A stable,rapidly converging conjugate gradient method for energy minimization

We apply Shanno's conjugate gradient algorithm to the problem of minimizing the potential energy function associated with molecular mechanical calculations. Shanno's algorithm is stable with respect to roundoff errors and inexact line searches and converges rapidly to a minimum. Equally important, this algorithm can improve the rate of convergence to a minimum by a factor of 5 relative to Fletcher-Reeves or Polak-Ribière minimizers when used within the molecular mechanics package AMBER. Comparable improvements are found for a limited number of simulations when the Polak-Ribière direction vector is incorporated into the Shanno algorithm.     

The conjugate gradient method applied to the direct second-order minimization of energy

The conjugate gradient method is proposed for minimizing the second-order Δε. Formulae for derivatives are expressed in a constructive way: they specify to which derivatives and with which weight each integral (belonging to a non-redundant list) contributes. The case of geminal functions is fully treated. A test calculation on the BeH molecule is shown.     

Analyzing electrochemical noise with Chebyshev’s discrete polynomials

The principles underlying a novel method intended for analyzing experimental data obtained when studying fluctuation processes are considered. The method in question is Chebyshev’s spectroscopy. The application of this method allows one to determine statistic characteristics of steady-state electrochemical noise against the background of severe deterministic interference without invoking the procedure of the fitting of the initial data. The potentialities of this novel method, which is intended for treating noise experiment, are demonstrated by examining model examples and analyzing the electrochemical noise generated by a lithium electrode placed in an aprotic organic electrolyte.     

Inelastic scattering of X-rays and gamma rays

Recent progress in the following topics will be outlined. Needs and opportunities for further work will also be indicated. The topics are as follows. Compton scattering by inner shell (K and L) electrons; non-resonant Raman and Compton scattering and spin-dependent Compton scattering; atomic single-differential scattering cross-sections and incoherent scattering function (ISF) approximation; resonant Raman–Compton scattering and resonant inelastic X-ray scattering (RIXS) with possible coherence effects; ultra-high-resolution studies.     

Inelastic and superelastic scattering of electrons from sodium

Recent experimental results of the NIST, Flinders and Münster groups on superelastic scattering of intermediate-energy polarized electrons from laser-excited polarized and unpolarized sodium atoms have been analyzed theoretically together with those on inelastic scattering data. Based on the Persival-Seaton hypothesis specific model-independent relations between correlation and polarization parameters measured in superelastic scattering experiments of different types have been suggested. The differential cross section as well as the parametersL _⊥,L ^S(T) _⊥, γ,r, and \(\bar S\) _A (J) for the 3²S?3² P transition in a broad range of scattering angels have been calculated within the distorted-wave approximation. Problem of constructing the e + Na optical potential is discussed.     

Inelastic neutron scattering studies of polyethylene and N-alkanes

High quality inelastic neutron scattering (INS) spectra of randomly oriented polycrystalline polyethylene, perdeuteropolyethylene and highly oriented polyethylene are presented. The instrumental resolution was significantly better than previous work and has revealed increased detail in the 0 − 600 cm⁻¹ region. For the polycrystalline sample, comparison with the best available dispersion curves shows that these qualitatively reproduce the INS spectrum, apart from the energy of the maximum in the in-plane C-C bending mode v5. For the oriented samples, comparison with calculated INS spectra show fair, but not exact, agreement with the experimental spectra.     

Inelastic scattering of fast electrons and the electron density of the scattering molecules

Theoretical and Experimental Chemistry -     

Inelastic incoherent neutron scattering studies of water interacting with biological macromolecules.

The interaction between water and biological macromolecules in living organisms is of fundamental importance in a range of processes. We have studied water-DNA and water-proteolipid membrane systems over a range of hydration states using inelastic incoherent neutron scattering. We find a relatively sharp transition for both systems at a water concentration above which bulk solvent can be detected. Below this concentration, bulk water is essentially absent, i.e., all the water in the system is interacting with the biological macromolecules. This water is strongly perturbed as judged by its energy transfer spectrum, with a broader and lower energy transition than bulk water in the 50-75 meV (approximately 400-600 cm(-1)) range. Taking into account the differing geometry of (cylindrical) DNA and (planar) membranes, the number of water shells perturbed by each system was estimated. A conclusion is that in living organisms a large proportion of the cellular water will be in a state quite distinct from bulk water. The data add to the growing evidence that water structure in the vicinity of biological macromolecules is unusual and that the proximal water behaves differently compared to the bulk solvent.     

Inelastic neutron scattering in the glassy and metastable phases of methoxy-benzylidene-butyl-aniline

The inelastic neutron scattering (INS) spectra were measured in the glassy and in the metastable phases of methoxy-benzylidene-butyl-aniline. For comparison, the spectrum of benzylidene-aniline was also recorded. Complementary information was provided by Raman scattering measurements which analyzed more accurately the vibrational motions. Strong differences between the INS and Raman spectra were evidenced. The assignment of some lines is discussed to elucidate the respective role of the core and the tail of the molecule in the appearance of the successive metastable phases.     

Inelastic scattering of vibrationally excited KBr BY Ar and CO2

Scattering of highly vibrationally excited potassium bromide by argon and carbon dioxide has been investigated. Velocity resolved KBr scattering intensities indicate that highly translationally inelastic collisions occur in both systems and, in the CO₂ system, show effects due to VT, VV competition.     

Inelastic light scattering from the liquid crystal and solid phases of MBBA

Brillouin spectra from 4-methoxybenzylidene-4'-n-butylaniline were measured for the nematic phase, a quenched liquid crystal (phase C₀), and a partially ordered structure (phase C₁). The difference in the velocities of the longitudinal hyper-sound waves in the nematic and the quenched liquid crystal structures is associated with temperature and relaxation effects.     

Inelastic scattering of OH(X2Pi) with Ar and He: a combined polarization spectroscopy and quantum scattering study

One-colour polarization spectroscopy (PS) on the OH A (2)Sigma(+)- X (2)Pi(0,0) band has been used to measure the removal of bulk rotational angular momentum alignment of ground-state OH(X (2)Pi) in collisions with He and Ar. Pseudo-first-order PS signal decays at different collider partial pressures were used to determine second-order decay rate constants for the X (2)Pi(3/2), J = 1.5-6.5, e states. The PS signal decay rate constant, k(PS), is sensitive to all processes that remove population and destroy polarization. The contribution to k(PS) from pure (elastic) alignment depolarization within the initial level, k(DEP), can be extracted by subtracting the independently measured or predicted sum of the rate constants for total rotational energy transfer (RET), k(RET), and for Lambda-doublet changing, k(Lambda), collisions from k(PS). Literature values of k(RET) and k(Lambda) are available from experiments with He and Ar, and from quantum scattering calculations for Ar only. We therefore also present the results of new, exact, fully quantum mechanical calculations of k(RET) and k(Lambda) on the most recent ab initio OH(X)-He potential energy surface of Lee et al. [J. Chem. Phys. 2000, 113, 5736]. The results for k(DEP) from this subtraction for He are found to be modest, around 0.4 x 10(-10) cm(3) s(-1), whereas for Ar k(DEP) is found to range between 0.6 +/- 0.2 x 10(-10) cm(3) s(-1) and 1.7 +/- 0.3 x 10(-10) cm(3) s(-1), comparable to total population removal rate constants. The differences between k(DEP) for the two colliders are most likely explained by the presence of a substantially deeper attractive well for Ar than for He. The measurement of k(DEP) may provide a useful new tool that is more sensitive to the form of the long-range part of the intermolecular potential than rotational state-changing collisions.     

Inelastic neutron scattering spectrum of cyclotrimethylenetrinitramine: a comparison with solid-state electronic structure calculations

Solid-state geometry optimizations and corresponding normal-mode analysis of the widely used energetic material cyclotrimethylenetrinitramine (RDX) were performed using density functional theory with both the generalized gradient approximation (BLYP and BP functionals) and the local density approximation (PWC and VWN functionals). The structural results were found to be in good agreement with experimental neutron diffraction data and previously reported calculations based on the isolated-molecule approximation. The vibrational inelastic neutron scattering (INS) spectrum of polycrystalline RDX was measured and compared with simulated INS constructed from the solid-state calculations. The vibrational frequencies calculated from the solid-state methods had average deviations of 10 cm(-1) or less, whereas previously published frequencies based on an isolated-molecule approximation had deviations of 65 cm(-1) or less, illustrating the importance of including crystalline forces. On the basis of the calculations and analysis, it was possible to assign the normal modes and symmetries, which agree well with previous assignments. Four possible "doorway modes" were found in the energy range defined by the lattice modes, which were all found to contain fundamental contributions from rotation of the nitro groups.     

Inelastic scattering and chemisorption of CO on a Pt(111) surface

A semiclassical model is used to calculate energy transfer in collisions between CO and a Pt(111) surface. The sticking probability is found to be as large as 0.7–0.8 for small collision energies (≈0.14 eV). At higher energies (≈5 eV) it decreases to ≈0.3. Strong interaction between the adsorbed molecule and the phonons is observed.     

Inelastic scattering and energy loss of swift electron beams in biologically relevant materials

The inelastic mean free path and the stopping power of swift electrons in relevant biomaterials, such as liquid water, DNA, protein, lipid, carotene, sugar, and ice are calculated in the framework of the dielectric formalism. The Mermin Energy Loss Function – Generalized Oscillator Strength model is used to determine the energy loss function of these materials for arbitrary energy and momentum transfer using electron energy‐loss spectroscopy data as input. To ensure the consistency of the model, efforts are made so that both the Kramers–Kronig and f‐sum rules are fulfilled to better than 2%. Our findings indicate sizeable differences in the inelastic mean free path and stopping power among these biomaterials for low‐energy electrons. For example, at 100‐eV electron energy, the inelastic mean free path in protein is 25% smaller than for water and around 10% smaller than for the other biomaterials. The stopping power values of protein, DNA, and sugar are rather similar but 20% larger than for water. Taking into account these results, we conclude that electron interactions with living tissues at the nanometric scale cannot be reliably described using only liquid water as the surrogate of the biological target. Copyright © 2016 John Wiley & Sons, Ltd.     

Inelastic neutron scattering studies of the interaction between water and some amino acids

The interaction between water and some of amino acids (glycine, L-glutamine, L-threonine, L-cysteine and L-serine) was studied by inelastic incoherent neutron scattering (IINS). The vibrational spectra of dry amino acids and amino acids with a water content (e.g., 1 mol water/1 mol amino acid) were recorded. Comparing the difference spectra obtained by subtracting the spectrum of dry sample from those of wet sample with the spectra of ice Ih, we obtained that the difference spectrum for serine changed greatly from normal ice spectrum; but on the other hand, the difference spectra for the other amino acids such as glycine, glutamine, threonine, and cysteine changed slightly. The results demonstrate that serine has stronger hydrophilic character than glycine, glutamine, threonine, and cysteine. This is the first time the hydrophilic or hydrophobic character of amino acids was studied by using inelastic neutron scattering techniques, which provides important information for theoretical modeling and force field refinement for the interaction between water and the amino acids studied here.     

Inelastic incoherent neutron scattering measurements of intact cells and tissues and detection of interfacial water

We have previously used inelastic incoherent neutron scattering spectroscopy to investigate the properties of aqueous suspensions of biomolecules as a function of hydration. These experiments led to the identification of signals corresponding to interfacial (hydration) water at low water content. A prediction from these studies was that in the crowded environment inside living cells, a significant proportion of the water would be interfacial, with profound implications for biological function. Here we describe the first inelastic incoherent neutron scattering spectroscopy studies of living cells and tissues. We find that the interfacial water signal is similar to that observed for water interacting with purified biomolecules and other solutes, i.e., it is strongly perturbed in the librational and translational intermolecular optical regions of the spectrum at 20-150 meV. The ratio of interfacial water compared to total water in cells (approximately 30%) is in line with previous experimental data for hydration water and calculations based on simple assumptions.     

Inelastic neutron scattering and infrared spectroscopic study of furan adsorption on alkali-metal cation-exchanged faujasites.

Inelastic neutron scattering (INS) as well as infrared (IR) transmission and diffuse reflection infrared Fourier transform (DRIFT) spectra of furan adsorbed on Li-LSX, NaY, NaX, K-LSX, and CsNaX zeolites have been measured in the range 2000-200 and 4000-1300 cm(-1), respectively. On the basis of an assignment of normal modes of furan taken from the literature and our own quantum chemical calculations of vibrational frequencies, the observed frequency shifts between bulk furan and furan adsorbed on the zeolites mentioned above have been interpreted in view of the interactions between furan and zeolite. For an explanation of frequency shifts of CH out-of-plane bendings, CH stretchings and some ring vibrations, it has to be assumed that in addition to the interaction between furan and the corresponding cation of the zeolite, a further interaction between the CH bonds and lattice oxygen atoms exists.