Dynamical structure of peptide molecules: Fourier transform microwave spectroscopy and ab initio calculations of N-methylformamide

Rotational spectra of both trans and cis forms of the N-methylformamide normal as well as deuterated (HCONDCH₃, referred to as N-D) species were observed by Fourier transform microwave spectroscopy in the frequency region from 5 to 118 GHz. Samples were prepared in the form of a beam by a pulsed jet valve maintained at 50 °C and were introduced in a high-vacuum cavity cell, with either Ne or Ar as a carrier gas at a backing pressure of 100 kPa. The observed spectra were analyzed to yield molecular parameters including rotational constants and barrier, V₃, to CH₃ internal-rotation: 53.9 (6) and 301 (4) cm⁻¹ for the trans and cis forms of the normal species, respectively, and 41.9 (6) and 309 (4) cm⁻¹ for the trans and cis forms of the N-D species, respectively. Spectra of four trans isotopologues with ¹³C, ¹⁵N, or ¹⁸O singly-substituted in the internal-rotation A state were observed and analyzed to derive the r_s structure of the trans form. For comparison with the experimental data, ab initio calculations were carried out at MP2/6-31G∗∗ level to derive molecular structure, potential barrier to CH₃ internal rotation, and the energy difference between the cis and trans forms. An extensive coupling was found between the CH₃ internal rotation and N-H out-of-plane bending, suggesting that the potential function for the CH₃ internal-rotation deviates considerably from a simple cos(3α) form. The effects of the V₆ term is briefly discussed.     

Molecular dynamics simulations of structural disordering and forming defects in a milling process for selenium

In our previous paper, structural changes of selenium powders ground by a planetary ball mill at various rotational speeds were investigated for the nanostructural modification of particles using mechanical grinding process. The experimental results indicated that the amorphisation of Se by grinding accompanies lattice strain, and the lattice strain arises from impact energy which is more than an energy related to intermolecular interaction. In this paper, molecular dynamics simulations of selenium have been carried out under compressing conditions of various pressure strengths for obtaining information of the lattice strain at atomic level. Then, dynamical behaviour of atomic configuration has been discussed in this process. The structural disordering and formation of the structural defects were estimated by deviations of bond length and angle and the number of created defects before and after compressing from simulated results. The disordering took place during compressing at various pressure strengths, and the disordered atoms return to their initial positions at lower pressure. Stable disordered state and defects after the compression can however remain by compression at more than a certain pressure strength mainly associated with binding energy of selenium.     

Clathrate-formation mediated adsorption of methane on Cu-complex crystals

We measured adsorption and desorption isotherms of methane on [Cu(4, 4'-bipyridine)2(BF4)2] (LPC) at 258, 273, and 303 K. Adsorption proceeds almost vertically at a definite pressure, which is named gate pressure. The lower the measurement temperature, the smaller the gate pressure. The temperature dependence of the gate pressure is expressed by the Clapeyron-Clausius equation, giving a thermodynamic evidence on the clathrate formation between the Cu complex and methane.     

Effects of hydrophilic chain length on the characteristics of the micelles of pentaoxyethylene n-decyl C10E5 and hexaoxyethylene n-decyl C10E6 ethers

Wormlike micelles of nonionic surfactants pentaoxyethylene decyl ether C(10)E(5) and hexaoxyethylene decyl ether C(10)E(6) in dilute aqueous solutions were characterized by static (SLS) and dynamic light scattering (DLS) experiments at several temperatures T below the critical points. The SLS results were analyzed with the aid of the molecular thermodynamic theory for SLS from micelle solutions formulated with the wormlike spherocylinder model, thereby yielding the molar mass M(w) of the micelles as a function of c and the cross-sectional diameter d of 2.6 nm for both C(10)E(5) and C(10)E(6) micelles. It has been found that the micelles grow in size with increasing c and T, following the relation M(w) proportional, variant c(1/2) in conformity with the theoretical prediction for highly extended polymerlike micelles. The hydrodynamic radius R(H) of the micelles as a function of M(w) was found to be also well described by the corresponding theories for the wormlike spherocylinder model. The results of the stiffness parameter lambda(-1) show that both micelles are rather stiff compared with those formed with other polyoxyethylene alkyl ethers C(i)E(j) but far from rigid rods. The values of the spacing s between two adjacent hexaoxyethylene chains on the micellar surface were found to be substantially the same for both micelles.     

Observation of the transient rotator phase of n-hexadecane in emulsified droplets with time-resolved two-dimensional small- and wide-angle X-ray scattering

Crystallization of n-hexadecane in emulsion droplets was studied using time-resolved two-dimensional small- and wide-angle x-ray scattering with differential scanning calorimetry (2D-SAXS-WAXS-in situ DSC) which provides information about both nano- and subnanoscale structural change. n-hexadecane in droplets reproducibly crystallized into the stable triclinic phase via a transient-rotator phase. This is in contrast with previous results that the rotator phase of n-hexadecane was observed only occasionally for bulk samples. Thus we confirmed the existence of rotator phase in n-hexadecane, which is important for the study of crystallization of soft materials. We suggest that the rotator phase at the interface of oil and water plays a precursor role for bulk crystallization. This study demonstrates that 2D-SAXS-WAXS-in situ DSC is a powerful tool for the study of a transient phase.     

Hydrophobic scale: a second parameter to elucidating various specific ligand-protein interactions

In the sequence Fourier analysis (SFA) of specific interactions such as those between fibroblast growth factors (FGFs)/FGF receptors (FGFRs), bone morphogenetic proteins (BMPs)/BMP receptors (BMPRs), or tumor repressor protein p53/mouse double minute 2 homolog (MDM2), the characteristic frequency peak(s) could be observed with the hydrophobic scale for 20 amino acids as well as 4 nucleotides as the physicochemical parameter, but not successfully with the absolute electronegativity scale. This result implies that these two independent scales should be appropriately selected in various specific ligand-protein interactions, though the critical difference has to be determined.     

Interpretation of Hund's multiplicity rule for the carbon atom

Hund's multiplicity rule is investigated for the carbon atom using quantum Monte Carlo methods. Our calculations give an accurate account of electronic correlation and obey the virial theorem to high accuracy. This allows us to obtain accurate values for each of the energy terms and therefore to give a convincing explanation of the mechanism by which Hund's rule operates in carbon. We find that the energy gain in the triplet with respect to the singlet state is due to the greater electron-nucleus attraction in the higher spin state, in accordance with Hartree-Fock calculations and studies including correlation. The method used here can easily be extended to heavier atoms.     

Internal Rotation of the Hydroxyl Group in Isopropanol and the Chirality of the Gauche Form: Fourier Transform Microwave Spectroscopy of (CH(3))(2)CHOD

The rotational spectrum of the deuterated isopropanol (CH(3))(2)CHOD has been observed by Fourier transform microwave spectroscopy and analyzed to yield tunneling splitting of 4431.4613 (17) MHz, between the antisymmetric and the symmetric gauche forms, which is much larger than the 2400 MHz estimated from the internal-rotation potential function reported in the literature. The potential function for the OH internal rotation has been examined in view of the discrepancy between the observed and estimated tunneling splitting, and it was accounted for by taking into account isotope effects on the potential constants. The deuterium quadrupole coupling effect has been included together with the Coriolis terms in the off-diagonal block of the Hamiltonian matrix for the gauche form. The deuterium quadrupole coupling constants obtained for the trans form were employed to calculate the components of the coupling constants as functions of the internal-rotation angle, and the components at around 120 degrees were compared with the values observed for the gauche form, thereby leading to unambiguous determination of the signs of the constants in the off-diagonal block; the signs are not obtainable from an ordinary analysis of the rotational spectra. The chirality of the gauche form was discussed by placing special emphasis on the effect of intermolecular interactions between two chiral molecules. Copyright 2001 Academic Press.     

Effects of Cs treatment on field emission properties of capped carbon nanotubes

Within the methodology [M. Khazaei, A.A. Farajian, Y. Kawazoe, Phys. Rev. Lett. 95 (2005) 177602] based on first-principles electronic structure calculations, the effects of Cs treatment on current emissions and emission patterns of capped carbon nanotubes are considered at low deposition densities when the nanotubes are under an electric field 0.2 V/Å. The results show that the current emission from the cap with one adsorbed Cs is 3.4 times larger than the cap without any Cs. It is 9.6 times larger in the cap with two adsorbed Cs atoms. After Cs deposition the emission patterns become asymmetric (current emission from the carbon atoms located at the topmost pentagon ring close to Cs atoms is larger than the other atomic sites). There are very few localized states on Cs atoms. Hence, although the tunneling probability of electron emission from Cs atoms is significant, there is no current from Cs atoms. In addition, the effect of Cs on work function reduction of nanotubes is explained in terms of Cs deposition densities and the surface dipole moments.