses and bond order calculations. Finally, 13C NMR and UV-vis-NIR spectra were simulated to provide valuable information for future experiments.

Energy and Spectroscopic Characterization of the Isomers of C4H3-, C6H3-, and C6H5-

NASA Technical Reports Server (NTRS)

Wright, Danielle; Bera, Partha P.; Lee, Timothy J.

2015-01-01

Organic and inorganic molecules, neutral and ions have been observed in the interstellar medium. A few anions of organic molecules have also been observed recently. The Cassini spacecraft in the upper atmosphere of Titan has observed anions of large organic molecules. In this project we have studied the physical and spectroscopic properties of C4H3-, C6H3-, and C6H5-. We have optimized the geometrical structures of all low-lying isomers of the anions, calculated rotational, and harmonic vibrational frequencies of the anions mentioned above using the B3LYP density functional along with the augmented correlation consistent polar valence triple zeta (aug-cc-pVTZ) basis set. We have found many low-lying isomers on the potential energy surface of these anions.

A Possible Progenitor of the Interstellar Sulfide Bond: Rovibrational Characterization of the Hydrogen Disulfide Cation HSSH+

NASA Astrophysics Data System (ADS)

Fortenberry, Ryan C.; Francisco, Joseph S.

2018-03-01

{\\tilde{X}}2A\\prime\\prime S2H (HSS) has been observed very recently in the interstellar medium, specifically in the Horsehead nebula. The protonated form, S2H2 +, is believed to be a necessary intermediate in its creation in the gas phase in UV-irradiated regions. However, little is known about this radical cation. This work showcases that the trans-HSSH+ isomer is 0.12 eV lower in energy than the cis with a 1.05 eV upper limit to the torsional rotation barrier. Additionally, the vibrational frequencies and rotational constants for both structures are provided in full here for the first time. The cis isomer is likely the more detectable since it possesses a permanent dipole moment and has a high-intensity vibrational frequency for the antisymmetric H‑S‑S bend at 926 cm‑1 (10.8 μm), in the heart of the mid-IR spectral range. A third isomer, H2S‑S+ is also reported herein lying ∼0.9 eV in energy above trans-HSSH+. This isomer could play a role in the formation of S2H since it would be kinetically favored in the reaction of sulfur cations with hydrogen sulfide. Further assessment of this third, higher-energy isomer is left for future work.

More than 170 polyunsaturated tocopherol-related compounds in a vitamin E capsule: Countercurrent chromatographic enrichment, gas chromatography/mass spectrometry analysis and preliminary identification of the potential artefacts.

PubMed

Hammann, Simon; Kröpfl, Alexander; Vetter, Walter

2016-12-09

Tocopherols and tocotrienols (usually summed up as vitamin E) are a class of structurally related natural antioxidants. Commonly, only some of the eight classic representatives (four tocopherols and four tocotrienols) are found with varied composition in food. In this study we fractionated 230mg oil from commercial vitamin E supplement capsules by countercurrent chromatography (CCC) and subsequent analysis by gas chromatography with mass spectrometry (GC/MS) of silylated CCC fractions showed that these eight isomers represented only about 70% of total tocopherol compounds. Detailed analysis enabled the detection of 161T 3 isomers (α-, γ- and δ-T 3 ) along with 18 tetra- and several penta-unsaturated isomers (tocools), two tocomonoenol isomers, and several degradation products with shorter isoprenoid side chain (apo-tocools). Altogether, over 170 tocool compounds, most likely artefacts which originated from an inappropriate oil refining process were described in this study. Silver ion high performance liquid chromatography (Ag + -HPLC) was used to separate one fraction rich in γ-T 3 into four peaks each consisting of at least five peaks according to GC/MS. About ten γ-T 3 isomers were also detected in rice bran oils from one producer bought retail in Germany. Copyright © 2016 Elsevier B.V. All rights reserved.

Theoretical study of the photo-isomerisation reactions of 1,2-dihydro-1,2-phosphaborine and 1,2-dihydro-1,2-alumazaine

NASA Astrophysics Data System (ADS)

Su, Ming-Der

2015-07-01

The mechanisms of the photochemical isomerisation reactions are investigated theoretically using the model systems, 1,2-dihydro-1,2-phosphaborine (5) and 1,2-dihydro-1,2-alumazaine (6), using the CAS(6,6)/6-311G(d,p) and MP2-CAS-(6,6)/6-311++G(3df,3pd)//CAS(6,6)/6-311G(d,p) methods. For each model reactant, three reaction pathways, which lead to three kinds of photo-isomers, are examined. The structures of the conical intersections, which play a key role in such photo-rearrangements, are determined. The thermal (or dark) reactions of the reactant species are also examined, using the same level of theory, to provide a qualitative explanation of the reaction pathways. These model investigations demonstrate that the preferred reaction route for these two aromatic heterocyclics is as follows: reactant → Franck-Condon region → conical intersection → photoproduct. The theoretical evidences anticipate that after irradiation of 5, the photoproduct yield of the Dewar BP-isomer, 8, should be larger than that of the Dewar BP-isomer, 7, whereas no Dewar BP-isomer 9 can be observed. Moreover, the present theoretical data predict after irradiation of 6, all three Dewar AlN-isomers (10, 11, and 12) and the starting molecule, 6, are produced.

Superbasic amidine monodentate ligands in fac-[Re(CO)3(5,5'-Me2bipy)(amidine)]BF4 complexes: dependence of amidine configuration on the remote nitrogen substituents.

PubMed

Perera, Theshini; Fronczek, Frank R; Marzilli, Patricia A; Marzilli, Luigi G

2010-08-02

Addition of various RNH(2) to fac-[Re(CO)(3)(5,5'-Me(2)bipy)(CH(3)CN)]BF(4) (1) converts the acetonitrile ligand to the amidine ligand (a superbase) in fac-[Re(CO)(3)(5,5'-Me(2)bipy)(HNC(CH(3))NHR)]BF(4) products. Each complex has four conceivable isomers (E, E', Z, and Z') because the amidine CN bonds have double-bond character, and the two remote NHR group substituents are different. The reaction of 1 in acetonitrile is complete in 6 to 96 h (25 degrees C) and forms fac-[Re(CO)(3)(5,5'-Me(2)bipy)(HNC(CH(3))NHR)]BF(4) E' and Z isomers. Only the E' isomer formed crystals (R = methyl, isopropyl, isobutyl, tert-butyl, and benzyl). Upon dissolution of such crystals in acetonitrile-d(3), NMR spectra with highly dominant E' signals gradually changed (approximately 15 min at room temperature) to spectra with signals for an equilibrium mixture of E' and Z isomers. Such slow E'-to-Z isomer interchange is also indicated by 2D ROESY NMR data used primarily to assign solution structure. Equilibrium ratios (E':Z) of approximately 65:35 for R = methyl, isopropyl, and isobutyl and 83:17 for R = tert-butyl demonstrate that increasing the remote NHR group steric bulk above a threshold size favors the E' isomer. Consistent with this trend, fac-[Re(CO)(3)(5,5'-Me(2)bipy)(HNC(CH(3))NH(2))]BF(4), with a remote NH(2) (low bulk) group, favors the Z isomer. In contrast, although the remote NH(benzyl) group in fac-[Re(CO)(3)(5,5'-Me(2)bipy)(HNC(CH(3))NH(CH(2)C(6)H(5))]BF(4) has only moderate bulk, the E' isomer has high abundance as a result of favorable 5,5'-Me(2)bipy/benzyl stacking, evidence for which is present in both solid and solution states. The fac-[Re(CO)(3)(5,5'-Me(2)bipy)(HNC(CH(3))NHR)]BF(4) E isomer can be detected in solvents of low polarity. However, the Z' isomer was not observed, undoubtedly because unfavorable remote-group clashes with the equatorial ligands destabilize this isomer. Challenge studies with a 5-fold excess of 4-dimethylaminopyridine in acetonitrile-d(3) establish that fac-[Re(CO)(3)(5,5'-Me(2)bipy)(HNC(CH(3))NHCH(CH(3))(2))]BF(4) is robust because the isopropylamidine ligand was not displaced, consistent with the superbase character of amidine ligands.

Montelukast photodegradation: elucidation of Ф-order kinetics, determination of quantum yields and application to actinometry.

PubMed

Maafi, Mounir; Maafi, Wassila

2014-08-25

A recently developed Ф-order semi-emperical integrated rate-law for photoreversible AB(2Ф) reactions has been successfully applied to investigate Montelukast sodium (Monte) photodegradation kinetics in ethanol. The model equations also served to propose a new stepwise kinetic elucidation method valid for any AB(2Ф) system and its application to the determination of Monte's forward (Ф(λ(irr))(A-->B)) and reverse (Ф(λ(irr))(B-->A)) quantum yields at various irradiation wavelengths. It has been found that Ф(λ(irr))(A-->B) undergoes a 15-fold increase with wavelength between 220 and 360 nm, with the spectral section 250-360 nm representing Monte effective photodegradation causative range. The reverse quantum yield values were generally between 12 and 54% lower than those recorded for Ф(λ(irr))(A-->B), with the trans-isomer (Monte) converting almost completely to its cis-counterpart at high irradiation wavelengths. Furthermore, the potential use of Monte as an actinometer has been investigated, and an actinometric method was proposed. This study demonstrated the usefulness of Monte for monochromatic light actinometry for the dynamic range 258-380 nm. Copyright © 2014 Elsevier B.V. All rights reserved.

Photoelectron Spectroscopy of Substituted Phenylnitrenes

NASA Astrophysics Data System (ADS)

Wijeratne, Neloni R.; Da Fonte, Maria; Wenthold, Paul G.

2009-06-01

Nitrenes are unusual molecular structures with unfilled electronic valences that are isoelectronic with carbenes. Although, both can be generated by either thermal or photochemical decomposition of appropriate precursors they usually exhibit different reactivities. In this work, we carry out spectroscopic studies of substituted phenylnitrene to determine how the introduction of substituents will affect the reactivity and its thermochemical properties. All studies were carried out by using the newly constructed time-of-flight negative ion photoelectron spectrometer (NIPES) at Purdue University. The 355 nm photoelectron spectra of the o-, m-, and p-chlorophenyl nitrene anions are fairly similar to that measured for phenylnitrene anion. All spectra show low energy triplet state and a high energy singlet state. The singlet state for the meta isomer is well-resolved, with a well defined origin and observable vibrational structure. Whereas the singlet states for the ortho and para isomers have lower energy onsets and no resolved structure. The isomeric dependence suggests that the geometry differences result from the resonance interaction between the nitrogen and the substituent. Quinoidal resonance structures are possible for the open-shell singlet states of the o- and p-chlorinated phenyl nitrenes. The advantages of this type of electronic structures for the open-shell singlet states is that the unpaired electrons can be more localized on separate atoms in the molecules, minimizing the repulsion between. Because the meta position is not in resonance with the nitrenes, substitution at that position should not affect the structure of the open-shell singlet state. The measured electron affinities (EA) of the triplet phenylnitrenes are in excellent agreement with the values predicted by electronic structure calculations. The largest EA, 1.82 eV is found for the meta isomer, with para being the smallest, 1.70 eV.

New two-dimensional V-V binary compounds with a honeycomb-like structure: a first-principles study

NASA Astrophysics Data System (ADS)

Xiao, Wen-Zhi; Xiao, Gang; Rong, Qing-Yan; Wang, Ling-Ling

2018-03-01

We systematically search for the stable structures of two-dimensional (2D) V-V binary compounds with honeycomb-like structure by using the first-principles calculation. We identify 26 stable structures out of 54 2D V-V compounds based on various assessments of stabilities: total energy, thermodynamics, and mechanics. Among them, 12 2D V-V compounds are previously unrecognized structures. For each class V-V isomer, the most stable structures are found to be β-AsP, β-SbAs, α-BiAs, α-BiSb, α 2-SbP, and α 2-BiP. For all isomers of the AsP, they are always stable, and hence PAs monolayer is most likely to be prepared experimentally. All the stable structures are semiconductors with bandgaps ranging from 0.06 eV to 2.52 eV at the Heyd-Scuseria-Ernzerhof level. Therefore, they are potential materials for versatile semiconductor devices. Our findings provide a new clue to facilitate the design of 2D materials for potential applications.

Isolating isomers of perfluorocarboxylates in polar bears (Ursus maritimus) from two geographical locations.

PubMed

De Silva, Amila O; Mabury, Scott A

2004-12-15

The source of involatile, anthropogenic perfluorocarboxylate anions (PFCAs) in biota from remote regions is of heightened interest due to the persistence, toxicity, and bioaccumulation of these materials. Large-scale production of fluorinated compounds is carried out primarily by one of two methods: electrochemical fluorination (ECF) and telomerization. Products of the two processes may be distinguished based on constitutional isomer pattern as ECF products are characteristically comprised of a variety of constitutional isomers. The objective of this research was to develop a method for identifying the constitutional isomer profile of PFCAs in environmental samples and to apply the method to polar bear livers from two different locations. Resolution of constitutional isomers of derivatized PFCAs (8-13 carbons) was accomplished via GC-MS. Seven isomers of an authentic ECF perfluorooctanoate (PFOA) standard were separated. The linear isomer comprised 78% of this standard. Isomer profiles of PFCAs in liver samples of 15 polar bears (Ursus maritimus) from the Canadian Arctic and eastern Greenland were determined by GC-MS. The PFOA isomer pattern in Greenland polar bear samples showed a variety of branched isomers while only the linear PFOA isomer was determined in Canadian samples. Samples of both locations had primarily (>99%) linear isomers of perfluorononanoate and perfluorotridecanoate. Branched isomers of perfluorodecanoate, perfluoroundecanoate, and perfluorododecanoate were determined in the polar bear samples. Unlike the PFOA isomer signature, only a single branched isomer peak on the chromatograms was observed for these longer chain PFCAs. The presence of branched isomers suggests some contribution from ECF sources. However, in comparison to the amount of branched isomers in the ECF PFOA standard, such minor percentages of branched PFCAs may suggest additional input from an exclusively linear isomer source.

On-demand photoinitiated polymerization

DOEpatents

Boydston, Andrew J; Grubbs, Robert H; Daeffler, Chris; Momcilovic, Nebojsa

2015-01-13

Compositions and methods for adjustable lenses are provided. In some embodiments, the lenses contain a lens matrix material, a masking compound, and a prepolymer. The lens matrix material provides structure to the lens. The masking compound is capable of blocking polymerization or crosslinking of the prepolymer, until photoisomerization of the compound is triggered, and the compound is converted from a first isomer to a second isomer having a different absorption profile. The prepolymer is a composition that can undergo a polymerization or crosslinking reaction upon photoinitiation to alter one or more of the properties of the lenses.

On-demand photoinitiated polymerization

DOEpatents

Boydston, Andrew J; Grubbs, Robert H; Daeffler, Chris; Momcilovic, Nebojsa

2013-12-10

Compositions and methods for adjustable lenses are provided. In some embodiments, the lenses contain a lens matrix material, a masking compound, and a prepolymer. The lens matrix material provides structure to the lens. The masking compound is capable of blocking polymerization or crosslinking of the prepolymer, until photoisomerization of the compound is triggered, and the compound is converted from a first isomer to a second isomer having a different absorption profile. The prepolymer is a composition that can undergo a polymerization or crosslinking reaction upon photoinitiation to alter one or more of the properties of the lenses.

Nuclear states with anomalously large radius (size isomers)

DOE Office of Scientific and Technical Information (OSTI.GOV)

Ogloblin, A. A.; Demyanova, A. S., E-mail: a.s.demyanova@bk.ru; Danilov, A. N.

2016-07-15

Methods of determination of the nuclear excited state radii are discussed together with the recently obtained data on the states of some light nuclei having abnormally large radii (size isomers). It is shown that such states include excited neutron-halo states in {sup 9}Be, {sup 11}Be, and {sup 13}C and some alpha-cluster states in {sup 12}C, {sup 11}B, and {sup 13}C. Among the latter ones, there is the well-known Hoyle state in {sup 12}C—the structure of this state exhibit rudimentary features of alpha-particle states.

The HNC/HCN ratio in star-forming regions

DOE Office of Scientific and Technical Information (OSTI.GOV)

Graninger, Dawn M.; Öberg, Karin I.; Herbst, Eric

2014-05-20

HNC and HCN, typically used as dense gas tracers in molecular clouds, are a pair of isomers that have great potential as a temperature probe because of temperature dependent, isomer-specific formation and destruction pathways. Previous observations of the HNC/HCN abundance ratio show that the ratio decreases with increasing temperature, something that standard astrochemical models cannot reproduce. We have undertaken a detailed parameter study on which environmental characteristics and chemical reactions affect the HNC/HCN ratio and can thus contribute to the observed dependence. Using existing gas and gas-grain models updated with new reactions and reaction barriers, we find that in staticmore » models the H + HNC gas-phase reaction regulates the HNC/HCN ratio under all conditions, except for very early times. We quantitatively constrain the combinations of H abundance and H + HNC reaction barrier that can explain the observed HNC/HCN temperature dependence and discuss the implications in light of new quantum chemical calculations. In warm-up models, gas-grain chemistry contributes significantly to the predicted HNC/HCN ratio and understanding the dynamics of star formation is therefore key to model the HNC/HCN system.« less

A theoretical study of the hydrogen bonding between the vic-, cis- and trans-C 2H 2F 2 isomers and hydrogen fluoride

NASA Astrophysics Data System (ADS)

Rusu, Victor H.; da Silva, João Bosco P.; Ramos, Mozart N.

2009-04-01

MP2/6-31++G(d,p) and B3LYP/6-31++G(d,p) theoretical calculations have been employed to investigate the hydrogen bonding formation involving the vic-, cis- and trans-C 2H 2F 2 isomers and hydrogen fluoride. Our calculations have revealed for each isomer the preferential existence of two possible hydrogen-bonded complexes: a non-cyclic complex and a cyclic complex. For all the three isomers the binding energies for the non-cyclic and cyclic hydrogen complexes are essentially equal using both the MP2 and B3LYP calculations, being that the cyclic structure is slightly more stable. For instance, the binding energies including BSSE and ZPE corrections for the non-cyclic and cyclic structures of cis-C 2H 2F···HF are 8.7 and 9.0 kJ mol -1, respectively, using B3LYP calculations. The cyclic complex formation reduces the polarity, in contrast to what occurs with the non-cyclic complex. This result is more accentuated in vic-C 2H 2F 2···HF. In this latter, Δ μ(cyclic) is -3.07 D, whereas Δ μ(non-cyclic) is +1.92 D using B3LYP calculations. Their corresponding MP2 values are +0.44 D and -1.89 D, respectively. As expected, the complexation produces an H sbnd F stretching frequency downward shift, whereas its IR intensity is enhanced. On the other hand, the vibrational modes of the vic-, cis- and trans-C 2H 2F 2 isomers are little affected by complexation. The new vibrational modes due to hydrogen bonding formation show several interesting features, in particular the HF bending modes which are pure rotations in the free molecule.

Strategies to distinguish new synthetic cannabinoid FUBIMINA (BIM-2201) intake from its isomer THJ-2201: metabolism of FUBIMINA in human hepatocytes.

PubMed

Diao, Xingxing; Scheidweiler, Karl B; Wohlfarth, Ariane; Zhu, Mingshe; Pang, Shaokun; Huestis, Marilyn A

Since 2013, a new drugs-of-abuse trend attempts to bypass drug legislation by marketing isomers of scheduled synthetic cannabinoids (SCs), e.g., FUBIMINA (BIM-2201) and THJ-2201. It is much more challenging to confirm a specific isomer's intake and distinguish it from its structural analog because the isomers and their major metabolites usually have identical molecular weights and display the same product ions. Here, we investigated isomers FUBIMINA and THJ-2201 and propose strategies to distinguish their consumption. THJ-2201 was scheduled in the US, Japan, and Europe; however, FUBIMINA is easily available on the Internet. We previously investigated THJ-2201 metabolism in human hepatocytes, but human FUBIMINA metabolism is unknown. We aim to characterize FUBIMINA metabolism in human hepatocytes, recommend optimal metabolites to confirm its consumption, and propose strategies to distinguish between intakes of FUBIMINA and THJ-2201. FUBIMINA (10 μM) was incubated in human hepatocytes for 3 h, and metabolites were characterized with high-resolution mass spectrometry (HR-MS). We identified 35 metabolites generated by oxidative defluorination, further carboxylation, hydroxylation, dihydrodiol formation, glucuronidation, and their combinations. We recommend 5'-OH-BIM-018 (M34), BIM-018 pentanoic acid (M33), and BIM-018 pentanoic acid dihydrodiol (M7) as FUBIMINA specific metabolites. THJ-2201 produced specific metabolite markers 5'-OH-THJ-018 (F26), THJ-018 pentanoic acid (F25), and hydroxylated THJ-2201 (F13). Optimized chromatographic conditions to achieve different retention times and careful selection of specific product ion spectra enabled differentiation of isomeric metabolites, in this case FUBIMINA from THJ-2201. Our HR-MS approach should be applicable for differentiating future isomeric SCs, which is especially important when different isomers have different legal status.

Providing theoretical data for detection of four formamidic acid isomers in astrophysical media

NASA Astrophysics Data System (ADS)

Vichietti, R. M.; da Silva, A. B. F.; Haiduke, R. L. A.

2018-03-01

We present a theoretical study, so that molecular data (geometrical parameters, vibrational frequencies, infrared intensities, electronic energies, enthalpies, and Gibbs energies) of four formamidic acid (FA) isomers (labeled here as FA1, FA2, FA3, and FA4) and formamide (HCONH2) are obtained from CCSD/cc-pVTZ, CCSD/aug-cc-pVTZ, CCSD/cc-pVQZ, and CCSD(T)/cc-pVTZ calculations. Furthermore, on the basis of insufficient or even lacking theoretical and experimental results in the literature, we employed the aforementioned theory levels to determine benchmark values of dipole moments and rotational constants for these four FA isomers in order to contribute for their detection in astrophysical environments. Besides, we provide for the first time data about forward and reverse rate constants (200-4000 K) and Arrhenius' parameters for each interconversion reaction between pairs of FA isomers as well as for the tautomeric process involving FA4 and formamide, which were calculated from a Complete Basis Set (CBS) extrapolation equation obtained at CCSD/cc-pVTZ optimized geometries. Our kinetic analysis indicated a faster interconversion between the FA structures in comparison with the FA4 ↔ HCONH2 process, suggesting that these isomers could co-exist in astrophysical media. Finally, we estimated that these isomers may be detected with relative abundances, [FAx]/[HCONH2] (x = 1, 2, 3, and 4), between ∼0.01 and ∼0.1% in astrophysical sources at chemical equilibrium conditions and temperatures around 1000 K. However, these ratios can become as high as ∼1, ∼3, and ∼5%, respectively, in hotter regions with temperatures around 2000, 3000, and 4000 K (expected, for example, in massive star-forming regions).

Fluorescence of carotenoids. Effect of oxygenation and cis/trans isomerization

NASA Astrophysics Data System (ADS)

Jørgensen, Kevin; Stapelfeldt, Henrik; Skibsted, Leif H.

1992-03-01

C 40 carotenoids fall, with respect to fluorescence in homogeneous solution, into two distinct groups depending on the presence of a CO group in the molecule. Excitation spectra agree with absorption spectra for the carbonyl derivatives astaxanthin and canthaxanthin. In contrast, zeaxanthin and isomers of β-carotene have a twentyfold increase in fluorescence quantum yield for excitation around 350 nm compared to excitation near the absorption maximum (at approximatively 430 nm). These differences are interpreted in terms of the role of non-emitting 1(n, π*) states related to the CO group in facilitating non-radiative deactivation of higher 1(π, π*) states.

Catalytic homogeneous hydrogenation of compounds containing X --> O semipolar bonds (X = N, S, P) with para-hydrogen as a promising route for preparation of para-water.

PubMed

Ustynyuk, Yuri A; Gavrikov, Alexei V; Sergeyev, Nikolay M

2006-11-28

The quantum-chemical simulation (DFT, PBE, TZ2p basis set) of the mechanism of catalytic hydrogenation of compounds containing R(n)X --> O semipolar bonds (R(n)X = N(2), Me(2)S, C(5)H(5)N, Ph(3)P) on the Wilkinson catalyst (Ph(3)P)(3)RhCl with para-hydrogen showed that this process proceeds with retention of proton nuclear spin correlation, which enables a principal possibility to synthesize para-H(2)O, i.e. the nuclear spin isomer of water with antiparallel proton spins, using this route.

Table of superdeformed nuclear bands and fission isomers (from Nuclear Data Sheets, v.78, issue 1, May 1996)

DOE Office of Scientific and Technical Information (OSTI.GOV)

Singh, B.; Firestone, R B.; Chu, S Y.F.

As part of a committment to maintain nuclear structure data as current as possible in the Evaluated Nuclear Structure Data File (ENSDF) and the Table of Isotopes, the author have been updating the information on superdeformed and hyperdeformed nuclear bands. As of February, 1996, they have compiled data for 161 superdeformed bands and 47 fission isomers identified in 93 nuclides for this publication. This is an increase of 75 superdeformed bands and 20 new nuclides since the first edition in 1994. Partial data for superdeformed bands and fission isomers are shown in the band drawings. For each nuclide there ismore » a complete level table listing both normal (taken from the ENSDF file) and superdeformed band assignments; level energy, spin, parity, half-life, magnetic moments, decay branchings; and the energies, final levels, relative intensities, multipolarities, and mixing ratios for transitions deexciting each level. Mass excess, decay energies, and proton and neutron separation energies are also provided from the evaluation of Audi and Wapstra. For superdeformed and hyperdeformed bands they provide the following quantities: level energies; level half-lives; level spins; and gamma ray energies.« less

Isomeric Detergent Comparison for Membrane Protein Stability: Importance of Inter-Alkyl-Chain Distance and Alkyl Chain Length.

PubMed

Cho, Kyung Ho; Hariharan, Parameswaran; Mortensen, Jonas S; Du, Yang; Nielsen, Anne K; Byrne, Bernadette; Kobilka, Brian K; Loland, Claus J; Guan, Lan; Chae, Pil Seok

2016-12-14

Membrane proteins encapsulated by detergent micelles are widely used for structural study. Because of their amphipathic property, detergents have the ability to maintain protein solubility and stability in an aqueous medium. However, conventional detergents have serious limitations in their scope and utility, particularly for eukaryotic membrane proteins and membrane protein complexes. Thus, a number of new agents have been devised; some have made significant contributions to membrane protein structural studies. However, few detergent design principles are available. In this study, we prepared meta and ortho isomers of the previously reported para-substituted xylene-linked maltoside amphiphiles (XMAs), along with alkyl chain-length variation. The isomeric XMAs were assessed with three membrane proteins, and the meta isomer with a C 12 alkyl chain was most effective at maintaining solubility/stability of the membrane proteins. We propose that interplay between the hydrophile-lipophile balance (HLB) and alkyl chain length is of central importance for high detergent efficacy. In addition, differences in inter-alkyl-chain distance between the isomers influence the ability of the detergents to stabilise membrane proteins. © 2016 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

Quantum Dot and Polymer Composite Cross-Reactive Array for Chemical Vapor Detection.

PubMed

Bright, Collin J; Nallon, Eric C; Polcha, Michael P; Schnee, Vincent P

2015-12-15

A cross-reactive chemical sensing array was made from CdSe Quantum Dots (QDs) and five different organic polymers by inkjet printing to create segmented fluorescent composite regions on quartz substrates. The sensor array was challenged with exposures from two sets of analytes, including one set of 14 different functionalized benzenes and one set of 14 compounds related to security concerns, including the explosives trinitrotoluene (TNT) and ammonium nitrate. The array was broadly responsive to analytes with different chemical functionalities due to the multiple sensing mechanisms that altered the QDs' fluorescence. The sensor array displayed excellent discrimination between members within both sets. Classification accuracy of more than 93% was achieved, including the complete discrimination of very similar dinitrobenzene isomers and three halogenated, substituted benzene compounds. The simple fabrication, broad responsivity, and high discrimination capacity of this type of cross-reactive array are ideal qualities for the development of sensors with excellent sensitivity to chemical and explosive threats while maintaining low false alarm rates.

Isomer-delayed γ -ray spectroscopy of A =159 -164 midshell nuclei and the variation of K -forbidden E 1 transition hindrance factors

NASA Astrophysics Data System (ADS)

Patel, Z.; Walker, P. M.; Podolyák, Zs.; Regan, P. H.; Berry, T. A.; Söderström, P.-A.; Watanabe, H.; Ideguchi, E.; Simpson, G. S.; Nishimura, S.; Wu, Q.; Xu, F. R.; Browne, F.; Doornenbal, P.; Lorusso, G.; Rice, S.; Sinclair, L.; Sumikama, T.; Wu, J.; Xu, Z. Y.; Aoi, N.; Baba, H.; Bello Garrote, F. L.; Benzoni, G.; Daido, R.; Dombrádi, Zs.; Fang, Y.; Fukuda, N.; Gey, G.; Go, S.; Gottardo, A.; Inabe, N.; Isobe, T.; Kameda, D.; Kobayashi, K.; Kobayashi, M.; Komatsubara, T.; Kojouharov, I.; Kubo, T.; Kurz, N.; Kuti, I.; Li, Z.; Matsushita, M.; Michimasa, S.; Moon, C.-B.; Nishibata, H.; Nishizuka, I.; Odahara, A.; Şahin, E.; Sakurai, H.; Schaffner, H.; Suzuki, H.; Takeda, H.; Tanaka, M.; Taprogge, J.; Vajta, Zs.; Yagi, A.; Yokoyama, R.

2017-09-01

Excited states have been studied in 159Sm, 161Sm, 162Sm (Z =62 ), 163Eu (Z =63 ), and 164Gd (Z =64 ), populated by isomeric decay following 238U projectile fission at RIBF, RIKEN. The isomer half-lives range from 50 ns to 2.6 μ s . In comparison with other published data, revised interpretations are proposed for 159Sm and 163Eu. The first data for excited states in 161Sm are presented, where a 2.6-μ s isomer is assigned a three-quasiparticle, Kπ=17 /2- structure. The interpretation is supported by multi-quasiparticle Nilsson-BCS calculations, including the blocking of pairing correlations. A consistent set of reduced E 1 hindrance factors is obtained. Limited evidence is also reported for isomeric decay in 163Sm, 164Eu, and 165Eu.

Revisiting shape selectivity in liquid chromatography for polycyclic aromatic hydrocarbons (PAHs) - six-ring and seven-ring Cata-condensed PAH isomers of molecular mass 328 Da and 378 Da.

PubMed

Oña-Ruales, Jorge O; Sander, Lane C; Wilson, Walter B; Wise, Stephen A

2018-01-01

The relationship of reversed-phase liquid chromatography (RPLC) retention on a polymeric C 18 stationary phase and the shape of polycyclic aromatic hydrocarbons (PAHs) was investigated for three-ring to seven-ring cata-condensed isomers. We report the first RPLC separation for six-ring and seven-ring cata-condensed PAH isomers. Correlations of LC retention and shape parameters (length-to-breath ratio, L/B and thickness, T) were investigated for 2 three-ring isomers (molecular mass 178 Da), 5 four-ring isomers (molecular mass 228 Da), 11 five-ring isomers (molecular mass 278 Da), 17 six-ring isomers (molecular mass 328 Da), and 20 seven-ring isomers (molecular mass 378 Da). Significant linear correlations were found for all isomer groups (r = 0.71 to 0.94). Nonplanarity of the PAH isomers was found to influence retention (i.e., nonplanar isomers eluting earlier than expected based on L/B) and linear correlations of retention vs. T for isomer groups containing nonplanar isomers were significant (r = 0.71 to 0.86). Graphical abstract.

Theoretical Studies on Structures and Relative Stability for Polynitrohexaazaadamantanes

NASA Astrophysics Data System (ADS)

Xu, Xiao-juan; Xiao, He-ming; Wang, Gui-xiang; Ju, Xue-hai

2006-10-01

The density function theory at the B3LYP/6-31G* level was employed to study the structures, including the total energies (EZPE), the geometries, the oxygen balances (OB100), the dipole moments, of polynitro-hexaazaadamantanes (PNHAAs) and the potential candidates of high energy density compounds (HEDCs). The structural parameters of PNHAAs, such as the the maximum N—NO2 bond length (LBmax), the least N—N Mulliken population (BN—N), the least negative charge on the nitro group (QNO2) and OB100, were studied to predict their relative stability or sensitivity (the easiness for initiating a detonation, high sensitivity means low stability). It was found that the same conclusion was drawn from the four parameters. With the number of nitro groups increasing, the stabilities of these compounds decrease. OB100 failed in identifying the isomers, but the EZPE energy and the dipole moment were considered to give more reliable results for the isomers.

Optically active single-walled carbon nanotubes

NASA Astrophysics Data System (ADS)

Peng, Xiaobin; Komatsu, Naoki; Bhattacharya, Sumanta; Shimawaki, Takanori; Aonuma, Shuji; Kimura, Takahide; Osuka, Atsuhiro

2007-06-01

The optical, electrical and mechanical properties of single-walled carbon nanotubes (SWNTs) are largely determined by their structures, and bulk availability of uniform materials is vital for extending their technological applications. Since they were first prepared, much effort has been directed toward selective synthesis and separation of SWNTs with specific structures. As-prepared samples of chiral SWNTs contain equal amounts of left- and right-handed helical structures, but little attention has been paid to the separation of these non-superimposable mirror image forms, known as optical isomers. Here, we show that optically active SWNT samples can be obtained by preferentially extracting either right- or left-handed SWNTs from a commercial sample. Chiral `gable-type' diporphyrin molecules bind with different affinities to the left- and right-handed helical nanotube isomers to form complexes with unequal stabilities that can be readily separated. Significantly, the diporphyrins can be liberated from the complexes afterwards, to provide optically enriched SWNTs.

[Ligands of cholinesterases of ephedrine and pseudoephedrine structure].

PubMed

Basova, N E; Kormilitsin, B N; Perchenok, A Yu; Rozengatt, E V; Saakov, V S; Suvorov, A A

2013-01-01

The paper is a review of literature data on interaction of the mammalian erythrocyte acetylcholinesterase and blood serum butyrylcholinesterase with a group of isomer complex ester derivatives (acetates, propionates, butyrates, valerates, and isobutyrates) of bases and iodomethylates of ephedrine and its enantiomer pseudoephedrine. For 20 alkaloid monoesters, parameters of enzymatic hydrolysis are determined and their certain specificity toward acetylcholinesterase is revealed, whereas 5 diesters of iodomethylates of pseudoephedrine were hydrolyzed only by butyrylcholinesterase. The studied 20 aklaloid diesters and 10 trimethylammonium derivatives turned out to be non-competitive reversible inhibitors of acetylcholinesterase and competitive inhibitors of butyrylcholinesterase. The performed for the first time isomer and enantiomer analysis "structure-efficiency" has shown that in most cases it is possible to state the greater comlementarity of the catalytical surface of enzymes for ligands of the pseudoephedrine structure, such differentiation being realized more often at the reversible inhibition of enzymes. pseudoephedrine.

Structure and stability of M6N8 clusters (M = Si, Ge, Sn, Ti).

PubMed

Davydova, Elena I; Timoshkin, Alexey Y; Frenking, Gernot

2010-06-10

The structures and stabilities of the M(6)N(8) clusters (M = Si, Ge, Sn, Ti) have been theoretically studied at DFT and ab initio levels of theory. Two new isomers have been considered: cage-like molecules and propeller-like molecules. It is shown that only for M = Si are both isomers true minima on the potential energy surface. The thermodynamics of the dissociation process (1/6)M(6)N(8) --> (1/3)M(3)N(4) is discussed. For each M(3)N(4) molecule, four structures with different multiplicity are considered. The thermodynamic analysis shows that independently of the multiplicity of M(3)N(4) nitrides all M(6)N(8) clusters are stable in the gas phase in a wide temperature range and could be potential intermediates in chemical vapor deposition of the nitride materials.

Endosulfan leaching from Typic Argiudolls in soybean tillage areas and groundwater pollution implications.

PubMed

Grondona, Sebastián I; Gonzalez, Mariana; Martínez, Daniel E; Massone, Héctor E; Miglioranza, Karina S B

2014-06-15

Endosulfan has been recently added to Persistent Organic Pollutants (POPs) list and due to its extensive and massive use and environmental persistence constitutes a potential hazard to groundwater resources. Undisturbed soil columns were used to evaluate endosulfan leaching in two series of Typic Argiudolls considering natural and agricultural land use. Columns were spiked with 10μgL(-1) of technical endosulfan and eluted under saturated flow with five pore volumes of distilled water. Alfa and beta isomer residues were detected in the upper soil level, with decreasing values through the profile, being influenced by soil texture and land use. The endosulfan sulfate metabolite was mainly found in the upper level linked to high dehydrogenase activity. Results from leachates (total endosulfan 27-87ngL(-1)) showed higher α-isomer mobility, and suggest alkaline hydrolysis of both endosulfan isomers. The agricultural use modified the physico-chemical properties and structure of soils leading to vertical migration of endosulfan isomers under saturated conditions. Intact column test provided information close to field data showing its utility for the assessment of groundwater pollution by endosulfan. Copyright © 2014 Elsevier B.V. All rights reserved.

Stable isomers and electronic, vibrational, and optical properties of WS2 nano-clusters: A first-principles study

NASA Astrophysics Data System (ADS)

Hafizi, Roohollah; Hashemifar, S. Javad; Alaei, Mojtaba; Jangrouei, MohammadReza; Akbarzadeh, Hadi

2016-12-01

In this paper, we employ an evolutionary algorithm along with the full-potential density functional theory (DFT) computations to perform a comprehensive search for the stable structures of stoichiometric (WS2)n nano-clusters (n = 1 - 9), within three different exchange-correlation functionals. Our results suggest that n = 5 and 8 are possible candidates for the low temperature magic sizes of WS2 nano-clusters while at temperatures above 500 Kelvin, n = 7 exhibits a comparable relative stability with n = 8. The electronic properties and energy gap of the lowest energy isomers were computed within several schemes, including semilocal Perdew-Burke-Ernzerhof and Becke-Lee-Yang-Parr functionals, hybrid B3LYP functional, many body based DFT+GW approach, ΔSCF method, and time dependent DFT calculations. Vibrational spectra of the lowest lying isomers, computed by the force constant method, are used to address IR spectra and thermal free energy of the clusters. Time dependent density functional calculation in a real time domain is applied to determine the full absorption spectra and optical gap of the lowest energy isomers of the WS2 nano-clusters.

Sequence and Solution Effects on the Prevalence of d-Isomers Produced by Deamidation

PubMed Central

2017-01-01

Deamidation of asparagine is a spontaneous and irreversible post-translational modification associated with a growing list of human diseases. While pervasive, deamidation is often overlooked because it represents a relatively minor chemical change. Structural and functional characterization of this modification is complicated because deamidation of asparagine yields four isomeric forms of Asp. Herein, radical directed dissociation (RDD), in conjunction with mass spectrometry, is used to identify and quantify all four isomers in a series of model peptides that were subjected to various deamidation conditions. Although primary sequence significantly influences the rate of deamidation, it has little impact on the relative proportions of the product isomers. Furthermore, the addition of ammonia can be used to increase the rate of deamidation without significantly perturbing isomer populations. Conversely, external factors such as buffer conditions and temperature alter product distributions but exhibit less dramatic effects on the deamidation rate. Strikingly, the common laboratory and biologically significant bicarbonate buffer is found to strongly promote racemization, yielding increased amounts of d-Asp and d-isoAsp. These outcomes following deamidation have broad implications in human aging and should be considered during the development of protein-based therapeutics. PMID:28984444

Structural evolution study of 1-2 nm gold clusters

NASA Astrophysics Data System (ADS)

Beltrán, M. R.; Suárez Raspopov, R.; González, G.

2011-12-01

We have explored lowest energy minima structures of gold atom clusters both, charged and neutral (Aun^{ν}νn with n = 20, 28, 34, 38, 55, 75, 101, 146, 147, 192, 212 atoms and ν = 0, ±1). The structures have been obtained from first principles generalized gradient approximation, density functional theory (DFT) calculations based on norm-conserving pseudopotentials and numerical atomic basis sets. We have found two new disordered or defective isomers lower in energy than their ordered counterparts for n = 101, 147. The purpose of this work is to systematically study the difference between the electronic properties of the two lowest ordered and disordered isomers for each size. Our results agree with previous first principle calculations and with some recent experimental results (Au20 and Au101). For each case we report total energies, binding energies, ionization potentials, electron affinities, density of states, highest occupied molecular orbital-lowest unoccupied molecular orbital (HOMO-LUMO) gaps, Housdorff chirality measure index and their simulated image in a high resolution transmission electron microscopy (HRTEM). The calculated properties of the two low lying (ordered and disordered) isomers show clear differences as to be singled out in a suitable experimental setting. An extensive discussion on the evolution with size of the cohesive energy, the ionization potentials, the electron affinities, the HOMO-LUMO gaps and their index of chirality to determine the crossover between them is given.

Evolution of the properties of Al(n)N(n) clusters with size.

PubMed

Costales, Aurora; Blanco, M A; Francisco, E; Pandey, Ravindra; Martín Pendás, A

2005-12-29

A global optimization of stoichiometric (AlN)(n) clusters (n = 1-25, 30, 35, ..., 95, 100) has been performed using the basin-hopping (BH) method and describing the interactions with simple and yet realistic interatomic potentials. The results for the smaller isomers agree with those of previous electronic structure calculations, thus validating the present scheme. The lowest-energy isomers found can be classified in three different categories according to their structural motifs: (i) small clusters (n = 2-5), with planar ring structures and 2-fold coordination, (ii) medium clusters (n = 6-40), where a competition between stacked rings and globular-like empty cages exists, and (iii) large clusters (n > 40), large enough to mix different elements of the previous stage. All the atoms in small and medium-sized clusters are in the surface, while large clusters start to display interior atoms. Large clusters display a competition between tetrahedral and octahedral-like features: the former lead to a lower energy interior in the cluster, while the latter allow for surface terminations with a lower energy. All of the properties studied present different regimes according to the above classification. It is of particular interest that the local properties of the interior atoms do converge to the bulk limit. The isomers with n = 6 and 12 are specially stable with respect to the gain or loss of AlN molecules.

Characterisation of different polymorphs of tris(8-hydroxyquinolinato)aluminium(III) using solid-state NMR and DFT calculations

PubMed Central

Goswami, Mithun; Nayak, Pabitra K; Periasamy, N; Madhu, PK

2009-01-01

Background Organic light emitting devices (OLED) are becoming important and characterisation of them, in terms of structure, charge distribution, and intermolecular interactions, is important. Tris(8-hydroxyquinolinato)-aluminium(III), known as Alq3, an organomettalic complex has become a reference material of great importance in OLED. It is important to elucidate the structural details of Alq3 in its various isomeric and solvated forms. Solid-state nuclear magnetic resonance (NMR) is a useful tool for this which can also complement the information obtained with X-ray diffraction studies. Results We report here 27Al one-dimensional (1D) and two-dimensional (2D) multiple-quantum magic-angle spinning (MQMAS) NMR studies of the meridional (α-phase) and the facial (δ-phase) isomeric forms of Alq3. Quadrupolar parameters are estimated from the 1D spectra under MAS and anisotropic slices of the 2D spectra and also calculated using DFT (density functional theory) quantum-chemical calculations. We have also studied solvated phase of Alq3 containing ethanol in its lattice. We show that both the XRD patterns and the quadrupolar parameters of the solvated phase are different from both the α-phase and the δ-phase, although the fluorescence emission shows no substantial difference between the α-phase and the solvated phase. Moreover, we have shown that after the removal of ethanol from the matrix the solvated Alq3 has similar XRD patterns and quadrupolar parameters to that of the α-phase. Conclusion The 2D MQMAS experiments have shown that all the different modifications of Alq3 have 27Al in single unique crystallographic site. The quadrupolar parameters predicted using the DFT calculation under the isodensity polarisable continuum model resemble closely the experimentally obtained values. The solvated phase of Alq3 containing ethanol has structural difference from the α-phase of Alq3 (containing meridional isomer) from the solid-state NMR studies. Solid-state NMR can hence be used as an effective complementary tool to XRD for characterisation and structural elucidation. PMID:19900275

Characterisation of different polymorphs of tris(8-hydroxyquinolinato)aluminium(III) using solid-state NMR and DFT calculations.

PubMed

Goswami, Mithun; Nayak, Pabitra K; Periasamy, N; Madhu, P K

2009-11-09

Organic light emitting devices (OLED) are becoming important and characterisation of them, in terms of structure, charge distribution, and intermolecular interactions, is important. Tris(8-hydroxyquinolinato)-aluminium(III), known as Alq3, an organomettalic complex has become a reference material of great importance in OLED. It is important to elucidate the structural details of Alq3 in its various isomeric and solvated forms. Solid-state nuclear magnetic resonance (NMR) is a useful tool for this which can also complement the information obtained with X-ray diffraction studies. We report here 27Al one-dimensional (1D) and two-dimensional (2D) multiple-quantum magic-angle spinning (MQMAS) NMR studies of the meridional (alpha-phase) and the facial (delta-phase) isomeric forms of Alq3. Quadrupolar parameters are estimated from the 1D spectra under MAS and anisotropic slices of the 2D spectra and also calculated using DFT (density functional theory) quantum-chemical calculations. We have also studied solvated phase of Alq3 containing ethanol in its lattice. We show that both the XRD patterns and the quadrupolar parameters of the solvated phase are different from both the alpha-phase and the delta-phase, although the fluorescence emission shows no substantial difference between the alpha-phase and the solvated phase. Moreover, we have shown that after the removal of ethanol from the matrix the solvated Alq3 has similar XRD patterns and quadrupolar parameters to that of the alpha-phase. The 2D MQMAS experiments have shown that all the different modifications of Alq3 have 27Al in single unique crystallographic site. The quadrupolar parameters predicted using the DFT calculation under the isodensity polarisable continuum model resemble closely the experimentally obtained values. The solvated phase of Alq3 containing ethanol has structural difference from the alpha-phase of Alq3 (containing meridional isomer) from the solid-state NMR studies. Solid-state NMR can hence be used as an effective complementary tool to XRD for characterisation and structural elucidation.

Alkyl nitrate formation from the reactions of C8-C14 n-alkanes with OH radicals in the presence of NO(x): measured yields with essential corrections for gas-wall partitioning.

PubMed

Yeh, Geoffrey K; Ziemann, Paul J

2014-09-18

In this study, C8-C14 n-alkanes were reacted with OH radicals in the presence of NO(x) in a Teflon film environmental chamber and isomer-specific yields of alkyl nitrates were determined using gas chromatography. Because results indicated significant losses of alkyl nitrates to chamber walls, gas-wall partitioning was investigated by monitoring the concentrations of a suite of synthesized alkyl nitrates added to the chamber. Gas-to-wall partitioning increased with increasing carbon number and with proximity of the nitrooxy group to the terminal carbon, with losses as high as 86%. The results were used to develop a structure-activity model to predict the effects of carbon number and isomer structure on gas-wall partitioning, which was used to correct the measured yields of alkyl nitrate isomers formed in chamber reactions. The resulting branching ratios for formation of secondary alkyl nitrates were similar for all isomers of a particular carbon number, and average values, which were almost identical to alkyl nitrate yields, were 0.219, 0.206, 0.254, 0.291, and 0.315 for reactions of n-octane, n-decane, n-dodecane, n-tridecane, and n-tetradecane, respectively. The increase in average branching ratios and alkyl nitrate yields with increasing carbon number to a plateau value of ∼0.30 at about C13-C14 is consistent with predictions of a previously developed model, indicating that the model is valid for alkane carbon numbers ≥C3.

Synthesis of framework isomer MOFs containing zinc and 4-tetrazolyl benzenecarboxylic acid via a structure directing solvothermal approach

DOE PAGES

Ordonez, Carlos; Kinnibrugh, Tiffany L.; Xu, Hongwu; ...

2015-04-02

The solvothermal synthesis of framework isomers was carried out using the hybrid carboxylate and tetrazolate functional ligand, 4-tetrazolyl benzenecarboxylic acid (H₂TBC, TBC = 4-tetrazolyl benzenecarboxylate) and zinc. H₂TBC was also synthesized with the solvothermal approach, and is referred herein as structure 1. Using single-crystal X-ray diffraction, we found that the tetrazolate groups of TBC show an unusual “opposite-on” coordination mode with zinc. Three previously characterized metal-organic frameworks (MOFs) were obtained by systematically changing the solvents of the H₂TBC-Zn reaction, (1) ZnTBC, 2, which has a non-porous structure; (2) Zn₂(TBC)₂(H2O), 3, which has an amphiphilic pore structure and (3) Zn₂(TBC)₂{guest}, 4,more » which is porous and has channels containing uncoordinated N heteroatoms. Fluorescence spectra of 4 reveal a strong blue emission mainly from the TBC ligands.« less

Identification of carbohydrate anomers using ion mobility-mass spectrometry.

PubMed

Hofmann, J; Hahm, H S; Seeberger, P H; Pagel, K

2015-10-08

Carbohydrates are ubiquitous biological polymers that are important in a broad range of biological processes. However, owing to their branched structures and the presence of stereogenic centres at each glycosidic linkage between monomers, carbohydrates are harder to characterize than are peptides and oligonucleotides. Methods such as nuclear magnetic resonance spectroscopy can be used to characterize glycosidic linkages, but this technique requires milligram amounts of material and cannot detect small amounts of coexisting isomers. Mass spectrometry, on the other hand, can provide information on carbohydrate composition and connectivity for even small amounts of sample, but it cannot be used to distinguish between stereoisomers. Here, we demonstrate that ion mobility-mass spectrometry--a method that separates molecules according to their mass, charge, size, and shape--can unambiguously identify carbohydrate linkage-isomers and stereoisomers. We analysed six synthetic carbohydrate isomers that differ in composition, connectivity, or configuration. Our data show that coexisting carbohydrate isomers can be identified, and relative concentrations of the minor isomer as low as 0.1 per cent can be detected. In addition, the analysis is rapid, and requires no derivatization and only small amounts of sample. These results indicate that ion mobility-mass spectrometry is an effective tool for the analysis of complex carbohydrates. This method could have an impact on the field of carbohydrate synthesis similar to that of the advent of high-performance liquid chromatography on the field of peptide assembly in the late 1970s.

Identification of carbohydrate anomers using ion mobility-mass spectrometry

NASA Astrophysics Data System (ADS)

Hofmann, J.; Hahm, H. S.; Seeberger, P. H.; Pagel, K.

2015-10-01

Carbohydrates are ubiquitous biological polymers that are important in a broad range of biological processes. However, owing to their branched structures and the presence of stereogenic centres at each glycosidic linkage between monomers, carbohydrates are harder to characterize than are peptides and oligonucleotides. Methods such as nuclear magnetic resonance spectroscopy can be used to characterize glycosidic linkages, but this technique requires milligram amounts of material and cannot detect small amounts of coexisting isomers. Mass spectrometry, on the other hand, can provide information on carbohydrate composition and connectivity for even small amounts of sample, but it cannot be used to distinguish between stereoisomers. Here, we demonstrate that ion mobility-mass spectrometry--a method that separates molecules according to their mass, charge, size, and shape--can unambiguously identify carbohydrate linkage-isomers and stereoisomers. We analysed six synthetic carbohydrate isomers that differ in composition, connectivity, or configuration. Our data show that coexisting carbohydrate isomers can be identified, and relative concentrations of the minor isomer as low as 0.1 per cent can be detected. In addition, the analysis is rapid, and requires no derivatization and only small amounts of sample. These results indicate that ion mobility-mass spectrometry is an effective tool for the analysis of complex carbohydrates. This method could have an impact on the field of carbohydrate synthesis similar to that of the advent of high-performance liquid chromatography on the field of peptide assembly in the late 1970s.

Power optimization in logic isomers

NASA Technical Reports Server (NTRS)

Panwar, Ramesh; Rennels, David; Alkalaj, Leon

1993-01-01

Logic isomers are labeled, 2-isomorphic graphs that implement the same logic function. Logic isomers may have significantly different power requirements even though they have the same number of transistors in the implementation. The power requirements of the isomers depend on the transition activity of the input signals. The power requirements of isomorphic graph isomers of n-input NAND and NOR gates are shown. Choosing the less power-consuming isomer instead of the others can yield significant power savings. Experimental results on a ripple-carry adder are presented to show that the implementation using the least power-consuming isomers requires approximately 10 percent less power than the implementation using the most power-consuming isomers. Simulations of other random logic designs also confirm that designs using less power-consuming isomers can reduce the logic power demand by approximately 10 percent as compared to designs using more power-consuming isomers.

An In Silico Study on the Isomers of Pentacene: The Case for Air-Stable and Alternative C22H14 Acenes for Organic Electronics.

PubMed

Jones, Leighton; Lin, Long

2017-04-13

Pentacene is one of the most investigated candidates for organic thin film transistor (OTFT) applications over the last few decades even though it unstable in air (E g = 1.80 eV), owing in part to its planar nature and high charge-transfer mobilities as both a single crystal (35 cm 2 V -1 s -1 ) and as a thin-film (3.0 cm 2 V -1 s -1 ). Until now, picene is the only isomer of pentacene to be investigated for organic electronic applications, due to its greater stability (E g = 4.21 eV) and high-charge transfer mobility (3.0 cm 2 V -1 s -1 ); even benefiting from oxygen doping. In the present study, a total of 12 fused-ring isomers (including pentacene, picene and ten other structures) of the formula C 22 H 14 were analyzed and investigated for their electronic and optical properties for worth in OTFT applications. We screened several pure and hybrid DFT functionals against the experimental frontier molecular orbitals (FMOs) of pentacene, then deployed Marcus Theory, Koopmans' Theorem and Green's function with the P3 electron propagator variant, for the internal hole reorganization energy, the hole transfer integral (via the "splitting-in-dimer method" at d = 3.0, 3.5, and 4.0 Å), the charge transfer rate constant, and vertical ionization energies. Using these as a basis, we studied pentacene's isomers and found that the four nonplanar structures, namely, benzo[g]chrysene (3), naphtho[c]phenanthrene (7), benzo[c]chrysene (11) and dibenzo[c,c']phenthrene (12), are (I) more stable than pentacene, by up to 2 eV, and (II) have relatively similar ionization energies (7.5-7.6 eV) to those of picene's experimental value (7.51 eV). The largest charge transfer rates at 3.5 Å dimer separations were given by the isomers benzo[b]chrysene 4, naphtha[c]phenanthrene 7, dibenzo[a,c]anthracene 8 and benzo[a]tetracene 10 and found to be 2.92, 1.72, 1.30, and 3.09 × 10 14 s -1 respectively. In comparison to that of pentacene (K CT = 3.97 × 10 14 s -1 ), these unusual isomers are thus promising air-stable and alternative candidates for organic electronic applications.

Shellwise Mackay transformation in iron nanoclusters.

PubMed

Rollmann, Georg; Gruner, Markus E; Hucht, Alfred; Meyer, Ralf; Entel, Peter; Tiago, Murilo L; Chelikowsky, James R

2007-08-24

Structure and magnetism of iron clusters with up to 641 atoms have been investigated by means of density functional theory calculations including full geometric optimizations. Body-centered cubic (bcc) isomers are found to be lowest in energy when the clusters contain more than about 100 atoms. In addition, another stable conformation has been identified for magic-number clusters, which lies well within the range of thermal energies as compared to the bcc isomers. Its structure is characterized by a close-packed particle core and an icosahedral surface, while intermediate shells are partially transformed along the Mackay path between icosahedral and cuboctahedral geometry. The gradual transformation results in a favorable bcc environment for the subsurface atoms. For Fe55, the shellwise Mackay-transformed morphology is a promising candidate for the ground state.

Stepwise Internal Energy Control for Protonated Methanol Clusters by Using the Inert Gas Tagging

NASA Astrophysics Data System (ADS)

Shimamori, Takuto; Kuo, Jer-Lai; Fujii, Asuka

2016-06-01

Preferred isomer structures of hydrogen-bonded clusters should depend on their temperature because of the entropy term in the free energy. To observe such temperature dependence, we propose a new approach to control the internal energy (vibrational temperature) of protonated clusters in the gas phase. We performed IR spectroscopy of protonated methanol clusters, H+ (CH{_3}OH) {_n}, n= 5 and 7, with the tagging by various inert gas species (Ar, CO{_2}, CO, CS{_2}, C{_2}H{_2}, and C{_6}H{_6}). We found that vibrational temperature of the tagged clusters raises with increase of the interaction energy with the tag species, and the observed cluster structures follow the theoretical prediction of the temperature dependence of the isomer population.

Quantum optimal control pathways of ozone isomerization dynamics subject to competing dissociation: A two-state one-dimensional model

DOE Office of Scientific and Technical Information (OSTI.GOV)

Kurosaki, Yuzuru, E-mail: kurosaki.yuzuru@jaea.go.jp; Ho, Tak-San, E-mail: tsho@Princeton.EDU; Rabitz, Herschel, E-mail: hrabitz@Princeton.EDU

We construct a two-state one-dimensional reaction-path model for ozone open → cyclic isomerization dynamics. The model is based on the intrinsic reaction coordinate connecting the cyclic and open isomers with the O{sub 2} + O asymptote on the ground-state {sup 1}A{sup ′} potential energy surface obtained with the high-level ab initio method. Using this two-state model time-dependent wave packet optimal control simulations are carried out. Two possible pathways are identified along with their respective band-limited optimal control fields; for pathway 1 the wave packet initially associated with the open isomer is first pumped into a shallow well on the excitedmore » electronic state potential curve and then driven back to the ground electronic state to form the cyclic isomer, whereas for pathway 2 the corresponding wave packet is excited directly to the primary well of the excited state potential curve. The simulations reveal that the optimal field for pathway 1 produces a final yield of nearly 100% with substantially smaller intensity than that obtained in a previous study [Y. Kurosaki, M. Artamonov, T.-S. Ho, and H. Rabitz, J. Chem. Phys. 131, 044306 (2009)] using a single-state one-dimensional model. Pathway 2, due to its strong coupling to the dissociation channel, is less effective than pathway 1. The simulations also show that nonlinear field effects due to molecular polarizability and hyperpolarizability are small for pathway 1 but could become significant for pathway 2 because much higher field intensity is involved in the latter. The results suggest that a practical control may be feasible with the aid of a few lowly excited electronic states for ozone isomerization.« less

Reaction between peroxynitrite and triphenylphosphonium-substituted arylboronic acid isomers–Identification of diagnostic marker products and biological implications

PubMed Central

Sikora, Adam; Zielonka, Jacek; Adamus, Jan; Debski, Dawid; Dybala-Defratyka, Agnieszka; Michalowski, Bartosz; Joseph, Joy; Hartley, Richard C.; Murphy, Michael P.; Kalyanaraman, Balaraman

2013-01-01

Aromatic boronic acids react rapidly with peroxynitrite (ONOO−) to yield phenols as major products. This reaction was used to monitor ONOO− formation in cellular systems. Previously, we proposed that the reaction between ONOO− and arylboronates (PhB(OH)2) yields a phenolic product (major pathway) and a radical pair PhB(OH)2O•−…•NO2 (minor pathway). [Sikora A. et al., Chem Res Toxicol 24, 687-97, 2011]. In this study, we investigated the influence of a bulky triphenylphosphonium (TPP) group on the reaction between ONOO− and mitochondria-targeted arylboronate isomers (o-, m-, and p-MitoPhB(OH)2). Results from the electron paramagnetic resonance (EPR) spin-trapping experiments unequivocally showed the presence of a phenyl radical intermediate from meta and para isomers, and not from the ortho isomer. The yield of o-MitoPhNO2 formed from the reaction between o-MitoPhB(OH)2 and ONOO− was not diminished by phenyl radical scavengers, suggesting a rapid fragmentation of the o-MitoPhB(OH)2O•− radical anion with subsequent reaction of the resulting phenyl radical with •NO2 in the solvent cage. The DFT quantum mechanical calculations showed that the energy barrier for the dissociation of o-MitoPhB(OH)2O•− radical anion is significantly lower than that of m-MitoPhB(OH)2O•− and p-MitoPhB(OH)2O•− radical anions. The nitrated product, o-MitoPhNO2, is not formed by nitrogen dioxide radical generated by myeloperoxidase in the presence of nitrite anion and hydrogen peroxide, indicating that this specific nitrated product may be used as a diagnostic marker product for ONOO−. Incubation of o-MitoPhB(OH)2 with RAW 264.7 macrophages activated to produce ONOO− yielded the corresponding phenol o-MitoPhOH as well as the diagnostic nitrated product, o-MitoPhNO2. We conclude that the ortho isomer probe reported here is most suitable for specific detection of ONOO− in biological systems. PMID:23611338

Solution structure and thermodynamics of 2',5' RNA intercalation.

PubMed

Horowitz, Eric D; Lilavivat, Seth; Holladay, Benjamin W; Germann, Markus W; Hud, Nicholas V

2009-04-29

As a means to explore the influence of the nucleic acid backbone on the intercalative binding of ligands to DNA and RNA, we have determined the solution structure of a proflavine-bound 2',5'-linked octamer duplex with the sequence GCCGCGGC. This structure represents the first NMR structure of an intercalated RNA duplex, of either backbone structural isomer. By comparison with X-ray crystal structures, we have identified similarities and differences between intercalated 3',5' and 2',5'-linked RNA duplexes. First, the two forms of RNA have different sugar pucker geometries at the intercalated nucleotide steps, yet have the same interphosphate distances. Second, as in intercalated 3',5' RNA, the phosphate backbone angle zeta at the 2',5' RNA intercalation site prefers to be in the trans conformation, whereas unintercalated 2',5' and 3',5' RNA prefer the -gauche conformation. These observations provide new insights regarding the transitions required for intercalation of a phosphodiester-ribose backbone and suggest a possible contribution of the backbone to the origin of the nearest-neighbor exclusion principle. Thermodynamic studies presented for intercalation of both structural RNA isomers also reveal a surprising sensitivity of intercalator binding enthalpy and entropy to the details of RNA backbone structure.

Chemical Methods to Prepare [60]Fulleranes

NASA Astrophysics Data System (ADS)

Briggs, Jonathan B.; Miller, Glen P.

Most known chemical methods to prepare hydrogenated [60]fullerenes or [60]fulleranes are described with an emphasis on those methods that are of historical significance and/or convenient, scalable and high yielding. Separate sections are dedicated to C60H2, C60H4-16, C60H18, C60H36, and C60H>36. The simplest of all [60]fullerane derivatives, 1,2-C60H2, is prepared in good isolated yield using either a NaBH4 reduction (59% isolated) or a Zn(Cu) couple reduction (66% isolated). A few C60H4 (e.g., 1,2,3,4-C60H4) and C60H6 (e.g., 1,2,33,41,42,50-C60H6) isomers have been formed and identified using structure sensitive analytical techniques but evidence for [60]fulleranes of formula C60H8-16 is based largely upon structure insensitive mass spectrometry data. Crown shaped C 3v C60H18 is the only [60]fullerane species that can be produced in high yield using multiple synthetic methods. It is a stable, easily isolable species of limited solubility that persists for years. Of the synthetic methodologies available, the polyamine chemistries [conventional heating or microwave irradiation] are best because the yields are excellent, the reactions are scalable, only standard glassware is required, the work-up is simple, and no purification is required. Birch reductions, transfer hydrogenations and Zn-acid conditions all lead to mixtures of C60H36 isomers in good yield. Of these methods, the transfer hydrogenation reaction gives the cleanest product slate with formation of three isomers possessing C 1 symmetry (60-70%), C 3 symmetry (25-30%) and T symmetry (2-5%), respectively. The formation of [60]fulleranes with more than 36 hydrogens is well documented but the products have generally escaped characterization by structure sensitive analytical techniques. No single isomer of formula C60H>36 has ever been isolated.

Molecular dynamics simulation of the enterostatin APGPR and VPDPR peptides in water

NASA Astrophysics Data System (ADS)

Trucco, Gabriella; Fornili, Sandro L.

2007-09-01

We report on structural and dynamic properties in water of all the isomers of both peptides related to the trans and cis conformations of the peptide bonds preceding the proline (Pro) residues. Free-energy calculations indicate that the isomers having the Pro closer to the N-terminus (Pro1) in trans and the Pro2 in cis conformations are the most populated. Furthermore, the backbone is more flexible for APGPR than for VPDPR, and its conformation is more stable in the hydrophilic C-terminal moiety than in the hydrophobic N-terminal region.

Can honey bees discriminate between floral-fragrance isomers?

PubMed

Aguiar, João Marcelo Robazzi Bignelli Valente; Roselino, Ana Carolina; Sazima, Marlies; Giurfa, Martin

2018-05-24

Many flowering plants present variable complex fragrances, which usually include different isomers of the same molecule. As fragrance is an essential cue for flower recognition by pollinators, we ask if honey bees discriminate between floral-fragrance isomers in an appetitive context. We used the olfactory conditioning of the proboscis extension response (PER), which allows training a restrained bee to an odor paired with sucrose solution. Bees were trained under an absolute (a single odorant rewarded) or a differential conditioning regime (a rewarded vs. a non-rewarded odorant) using four different pairs of isomers. One hour after training, discrimination and generalization between pairs of isomers were tested. Bees trained under absolute conditioning exhibited high generalization between isomers and discriminated only one out of four isomer pairs; after differential conditioning, they learned to differentiate between two out of four pairs of isomers but in all cases generalization responses to the non-rewarding isomer remained high. Adding an aversive taste to the non-rewarded isomer facilitated discrimination of isomers that otherwise seemed non-discriminable, but generalization remained high. Although honey bees discriminated isomers under certain conditions, they achieved the task with difficulty and tended to generalize between them, thus showing that these molecules were perceptually similar to them. We conclude that the presence of isomers within floral fragrances might not necessarily contribute to a dramatic extent to floral odor diversity. © 2018. Published by The Company of Biologists Ltd.

Structures and physical properties of gaseous metal cationized biological ions.

PubMed

Burt, Michael B; Fridgen, Travis D

2012-01-01

Metal chelation can alter the activity of free biomolecules by modifying their structures or stabilizing higher energy tautomers. In recent years, mass spectrometric techniques have been used to investigate the effects of metal complexation with proteins, nucleobases and nucleotides, where small conformational changes can have significant physiological consequences. In particular, infrared multiple photon dissociation spectroscopy has emerged as an important tool for determining the structure and reactivity of gas-phase ions. Unlike other mass spectrometric approaches, this method is able to directly resolve structural isomers using characteristic vibrational signatures. Other activation and dissociation methods, such as blackbody infrared radiative dissociation or collision-induced dissociation can also reveal information about the thermochemistry and dissociative pathways of these biological ions. This information can then be used to provide information about the structures of the ionic complexes under study. In this article, we review the use of gas-phase techniques in characterizing metal-bound biomolecules. Particular attention will be given to our own contributions, which detail the ability of metal cations to disrupt nucleobase pairs, direct the self-assembly of nucleobase clusters and stabilize non-canonical isomers of amino acids.

Properties of the Only Thorium Fullerene, Th@C84, Uncovered.

PubMed

Kaminský, Jakub; Vícha, Jan; Bouř, Petr; Straka, Michal

2017-04-27

Only a single thorium fullerene, Th@C 84 , has been reported to date (Akiyama, K.; et al. J. Nucl. Radiochem. Sci. 2002, 3, 151-154). Although the system was characterized by UV-vis and XANES (X-ray absorption near edge structure) spectra, its structure and properties remain unknown. In this work we used the density functional calculations to identify molecular and electronic structure of the Th@C 84 . Series of molecular structures satisfying the ThC 84 stoichiometric formula were studied comprising 24 IPR and 110 non-IPR Th@C 84 isomers as well as 9 ThC 2 @C 82 IPR isomers. The lowest energy structure is Th@C 84 -C s (10) with the singlet ground state. Its predicted electronic absorption spectra are in agreement with the experimentally observed ones. The bonding between the cage and Th was characterized as polar covalent with Th in formal oxidation state IV. The NMR chemical shifts of Th@C 84 -C s (10) were predicted to guide the future experimental efforts in identification of this compound.

Structure, stability, thermodynamic properties, and IR spectra of the protonated water decamer H+(H2O)10.

PubMed

Karthikeyan, S; Kim, Kwang S

2009-08-13

Protonated water clusters H+(H2O)n favor two-dimensional (2D) structures for n < or = 7 at low temperatures. At 0 K, the 2D and three-dimensional (3D) structures for n = 8 are almost isoenergetic, and the 3D structures for n > 9 tend to be more stable. However, for n = 9, the netlike structures are likely to be more stable above 150 K. In this regard, we investigate the case of n = 10 to find which structure is more stable between the 3D structure and the netlike structure around 150 and 250 K. We use density functional theory, Møller-Plesset second-order perturbation theory, and coupled cluster theory with single, double, and perturbative triple excitations (CCSD(T)). At the complete basis set limit for the CCSD(T) level of theory, three isomers of 3D cage structure are much more stable in zero point energy corrected binding energy and in free binding energies at 150 K than the lowest energy netlike structures, while the netlike structure would be more stable around approximately 250 K. The predicted vibrational spectra are in good agreement with the experiment. One of the three isomers explains the experimental IR observation of an acceptor (A) type peak of a dangling hydrogen atom.

Communication: Ion mobility of the radical cation dimers: (Naphthalene)2+• and naphthalene+•-benzene: Evidence for stacked sandwich and T-shape structures

NASA Astrophysics Data System (ADS)

Platt, Sean P.; Attah, Isaac K.; Aziz, Saadullah; El-Shall, M. Samy

2015-05-01

Dimer radical cations of aromatic and polycyclic aromatic molecules are good model systems for a fundamental understanding of photoconductivity and ferromagnetism in organic materials which depend on the degree of charge delocalization. The structures of the dimer radical cations are difficult to determine theoretically since the potential energy surface is often very flat with multiple shallow minima representing two major classes of isomers adopting the stacked parallel or the T-shape structure. We present experimental results, based on mass-selected ion mobility measurements, on the gas phase structures of the naphthalene+ṡ ṡ naphthalene homodimer and the naphthalene+ṡ ṡ benzene heterodimer radical cations at different temperatures. Ion mobility studies reveal a persistence of the stacked parallel structure of the naphthalene+ṡ ṡ naphthalene homodimer in the temperature range 230-300 K. On the other hand, the results reveal that the naphthalene+ṡ ṡ benzene heterodimer is able to exhibit both the stacked parallel and T-shape structural isomers depending on the experimental conditions. Exploitation of the unique structural motifs among charged homo- and heteroaromatic-aromatic interactions may lead to new opportunities for molecular design and recognition involving charged aromatic systems.

Electronic structure investigation of neutral titanium oxide molecules TixOy

NASA Astrophysics Data System (ADS)

Jeong, K. S.; Chang, Ch; Sedlmayr, E.; Sülzle, D.

2000-09-01

Electronic and structural properties of energetically low-lying isomers of isolated TixOy (x = 1-6, y = 1-12) molecular systems have been investigated by density functional theoretical methods. A variety of stationary points are thoroughly characterized. We report total cluster energies, equilibrium geometries and harmonic vibrational wavenumbers.

Locomotor activity and tissue levels following acute administration of lambda- and gamma-cyhalothrin in rats

DOE Office of Scientific and Technical Information (OSTI.GOV)

Moser, Virginia C., E-mail: Moser.ginger@epa.gov

Pyrethroids produce neurotoxicity that depends, in part, on the chemical structure. Common behavioral effects include locomotor activity changes and specific toxic syndromes (types I and II). In general these neurobehavioral effects correlate well with peak internal dose metrics. Products of cyhalothrin, a type II pyrethroid, include mixtures of isomers (e.g., λ-cyhalothrin) as well as enriched active isomers (e.g., γ-cyhalothrin). We measured acute changes in locomotor activity in adult male rats and directly correlated these changes to peak brain and plasma concentrations of λ- and γ-cyhalothrin using a within-subject design. One-hour locomotor activity studies were conducted 1.5 h after oral gavagemore » dosing, and immediately thereafter plasma and brains were collected for analyzing tissue levels using LC/MS/MS methods. Both isomers produced dose-related decreases in activity counts, and the effective dose range for γ-cyhalothrin was lower than for λ-cyhalothrin. Doses calculated to decrease activity by 50% were 2-fold lower for the γ-isomer (1.29 mg/kg) compared to λ-cyhalothrin (2.65 mg/kg). Salivation, typical of type II pyrethroids, was also observed at lower doses of γ-cyhalothrin. Administered dose correlated well with brain and plasma concentrations, which furthermore showed good correlations with activity changes. Brain and plasma levels were tightly correlated across doses. While γ-cyhalothrin was 2-fold more potent based on administered dose, the differences based on internal concentrations were less, with γ-cyhalothrin being 1.3- to 1.6-fold more potent than λ-cyhalothrin. These potency differences are consistent with the purity of the λ-isomer (approximately 43%) compared to the enriched isomer γ-cyhalothrin (approximately 98%). Thus, administered dose as well as differences in cyhalothrin isomers is a good predictor of behavioral effects. - Highlights: • Acute changes in locomotor activity were produced by λ- and γ-cyhalothrin. • γ-Cyhalothrin was about 2-fold more potent than λ-cyhalothrin. • Brain and plasma levels were tightly correlated across doses. • Activity changes correlated well with brain and plasma concentrations.« less

A Mechanistical Study on the Formation of Dimethyl Ether (CH3OCH3) and Ethanol (CH3CH2OH) in Methanol-containing Ices and Implications for the Chemistry of Star-forming Regions

NASA Astrophysics Data System (ADS)

Bergantini, Alexandre; Góbi, Sándor; Abplanalp, Matthew J.; Kaiser, Ralf I.

2018-01-01

The underlying formation mechanisms of complex organic molecules (COMs)—in particular, structural isomers—in the interstellar medium (ISM) are largely elusive. Here, we report new experimental findings on the role of methanol (CH3OH) and methane (CH4) ices in the synthesis of two C2H6O isomers upon interaction with ionizing radiation: ethanol (CH3CH2OH) and dimethyl ether (CH3OCH3). The present study reproduces the interstellar abundance ratios of both species with ethanol to dimethyl ether branching ratios of (2.33 ± 0.14):1 suggesting that methanol and methane represents the key precursor to both isomers within interstellar ices. Exploiting isotopic labeling combined with reflectron time-of-flight mass spectrometry (Re-TOF-MS) after isomer selective vacuum ultra-violet (VUV) photoionization of the neutral molecules, we also determine the formation mechanisms of both isomers via radical–radical recombination versus carbene (CH2) insertion with the former pathway being predominant. Formation routes to higher molecular weight reaction products such as ethylene glycol (HOCH2CH2OH), dimethyl peroxide (CH3OOCH3), and methoxymethanol (CH3OCH2OH) are discussed briefly as well.

Exciton Resonances in Novel Silicon Carbide Polymers

NASA Astrophysics Data System (ADS)

Burggraf, Larry; Duan, Xiaofeng

2015-05-01

A revolutionary technology transformation from electronics to excitionics for faster signal processing and computing will be advantaged by coherent exciton transfer at room temperature. The key feature required of exciton components for this technology is efficient and coherent transfer of long-lived excitons. We report theoretical investigations of optical properties of SiC materials having potential for high-temperature excitonics. Using Car-Parinello simulated annealing and DFT we identified low-energy SiC molecular structures. The closo-Si12C12 isomer, the most stable 12-12 isomer below 1100 C, has potential to make self-assembled chains and 2-D nanostructures to construct exciton components. Using TDDFT, we calculated the optical properties of the isomer as well as oligomers and 2-D crystal formed from the isomer as the monomer unit. This molecule has large optical oscillator strength in the visible. Its high-energy and low-energy transitions (1.15 eV and 2.56 eV) are nearly pure one-electron silicon-to-carbon transitions, while an intermediate energy transition (1.28 eV) is a nearly pure carbon-to-silicon one-electron charge transfer. These results are useful to describe resonant, coherent transfer of dark excitons in the nanostructures. Research supported by the Air Force Office of Scientific Research.

Influence of high hydrostatic pressure on Alq3, Gaq3, and Inq3 (q = 8-hydroxyquinoline).

PubMed

Hernández, Ignacio; Gillin, William P

2009-10-29

We have studied the spectroscopic properties of OLED materials Alq(3), Gaq(3) and Inq(3) (q = 8-hydroxyquinoline) under pressure. We discuss the results in terms of the influence of structural modifications, the isomeric state and the enhancement of the intermolecular interaction. As-grown Alq(3), Gaq(3), Inq(3) containing meridional (mer) isomer experience a red shift of nearly 90 nm (2400 cm(-1)) in the 0-8 GPa range. Abrupt changes in the photoluminescence occur during compression at intermediate pressures for all materials. We assign them to a phase transition, its critical pressure depending on the central cation. All three samples experience an amorphization at P approximately 6 GPa, with associated changes in the spectroscopic properties. The pressure-induced phase transitions present hysteresis to ambient conditions. Photoluminescence lifetime decreases in all cases in the explored pressure range. In the case of facial isomer containing polymorphs of Alq(3), luminescence does not change its energy significantly. The most significant spectroscopic change observed in fac-isomer containing materials corresponds to gamma-Alq(3), which presents a low energy component that gains relative importance when pressure is increased. We ascribe this phenomenon to the presence of sensitized mer isomer impurities.

High-spin structures in 132Xe and 133Xe and evidence for isomers along the N =79 isotones

NASA Astrophysics Data System (ADS)

Vogt, A.; Siciliano, M.; Birkenbach, B.; Reiter, P.; Hadyńska-Klek, K.; Wheldon, C.; Valiente-Dobón, J. J.; Teruya, E.; Yoshinaga, N.; Arnswald, K.; Bazzacco, D.; Blazhev, A.; Bracco, A.; Bruyneel, B.; Chakrawarthy, R. S.; Chapman, R.; Cline, D.; Corradi, L.; Crespi, F. C. L.; Cromaz, M.; de Angelis, G.; Eberth, J.; Fallon, P.; Farnea, E.; Fioretto, E.; Fransen, C.; Freeman, S. J.; Fu, B.; Gadea, A.; Gelletly, W.; Giaz, A.; Görgen, A.; Gottardo, A.; Hayes, A. B.; Hess, H.; Hetzenegger, R.; Hirsch, R.; Hua, H.; John, P. R.; Jolie, J.; Jungclaus, A.; Karayonchev, V.; Kaya, L.; Korten, W.; Lee, I. Y.; Leoni, S.; Liang, X.; Lunardi, S.; Macchiavelli, A. O.; Menegazzo, R.; Mengoni, D.; Michelagnoli, C.; Mijatović, T.; Montagnoli, G.; Montanari, D.; Müller-Gatermann, C.; Napoli, D.; Pearson, C. J.; Podolyák, Zs.; Pollarolo, G.; Pullia, A.; Queiser, M.; Recchia, F.; Regan, P. H.; Régis, J.-M.; Saed-Samii, N.; Şahin, E.; Scarlassara, F.; Seidlitz, M.; Siebeck, B.; Sletten, G.; Smith, J. F.; Söderström, P.-A.; Stefanini, A. M.; Stezowski, O.; Szilner, S.; Szpak, B.; Teng, R.; Ur, C.; Warner, D. D.; Wolf, K.; Wu, C. Y.; Zell, K. O.

2017-08-01

The transitional nuclei 132Xe and 133Xe are investigated after multinucleon-transfer (MNT) and fusion-evaporation reactions. Both nuclei are populated (i) in 136Xe+208Pb MNT reactions employing the high-resolution Advanced GAmma Tracking Array (AGATA) coupled to the magnetic spectrometer PRISMA, (ii) in the 136Xe+198Pt MNT reaction employing the GAMMASPHERE spectrometer in combination with the gas-detector array CHICO, and (iii) as an evaporation residue after a 130Te(α ,x n )134 -x nXe fusion-evaporation reaction employing the HORUS γ -ray array at the University of Cologne. The high-spin level schemes are considerably extended above the Jπ=(7-) and (10+) isomers in 132Xe and above the 11 /2- isomer in 133Xe. The results are compared to the high-spin systematics of the Z =54 as well as the N =78 and N =79 chains. Furthermore, evidence is found for a long-lived (T1 /2≫1 μ s ) isomer in 133Xe which closes a gap along the N =79 isotones. Shell-model calculations employing the SN100PN and PQM130 effective interactions reproduce the experimental findings and provide guidance to the interpretation of the observed high-spin features.

High-spin structures in Xe 132 and Xe 133 and evidence for isomers along the N = 79 isotones

DOE Office of Scientific and Technical Information (OSTI.GOV)

Vogt, A.; Siciliano, M.; Birkenbach, B.

In this study, the transitional nuclei 132Xe and 133Xe are investigated after multinucleon-transfer (MNT) and fusion-evaporation reactions. Both nuclei are populated (i) in 136Xe + 208Pb MNT reactions employing the high-resolution Advanced GAmma Tracking Array (AGATA) coupled to the magnetic spectrometer PRISMA, (ii) in the 136Xe + 198Pt MNT reaction employing the GAMMASPHERE spectrometer in combination with the gas-detector array CHICO, and (iii) as an evaporation residue after a 130Te (α,xn) 134-xnXe fusion-evaporation reaction employing the HORUS γ -ray array at the University of Cologne. The high-spin level schemes are considerably extended above the J π = (7 -) andmore » (10 +) isomers in 132Xe and above the 11/2 - isomer in 133Xe. The results are compared to the high-spin systematics of the Z = 54 as well as the N = 78 and N = 79 chains. Furthermore, evidence is found for a long-lived (T 1/2 » 1 μs) isomer in 133Xe which closes a gap along the N = 79 isotones. Finally, shell-model calculations employing the SN100PN and PQM130 effective interactions reproduce the experimental findings and provide guidance to the interpretation of the observed high-spin features.« less

High-spin structures in Xe 132 and Xe 133 and evidence for isomers along the N = 79 isotones

DOE PAGES

Vogt, A.; Siciliano, M.; Birkenbach, B.; ...

2017-08-24

In this study, the transitional nuclei 132Xe and 133Xe are investigated after multinucleon-transfer (MNT) and fusion-evaporation reactions. Both nuclei are populated (i) in 136Xe + 208Pb MNT reactions employing the high-resolution Advanced GAmma Tracking Array (AGATA) coupled to the magnetic spectrometer PRISMA, (ii) in the 136Xe + 198Pt MNT reaction employing the GAMMASPHERE spectrometer in combination with the gas-detector array CHICO, and (iii) as an evaporation residue after a 130Te (α,xn) 134-xnXe fusion-evaporation reaction employing the HORUS γ -ray array at the University of Cologne. The high-spin level schemes are considerably extended above the J π = (7 -) andmore » (10 +) isomers in 132Xe and above the 11/2 - isomer in 133Xe. The results are compared to the high-spin systematics of the Z = 54 as well as the N = 78 and N = 79 chains. Furthermore, evidence is found for a long-lived (T 1/2 » 1 μs) isomer in 133Xe which closes a gap along the N = 79 isotones. Finally, shell-model calculations employing the SN100PN and PQM130 effective interactions reproduce the experimental findings and provide guidance to the interpretation of the observed high-spin features.« less

Insights into the Competing Mechanisms and Origin of Enantioselectivity for N-Heterocyclic Carbene-Catalyzed Reaction of Aldehyde with Enamide

NASA Astrophysics Data System (ADS)

Qiao, Yan; Chen, Xinhuan; Wei, Donghui; Chang, Junbiao

2016-12-01

Hydroacylation reactions and aza-benzoin reactions have attracted considerable attention from experimental chemists. Recently, Wang et al. reported an interesting reaction of N-heterocyclic carbene (NHC)-catalyzed addition of aldehyde to enamide, in which both hydroacylation and aza-benzoin reactions may be involved. Thus, understanding the competing relationship between them is of great interest. Now, density functional theory (DFT) investigation was performed to elucidate this issue. Our results reveal that enamide can tautomerize to its imine isomer with the assistance of HCO3-. The addition of NHC to aldehydes formed Breslow intermediate, which can go through cross-coupling with enamide via hydroacylation reaction or its imine isomer via aza-benzoin reaction. The aza-benzoin reaction requires relatively lower free energy barrier than the hydroacylation reaction. The more polar characteristic of C=N group in the imine isomers, and the more advantageous stereoelectronic effect in the carbon-carbon bond forming transition states in aza-benzoin pathway were identified to determine that the imine isomer can react with the Breslow intermediate more easily. Furthermore, the origin of enantioselectivities for the reaction was explored and reasonably explained by structural analyses on key transition states. The work should provide valuable insights for rational design of switchable NHC-catalyzed hydroacylation and aza-benzoin reactions with high stereoselectivity.

LC-MS n Analysis of Isomeric Chondroitin Sulfate Oligosaccharides Using a Chemical Derivatization Strategy

NASA Astrophysics Data System (ADS)

Huang, Rongrong; Pomin, Vitor H.; Sharp, Joshua S.

2011-09-01

Improved methods for structural analyses of glycosaminoglycans (GAGs) are required to understand their functional roles in various biological processes. Major challenges in structural characterization of complex GAG oligosaccharides using liquid chromatography-mass spectrometry (LC-MS) include the accurate determination of the patterns of sulfation due to gas-phase losses of the sulfate groups upon collisional activation and inefficient on-line separation of positional sulfation isomers prior to MS/MS analyses. Here, a sequential chemical derivatization procedure including permethylation, desulfation, and acetylation was demonstrated to enable both on-line LC separation of isomeric mixtures of chondroitin sulfate (CS) oligosaccharides and accurate determination of sites of sulfation by MS n . The derivatized oligosaccharides have sulfate groups replaced with acetyl groups, which are sufficiently stable to survive MS n fragmentation and reflect the original sulfation patterns. A standard reversed-phase LC-MS system with a capillary C18 column was used for separation, and MS n experiments using collision-induced dissociation (CID) were performed. Our results indicate that the combination of this derivatization strategy and MS n methodology enables accurate identification of the sulfation isomers of CS hexasaccharides with either saturated or unsaturated nonreducing ends. Moreover, derivatized CS hexasaccharide isomer mixtures become separable by LC-MS method due to different positions of acetyl modifications.

Ligand Binding Phenomena that Pertain to the Metabolic Function of Renalase

PubMed Central

Beaupre, Brett A.; Roman, Joseph V.; Hoag, Matthew R.; Meneely, Kathleen M.; Silvaggi, Nicholas R.; Lamb, Audrey L.; Moran, Graham R.

2017-01-01

Renalase catalyzes the oxidation of isomers of β-NAD(P)H that carry the hydride in the 2 or 6 positions of the nicotinamide base to form β-NAD(P)+. This activity is thought to alleviate inhibition of multiple β-NAD(P)-dependent enzymes of primary and secondary metabolism by these isomers. Here we present evidence for a variety of ligand binding phenomena relevant to the function of renalase. We offer evidence of the potential for primary metabolism inhibition with structures of malate dehydrogenase and lactate dehydrogenase bound to the 6-dihydroNAD isomer. The previously observed preference of renalase from Pseudomonas for NAD-derived substrates over those derived from NADP is accounted for by the structure of the enzyme in complex with NADPH. We also show that nicotinamide nucleosides and mononucloetides reduced in the 2- and 6-positions are renalase substrates, but bind weakly. A seven-fold enhancement of acquisition (kred/Kd) for 6-dihydronicotinamide riboside was observed for human renalase in the presence of ADP. However, generally the addition of complement ligands, ADP for mononucloetide or AMP for nucleoside substrates, did not enhance the reductive half-reaction. Non-substrate nicotinamide nucleosides or nucleotides bind weakly suggesting that only β-NADH and β-NADPH compete with dinucleotide substrates for access to the active site. PMID:27769837

LC-MSn Analysis of Isomeric Chondroitin Sulfate Oligosaccharides Using a Chemical Derivatization Strategy

PubMed Central

Huang, Rongrong; Pomin, Vitor H.; Sharp, Joshua S.

2011-01-01

Improved methods for structural analyses of glycosaminoglycans (GAGs) are required to understand their functional roles in various biological processes. Major challenges in structural characterization of complex GAG oligosaccharides using liquid chromatography-mass spectrometry (LC-MS) include the accurate determination of the patterns of sulfation due to gas-phase losses of the sulfate groups upon collisional activation and inefficient on-line separation of positional sulfation isomers prior to MS/MS analyses. Here, a sequential chemical derivatization procedure including permethylation, desulfation, and acetylation was demonstrated to enable both on-line LC separation of isomeric mixtures of chondroitin sulfate (CS) oligosaccharides and accurate determination of sites of sulfation by MSn. The derivatized oligosaccharides have sulfate groups replaced with acetyl groups, which are sufficiently stable to survive MSn fragmentation and reflect the original sulfation patterns. A standard reversed-phase LC-MS system with a capillary C18 column was used for separation, and MSn experiments using collision-induced dissociation (CID) were performed. Our results indicate that the combination of this derivatization strategy and MSn methodology enables accurate identification of the sulfation isomers of CS hexasaccharides with either saturated or unsaturated nonreducing ends. Moreover, derivatized CS hexasaccharide isomer mixtures become separable by LC-MS method due to different positions of acetyl modifications. PMID:21953261

Characterization of the Antinociceptive Effects of the Individual Isomers of Methadone Following Acute and Chronic Administration

PubMed Central

Morgan, Richard W.; Nicholson, Katherine L.

2011-01-01

Methadone is a long-acting opioid used in the treatment of various pain states and substitution therapy in heroin addiction. Extensive behavioral characterization has been carried out utilizing the racemate, but limited investigation has been performed with the individual isomers. While the l-isomer is a potent opioid agonist, the d-isomer has weak μ opioid activity and has also been shown to possess N-methyl-d-aspartate (NMDA) antagonist properties in vitro. The acute antinociceptive effects of the isomers were evaluated in rats using a warm water tail withdrawal procedure at two stimulus intensities (50° and 55° C). Increasing dose ratios of d- to l-methadone were administered chronically to determine the ability of the d-isomer to modulate antinociceptive tolerance to the l-isomer. Acutely, both l- (0.1-5.6 mg/kg, sc) and d- (3.0-56.0 mg/kg, sc) methadone produced antinociception though the efficacy of the d-isomer was limited at 55° C. These effects were dose-dependently blocked by naltrexone (0.01-1.0 mg/kg, sc). Administered chronically, d-methadone (1.7-10 mg/kg, sc) dose-dependently blocked tolerance development to the l-isomer (1.7 mg/kg, sc). These findings support the antinociceptive effects of the isomers being opioid receptor mediated with the l-isomer functioning as a full efficacy agonist whereas the d-isomer appears to have lower efficacy. The ability of nonracemic doses of the d-isomer to prevent tolerance development to the l-isomer may be attributed to partial μ agonist activity however NMDA antagonist activity cannot be discounted. PMID:21836464

Infrared Spectroscopy of the Mass 31 Cation: Protonated Formaldehyde VS. The Triplet Methoxy Cation

NASA Astrophysics Data System (ADS)

Mosley, J. D.; Cheng, T. C.; Duncan, M. A.

2012-06-01

The m/z=31 cation is produced by ionization and fragmentation of methanol, ethanol, dimethyl ether, etc. Two structures have been proposed, protonated formaldehyde (^1CH_2OH^+) and the triplet methoxy cation (^3CH_3O^+). The infrared spectrum of the mass 31 cation is obtained using infrared photodissociation spectroscopy with Ar tagging. The spectrum reveals the presence of two stable isomers, protonated formaldehyde (^1CH_2OH^+) and the triplet methoxy cation (^3CH_3O^+). The triplet methoxy cation has been studied extensively and is predicted to interconvert to protonated formaldehyde through an essentially barrierless process on a timescale much faster than our experiment (>100 μs). The presence of two structural isomers is verified by comparison of spectra from different precursors and spectra of different temperature ions from the same precursor.

Analysis of the Nuclear Structure of 186 Re Using Neutron-Induced Reactions

NASA Astrophysics Data System (ADS)

Matters, David; McClory, John; Carroll, James; Chiara, Chris; Fotiades, Nikolaos; Devlin, Matt; Nelson, Ron O.

2015-04-01

Evaluated nuclear structure data for 186 Re identifies the majority of spin-parity assignments as tentative, with approximate values associated with the energies of several levels and transitions. In particular, the absence of known transitions that feed the Jπ =8+ isomer motivates their discovery, which would have astrophysical implications and a potential application in the development of an isomer power source. Using the GErmanium Array for Neutron Induced Excitations (GEANIE) spectrometer at the Los Alamos Neutron Science Center (LANSCE) Weapons Neutron Research (WNR) facility, the (n,2n γ) and (n,n' γ) reactions in a 99.52% enriched 187 Re target were used to measure γ-ray excitation functions in 186 Re and 187 Re, respectively. A preliminary analysis of the data obtained from the experiment reveals several new transitions in 186 Re and 187 Re.

IRMPD Spectroscopy Sheds New (Infrared) Light on the Sulfate Pattern of Carbohydrates.

PubMed

Schindler, B; Barnes, L; Gray, C J; Chambert, S; Flitsch, S L; Oomens, J; Daniel, R; Allouche, A R; Compagnon, I

2017-03-16

IR spectroscopy of gas-phase ions is proposed to resolve positional isomers of sulfated carbohydrates. Mass spectrometric fingerprints and gas-phase vibrational spectra in the near and mid-IR regions were obtained for sulfated monosaccharides, yielding unambiguous signatures of sulfated isomers. We report the first systematic exploration of the biologically relevant but notoriously challenging deprotonated state in the near IR region. Remarkably, anions displayed very atypical vibrational profiles, which challenge the well-established DFT (Density Functionnal Theory) modeling. The proposed approach was used to elucidate the sulfate patterns in glycosaminoglycans, a ubiquitous class of mammalian carbohydrates, which is regarded as a major challenge in carbohydrate structural analysis. Isomeric glycosaminoglycan disaccharides from heparin and chondroitin sources were resolved, highlighting the potential of infrared multiple photon dissociation spectroscopy as a novel structural tool for carbohydrates.

The Existence of a Designer Al=Al Double Bond in the LiAl2 H4- Cluster Formed by Electronic Transmutation.

PubMed

Lundell, Katie A; Zhang, Xinxing; Boldyrev, Alexander I; Bowen, Kit H

2017-12-22

The Al=Al double bond is elusive in chemistry. Herein we report the results obtained via combined photoelectron spectroscopy and ab initio studies of the LiAl 2 H 4 - cluster that confirm the formation of a conventional Al=Al double bond. Comprehensive searches for the most stable structures of the LiAl 2 H 4 - cluster have shown that the global minimum isomer I possesses a geometric structure which resembles that of Si 2 H 4 , demonstrating a successful example of the transmutation of Al atoms into Si atoms by electron donation. Theoretical simulations of the photoelectron spectrum discovered the coexistence of two isomers in the ion beam, including the one with the Al=Al double bond. © 2017 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

Supramolecular assembly of (Z)-ethyl 2-cyano-3-((4-fluorophenyl)amino) acrylate, crystal structure, Hirshfeld surface analysis and DFT studies

NASA Astrophysics Data System (ADS)

Matos, Catiúcia R. M. O.; Vitorino, Letícia S.; de Oliveira, Pedro H. R.; de Souza, Maria Cecília B. V.; Cunha, Anna C.; Boechat, Fernanda da C. S.; Resende, Jackson A. L. C.; Carneiro, José Walkimar de M.; Ronconi, Célia M.

2016-09-01

A mixture of the E and Z isomers of ethyl 2-cyano-3-((4-fluorophenyl)amino) acrylate was synthesized and characterized by elemental analysis, attenuated total reflectance-Fourier transform infrared spectroscopy, 1H and 13C nuclear magnetic resonance spectroscopy. The structure of the Z isomer was determined by single crystal X-ray diffraction, which revealed a three-dimensional supramolecular network governed by Csbnd H⋯N, Csbnd H⋯O, and Csbnd H⋯F hydrogen bonds and π⋯π stacking interactions. The combination of these interactions plays an important role in stabilizing the self-assembly process and the molecular conformation. Hirshfeld surface analysis indicated the roles of the noncovalent interactions in the crystal packing, which were quantified by fingerprint plots and DFT calculations.

Thermochemistry and kinetics for 2-butanone-1-yl radical (CH2·C(═O)CH2CH3) reactions with O2.

PubMed

Sebbar, N; Bozzelli, J W; Bockhorn, H

2014-01-09

Thermochemistry of reactants, intermediates, transition state structures, and products along with kinetics on the association of CH2·C(═O)CH2CH3 (2-butanone-1-yl) with O2 and dissociation of the peroxy adduct isomers are studied. Thermochemical properties are determined using ab initio (G3MP2B3 and G3) composite methods along with density functional theory (B3LYP/6-311g(d,p)). Entropy and heat capacity contributions versus temperature are determined from structures, vibration frequencies, and internal rotor potentials. The CH2·C(═O)CH2CH3 radical + O2 association results in a chemically activated peroxy radical with 27 kcal mol(-1) excess of energy. The chemically activated adduct can react to stabilized peroxy or hydroperoxide alkyl radical adducts, further react to lactones plus hydroxyl radical, or form olefinic ketones and a hydroperoxy radical. Kinetic parameters are determined from the G3 composite methods derived thermochemical parameters, and quantum Rice-Ramsperger-Kassel (QRRK) analysis to calculate k(E) with master equation analysis to evaluate falloff in the chemically activated and dissociation reactions. One new, not previously reported, peroxy chemistry reaction is presented. It has a low barrier path and involves a concerted reaction resulting in olefin formation, H2O elimination, and an alkoxy radical.

Formation of solvate structures by the ortho-, meta-, and para-isomers of hydroxybenzoic acid in supercritical fluid

NASA Astrophysics Data System (ADS)

Antipova, M. L.; Gurina, D. L.; Odintsova, E. G.; Petrenko, V. E.

2017-04-01

The solvate structures formed by the ortho-, meta-, and para-isomers of hydroxybenzoic acid ( o-HBA, m-HBA, and p-HBA) with a polar co-solvent (methanol at a concentration of 0.030 and 0.035 mole fractions) in supercritical carbon dioxide at a constant density of 0.7 g/cm3 and temperatures of 318 and 328 K have been studied by the classic molecular dynamics. It has been determined that a stable hydrogen-bonded complex with the co-solvent forms via the hydrogen of the carboxyl group for all isomers. The probability of this complex existence is high at all temperatures and concentrations. In the o-HBA molecule, the other functional groups are engaged in the intramolecular hydrogen bond, but not involved in interactions with methanol. It has been found that m-HBA and p-HBA can be involved in hydrogen bonds with methanol via hydroxyl hydrogen and oxygen atoms; they are characterized by the presence of one more co-solvent molecule (rarely, two molecules) in their solvation shell and intermittent formations/breakages of hydrogen bonds via other functional groups. These bonds are far less stable, and their formation is sensitive to change of temperature and co-solvent concentration. It has been concluded that the degree of selective solvation of m-HBA and p-HBA by co-solvent molecules is approximately the same, but the rate of structural rearrangements in the nearest environment of m-HBA is higher than that of p-HBA.

Structural Determination and Occurrence in Ahiflower Oil of Stearidonic Acid Trans Fatty Acids.

PubMed

Delmonte, Pierluigi; Milani, Andrea; Bhangley, Shivani

2018-02-01

Several marine oils and seed oils on the market contain relevant quantities of stearidonic acid (18:4n-3, SDA). The formation of 18:4n-3 trans fatty acids (tFA) during the refining of these oils necessitates the development of a method for their quantification. In this study, 18:4n-3 was isolated from Ahiflower and isomerized to obtain its 16 geometric isomers. The geometric isomers of 18:4n-3 were isolated by silver ion HPLC (Ag + -HPLC) and characterized by partial reduction with hydrazine followed by gas chromatography analysis. The elution order of all 16 isomers was established using a 100 m × 0.25 mm 100% poly(biscyanopropyl siloxane) capillary column and at the elution temperature of 180 °C. The 4 mono-trans-18:4n-3 isomers produced during the refining of oils rich in 18:4n-3 were chromatographically resolved from each other, but c6,t9,c12,c15-18:4 coeluted with the tetra-cis isomer. These 2 fatty acids (FA) were resolved by reducing the separation temperature to 150 °C, but this change caused tetra-cis-18:4n-3 to coelute with t6,c9,c12,c15-18:4. Combining the results from 2 isothermal separations (180 and 150 °C) was necessary to quantify the 4 mono-trans 18:4n-3 FA in Ahiflower oil. Published 2018. This article is a U.S. Government work and is in the public domain in the USA.

1,2-Dichlorohexafluoro-Cyclobutane (1,2-c-C4F6Cl2, R-316c) a Potent Ozone Depleting Substance and Greenhouse Gas: Atmospheric Loss Processes, Lifetimes, and Ozone Depletion and Global Warming Potentials for the (E) and (Z) stereoisomers

NASA Technical Reports Server (NTRS)

Papadimitriou, Vassileios C.; McGillen, Max R.; Smith, Shona C.; Jubb, Aaron M.; Portmann, Robert W.; Hall, Bradley D.; Fleming, Eric L.; Jackman, Charles H.; Burkholder, James B.

2013-01-01

The atmospheric processing of (E)- and (Z)-1,2-dichlorohexafluorocyclobutane (1,2-c-C4F6Cl2, R-316c) was examined in this work as the ozone depleting (ODP) and global warming (GWP) potentials of this proposed replacement compound are presently unknown. The predominant atmospheric loss processes and infrared absorption spectra of the R-316c isomers were measured to provide a basis to evaluate their atmospheric lifetimes and, thus, ODPs and GWPs. UV absorption spectra were measured between 184.95 to 230 nm at temperatures between 214 and 296 K and a parametrization for use in atmospheric modeling is presented. The Cl atom quantum yield in the 193 nm photolysis of R- 316c was measured to be 1.90 +/- 0.27. Hexafluorocyclobutene (c-C4F6) was determined to be a photolysis co-product with molar yields of 0.7 and 1.0 (+/-10%) for (E)- and (Z)-R-316c, respectively. The 296 K total rate coefficient for the O(1D) + R-316c reaction, i.e., O(1D) loss, was measured to be (1.56 +/- 0.11) × 10(exp -10)cu cm/ molecule/s and the reactive rate coefficient, i.e., R-316c loss, was measured to be (1.36 +/- 0.20) × 10(exp -10)cu cm/molecule/s corresponding to a approx. 88% reactive yield. Rate coefficient upper-limits for the OH and O3 reaction with R-316c were determined to be <2.3 × 10(exp -17) and <2.0 × 10(exp -22)cu cm/molecule/s, respectively, at 296 K. The quoted uncertainty limits are 2(sigma) and include estimated systematic errors. Local and global annually averaged lifetimes for the (E)- and (Z)-R-316c isomers were calculated using a 2-D atmospheric model to be 74.6 +/- 3 and 114.1 +/-10 years, respectively, where the estimated uncertainties are due solely to the uncertainty in the UV absorption spectra. Stratospheric photolysis is the predominant atmospheric loss process for both isomers with the O(1D) reaction making a minor, approx. 2% for the (E) isomer and 7% for the (Z) isomer, contribution to the total atmospheric loss. Ozone depletion potentials for (E)- and (Z)-R-316c were calculated using the 2-D model to be 0.46 and 0.54, respectively. Infrared absorption spectra for (E)- and (Z)-R-316c were measured at 296 K and used to estimate their radiative efficiencies (REs) and GWPs; 100-year time-horizon GWPs of 4160 and 5400 were obtained for (E)- and (Z)-R-316c, respectively. Both isomers of R-316c are shown in this work to be long-lived ozone depleting substances and potent greenhouse gases.

Formation of cyanoallene (buta-2, 3-dienenitrile) in the interstellar medium: a quantum chemical and spectroscopic study

NASA Astrophysics Data System (ADS)

Singh, Amresh; Shivani; Misra, Alka; Tandon, Poonam

2014-03-01

The interstellar medium, filling the vast space between stars, is a rich reservoir of molecular material ranging from simple diatomic molecules to more complex, astrobiologically important molecules such as vinylcyanide, methylcyanodiaccetylene, cyanoallene, etc. Interstellar molecular cyanoallene is one of the most stable isomers of methylcynoacetylene. An attempt has been made to explore the possibility of forming cyanoallene in interstellar space by radical-radical and radical-molecule interaction schemes in the gaseous phase. The formation of cyanoallene starting from some simple, neutral interstellar molecules and radicals has been studied using density functional theory. The reaction energies and structures of the reactants and products show that the formation of cyanoallene is possible in the gaseous phase. Both of the considered reaction paths are totally exothermic and barrierless, thus giving rise to a high probability of occurrence. Rate constants for each step in the formation process of cyanoallene in both the reaction paths are estimated. A full vibrational analysis has been attempted for cyanoallene in the harmonic and anharmonic approximations. Anharmonic spectroscopic parameters such as rotational constants, rotation-vibration coupling constants and centrifugal distortion constants have been calculated.

Kinetics of photoirradiation-induced synthesis of soy oil-conjugated linoleic acid isomers.

PubMed

Jain, Vishal P; Proctor, Andrew

2007-02-07

Photoirradiation of soy oil with UV/visible light has been shown to produce significant amounts of trans,trans conjugated linoleic acid (CLA) isomers through conversion of various synthesized intermediate cis,trans isomers. The objective of this study was to determine the kinetics of CLA isomers synthesis to better understand the production of various isomers. Soy oil was irradiated with UV/visible light for 144 h in the presence of an iodine catalyst and CLA isomers analyzed by gas chromatography (GC). Arrhenius plots were developed for the conversion of soy oil linoleic acid (A) to form cis-, trans/trans-, cis-CLA (B), conversion of cis-, trans/trans-, cis-CLA to form trans,trans-CLA (C) with respect to B, and formation of trans,trans-CLA isomers with respect to C. The kinetics of consumption of linoleic acid (LA) to form cis-, trans/trans-, cis-CLA was found to be of second-order with a rate constant of 9.01 x 10-7 L/mol s. The rate of formation of cis-, trans/trans-, cis-CLA isomers depends on the rate of formation from LA and its rate of consumption to form trans,trans-CLA isomers. The conversion of cis-, trans/trans-, cis-CLA isomers to trans,trans-CLA isomers was found to be of first-order with a rate constant of 2.75 x 10-6 s-1. However, the formation of thermodynamically stable trans,trans-CLA isomers (C) with respect to C was found to be a zero-order reaction with a rate constant of 10.66 x 10-7 mol/L s. The consumption of LA was found to be the rate-determining step in the CLA isomers formation reaction mechanism. The findings provide a better understanding of the mechanism of CLA isomers synthesis by photoirradiation and the factors controlling the ratio of various isomers.

Total Synthesis and Structural Revision of Antibiotic CJ-16,264.

PubMed

Nicolaou, K C; Shah, Akshay A; Korman, Henry; Khan, Tabrez; Shi, Lei; Worawalai, Wisuttaya; Theodorakis, Emmanuel A

2015-08-03

The total synthesis and structural revision of antibiotic CJ-16,264 is described. Starting with citronellal, the quest for the target molecule featured a novel bis-transannular Diels-Alder reaction that casted stereoselectively the decalin system and included the synthesis of six isomers before demystification of its true structure. © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Framework fluxionality of organometallic oxides: synthesis, crystal structure, EXAFS, and DFT studies on [[Ru(eta6-arene)]4Mo4O16] complexes.

PubMed

Laurencin, Danielle; Garcia Fidalgo, Eva; Villanneau, Richard; Villain, Françoise; Herson, Patrick; Pacifico, Jessica; Stoeckli-Evans, Helen; Bénard, Marc; Rohmer, Marie-Madeleine; Süss-Fink, Georg; Proust, Anna

2004-01-05

Reactions of the molybdates Na(2)MoO4.2 H2O and (nBu(4)N)2[Mo2O7] with [[Ru(arene)Cl(2)](2)] (arene=C(6)H5CH3, 1,3,5-C6H3(CH3)(3), 1,2,4,5-C6H2(CH3)4) in water or organic solvents led to formation of the triple-cubane organometallic oxides [[Ru(eta(6)-arene)](4)Mo4O16], whose crystal and molecular structures were determined. Refluxing triple cubane [[Ru(eta(6)-C6H5CH3)](4)Mo4O16] in methanol caused partial isomerization to the windmill form. The two isomers of [[Ru(eta(6)-C6H5CH3)](4)Mo4O16] were characterized by Raman and Mo K-edge X-ray absorption spectroscopy (XAS), both in the solid-state and in solution. This triple-cubane isomer was also used as a spectroscopic model to account for isomerization of the p-cymene windmill [[Ru(eta(6)-1,4-CH3C6H4CH(CH3)2)](4)Mo4O16] in solution. Using both Raman and XAS techniques, we were then able to determine the ratio between the windmill and triple-cubane isomers in dichloromethane and in chloroform. Density functional calculations on [[Ru(eta(6)-arene)](4)Mo4O16] (arene=C6H6, C6H5CH3, 1,3,5-C6H3(CH3)3, 1,4-CH3C6H4CH(CH3)2, C6(CH3)6) suggest that the windmill form is intrinsically more stable, provided the complexes are assumed to be isolated. Intramolecular electrostatic interactions and steric bulk induced by substituted arenes were found to modulate but not to reverse the energy difference between the isomers. The stability of the triple-cubane isomers should therefore be accounted for by effects of the surroundings that induce a shift in the energy balance between both forms.

Stereodynamics and edge-to-face CH-π aromatic interactions in imino compounds containing heterocyclic rings.

PubMed

González-Rosende, M Eugenia; Castillo, Encarna; Jennings, W Brian; Malone, John F

2017-02-07

By comparison with close contact interactions between benzene rings there is a paucity of experimental data available for attractive interactions involving aromatic heterocyclic rings, especially for small molecules in solution. Herein we describe aromatic heterocyclic and carbocyclic edge-to face interactions and conformational stereodynamics of N-1,2-diphenylethyl imines bearing a phenyl group and either a 2-pyridyl, 3-pyridyl, 2-thiophene or 2-furanyl moiety on the imino carbon. X-ray crystal structures have been determined for two compounds. Slow rotation about the phenyl-imino bond in the E-isomers and around the heterocycle-imino bond in the Z-isomers of the pyridyl compounds was observed at low temperatures by NMR. Abnormally large shielding of one ortho hydrogen indicates that both the imino phenyl and heterocycle rings can engage in an edge-to-face interaction with the N-terminal phenyl moiety in the appropriate isomer. Some rotational barriers around the phenyl-imino and heterocycle-imino bonds were measured.

Boomerang-type substitution reaction: reactivity of fullerene epoxides and a halofullerenol.

PubMed

Jia, Zhenshan; Zhang, Xiang; Zhang, Gaihong; Huang, Shaohua; Fang, Hao; Hu, Xiangqing; Li, Yuliang; Gan, Liangbing; Zhang, Shiwei; Zhu, Daoben

2007-02-05

The C(s)-symmetric fullerene chlorohydrin C60(Cl)(OH)(OOtBu)4 reacts with 4-dimethylaminopyridine (DMAP) and 1,4-diazabicyclo[2.2.2]octane (DABCO) to yield two isomers with the formula C60(O)(OOtBu)4 in good yields. These isomers differ with respect to the location of the epoxy functionality. The one from DMAP is C(s) symmetric, whereas that from DABCO is C1 symmetric with the epoxy group on the central pentagon. Two different mechanisms are proposed to explain the chemoselectivity of these reactions. The reaction with DMAP involves single-electron transfer as the key step; DMAP acts as the electron donor. A combination of an oxygen-atom shift and S(N)2'' processes (boomerang substitution) are responsible for the formation of isomer with DACBO. Various related reactions support the proposed mechanisms. The structures of new fullerene derivatives were determined by spectroscopy, single-crystal X-ray analysis, and chemical correlation experiments.

A Nonequilibrium Rate Formula for Collective Motions of Complex Molecular Systems

NASA Astrophysics Data System (ADS)

Yanao, Tomohiro; Koon, Wang Sang; Marsden, Jerrold E.

2010-09-01

We propose a compact reaction rate formula that accounts for a non-equilibrium distribution of residence times of complex molecules, based on a detailed study of the coarse-grained phase space of a reaction coordinate. We take the structural transition dynamics of a six-atom Morse cluster between two isomers as a prototype of multi-dimensional molecular reactions. Residence time distribution of one of the isomers shows an exponential decay, while that of the other isomer deviates largely from the exponential form and has multiple peaks. Our rate formula explains such equilibrium and non-equilibrium distributions of residence times in terms of the rates of diffusions of energy and the phase of the oscillations of the reaction coordinate. Rapid diffusions of energy and the phase generally give rise to the exponential decay of residence time distribution, while slow diffusions give rise to a non-exponential decay with multiple peaks. We finally make a conjecture about a general relationship between the rates of the diffusions and the symmetry of molecular mass distributions.

Reorienting the Fab Domains of Trastuzumab Results in Potent HER2 Activators

PubMed Central

Scheer, Justin M.; Sandoval, Wendy; Elliott, J. Michael; Shao, Lily; Luis, Elizabeth; Lewin-Koh, Sock-Cheng; Schaefer, Gabriele; Vandlen, Richard

2012-01-01

The structure of the Fab region of antibodies is critical to their function. By introducing single cysteine substitutions into various positions of the heavy and light chains of the Fab region of trastuzumab, a potent antagonist of HER2, and using thiol chemistry to link the different Fabs together, we produced a variety of monospecific F(ab′)2-like molecules with activities spanning from activation to inhibition of breast tumor cell growth. These isomers (or bis-Fabs) of trastuzumab, with varying relative spatial arrangements between the Fv-regions, were able to either promote or inhibit cell-signaling activities through the PI3K/AKT and MAPK pathways. A quantitative phosphorylation mapping of HER2 indicated that the agonistic isomers produced a distinct phosphorylation pattern associated with activation. This study suggests that antibody geometric isomers, found both in nature and during synthetic antibody development, can have profoundly different biological activities independent of their affinities for their target molecules. PMID:23284778

C60H_2: Synthesis of the Simplest C60 Hydrocarbon Derivative

NASA Astrophysics Data System (ADS)

Henderson, Craig C.; Cahill, Paul A.

1993-03-01

The reaction of C60 with BH_3:tetrahydrofuran in toluene followed by hydrolysis yielded C60H_2. This product was separated by high-performance liquid chromatography and characterized as the addition product of H_2 to a 6,6-ring fusion (1a1b isomer). The ^1H nuclear magnetic resonance (NMR) spectrum of the product remained a sharp singlet between -80^circ and +100^circC, which suggests a static structure on the NMR time scale. Hydrolysis of the proposed borane addition product with acetic acid-d_1 or D_2O yielded C60HD, and its ^3JHD coupling constant is consistent with vicinal addition. The observation of a single C60H_2 isomer is in complete agreement with earlier calculations that indicated that at most 2 of the 23 possible isomers of C60 would be observable at equilibrium at room temperature. These results suggest that organoborane chemistry may be applied to further functionalization of fullerenes.

Designing efficient photochromic dithienylethene dyads.

PubMed

Fihey, Arnaud; Jacquemin, Denis

2015-06-01

Aiming at designing more efficient multiphotochromes, we investigate with the help of ab initio tools the impact of the substitution on a series of dimers constituted of two dithienylethene (DTE) moieties, strongly coupled to each other through an ethynyl linker. The electronic structure and the optical properties of a large panel of compounds, substituted on different positions by various types of electroactive groups, have been compared with the aim of designing a dyad in which the three possible isomers (open-open, closed-open, closed-closed) can be reached. We show that appending the reactive carbons atoms of the DTE core with electroactive groups on one of the two photochromes allows cyclisation to be induced on a specific moiety, which leads to the formation of the desired closed-open isomer. Substituting the lateral positions of the thiophene rings provides further control of the topology of the frontier molecular orbitals, so that the electronic transition inducing the second ring closure stands out in the spectrum of the intermediate isomer.

Collaborative Physical Chemistry Projects Involving Computational Chemistry

NASA Astrophysics Data System (ADS)

Whisnant, David M.; Howe, Jerry J.; Lever, Lisa S.

2000-02-01

The physical chemistry classes from three colleges have collaborated on two computational chemistry projects using Quantum CAChe 3.0 and Gaussian 94W running on Pentium II PCs. Online communication by email and the World Wide Web was an important part of the collaboration. In the first project, students used molecular modeling to predict benzene derivatives that might be possible hair dyes. They used PM3 and ZINDO calculations to predict the electronic spectra of the molecules and tested the predicted spectra by comparing some with experimental measurements. They also did literature searches for real hair dyes and possible health effects. In the final phase of the project they proposed a synthetic pathway for one compound. In the second project the students were asked to predict which isomer of a small carbon cluster (C3, C4, or C5) was responsible for a series of IR lines observed in the spectrum of a carbon star. After preliminary PM3 calculations, they used ab initio calculations at the HF/6-31G(d) and MP2/6-31G(d) level to model the molecules and predict their vibrational frequencies and rotational constants. A comparison of the predictions with the experimental spectra suggested that the linear isomer of the C5 molecule was responsible for the lines.

New chemical sources of energy: A theoretical study

NASA Astrophysics Data System (ADS)

Chaban, Galina

The research presented in this dissertation employs methods of quantum chemistry for the search of highly energetic chemical compounds that can have applications as possible energy sources. The areas of research include: (1) improvement of orbital optimization methods for different types of wavefunctions which leads to substantial savings of computer time and memory; (2) predicting new high energy isomers for singlet and triplet states of Nsb3F and their kinetic stability with respect to isomerisation and dissociation reactions; (3) estimation of minimum energy reaction paths for dissociation reactions of high energy isomers of Nsb2Osb2 including potential energy barriers and minimum energy crossing points between the closest singlet and triplet states; (4) investigation of thermodynamic and kinetic stability of Van der Waals complexes M-Hsb2 (M = Li, Be, B, C, Na, Mg, Al, Si) that can play an important role in improvement of energetic properties of hydrogen based rocket fuels; (5) mapping of the potential energy surface for AlHsb2 compound in the region of crossing between sp2Bsb2 and sp2Asb1 electronic states and predicting the kinetic stability of Al complex, which suggests that Al may be among the promising candidates for inclusion into solid hydrogen for the purpose of energy storage.

Spectroscopic Investigation of O-,M-, and P-Cyanostyrenes

NASA Astrophysics Data System (ADS)

Korn, Joseph A.; Knezz, Stephanie N.; McMahon, Robert J.; Zwier, Timothy S.

2014-06-01

The atmosphere of Titan contains nitrogen, methane, and a rich mixture of more complex hydrocarbons and nitriles produced by photochemical processing. Data from the 2005 Cassini-Huygens mission suggests that among the more complex compounds are substituted benzenes that are themselves precursors to large polymeric tholins. Nitriles are particularly prevalent in Titan's atmosphere due to the dominance of N2 in the atmosphere. The cyanostyrenes are of particular interest, in part because they have the same molecular formula (C9H7N) as quinoline, a prototypical heteroaromatic, and therefore could engage in photochemical isomerization to form this molecule of significant pre-biotic relevance. As a first step in understanding the pathways leading to heteroaromatics, we have studied the isotope-selective spectroscopy of o-,m-, and p-cyanostyrene under jet-cooled conditions relevant to Titan's atmosphere. In this talk, the excitation and emission spectra for the three isomers will be presented. Using a combination of resonant two-photon ionization, LIF excitation, and dispersed fluorescence spectroscopies, the vibronic spectroscopy of the three isomers were recorded and compared. The meta isomer has two conformational isomers, which have been distinguished and studied using hole-burning methods. The talk will compare and contrast the UV spectral signatures of the set of structural and conformational isomers of the cyanostyrenes, using the ethynylstyrene counterparts as points of comparison. Sebree, J. A.; Kidwell, N. M.; Selby, T. M.; Amberger, B. K.; McMahon, R. J.; Zwier, T. S., Photochemistry of Benzylallene: Ring-Closing Reactions to Form Naphthalene. Journal of the American Chemical Society 2012, 134 (2), 1153-1163. Selby, T. M.; Clarkson, J. R.; Mitchell, D.; Fitzpatrick, J. A. J.; Lee, H. D.; Pratt, D. W.; Zwier, T. S., Isomer-Specific Spectroscopy and Conformational Isomerization Energetics of o-, m-, and p-Ethynylstyrenes. The Journal of Physical Chemistry A 2005, 109 (20), 4484-4496.

Selected Reaction Monitoring to Differentiate and Relatively Quantitate Isomers of Sulfated and Unsulfated Core 1 O-Glycans from Salivary MUC7 Protein in Rheumatoid Arthritis*

PubMed Central

Flowers, Sarah A.; Ali, Liaqat; Lane, Catherine S.; Olin, Magnus; Karlsson, Niclas G.

2013-01-01

Rheumatoid arthritis is a common and debilitating systemic inflammatory condition affecting up to 1% of the world's population. This study aimed to investigate the immunological significance of O-glycans in chronic arthritis at a local and systemic level. O-Glycans released from synovial glycoproteins during acute and chronic arthritic conditions were compared and immune-reactive glycans identified. The sulfated core 1 O-glycan (Galβ1–3GalNAcol) was immune reactive, showing a different isomeric profile in the two conditions. From acute reactive arthritis, three isomers could be sequenced, but in patients with chronic rheumatoid arthritis, only a single 3-Gal sulfate-linked isomer could be identified. The systemic significance of this glycan epitope was investigated using the salivary mucin MUC7 in patients with rheumatoid arthritis and normal controls. To analyze this low abundance glycan, a selected reaction monitoring (SRM) method was developed to differentiate and relatively quantitate the core 1 O-glycan and the sulfated core 1 O-glycan Gal- and GalNAc-linked isomers. The acquisition of highly sensitive full scan linear ion trap MS/MS spectra in addition to quantitative SRM data allowed the 3- and 6-linked Gal isomers to be differentiated. The method was used to relatively quantitate the core 1 glycans from MUC7 to identify any systemic changes in this carbohydrate epitope. A statistically significant increase in sulfation was identified in salivary MUC7 from rheumatoid arthritis patients. This suggests a potential role for this epitope in chronic inflammation. This study was able to develop an SRM approach to specifically identify and relatively quantitate sulfated core 1 isomers and the unsulfated structure. The expansion of this method may afford an avenue for the high throughput investigation of O-glycans. PMID:23457413

Levitation effect in zeolites: Quasielastic neutron scattering and molecular dynamics study of pentane isomers in zeolite NaY.

PubMed

Borah, Bhaskar J; Jobic, H; Yashonath, S

2010-04-14

We report the quasielastic neutron scattering (QENS) and molecular dynamics (MD) investigations into diffusion of pentane isomers in zeolite NaY. The molecular cross section perpendicular to the long molecular axis varies for the three isomers while the mass and the isomer-zeolite interaction remains essentially unchanged. Both QENS and MD results show that the branched isomers neopentane and isopentane have higher self-diffusivities as compared with n-pentane at 300 K in NaY zeolite. This result provides direct experimental evidence for the existence of nonmonotonic, anomalous dependence of self-diffusivity on molecular diameter known as the levitation effect. The energetic barrier at the bottleneck derived from MD simulations exists for n-pentane which lies in the linear regime while no such barrier is seen for neopentane which is located clearly in the anomalous regime. Activation energy is in the order E(a)(n-pentane)>E(a)(isopentane)>E(a)(neopentane) consistent with the predictions of the levitation effect. In the liquid phase, it is seen that D(n-pentane)>D(isopentane)>D(neopentane) and E(a)(n-pentane)

Levitation effect in zeolites: Quasielastic neutron scattering and molecular dynamics study of pentane isomers in zeolite NaY

NASA Astrophysics Data System (ADS)

Borah, Bhaskar J.; Jobic, H.; Yashonath, S.

2010-04-01

We report the quasielastic neutron scattering (QENS) and molecular dynamics (MD) investigations into diffusion of pentane isomers in zeolite NaY. The molecular cross section perpendicular to the long molecular axis varies for the three isomers while the mass and the isomer-zeolite interaction remains essentially unchanged. Both QENS and MD results show that the branched isomers neopentane and isopentane have higher self-diffusivities as compared with n-pentane at 300 K in NaY zeolite. This result provides direct experimental evidence for the existence of nonmonotonic, anomalous dependence of self-diffusivity on molecular diameter known as the levitation effect. The energetic barrier at the bottleneck derived from MD simulations exists for n-pentane which lies in the linear regime while no such barrier is seen for neopentane which is located clearly in the anomalous regime. Activation energy is in the order Ea(n-pentane)>Ea(isopentane)>Ea(neopentane) consistent with the predictions of the levitation effect. In the liquid phase, it is seen that D(n-pentane)>D(isopentane)>D(neopentane) and Ea(n-pentane)

Distribution of perfluorooctane sulfonate isomers and predicted risk of thyroid hormonal perturbation in drinking water.

PubMed

Yu, Nanyang; Wang, Xiaoxiang; Zhang, Beibei; Yang, Jingping; Li, Meiying; Li, Jun; Shi, Wei; Wei, Si; Yu, Hongxia

2015-06-01

We documented the distribution of seven perfluorooctane sulfonate (PFOS) isomers in drinking water in Jiangsu Province, China. Compared to the 30% proportion of branched PFOS in technical PFOS, the levels of branched PFOS in drinking water increased to 31.8%-44.6% of total PFOS. Because of previous risk assessment without considering the PFOS isomer profile and the toxicity of individual PFOS isomers, here we performed a new health risk assessment of PFOS for thyroid hormonal perturbation in drinking water with the contribution from individual PFOS isomers. The risk quotients (RQs) of individual PFOS isomers indicated that linear PFOS contributed most to the risk among all the target PFOS isomers (83.0%-90.2% of the total PFOS RQ), and that risk from 6m-PFOS (5.2%-11.9% of the total PFOS RQ) was higher than that from other branched PFOS isomers. We found that the risks associated with PFOS in drinking water would be overestimated by 10.0%-91.7% if contributions from individual PFOS isomers were not considered. The results revealed that the PFOS isomer profile and the toxicity of individual PFOS isomers were important factors in health risk assessment of PFOS and should be considered in the future risk assessments. Copyright © 2015 Elsevier Ltd. All rights reserved.

21 CFR 1308.11 - Schedule I.

Code of Federal Regulations, 2014 CFR

2014-04-01

... nervous system, including its salts, isomers, and salts of isomers whenever the existence of such salts... on the central nervous system, including its salts, isomers, and salts of isomers: (1) Aminorex (Some...

A DNA-Encapsulated and Fluorescent Ag 10 6+ Cluster with a Distinct Metal-Like Core

DOE Office of Scientific and Technical Information (OSTI.GOV)

Petty, Jeffrey T.; Ganguly, Mainak; Rankine, Ian J.

Silver cluster–DNA complexes are optical chromophores, and pairs of these conjugates can be toggled from fluorescently dim to bright states using DNA hybridization. This paper highlights spectral and structural differences for a specific cluster pair. We have previously characterized a cluster with low emission and violet absorption that forms a compact structure with single-stranded oligonucleotides. We now consider its counterpart with blue absorption and strong green emission. This cluster develops with a single-stranded/duplex DNA construct and is favored by low silver concentrations with ≲8 Ag+:DNA, an oxygen atmosphere, and neutral pH. The resulting cluster displays key signatures of a molecularmore » metal with well-defined absorption/emission bands at 490/550 nm, and with a fluorescence quantum yield of 15% and lifetime of 2.4 ns. The molecular cluster conjugates with the larger DNA host because it chromatographically elutes with the DNA and it exhibits circular dichroism. The silver cluster is identified as Ag106+ using two modes of mass spectrometry and elemental analysis. Our key finding is that it adopts a low-dimensional shape, as determined from a Ag K-edge extended X-ray absorption fine structure analysis. The Ag0 in this oxidized cluster segregates from the Ag+ via a sparse number of metal-like bonds and a denser network of silver–DNA bonds. This structure contrasts with the compact, octahedral-like shape of the violet counterpart to the blue cluster, which is also a Ag106+ species. We consider that the blue- and violet-absorbing clusters may be isomers with shapes that are controlled by the secondary structures of their DNA templates.« less