The Effect of Fluoro Substitution upon the β‐Hairpin Fold of a β‐Tetrapeptide in Methanol

The importance of β‐peptides lies in their ability to mimic the conformational behavior of α‐peptides, even with a much shorter chain length, and in their resistance to proteases. To investigate the effect of substitution of β‐peptides on their dominant fold, we have carried out a molecular‐dynamics (MD) simulation study of two tetrapeptides, Ac‐(2R,3S)‐β^2,3hVal(αMe)‐(2S)‐β²hPhe‐(R)‐β³hLys‐(2R,3S)‐β^2,3‐Ala(αMe)‐NH₂, differing in the substitution at the C_α of Phe2 (pepF with F, and pepH with H). Three simulations, unrestrained (UNRES), using ³J‐coupling biasing with local elevation in combination with either instantaneous (INS) or time‐averaging (AVE) NOE distance restraining, were carried out for each peptide. In the unrestrained simulations, we find three (pepF) and two (pepH) NOE distance bound violations of maximally 0.22 nm that involve the terminal residues. The restrained simulations match both the NOE distance bounds and ³J‐values derived from experiment. The fluorinated peptide shows a slightly larger conformational variability than the non‐fluorinated one.     

Experimental and ab initio infrared study of χ-, κ‐ and α-aluminas formed from gibbsite

χ-, κ- and α-alumina phases formed by dehydration of micro-grained gibbsite between 773 and 1573 K are studied using infrared spectroscopy (IR). The structural transitions evidenced by X-ray diffraction (XRD) were interpreted by comparing IR measurements with ab initio simulations (except for the χ form whose complexity does not allow a reliable simulation). For each phase, IR spectrum presents specific bands corresponding to transverse optical (TO) modes of Al-O stretching and bending under 900 cm⁻¹. The very complex χ phase, obtained at 773 K, provides a distinctive XRD pattern in contrast with the IR absorbance appearing as a broad structure extending between 200 and 900 cm⁻¹ resembling the equivalent spectra for γ-alumina phase. κ-alumina is forming at 1173 K and its rich IR spectrum is in good qualitative agreement with ab initio simulations. This complexity reflects the large number of atoms in the κ-alumina unit cell and the wide range of internuclear distances as well as the various coordinances of both Al and O atoms. Ab initio simulations suggest that this form of transition alumina demonstrates a strong departure from the simple pattern observed for other transition alumina. At 1573 K, the stable α-Αl₂Ο₃ develops. Its IR spectra extends in a narrower energy range as compared to transition alumina and presents characteristics features similar to model α-Αl₂Ο₃⋅ Ab initio calculations show again a very good general agreement with the observed IR spectra for this phase. In addition, for both κ- and α-Αl₂Ο₃, extra modes, measured at high energy (above 790 cm⁻¹ for κ and above 650 cm⁻¹ for α), can originate from either remnant χ-alumina or from surface modes.     

Ion Interactions with the Carbon Nanotube Surface in Aqueous Solutions: Understanding the Molecular Mechanisms

We study the molecular mechanisms of alkali halide ion interactions with the single‐wall carbon nanotube surface in water by means of fully atomistic molecular dynamics simulations. We focus on the basic physical‐chemical principles of ion–nanotube interactions in aqueous solutions and discuss them in light of recent experimental findings on selective ion effects on carbon nanotubes.     

手性配合物[M(bipy)_3]~(2+)(M=Fe,Ru,Os)圆二色谱的理论解析

应用密度泛函理论,在DFT/B3LYP/LanL2DZ水平上优化了铁族配合物[M(bipy)3]2+(M=Fe,Ru,Os;bipy=2,2′-联吡啶)在溶液中的基态几何结构,并用TDDFT/B3LYP方法和相同的基组计算了该类配合物的激发能、旋转强度和振子强度,绘制了相应的圆二色谱.计算的谱带位置虽有一定的红移或蓝移,但各谱带的带形和符号均与实验谱吻合.对跃迁性质的分析表明,三个配合物在长波区,除[Fe(bipy)3]2+的第一个谱带是以d-d跃迁为主外,其他谱带均是荷移跃迁为主.短波区的两个强带则是以π-π*跃迁为主的激子耦合带:对于铁配合物,TDDFT可以正确预言其正负带的强度比,但对钌和锇配合物而言,由于对激子跃迁中荷移成份的贡献估计不足,计算的比值偏小.这一结论为进一步改进有关的计算模型指明了方向.     

Time‐dependent density functional theory study on the hydrogen bonding‐induced twisted intramolecular charge‐transfer excited states of 2‐(4′‐N,N‐dimethylaminophenyl)imidazo[4,5‐b]pyridine

In this work, the time‐dependent density functional theory (TDDFT) method was carried out to investigate the hydrogen‐bonded intramolecular charge‐transfer excited state of 2‐(4′‐N,N‐dimethylaminophenyl)imidazo[4,5‐b]pyridine (DMAPIP) in methanol (MeOH) solvent. All the geometric conformations of the ground state and locally excited (LE) state and the twisted intramolecular charge‐transfer (TICT) state for isolated DMAPIP and its hydrogen‐bonded complexes have been optimized. At the same time, the absorption and fluorescence spectra of DMAPIP and the hydrogen‐bonded complexes in different electronic states are also calculated. We theoretically demonstrated for the first time that the intermolecular hydrogen bond formed between DMAPIP and MeOH can induce the formation of the TICT state for DMAPIP in MeOH solvent. Therefore, the two components at 414 and 506 nm observed in the fluorescence spectra of DMAPIP in MeOH solvent were reassigned in this work. The fluorescence peak at 414 nm is confirmed to be the LE state. Furthermore, the red‐shifted shoulder at 506 nm should be originated from the hydrogen‐bonded TICT excited state. © 2010 Wiley Periodicals, Inc. J Comput Chem, 2010     

基于MATLAB软件对不同偏振光在不同介质中的传播过程的动态模拟

利用MATLAB软件对不同偏振光在真空、各向同性介质、线型各向异性介质以及圆型各向异性介质中的传播过程进行了三维动态模拟,能够加深学生对光的偏振概念以及各种偏振光与不同介质之间相互作用原理的理解。     

Time-dependent density functional theory study on electronic excited states of the hydrogen-bonded solute-solvent phenol-(H2O)n (n=3-5) clusters

The solute-solvent interactions of hydrogen-bonded phenol-(H₂O)_n (n=3-5) clusters in electronic excited states were investigated by means of the time-dependent density functional theory (TDDFT) method. The geometric structures and IR spectra in ground state, S₁ state, and T₁ state of the clusters, were calculated using the density functional theory (DFT) and TDDFT methods. Only the ring form isomer, the most stable one of the cluster, was considered in this study. Four, five and six intermolecular hydrogen bonds were formed in phenol-(H₂O)₃, phenol-(H₂O)₄, and phenol-(H₂O)₅ clusters, respectively. Based on the analysis of IR spectra, it is revealed that the “window region” between unshifted and shifted absorption bands in both S₁ and T₁ state becomes broader compared with that in ground state for the corresponding clusters. Furthermore, two interesting phenomenon were observed: (1) with the anticlockwise order of the ring formed by the intermolecular hydrogen bonds in the H-bonded phenol-(H₂O)_n (n=3-5) clusters, the strengths of the intermolecular hydrogen bonds decrease in all the S₀, S₁ and T₁ states; (2) upon electronic excitation, the smaller the distance between phenol and water is, the larger the change of intermolecular hydrogen bonds strength is. Moreover, the intermolecular hydrogen bond (phenolic OH is the H donor) is strengthened in excited state compared with that in ground state. But the intermolecular hydrogen bond (phenolic OH is the H acceptor) is weakened in excited state.     

The energy conserving particle-in-cell method

A new particle-in-cell (PIC) method, that conserves energy exactly, is presented. The particle equations of motion and the Maxwell’s equations are differenced implicitly in time by the midpoint rule and solved concurrently by a Jacobian-free Newton Krylov (JFNK) solver. Several tests show that the finite grid instability is eliminated in energy conserving PIC simulations, and the method correctly describes the two-stream and Weibel instabilities, conserving exactly the total energy. The computational time of the energy conserving PIC method increases linearly with the number of particles, and it is rather insensitive to the number of grid points and time step. The kinetic enslavement technique can be effectively used to reduce the problem matrix size and the number of JFNK solver iterations.