Disiloxane structure,H bonds,and mesomorphism

Translated from Zhurnal Prikladnoi Spektroskopii, Vol. 52, No. 4, pp. 627–635, April, 1990.     

Coarse-graining stiff bonds

The method of constraints in molecular dynamics is useful because it avoids the resolution of high frequency motions with very small time steps. However, the price to pay is that both the dynamics and the statistics of a constrained system differ from those of the unconstrained one. Instead of using constraints, we propose to dispose of high frequency motions by a coarse-graining procedure in which fast variables are eliminated. These fast variables are thus modeled as friction and thermal fluctuations. We illustrate the methodology with a simple model case, a diatomic molecule in a monoatomic solvent, in which the bond between the atoms of a diatomic molecule is stiff. Although the example is very simple and does not display the interesting effects of “wrong” statistics of the constrained system (i.e. the well-known issue connected to the Fixman potential), it is well suited to give the proof of concept of the whole procedure.     

K− decay,hydride bonds,and Z-dependence in kaonic atoms

The observed low values and striking variations in kaonic X-ray intensities were found to be not due to K^? decay. Measurements on H₂O and CH show greatly reduced X-ray intensities apparently due to the presence of the hydride bonds. A simple cascade calculation with an initial distribution in n = 30 that is statistical out to various l_max gave agreement with our absolute X-ray intensities. A correlation between l_max and atomic spacing is suggested.     

Metallic bonds in clusters

It is stressed that the characters of interatomic bonds in metals change somewhat with the size and geometry of clusters. This change reacts directly on the equilibrium configurations. Specific effects related to electron correlations are less marked than for more electropositive elements.     

Stable bonds and unstable bonds in Y(Pr)-123 system

The Pr content dependence of the bond lengths of Y–Cu, Y–O, O–O, Cu–O, Ba–Cu and Ba–O in PrBa₂Cu₃O_y are analyzed and discussed in detail. The different valence bonds can be divided into two groups: stable bonds and unstable bonds. Since the bond lengths and angles between every two ions among O2, Cu2 and O3 are very stable, we conclude that the three ions form an unchangeable triangle when the Pr doping changes. The triangle is called “fixed triangle”. This “fixed triangle” can slightly rotate around the Cu2 ions. It is just this rotation that leads to the unstable bonds. As the increase of the Pr content, the bond lengths between the two Cu(2)–O planes becomes larger and larger, the Cu(2)–O planes bend towards the Ba–O plane. The bonds lengths between the Cu(2)–O and Ba–O planes vary oppositely from those of Cu(2)–O, and become shorter and shorter. These changes connected with the superconductivity are discussed.     

Silicon before the bonds break

The diamond structure of silicon can be destroyed by a femtosecond-laser pulse in a process that is called nonthermal melting. Using a supercell of 800 atoms, we have performed ab initio molecular dynamics simulations on laser-excited potential energy surfaces for electronic excitation densities around the threshold for nonthermal melting. By introducing a quantitative measure for the resemblance of the atomic paths below and above this threshold, we show that the directions of the atomic motions are the same within 98% during 150–200 fs. The atomic pathways below the melting threshold, before the bonds break, are therefore quantitatively closely related to the atomic motions during the first stages of nonthermal melting.     

Hydrogen bonds in polymer folding

We studied the thermodynamics of a homopolymeric chain with both van der Waals and directed hydrogen bond interaction. The effect of hydrogen bonds is to reduce dramatically the entropy of low-lying states and to give rise to long-range order and to conformations displaying secondary structures. For compact polymers a transition is found between helix-rich states and low-entropy sheet-dominated states. The consequences of this transition for protein folding and, in particular, for the problem of prions are discussed.     

Intramolecular hydrogen bonds in sulfur-containing aminophenols

IR Fourier spectroscopy methods have been adopted to study intramolecular interactions that occur in CCl₄ solutions of antiviral derivatives of aminophenol. Analysis of the IR spectra showed that intramolecular bonds O–H···N, O–H···O=C, N–H···O=S=O, and O–H···O=S=O can occur in these compounds depending on the substituent on the amino group. Not only the presence of intramolecular O–H···N, O–H···O=S=O, and N– H···O=S=O hydrogen bonds in 2-amino-4,6-di-tert-butylphenol derivatives containing a sulfonamide fragment but also conformational equilibrium among these types of intramolecular interactions are essential for the manifestation of high efficiency in suppressing HIV-infection in cell culture.     

Hydrogen bonds of anti-HIV active aminophenols

Analysis of IR-Fourier spectra from solutions and crystals of antiviral sulfo-containing aminophenols has shown that various types of intramolecular and intermolecular interactions can occur in molecules of these compounds. Three types of intramolecular hydrogen bonds (O–H⋅⋅⋅N, O–H⋅⋅⋅O=S=O, and N–H⋅⋅⋅O=S=O) are formed in CCl₄ solutions of the sulfo-containing aminophenols. The formation of intermolecular H-bonds involving the NH- and OH-groups and the preservation of the intramolecular O–H⋅⋅⋅O=S=O H-bond are characteristic of the anti-HIV active aminophenol crystals. Spectral attributes are determined in order to distinguish between the anti-HIV active and inactive sulfo-containing aminophenols.     

Superconductivity in crystals with covalent bonds

Novel types of ground states associated with properties of heavy fermion systems are derived for crystals with covalent bonds generated by short-range exchange forces between valence electrons of atoms localized at lattice sites. It is shown that the short-range exchange forces can give rise to a narrow energy band in which electrons can exhibit an enormous effective mass. The same exchange forces provide the microscopic mechanism for spin-singlet pairing of electrons into Cooper pairs which are responsible for superconductivity in these systems. This superconductivity exhibits several different anisotropic superconducting states. The effective mass, Fermi energy, specific heat, Pauli susceptibility, critical temperatures and critical magnetic field of heavy fermion systems are calculated and compared with experimental data.The authors thank Dr. . Jano for discussions.     

Environment potential in closing bonds case

A method of an electronic structure calculation of cluster is suggested. It consists of an “effective” potential with an electron to close the torn valence bonds which appear inevitably in a finite-size-cluster model. The method is applied to the C₅ cluster representing the diamond lattice and is shown to be effective to nullify the pseudo-surface effects.     

Symmetric hydrogen bonds in ice X

Raman measurements on Ice VIII under pressures up to 50 GPa reveal strong line shifts, changes in isotope frequency ratio, intensity decreases, and the appearance of one new line around 38 GPa. These observations are consistent with the formation of symmetric hydrogen bonds and a new phase, Ice X, with cuprit structure.