An electron-rich three dimensional receptor based on a calixarene-tetrathiafulvalene assembly

The synthesis of a calix[4]arene scaffold persubstituted with four redox-active tetrathiafulvalene (TTF) moieties at the lower rim is described. This assembly strongly binds sodium cation, and the binding process is accompanied by a conformational change of the receptor, as shown from NMR titration and by an X-ray diffraction led on the complex. This dynamic behavior remarkably results in a modification of the electrochemical response of TTF probes, which behave independently after sodium complexation.     

Structural anomalies for a three dimensional isotropic core-softened potential

Using molecular dynamics simulations we investigate the structure of a system of particles interacting through a continuous core-softened interparticle potential. We found for the translational order parameter t a local maximum at a density rho(t-max) and a local minimum at rho(t-min)>rho(t-max). Between rho(t-max) and rho(t-min), the t parameter anomalously decreases upon increasing pressure. For the orientational order parameter Q(6) a maximum was observed at a density rho(t-max)相似文献   

A synthetic strategy for the preparation of cyclic peptide mimetics based on SET-promoted photocyclization processes

A novel method for the synthesis of cyclic peptide analogues has been developed. The general approach relies on the use of SET-promoted photocyclization reactions of peptides that contain N-terminal phthalimides as light absorbing electron acceptor moieties and C-terminal alpha-amidosilane or alpha-amidocarboxylate centers. Prototypical substrates are prepared by coupling preformed peptides with the acid chloride of N-phthalimidoglycine. Irradiation of these substrates results in the generation of cyclic peptide analogues in modest to good yields. The chemical efficiencies of these processes are not significantly affected by (1) the lengths of the peptide chains separating the phthalimide and alpha-amidosilane or alpha-amidocarboxylate centers and (2) the nature of the penultimate cation radical alpha-heterolytic fragmentation process (i.e., desilylation vs decarboxylation). An evaluation of the effects of N-alkyl substitution on the amide residues in the peptide chain showed that N-alkyl substitution does not have a major impact on the efficiencies of the photocyclization reactions but that it profoundly increases the stability of the cyclic peptide.     

Analysis of vibrational spectra of chlorotoluene based on density function theory calculations

The conformational behavior and structural stability of chlorotoluene were investigated by utilizing ab initio calculations with 6-31G* basis set at restricted Hartree-Fock (RHF) and density function theory (DFT) levels. The vibrational frequencies of chlorotoluene were computed at the RHF and DFT levels. Complete vibrational assignments were made on the basis of normal coordinate calculations for stable conformer of the molecule. RHF results without scaled quantum mechanical (SQM) force field procedure considered are in bad agreement with experimental values. Of the five DFT methods, BLYP reproduces the observed fundamental frequencies most satisfactorily with the mean absolute deviation of the non-CH stretching modes less than 10 cm(-1). Two hybrid DFT methods are found to yield frequencies, which are generally higher than the observed fundamental frequencies. When the calculated results are compared with 'experimental' frequencies, B3LYP method is found to be slightly more accurate for C-H stretching modes. The results indicate that BLYP calculation is a very promising approach for understanding the observed spectral features.     

Analysis of vibrational spectra of L-alanylglycine based on density functional theory calculations

FT Raman and IR spectra of the crystallized biologically active molecule, L-alanylglycine (L-Ala-Gly) have been recorded and analyzed. The equilibrium geometry, bonding features and harmonic vibrational frequencies of L-Ala-Gly have been investigated with the help of B3LYP density functional theory (DFT) method. The calculated molecular geometry has been compared with the experimental data. The assignments of the vibrational spectra have been carried out with the help of normal coordinate analysis (NCA) following the scaled quantum mechanical force field methodology (SQMFF). The optimized geometry shows the non-planarity of the peptide group of the molecule. Potential energy surface (PES) scan studies has also been carried out by ab initio calculations with B3LYP/6-311+G** basis set. The red shifting of NH3+ stretching wavenumber indicates the formation of N-H...O hydrogen bonding. The change in electron density (ED) in the sigma* antibonding orbitals and E2 energies have been calculated by natural bond orbital analysis (NBO) using DFT method. The NBO analysis confirms the occurrence of strong intermolecular hydrogen bonding in the molecule.     

Steered molecular dynamics studies of the potential of mean force of a Na+ or K+ ion in a cyclic peptide nanotube

Potential of mean force (PMF) profiles of a single Na+ or K+ ion passing through a cyclic peptide nanotube, cyclo[-(D-Ala-Glu-D-Ala-Gln)2-], in water are calculated to provide insight into ion transport and to understand the conductance difference between these two ions. The PMF profiles are obtained by performing steered molecular dynamics (SMD) simulations that are based on the Jarzynski equality. The computed PMF profiles for both ions show barriers of around 2.4 kcal/mol at the channel entrances and exits and energy wells in the middle of the tube. The energy barriers, so-called dielectric energy barriers, arise due to the desolvation of water molecules when ions move across the nanotube, and the energy wells appear as a result of attractive interactions between the cations and negatively charged carbonyl oxygens on the backbone of the tube. We find more and deeper energy wells in the PMF profile for Na+ than for K+, which suggests that Na+ ions have a longer residence time inside the nanotube and that permeation of Na+ ions is reduced compared to K+ ions. Calculations of the radial distribution functions (RDF) between the ions and oxygens in the water molecules and in carbonyl groups on the tube and an investigation of the orientations of the carbonyl groups show that, in contrast with the dynamic carbonyl groups observed in the selectivity filter of the KcsA ion channel, the carbonyl groups in the cyclic peptide nanotube are relatively rigid, with only slight reorientation of the carbonyl groups as the cations pass through. The rigidity of the carbonyl groups in the cyclic peptide nanotube can be attributed to their role in hydrogen bonding, which is responsible for the tube structure. Comparison of the PMF profiles with the electrostatic energy profiles calculated from the Poisson-Boltzmann (PB) equation, a dielectric continuum model, reveals that the dielectric continuum model breaks down in the confined region within the tube that governs ion transport.     

Structure and vibrational frequencies of 1-naphthaldehyde based on density functional theory calculations

The mid and far FTIR and Raman spectra were measured in the liquid state. The fundamental vibrational frequencies and intensity of vibrational bands were evaluated using density functional theory (DFT) and standard B3LYP/6-311+G** basis set combination. The vibrational spectra were interpreted, with the aid of normal coordinate analysis based on a scaled quantum mechanical (SQM) force field. The infrared and Raman spectra were also predicted from the calculated intensities. Comparison of simulated spectra with the experimental spectra provides important information about the ability of the computational method to describe the vibrational modes. Unambiguous vibrational assignment of all the fundamentals was made using the total energy distribution (TED).     

Exploring odd-even effects of simple oligomer-like DRCNnT series: a study based on density functional theory/time-dependent density functional theory calculations

Odd-even effects of short-circuit current density and power conversion efficiency (PCE) are an interesting phenomenon in some organic solar cells. Although some explanations have been given, why they behave in such a way is still an open question. In the present work, we investigate a set of acceptor-donor-acceptor simple oligomer-like small molecules, named the DRCNnT (n = 5-9) series, to give an insight into this phenomenon because the solar cells based on them have high PCE (up to 10.08%) and show strong odd-even effects in experiments. By modeling the DRCNnT series and using density functional theory, we have studied the ground-state electronic structures of the DRCNnT (n = 5-9) series in condensed phase. The calculated results reproduce the experimental trends well. Furthermore, we find that the exciton-binding energies of the DRCNnT series may be one of the key parameters to explain this phenomenon because they also show odd-even effects. In addition, by studying the effects of alkyl branch and terminal group on odd-even effects of dipole moment, we find that eliminating one or two alkyl branches does not break the odd-even effects of dipole moments, but eliminating one or two terminal groups does. Finally, we conclude that removing one alkyl branch close to the terminal group of DRCN5T can decrease highest occupied molecular orbital (HOMO) energy (thus increasing open circuit voltage) and increase dipole moment (thus enhancing charge separation and short-circuit current). This could be a new and simple method to increase the PCE of DRCN5T-based solar cells.     

The Ti@MoOx nanorod array as a three dimensional film electrode for micro-supercapacitors

Ti@MoO_x core–shell nanorod arrays with diameters within 100 nm were fabricated by electrodepositing MoO_x on a Ti nanorod array prepared by oblique angle deposition. A high areal capacitance of 27 mF cm^− 2 and satisfactory cycling stability were obtained. After post-annealing, MoO₂ grains were introduced to enhance the rate capability, suggesting a potential pseudocapacitive micro-electrode.     

Intermolecular potentials based on symmetry-adapted perturbation theory with dispersion energies from time-dependent density-functional calculations

Recently, three of us have proposed a method [Phys. Rev. Lett. 91, 33201 (2003)] for an accurate calculation of the dispersion energy utilizing frequency-dependent density susceptibilities of monomers obtained from time-dependent density-functional theory (DFT). In the present paper, we report numerical calculations for the helium, neon, water, and carbon dioxide dimers and show that for a wide range of intermonomer separations, including the van der Waals and short-range repulsion regions, the method provides dispersion energies with accuracies comparable to those that can be achieved using the current most sophisticated wave-function methods. If the dispersion energy is combined with (i) the electrostatic and first-order exchange interaction energies as defined in symmetry-adapted perturbation theory (SAPT) but computed using monomer Kohn-Sham (KS) determinants, and (ii) the induction energy computed using the coupled KS static response theory, (iii) the exchange-induction and exchange-dispersion energies computed using KS orbitals and orbital energies, the resulting method, denoted by SAPT(DFT), produces very accurate total interaction potentials. For the helium dimer, the only system with nearly exact benchmark values, SAPT(DFT) reproduces the interaction energy to within about 2% at the minimum and to a similar accuracy for all other distances ranging from the strongly repulsive to the asymptotic region. For the remaining systems investigated by us, the quality of the SAPT(DFT) interaction energies is so high that these energies may actually be more accurate than the best available results obtained with wave-function techniques. At the same time, SAPT(DFT) is much more computationally efficient than any method previously used for calculating the dispersion and other interaction energy components at this level of accuracy.     

Analysis of vibrational spectra of 5,6-dimethyl benzimidazole based on density functional theory calculations

The vibrational spectra of 5,6-dimethyl benzimidazole (5,6DBZ) have been computed using the standard B3LYP/6-311G** method and basis set combinations. The solid phase FT-IR and FT-Raman spectra were recorded in the region 4000-400 and 3500-100 cm(-1), respectively. A close agreement was achieved between the observed and calculated frequencies by employing normal coordinate calculations. The observed and simulated spectra were found to be well comparable.     

Synthesis of a cyclic peptide containing norlanthionine: effect of the thioether bridge on peptide conformation

Two diastereomeric analogues of ring C of nisin incorporating a novel norlanthionine residue have been synthesized via a triply orthogonal protecting group strategy. A full structural study was carried out by NMR, which elucidated the conformational properties of the two peptides and enabled the identity of each diastereoisomer to be proposed.     

Ion current surface for a double focusing mass spectrometer of reversed geometry

Ion currents obtained for fragmentations in a mass spectrometer of reversed geometry have been represented as three-dimensional surfaces, which are termed ‘ion current surfaces’. In addition to ion current, useful dimensions of the ion current surfaces are a parameter ln(|ρ|) where ρ = (V₀/V)(E/E₀) and a parameter ln(|m*|) where m* = (V₀/V)m_B. Each ion reaction occurring in the source and flight path gives rise to a pattern of peaks and ridges on the surface. If the major features of the surface corresponding to each ion reaction are projected onto the zero ion current plane, they are disposed in a characteristic trapezoidal pattern. All simple and linked modes of scanning correspond to cross-sections of the surfaces, and representing the scanning modes in this light facilitates the identification of ‘cross-talk’.     

Glucose biosensor based on three dimensional ordered macroporous self-doped polyaniline/Prussian blue bicomponent film

In this paper, a three dimensional ordered macroporous self-doped polyaniline/Prussian blue (3DOM SPAN/PB) bicomponent film was fabricated via the inverted crystal template technique using step-by-step electrodeposition. In this bicomponent film, PB not only acted as a redox mediator, but also presented increased stability in neutral or weak alkaline solution by the protection of SPAN layer on the top. A novel glucose biosensor was fabricated based on the large active surface area and excellent conductivity possessed by the 3DOM SPAN/PB film. The applying experimental conditions of the glucose biosensor have been optimized. Under the optimal conditions, the biosensor showed a wide linear range over three orders of magnitude in glucose concentrations (from 2 to 1600 μM) and a low detection limit of 0.4 μM. Moreover, the biosensor exhibited short response time, high selectivity and excellent operation stability, which can be applied to detect the blood sugar in real samples without any pretreatment.     

基于对苯二甲酸配体的含二维铅无机层的三维无机-有机杂化材料的合成及晶体结构(英文)

以对苯二甲酸作为配体,利用水热法合成了含二维(2D)铅无机层的三维(3D)无机-有机杂化材料[Pb2Cl(1,4-BDC)1.5]n(1);利用红外光谱、电感耦合等离子体原子发射光谱、X-射线衍射表征了产物的结构,利用热重分析测定了其热稳定性.结果表明,[Pb2Cl(1,4-BDC)1.5]n属于单斜晶系,P21/c空间群,其晶格参数为:a=0.599 000(10)nm,b=1.185 29(2)nm,c=1.847 37(3)nm,β=91.778 0(10)°,V=1.310 98(4)nm3,Z=4,R1=0.032 0,wR2=0.089 4,Rint=0.043 6.就化合物1的分子结构而言,由Pb—X—Pb(X=O或Cl)链接形成的2D无机层通过对苯二甲酸配体连接,构筑成具有3D骨架的无机-有机杂化材料.     

Analysis of vibrational spectra of 2 and 3-methylpiperidine based on density functional theory calculations

The experimental and theoretical vibrational spectra of 2 and 3-methylpiperidine (abbreviated as 2-MP and 3-MP) were studied. The FT-Infrared spectra of 2-MP and 3-MP molecules were recorded in the liquid phase. The structural and spectroscopic analysis of the title molecules were made by using density functional harmonic calculations. For the title molecules, only one form was found most stable structure by using B3LYP level with the 6-311G (d,p) basis set. Selected experimental bands were assigned and characterized based on the scaled theoretical wave numbers by their total energy distribution (TED).     

Electronic and spatial structure of five-membered oxygen-or sulfur-containing cyclic phosphorus and arsenic compounds based on quantum-chemical calculations

We have carried out nonempirical quantum-chemical calculations for five-membered heterocyclic molecules containing O or S atoms and also P or As atoms in the ring, using RHF/6-31G(d) and MP2/6-31G(d) methods with full optimization of their geometry. We have studied their electronic and spatial structure and the characteristics of the interaction between atoms in the molecules. __________ Translated from Khimiya Geterotsiklicheskikh Soedinenii, No. 4, pp. 629–634 April, 2006.     

Molecular conformations of a partially halogenated ether: A study based on infrared spectroscopy and density functional theory calculations

A new partially halogenated ether (ClCF₂CF(CF₃)OCF₂CH₃) has been synthesized and characterized using DSC, GC, ¹H and ¹⁹F NMR, IR. The experimental infrared spectra of this “flexible” molecule have been successfully interpreted on the basis of reliable Density Functional Theory calculations. An efficient method useful for the identification of the many stable conformers has been developed and applied. Infrared spectra of the stable conformers have been simulated after full geometry optimization. The results obtained allow detection of conformation-sensitive bands, making possible the interpretation of fine details in the spectra.