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1.
We present an analysis of the dynamics of single-walled carbon nanotube (SWCNT) chirality during growth, using the recently developed local chirality index (LOCI) method [ Kim et al. Phys. Rev. Lett. 2011 , 107 , 175505 ] in conjunction with quantum chemical molecular dynamics (QM/MD) simulations. Using (5,5) and (8,0) SWCNT fragments attached to an Fe(38) catalyst nanoparticle, growth was induced by periodically placing carbon atoms at the edge of the SWCNT. For both armchair and zigzag SWCNTs, QM/MD simulations indicate that defect healing-the process of defect removal during growth-is a necessary, but not sufficient, condition for chirality-controlled SWCNT growth. Time-evolution LOCI analysis shows that healing, while restoring the pristine hexagon structure of the growing SWCNT, also leads to changes in the local chirality of the SWCNT edge region and thus of the entire SWCNT itself. In this respect, we show that zigzag SWCNTs are significantly inferior in maintaining their chirality during growth compared to armchair SWCNTs.  相似文献   

2.
The title compound, C25H35N3O2, is a novel urea derivative. Pairs of intermolecular N—H...O hydrogen bonds join the molecules into centrosymmetric R22(12) and R22(18) dimeric rings, which are alternately linked into one‐dimensional polymeric chains along the [010] direction. The parallel chains are connected via C—H...O hydrogen bonds to generate a two‐dimensional framework structure parallel to the (001) plane. The title compound was also modelled by solid‐state density functional theory (DFT) calculations. A comparison of the molecular conformation and hydrogen‐bond geometry obtained from the X‐ray structure analysis and the theoretical study clearly indicates that the DFT calculation agrees closely with the X‐ray structure.  相似文献   

3.
Matrix‐assisted laser desorption/ionization in‐source decay (MALDI‐ISD) induces N–Cα bond cleavage via hydrogen transfer from the matrix to the peptide backbone, which produces a c′/z? fragment pair. Subsequently, the z? generates z′ and [z + matrix] fragments via further radical reactions because of the low stability of the z?. In the present study, we investigated MALDI‐ISD of a cyclic peptide. The N–Cα bond cleavage in the cyclic peptide by MALDI‐ISD produced the hydrogen‐abundant peptide radical [M + 2H]+? with a radical site on the α‐carbon atom, which then reacted with the matrix to give [M + 3H]+ and [M + H + matrix]+. For 1,5‐diaminonaphthalene (1,5‐DAN) adducts with z fragments, post‐source decay of [M + H + 1,5‐DAN]+ generated from the cyclic peptide showed predominant loss of an amino acid with 1,5‐DAN. Additionally, MALDI‐ISD with Fourier transform‐ion cyclotron resonance mass spectrometry allowed for the detection of both [M + 3H]+ and [M + H]+ with two 13C atoms. These results strongly suggested that [M + 3H]+ and [M + H + 1,5‐DAN]+ were formed by N–Cα bond cleavage with further radical reactions. As a consequence, the cleavage efficiency of the N–Cα bond during MALDI‐ISD could be estimated by the ratio of the intensity of [M + H]+ and [M + 3H]+ in the Fourier transform‐ion cyclotron resonance spectrum. Because the reduction efficiency of a matrix for the cyclic peptide cyclo(Arg‐Gly‐Asp‐D‐Phe‐Val) was correlated to its tendency to cleave the N–Cα bond in linear peptides, the present method could allow the evaluation of the efficiency of N–Cα bond cleavage for MALDI matrix development. Copyright © 2016 John Wiley & Sons, Ltd.  相似文献   

4.
An in depth study of the reactivity of an N‐heterocyclic carbene (NHC)‐stabilized silylene monohydride with alkynes is reported. The reaction of silylene monohydride 1 , tBu3Si(H)Si←NHC, with diphenylacetylene afforded silole 2 , tBu3Si(H)Si(C4Ph4). The density functional theory (DFT) calculations for the reaction mechanism of the [2+2+1] cycloaddition revealed that the NHC played a major part stabilizing zwitterionic transition states and intermediates to assist the cyclization pathway. A significantly different outcome was observed, when silylene monohydride 1 was treated with phenylacetylene, which gave rise to supersilyl substituted 1‐alkenyl‐1‐alkynylsilane 3 , tBu3Si(H)Si(CH?CHPh)(C?CPh). Mechanistic investigations using an isotope labelling technique and DFT calculations suggest that this reaction occurs through a similar zwitterionic intermediate and subsequent hydrogen abstraction from a second molecule of phenylacetylene.  相似文献   

5.
The hydroxycyclohexadienyl peroxy radicals (HO? C6H6? O2) produced from the reaction of OH‐benzene adduct with O2 were studied with density functional theory (DFT) calculations to determine their characteristics. The optimized geometries, vibrational frequencies, and total energies of 2‐hydroxycyclohexadienyl peroxy radical IIs and 4‐hydroxycyclohexadienyl peroxy radical IIIs were calculated at the following theoretical levels, B3LYP/6‐31G(d), B3LYP/6‐311G(d,p), and B3LYP/6‐311+G(d,p). Both were shown to contain a red‐shifted intramolecular hydrogen bond (O? H … O? H bond). According to atoms‐in‐molecules (AIM) analysis, the intramolecular hydrogen bond in the 2‐hydroxycyclohexadienyl peroxy radical IIs is stronger than that one in 4‐hydroxycyclohexadienyl peroxy radical IIIs, and the former is the most stable conformation among its isomers. Generally speaking, hydrogen bonding in these radicals plays an important role to make them more stable. Based on natural bond orbital (NBO) analysis, the stabilization energy between orbitals is the main factor to produce red‐shifted intramolecular hydrogen bond within these peroxy radicals. The hyperconjugative interactions can promote the transfer of some electron density to the O? H antibonding orbital, while the increased electron density in the O? H antibonding orbital leads to the elongation of the O? H bond and the red shift of the O? H stretching frequency. © 2006 Wiley Periodicals, Inc. Int J Quantum Chem, 2007  相似文献   

6.
Understanding both structure and dynamics is crucial for producing tailor‐made ionic liquids (ILs). We studied the vibrational and structural dynamics of medium versus weakly hydrogen‐bonded C?H groups of the imidazolium ring in ILs of the type [1‐alkyl‐3‐methylimidazolium][bis(trifluoromethanesulfonyl)imide] ([Cnmim][NTf2]), with n=1, 2, and 8, by time‐resolved coherent anti‐Stokes Raman scattering (CARS) and quantum‐classical hybrid (QCH) simulations. From the time series of the CARS spectra, dephasing times were extracted by modeling the full nonlinear response. From the QCH calculations, pure dephasing times were obtained by analyzing the distribution of transition frequencies. Experiments and calculations reveal larger dephasing rates for the vibrational stretching modes of C(2)?H compared with the more weakly hydrogen‐bonded C(4,5)?H. This finding can be understood in terms of different H‐bonding motifs and the fast interconversion between them. Differences in population relaxation rates are attributed to Fermi resonance interactions.  相似文献   

7.
The Schiff base enaminones (3Z)‐4‐(5‐ethylsulfonyl‐2‐hydroxyanilino)pent‐3‐en‐2‐one, C13H17NO4S, (I), and (3Z)‐4‐(5‐tert‐butyl‐2‐hydroxyanilino)pent‐3‐en‐2‐one, C15H21NO2, (II), were studied by X‐ray crystallography and density functional theory (DFT). Although the keto tautomer of these compounds is dominant, the O=C—C=C—N bond lengths are consistent with some electron delocalization and partial enol character. Both (I) and (II) are nonplanar, with the amino–phenol group canted relative to the rest of the molecule; the twist about the N(enamine)—C(aryl) bond leads to dihedral angles of 40.5 (2) and −116.7 (1)° for (I) and (II), respectively. Compound (I) has a bifurcated intramolecular hydrogen bond between the N—H group and the flanking carbonyl and hydroxy O atoms, as well as an intermolecular hydrogen bond, leading to an infinite one‐dimensional hydrogen‐bonded chain. Compound (II) has one intramolecular hydrogen bond and one intermolecular C=O...H—O hydrogen bond, and consequently also forms a one‐dimensional hydrogen‐bonded chain. The DFT‐calculated structures [in vacuo, B3LYP/6‐311G(d,p) level] for the keto tautomers compare favourably with the X‐ray crystal structures of (I) and (II), confirming the dominance of the keto tautomer. The simulations indicate that the keto tautomers are 20.55 and 18.86 kJ mol−1 lower in energy than the enol tautomers for (I) and (II), respectively.  相似文献   

8.
The metalloradical activation of ortho‐benzallylaryl N‐tosyl hydrazones with [Co(TPP)] (TPP=tetraphenylporphyrin) as the catalyst enabled the controlled exploitation of the single‐electron reactivity of the redox non‐innocent carbene intermediate. This method offers a novel route to prepare eight‐membered rings, using base metal catalysis to construct a series of unique dibenzocyclooctenes through selective Ccarbene?Caryl cyclization. The desired eight‐membered‐ring products were obtained in good to excellent yields. A large variety of aromatic substituents are tolerated. The proposed reaction mechanism involves intramolecular hydrogen atom transfer (HAT) to CoIII–carbene radical intermediates followed by dissociation of an ortho‐quinodimethane that undergoes 8π cyclization. The mechanism is supported by DFT calculations, and the presence of radical‐type intermediates was confirmed by trapping experiments.  相似文献   

9.
Electronic spectra of guanine in the gas phase and in water were studied by quantum mechanical/molecular mechanical (QM/MM) methods. Geometries for the excited‐state calculations were extracted from ground‐state molecular dynamics (MD) simulations using the self‐consistent‐charge density functional tight binding (SCC‐DFTB) method for the QM region and the TIP3P force field for the water environment. Theoretical absorption spectra were generated from excitation energies and oscillator strengths calculated for 50 to 500 MD snapshots of guanine in the gas phase (QM) and in solution (QM/MM). The excited‐state calculations used time‐dependent density functional theory (TDDFT) and the DFT‐based multireference configuration interaction (DFT/MRCI) method of Grimme and Waletzke, in combination with two basis sets. Our investigation covered keto‐N7H and keto‐N9H guanine, with particular focus on solvent effects in the low‐energy spectrum of the keto‐N9H tautomer. When compared with the vertical excitation energies of gas‐phase guanine at the optimized DFT (B3LYP/TZVP) geometry, the maxima in the computed solution spectra are shifted by several tenths of an eV. Three effects contribute: the use of SCC‐DFTB‐based rather than B3LYP‐based geometries in the MD snapshots (red shift of ca. 0.1 eV), explicit inclusion of nuclear motion through the MD snapshots (red shift of ca. 0.1 eV), and intrinsic solvent effects (differences in the absorption maxima in the computed gas‐phase and solution spectra, typically ca. 0.1–0.3 eV). A detailed analysis of the results indicates that the intrinsic solvent effects arise both from solvent‐induced structural changes and from electrostatic solute–solvent interactions, the latter being dominant. © 2009 Wiley Periodicals, Inc. J Comput Chem 2010  相似文献   

10.
We report the first example of using ultraviolet (UV) photodissociation action spectroscopy for the investigation of gas‐phase peptide cation‐radicals produced by electron transfer dissociation. z ‐Type fragment ions Gly‐Gly‐Lys+, coordinated to 18‐crown‐6‐ether (CE), are generated, selected by mass and photodissociated in the 200–400 nm region. The UVPD action spectra indicate the presence of valence‐bond isomers differing in the position of the Cα radical defect, (α‐Gly)‐Gly‐Lys+(CE), Gly‐(α‐Gly)‐Lys+(CE) and Gly‐Gly‐(α‐Lys+)(CE). The isomers are readily distinguishable by UV absorption spectra obtained by time‐dependent density functional theory (TD‐DFT) calculations. In contrast, conformational isomers of these radical types are calculated to have similar UV spectra. UV photodissociation action spectroscopy represents a new tool for the investigation of transient intermediates of ion‐electron reactions. Specifically, z ‐type cation radicals are shown to undergo spontaneous hydrogen atom migrations upon electron transfer dissociation. Copyright © 2015 John Wiley & Sons, Ltd.  相似文献   

11.
The structures of 4‐nitrobenzene‐1,2‐diamine [C6H7N3O2, (I)], 2‐amino‐5‐nitroanilinium chloride [C6H8N3O2+·Cl, (II)] and 2‐amino‐5‐nitroanilinium bromide monohydrate [C6H8N3O2+·Br·H2O, (III)] are reported and their hydrogen‐bonded structures described. The amine group para to the nitro group in (I) adopts an approximately planar geometry, whereas the meta amine group is decidedly pyramidal. In the hydrogen halide salts (II) and (III), the amine group meta to the nitro group is protonated. Compound (I) displays a pleated‐sheet hydrogen‐bonded two‐dimensional structure with R22(14) and R44(20) rings. The sheets are joined by additional hydrogen bonds, resulting in a three‐dimensional extended structure. Hydrohalide salt (II) has two formula units in the asymmetric unit that are related by a pseudo‐inversion center. The dominant hydrogen‐bonding interactions involve the chloride ion and result in R42(8) rings linked to form a ladder‐chain structure. The chains are joined by N—H...Cl and N—H...O hydrogen bonds to form sheets parallel to (010). In hydrated hydrohalide salt (III), bromide ions are hydrogen bonded to amine and ammonium groups to form R42(8) rings. The water behaves as a double donor/single acceptor and, along with the bromide anions, forms hydrogen bonds involving the nitro, amine, and ammonium groups. The result is sheets parallel to (001) composed of alternating R55(15) and R64(24) rings. Ammonium N—H...Br interactions join the sheets to form a three‐dimensional extended structure. Energy‐minimized structures obtained using DFT and MP2 calculations are consistent with the solid‐state structures. Consistent with (II) and (III), calculations show that protonation of the amine group meta to the nitro group results in a structure that is about 1.5 kJ mol−1 more stable than that obtained by protonation of the para‐amine group. DFT calculations on single molecules and hydrogen‐bonded pairs of molecules based on structural results obtained for (I) and for 3‐nitrobenzene‐1,2‐diamine, (IV) [Betz & Gerber (2011). Acta Cryst. E 67 , o1359] were used to estimate the strength of the N—H...O(nitro) interactions for three observed motifs. The hydrogen‐bonding interaction between the pairs of molecules examined was found to correspond to 20–30 kJ mol−1.  相似文献   

12.
The synthesis and structural analysis of a quintuple [6]helicene with a corannulene core is reported. The compound was synthesized from corannulene in three steps including a five‐fold intramolecular direct arylation. X‐ray crystallographic analysis revealed a C5‐symmetric propeller‐shaped structure and one‐dimensional alignment in the solid state. The enantiomers of the quintuple [6]helicene were successfully separated by HPLC, and the chirality of the two fractions was identified by CD spectroscopy. A kinetic study yielded a racemization barrier of 34.2 kcal mol?1, which is slightly lower than that of pristine [6]helicene. DFT calculations indicate a rapid bowl‐to‐bowl inversion of the corannulene moiety and a step‐by‐step chiral inversion pathway for the five [6]helicene moieties.  相似文献   

13.
(2S,3S)‐2,6‐Dimethylheptane‐1,3‐diol, C9H20O2, (I), was synthesized from the ketone (R)‐4‐benzyl‐3‐[(2R,3S)‐3‐hydroxy‐2,6‐dimethylheptanoyl]‐1,3‐oxazolidin‐2‐one, C19H27NO4, (II), containing C atoms of known chirality. In both structures, strong hydrogen bonds between the hydroxy groups form tape motifs. The contribution from weaker C—H...O hydrogen bonds is much more evident in the structure of (II), which furthermore contains an example of a direct short Osp3...Csp2 contact that represents a usually unrecognized type of intermolecular interaction.  相似文献   

14.
The planar 3,4‐diphosphinidenecyclobutene (DPCB) can be remarkably twisted into a C2‐type helical structure by dual coordination of a AuCl moiety. A prompt chirality control of the twisted DPCB skeleton ligated by the digold units affords the enantiopure structure by exchanging the chloride ligands for chiral [1,1′‐binaphthalene]‐2,2′‐dicarboxylate. The chirality of the diaurated 2,2′‐bis(diphenylphosphanyl)‐1,1′‐biphenyl (BIPHEP) system can be controlled prior to that of DPCB. Mixing of a DPCB‐bis(chlorogold) complex with the chiral silver salt dynamically leads to a single diastereomer, which was characterized by the 31P NMR spectrum and the CD couplet patterns in the visible (DPCB) area. The absolute configuration of the singly induced helical structure was assigned by the theoretical CD spectra determined by TD‐DFT calculations. Intramolecular alkoxycyclization of hexa‐4,5‐dien‐1‐ol catalyzed by the asymmetric DPCB‐digold structure were also attempted.  相似文献   

15.
Summary: A dextran monomer and a 10mer under constant pulling speed were studied using the atomistic simulations. Molecular dynamics (MD) with the new Amber-Glycam04 forcefield were performed. The main result of the present Amber-based MD simulations is that the experimental plateau of the force-extension dependence for dextran can be explained by a transition of the glucopyranose rings in the dextran monomers from a chair (4C1) to a inverted chair (1C4) conformation whereas chair to boat transitions occur at higher forces. Density functional (DFT) calculations of monomer were also performed for a monomer at different fixed end-to-end distances (lengths) to clarify the molecular mechanism of dextran extension. These DFT calculations confirm the existence of an inverted chair (1C4) conformation at intermediate extensions and its possible important contribution to the plateau in the experimental force-extension dependence of dextran.  相似文献   

16.
The crystal structures of two single‐enantiomer amidophosphoesters with an (O)2P(O)(N) skeleton, i.e. diphenyl [(R)‐(+)‐α‐methylbenzylamido]phosphate, (I), and diphenyl [(S)‐(?)‐α‐methylbenzylamido]phosphate, (II), both C20H20NO3P, are reported. In both structures, chiral one‐dimensional hydrogen‐bonded architectures, along [010], are mediated by N—H…OP interactions. The statistically identical assemblies include the noncentrosymmetric graph‐set motif C(4) and the compounds crystallize in the chiral space group P21. As a result of synergistic co‐operation from C—H…O interactions, a two‐dimensional superstructure is built including a noncentrosymmetric R44(22) hydrogen‐bonded motif. A Cambridge Structural Database survey was performed on (O)2P(O)(N)‐based structures in order to review the frequency of space groups observed in this family of compounds; the hydrogen‐bond motifs in structures with chiral space groups and the types of groups inducing chirality are discussed. The 2,3JX–P (X = H or C) coupling constants from the NMR spectra of (I) and (II) have been studied. In each compound, the two diastereotopic C6H5O groups are different, which is reflected in the different chemical shifts and some coupling constants.  相似文献   

17.
The three organic two‐photon‐absorbing cycloalkanone chromophores 2,4‐bis[4‐(diethylamino)benzylidene]cyclobutanone, C26H32N2O ( I ), 2,5‐bis[4‐(diethylamino)benzylidene]cyclopentanone, C27H34N2O ( II ), and 2,6‐bis[4‐(diethylamino)benzylidene]cyclohexanone, C28H36N2O ( III ), were obtained by a reaction between 4‐(diethylamino)benzaldehyde and the corresponding cycloalkanone and were characterized by single‐crystal X‐ray diffraction studies, as well as density functional theory (DFT) quantum‐chemical calculations. Molecules of this series have three main fragments, i.e. central acceptor (A) and two terminal donors (D1 and D2) and represent examples of the D1–π–A–π–D2 molecular design. All three compounds crystallize with two crystallographically independent molecules in the asymmetric unit ( A and B ) and are distinguished by the conformations of both the molecular Et2N—C6H4—C=C—C(=O)—C=C—C6H4—NEt2 backbone (arcuate or linear) and the terminal diethylamino substituents (syn‐ or antiperiplanar to the plane of the molecule). The central four‐ and five‐membered rings in I and II are almost planar, and the six‐membered ring in III adopts a sofa conformation. In the crystals of I – III , the two independent molecules A and B form hydrogen‐bonded [ A … B ] dimers via intermolecular C—H…O hydrogen bonds. Furthermore, the [ A … B ] dimers in I are bound by intermolecular C—H…O hydrogen bonds into two‐tier puckered layers, whereas in the crystals of II and III , the [ A … B ] dimers are stacked along the c and a axes, respectively. Taking into account the decreasing steric strain upon expanding the central ring, compound I might be more efficient as a two‐photon absorption chromophore than compounds II and III , which corresponds to the results of spectroscopic studies.  相似文献   

18.
We report here the development of hybrid quantum mechanics/molecular mechanics (QM/MM) interface between the plane‐wave density functional theory based CPMD code and the empirical force‐field based GULP code for modeling periodic solids and surfaces. The hybrid QM/MM interface is based on the electrostatic coupling between QM and MM regions. The interface is designed for carrying out full relaxation of all the QM and MM atoms during geometry optimizations and molecular dynamics simulations, including the boundary atoms. Both Born–Oppenheimer and Car–Parrinello molecular dynamics schemes are enabled for the QM part during the QM/MM calculations. This interface has the advantage of parallelization of both the programs such that the QM and MM force evaluations can be carried out in parallel to model large systems. The interface program is first validated for total energy conservation and parallel scaling performance is benchmarked. Oxygen vacancy in α‐cristobalite is then studied in detail and the results are compared with a fully QM calculation and experimental data. Subsequently, we use our implementation to investigate the structure of rhodium cluster (Rhn; n = 2 to 6) formed from Rh(C2H4)2 complex adsorbed within a cavity of Y‐zeolite in a reducible atmosphere of H2 gas. © 2016 Wiley Periodicals, Inc.  相似文献   

19.
Novel difluoromethylenated [70]fullerene derivatives, C70(CF2)n (n=1–3), were obtained by the reaction of C70 with sodium difluorochloroacetate. Two major products, isomeric C70(CF2) mono‐adducts with [6,6]‐open and [6,6]‐closed configurations, were isolated and their homofullerene and methanofullerene structures were reliably determined by a variety of methods that included X‐ray analysis and high‐level spectroscopic techniques. The [6,6]‐open isomer of C70(CF2) constitutes the first homofullerene example of a non‐hetero [70]fullerene derivative in which functionalisation involves the most reactive bond in the polar region of the cage. Voltammetric estimation of the electron affinity of the C70(CF2) isomers showed that it is substantially higher for the [6,6]‐open isomer (the 70‐electron π‐conjugated system is retained) than the [6,6]‐closed form, the latter being similar to the electron affinity of pristine C70. In situ ESR spectroelectrochemical investigation of the C70(CF2) radical anions and DFT calculations of the hyperfine coupling constants provide evidence for the first example of an inter‐conversion between the [6,6]‐closed and [6,6]‐open forms of a cage‐modified fullerene driven by an electrochemical one‐electron transfer. Thus, [6,6]‐closed C70(CF2) constitutes an interesting example of a redox‐switchable fullerene derivative.  相似文献   

20.
Density functional theory (DFT) and Fourth‐order Möller–Plesset (MP4) perturbation theory calculations are performed to examine the possibility of hydrogen storage in V‐capped VC3H3 complex. Stability of bare and H2 molecules adsorbed V‐capped VC3H3 complex is verified using DFT and MP4 method. Thermo‐chemistry calculations are carried out to estimate the Gibbs free corrected averaged H2 adsorption energy which reveals whether H2 adsorption on V‐capped VC3H3 complex is energetically favorable, at different temperatures. We use different exchange and correlation functionals employed in DFT to see their effect on H2 adsorption energy. Molecular dynamic (MD) simulations are performed to confirm whether this complex adsorbs H2 molecules at a finite temperature. We elucidate the correlation between H2 adsorption energy obtained from density functional calculations and retaining number of H2 molecules on VC3H3 complex during MDs simulations at various temperatures. © 2011 Wiley Periodicals, Inc. J Comput Chem, 2011  相似文献   

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