Theory of relaxation properties of two‐dimensional polymer networks, 2. Local dynamic characteristics

Using normal mode transformation obtained in Part 1 of this series^[1], the exact analytical expressions for the mean‐square displacements of junctions and non‐junction beads, the autocorrelation functions of the end‐to‐end chain vectors between neighboring junctions, and those of subchain vectors of a two‐dimensional regular network consisting of "bead and spring" Rouse chains are obtained. Contributions of intra‐ and interchain relaxation processes to the local dynamic characteristics considered are compared. The time behavior of dynamic quantities obtained is estimated for different scales of motions. The possibility of describing long‐time relaxation of a two‐dimensional network by a simplified coarse‐grained network model is demonstrated. It is shown that the local relaxation properties of a two‐dimensional polymer network (as well as a three‐dimensional network) on scales smaller than the average distance between cross‐links are very close to those of a single Rouse chain. The large‐scale collective relaxation of the polymer networks having a two‐dimensional connectivity differs considerably from that of the three‐dimensional networks.     

Dynamics of proton exchange in a model phosphonic acid‐functionalized polymer

The dynamics and mechanism of proton exchange in phosphonic acid‐functionalized polymers were studied using poly(vinyl‐phosphonic acid) (PVPA) as a model system along with quantum chemical calculations and Born–Oppenheimer molecular dynamics (BOMD) simulations at the B3LYP/TZVP level as model calculations. This theoretical study began with searching for the smallest, most active polymer segments and their intermediate conformations which could be involved in the local proton‐exchange process. The B3LYP/TZVP results confirmed that a low local dielectric environment and excess proton conditions are required to generate the intermediate conformations, and the shapes of the potential energy curves of the proton exchange between the two phosphonic acid functional groups are sensitive to the local conformational changes. In contrast, a high local dielectric environment increases the energy barriers, thereby preventing the proton from returning to the original functional group. Based on the static results, a mechanism for the proton exchange between the two functional groups involving fluctuations in the local dielectric environment and a local conformational change was proposed. The BOMD results confirmed the proposed mechanism by showing that the activation energies for the proton exchange in the hydrogen bond between two immobilized phosphonic acid moieties, obtained from the exponential relaxation behaviors of the envelopes of the velocity autocorrelation functions and the ¹H Nuclear Magnetic Resonance (NMR) line‐shape analyses, are too low to be the rate‐determining process. Instead, coupled librational motion in the backbone which leads to the interconversion between the two intermediate conformations possesses higher activation energy, and therefore represents one of the most important rate‐determining processes. These findings suggested that the rate of the proton exchange in the model phosphonic acid‐functionalized polymer is determined by the polymer mobility which, in this case, is the large‐amplitude librational motion of the vinyl backbone. © 2015 Wiley Periodicals, Inc.     

Understanding pre-structured motifs (PreSMos) in intrinsically unfolded proteins

Intrinsically unfolded proteins (IUPs) do not obey the golden rule of structural biology, 3D structure = function, as they manifest their inherent functions without resorting to three-dimensional structures. Absence of a compact globular topology in these proteins strongly implies that their ligand recognition processes should involve factors other than spatially well-defined binding pockets. Heteronuclear multidimensional (HetMulD) NMR spectroscopy assisted with a stable isotope labeling technology is a powerful tool for quantitatively investigating detailed structural features in IUPs. In particular, it allows us to delineate the presence and locations of pre-structured motifs (PreSMos) on a per-residue basis. PreSMos are the transient local structural elements that presage target-bound conformations and act as specificity determinants for IUP recognition by target proteins. Here, we present a brief chronicle of HetMulD NMR studies on IUPs carried out over the past two decades along with a discussion on the functional significance of PreSMos in IUPs.     

The dielectric properties of liquid-crystal random copolyesters of 4-hydroxybenzoic acid and 2-hydroxy 6-naphthoic acid

Dielectric measurments made from 1 Hz to 10 kHz and from -80 to 150°C on random copolyesters of 4-hydroxybenzoic acid (HBA) and 2-hydroxy 6-naphthoic acid (HNA) reveal three relaxation processes at low frequencies rather than the two seen at audio frequencies. The higher temperature α process is similar to a glass transition, with a high activation energy ～ 170 kcal/mol, but the two lower temperature processes are identified as local mode processes associated with the HNA and HBA moieties, respectively. It is shown that the observed value of the permittivity above the glass transition is lower than that which would be expected for ester groups rotating freely about the local chain axis, and it is suggested that this may be due to several factors including immobilization of dipoles in the crystalline regions, correlated motion of dipoles, and librational rather than rotational motion.     

Spectral researches on interaction of laser radiation with targets from titanium oxides

Spectral characteristics and kinetic processes of the laser-induced plasma used for the growth of films from titanium oxides were investigated. The experiments were carried out in vacuum, oxygen, and an oxygen radiofrequency discharge plasma and its afterglow. A collision-radiative model describing the state-to-state kinetics of titanium atoms and ions at various stages of flight of laser-induced plasma was proposed. It was shown that the conditions of local thermodynamic equilibrium are disturbed because of a fast gas-dynamic expansion of plasma. Nonetheless, the distribution functions of titanium atoms and ions over excited states are described by the Boltzmann formulas with different temperatures.     

A coarse-grain three-site-per-nucleotide model for DNA with explicit ions

The "three sites per nucleotide" (3SPN) model provides a coarse-grained representation of nucleic acids for simulation of molecular processes. Previously, this model has relied on an implicit representation of the surrounding ionic environment at the level of Debye-Hu?ckel theory. In this work, we eliminate this limitation and present an explicit representation of ions, both monovalent and divalent. The coarse-grain ion-ion and ion-phosphate potential energy functions are inferred from all-atom simulations and parameterized to reproduce key features of the local structure and organization of ions in bulk water and in the presence of DNA. The resulting model, 3SPN.1-I, is capable of reproducing the local structure observed in detailed atomistic simulations, as well as the experimental melting temperature of DNA for a range of DNA oligonucleotide lengths, CG-content, Na(+) concentration, and Mg(2+) concentration.     

Frontier orbital and density functional study of the variation of the hard–soft behavior of monoborane (BH3) and boron trifluoride (BF3) as a function of angles of reorganization from planar (D3h) to pyramidal (C3v) shape

In chemical response the BH₃ and BF₃ molecules undergo the physical process of planar (D_3h) to pyramidal (C_3v) reorganization in shape as the condition precedent to the event of chemical reaction under the requirement of symmetry. A frontier orbital and density functional study of the variation of the stability of electronic structures and chemical reactivity of associated with the physical process of D_3h to C_3v geometry reorganization has been performed. The theoretical parameters viz. eigenvalues of HOMO and LUMO, the HOMO and LUMO energy gap, the global hardness and global softness, the chemical potential, the condensed Fukui function, and local softness of B atom, the reaction site, have been computed over a wide range of ∠XBX angles. The nature of variation in the intrinsic chemical reactivity, global and local, of the molecules associated with their geometry reorganization during the chemical event of charge transfer interaction involving their frontier molecular orbitals has been quantitatively explored. The hardness profiles as a function of reaction coordinates are consistent with the principle of maximum hardness (PMH). Results demonstrate that the hardness and softness are not a static and invariable property of molecules but a dynamic and variable function of molecular structure. The hardness parameters and the HOMO–LUMO gap of the molecules are so modified with the distortion of molecular geometry that, after a certain stage of molecular deformation, the profiles of such parameters of the molecules intersect and cross each other, signifying that the relative order of the intrinsic hardness of their equilibrium geometry is reversed. The intrinsically hard molecule BF₃ becomes softer than the intrinsically soft molecule BH₃ as a consequence of structural distortion. The increase in chemical reactivity computed in terms of density functional parameters are transparent and justified in terms of the profiles of the eigenvalues of the frontier orbitals. The profiles of chemical potential reveal the inherent difference in the tendency of backdonation from two molecules. The computed values of Fukui functions and local softness parameters of the B atom site demonstrate that the concept of local softness can be exploited for a theoretical analysis and understanding of the characteristic chemical events of the molecules under consideration. The profiles of the Fukui functions and local softness parameters of the two molecules seem to reflect and reveal their intrinsic difference in the tendency of receiving donation in the LUMO (electrophilicity) and that of backdonation from the HOMO (nucleophilicity) and the inherent difference of overall reactivity of the two molecules by a simultaneous operation of two opposing processes of charge transfer. © 2003 Wiley Periodicals, Inc. Int J Quantum Chem, 2003     

An off-lattice, self-learning kinetic Monte Carlo method using local environments

We present a method called local environment kinetic Monte Carlo (LE-KMC) method for efficiently performing off-lattice, self-learning kinetic Monte Carlo (KMC) simulations of activated processes in material systems. Like other off-lattice KMC schemes, new atomic processes can be found on-the-fly in LE-KMC. However, a unique feature of LE-KMC is that as long as the assumption that all processes and rates depend only on the local environment is satisfied, LE-KMC provides a general algorithm for (i) unambiguously describing a process in terms of its local atomic environments, (ii) storing new processes and environments in a catalog for later use with standard KMC, and (iii) updating the system based on the local information once a process has been selected for a KMC move. Search, classification, storage and retrieval steps needed while employing local environments and processes in the LE-KMC method are discussed. The advantages and computational cost of LE-KMC are discussed. We assess the performance of the LE-KMC algorithm by considering test systems involving diffusion in a submonolayer Ag and Ag-Cu alloy films on Ag(001) surface.     

Effect of double bonds on the conducting properties of ciguatoxin 3C and tetrahydropyrane-based polymers: a theoretical study

The electronic structure of the ciguatoxin 3C is analyzed through the Kohn-Sham model by using two different kinds of basis sets: localized basis set (Gaussian functions) and nonlocalized basis set (plane wave functions). With the localized basis functions, two approximations are used for the exchange-correlation functional: the local density approximation and the generalized gradient approximation. With the nonlocalized basis set, just the local density approximation is used. The energy gap, obtained from the frontier molecular orbitals, for this molecule predicts that this system is a semiconductor, even when the number of double bonds is increased inside the structure. However, as large molecules built with the basic unit--the tetrahydropyrane--of the ciguatoxin 3C are found in nature, it suggests studying the gap in polymeric systems built with the basic unit of this molecule. It is demonstrated that the presence of double bonds reduces considerably the gap, indicating the possibility of forming conducting materials by introducing double bonds in this kind of molecular systems. Thus, molecules strongly linked with biological systems can be used as precursor to build electric conducting systems.     

Molecular dynamics simulations of local field factors

In the present work, the authors evaluate a scheme based on molecular dynamics to derive local field factors. These are given without any assumption of a cavity by fitting the Langevin functions to the order parameters obtained from the molecular dynamics simulations. The local field factors so obtained, with the detailed chromophore-solvent interactions and solvent structures taken into account, are much smaller than those calculated from the conventional Onsager and Lorentz models. A numerical demonstration is given for two typical organic chromophore molecules, p-nitroaniline and p-nitro-N,N-dimethylaniline dissolved in chloroform.     

两个典型氧桥三核铁(Ⅲ)配合物[Fe3O(O2CCH2OC6H5)6(3H2O)]和[Fe3O(TIEO)2(O2CPh)2Cl3]的局域自旋和磁性质的理论探讨

用从头算波函数(UHF或UDFT波函数)代替ZILSH方法中的半经验波函数得到了ABLSH方法，接着用该方法研究了两个典型氧桥三核铁(Ⅲ)配合物[Fe₃O(O₂CCH₂OC₆H₅)₆(3H₂O)]和[Fe₃O(TIEO)₂(O₂CPh)₂Cl₃]的局域自旋和磁性质。通过计算得到的局域自旋结果和前人的具有可比性，同时所得的磁交换耦合常数和实验值很吻合。该方法可作为研究海森堡型磁性系统(HM)的新工具。     

Microstructure of neat alcohols: a molecular dynamics study

Neat methanol and tert-butanol are studied by molecular dynamics with the focus on the microstructure of these two alcohols. The site-site radial distribution functions, the corresponding structure factors, and an effective local one-body density function are shown to be the appropriate statistical quantities that point in a complementary manner towards the same microstructure for any given liquid. Methanol is found to be a weakly associated liquid forming various chainlike patterns (open and closed) while tert-butanol is almost entirely associated and forms micellelike primary pattern. The presence of stable local microheterogeneity within homogeneous disordered phase appears as a striking feature of these liquids. The absence of any such apparent clustering in water--a stronger hydrogen bonding liquid--through the same two statistical quantities is analyzed.     

Local density augmentation and dynamic properties of hydrogen-and non-hydrogen-bonded supercritical fluids: a molecular dynamics study

The local density inhomogeneities in neat supercritical fluids were investigated via canonical molecular dynamics simulations. The selected systems under investigation were the polar and hydrogen-bonded fluid methanol as well as the quadrupolar non-hydrogen-bonded carbon dioxide one. Effective local densities, local density augmentation, and enhancement factors were calculated at state points along an isotherm close to the critical temperature of each system (T(r)=1.03). The results obtained reveal strong influence of the polarity and hydrogen bonding upon the intensity of the local density augmentation. It is found that this effect is sufficiently larger in the case of the polar and associated methanol in comparison to those predicted for carbon dioxide. For both fluids the local density augmentation values are maximized in the bulk density region near 0.7rho(c), a result that is in agreement with experiment. In addition, the local density dynamics of each fluid were investigated in terms of the appropriate time correlation functions. The behavior of these functions reveals that the bulk density dependence of the local density reorganization times is very sensitive to the specific intermolecular interactions and to the size of the local region. Also, the estimated local density reorganization time as a function of bulk density of each fluid was further analyzed and successfully related to two different time-scale relaxation mechanisms. Finally, the results obtained indicate a possible relationship between the single-molecule reorientational dynamics and the local density reorganization ones.     

局域平衡假设和反应-扩散过程

局域平衡假设作为不可逆过程热力学理论的基础通常被认为适用于一般条件下的物理化学过程。本文从玻耳兹曼方程和涨落的随机理论出发重新研究了局域平衡假设对反应—扩散过程的适用性。表明对于涉及非线性化学动力学的反应—扩散过程, 从随机理论得到的结果和局域平衡假设是不一致的。     

Stationary phase analysis of inelastic atomic collisions: Penning ionization

Analytica semi-classical expressions, based on a stationary phase analysis, are presented for the energy distribution of particles ejected in inelastic processes. The tabulation of basic functions yields a considerable savings of computer time. Numerical comparisons with quantal calculations are made for the Penning ionization process involving metastable helium and atomic hydrogen, using two different potentials proposed for the He*H(²Σ) state.