Molecular modeling of polymers: I. Correct and efficient enumeration of intrachain conformational energetics

Polymer conformational analyses can require being able to model the intramolecular energetics of a very long (infinite) chain employing calculations carried out on a relatively short chain sequence. A method to meet this need, based upon symmetry considerations and molecular mechanics energetics, has been developed. Given N equivalent degrees of freedom in a linear polymer chain, N unique molecular groups are determined within the chain. A molecular unit is defined as a group of atoms containing backbone rotational degrees of conformational freedom on each of its ends. The interaction of these N molecular groups, each with a finite number of nearest neighbors, properly describe the intramolecular energetics of a long (infinite) polymer chain. Thus, conformational energetics arising from arbitrarily distant neighbor interactions can be included in the estimation of statistical and thermodynamic properties of a linear polymeric system. This approach is called the polymer reduced interaction matrix method (PRIMM) and the results of applying it to isotactic polystyrene (I-PS) are presented by way of example.     

The electronic structures of polymeric beryllium hydride and polymeric boron hydride

The band structure of linear polymeric beryllium hydride is here calculated by anab initio technique. The doubly-degenerate valence band has symmetry and is composed of a berylliump orbital and an antisymmetric combination of the appropriate hydrogen 1s orbitals. The Koopmans' ionization potential is calculated to be 16.1 eV and the direct band gap, found atX, is 15.2 eV. The charge distribution shows an electron drift of approximately 0.15 electrons from beryllium to the hydrogen atoms. The total energy calculation indicates that polymeric beryllium hydride is more stable than the monomer while polymeric boron hydride is less stable than the monomeric species. From the polymeric boron hydride system, an alternating-bond model is more stable than a symmetric bond model. The energy band structures of both models reveal that electron delocalization along the polymer chain is weak.     

Three multinuclear Co(II), Zn(II) and Cd(II) complexes based on a single-armed salamo-type bisoxime: syntheses,structural characterizations and fluorescent properties

Three multinuclear complexes, [Co(L)(OAc)Co(CH₃CH₂OH)₂]·H₂O, [Zn(L)(OAc)Zn(CH₃OH)], and [{Cd(L)(OAc)Cd(CH₃OH)}₂], containing a single-armed salamo-type bisoxime H₃L have been synthesized and characterized structurally. The Co(II) complex forms a dimeric unit by intermolecular hydrogen bond interactions of neighboring dimeric molecules. The Zn(II) complex also forms a dimeric unit by intermolecular hydrogen bond interactions. Interesting features of the crystal structure include O?O short contacts. Meanwhile, self-assembling infinite 1-D, 2-D, and 3-D supramolecular structures are formed by intermolecular hydrogen bond and C–H?π interactions. The Cd(II) complex forms an infinite 2-D supramolecular structure by intermolecular hydrogen bond interactions. The photophysical properties of the Co(II), Zn(II), and Cd(II) complexes have also been discussed.     

Thermodynamics of the interaction of liquid-crystalline polypropyleneimine dendrimer with low-molecular-weight compounds studied by reversed-phase gas chromatography

The thermodynamic functions of dissolution of n-alkanes (C₇–C₉) and n-alkanols (C₅–C₈) in the liquid-crystalline and isotropic phases of polypropyleneimine dendrimer of the first generation at infinite dilution were determined by the reversed-phase gas chromatography. The dependences of the thermodynamic parameters of sorbates on the phase state of the dendrite solvent, hydrocarbon chain length, and polarity of low-molecular-weight components of mesogenic—nonmesogenic binary systems were considered. The role of dispersion forces and specific intermolecular interactions in the solutions under study was estimated. Saturated hydrocarbons are more compatible with columnar phases of the dendrimer than alcohols.     

Thermolytic behavior of polydienyllithium and polystyryllithium

UV absorption spectra of thermolyzed polybutadienyl- and polyisoprenyl-lithium reveal a chromophore group previously not recognized for such systems; its absorption band at 271 nm has been assigned to a structure with three conjugated double bonds. A two-step mechanism for the formation of this trienic structure is proposed: an intermolecular metallation of associated living ends is followed by lithium hydride (LiH) elimination. Along thermolysis the presence of a dienic structure was also recognized, the latter arising from intramolecular elimination of LiH. The trienyllithium structure is also considered to be an effective species for the observed molecular weight distribution (MWD) variations. The observed different extent of high molecular weight (HMW) for polyisoprenyl- and polybutadienyl-lithium is explained on the basis of a different stability of the intermediates present along the proposed reaction mechanism. The thermolytic behavior of polystyryllithium does not provide any significant change in MWD: the disappearance of the living chain ends, UV detected, is due to an intramolecular LiH elimination which obeys first-order kinetics. The influence of temperature and of the tetrahydrofuran (THF) level on kinetic rate constants was investigated. © 1996 John Wiley & Sons, Inc.     

Polymorphism of methyl 4‐amino‐3‐phenylisothiazole‐5‐carboxylate: an experimental and theoretical study

Being a close analogue of amflutizole, methyl 4‐amino‐3‐phenylisothiazole‐5‐carboxylate (C₁₁H₁₀N₂O₂S) was assumed to be capable of forming polymorphic structures. Noncentrosymmetric and centrosymmetric polymorphs have been obtained by crystallization from a series of more volatile solvents and from denser tetrachloromethane, respectively. Identical conformations of the molecule are found in both structures. The two polymorphs differ mainly in the intermolecular interactions formed by the amino group and in the type of stacking interactions between the π‐systems. The most effective method for revealing packing motifs in structures with intermolecular interactions of different types (hydrogen bonding, stacking, dispersion, etc.) is to study the pairwise interaction energies using quantum chemical calculations. Molecules form a column as the primary basic structural motif due to stacking interactions in both polymorphic structures under study. The character of a column (straight or zigzag) is determined by the orientations of the stacked molecules (in a `head‐to‐head' or `head‐to‐tail' manner). Columns bound by intermolecular N—H…O and N—H…N hydrogen bonds form a double column as the main structural motif in the noncentrosymmetric structure. Double columns in the noncentrosymmetric structure and columns in the centrosymmetric structure interact strongly within the ab crystallographic plane, forming a layer as a secondary basic structural motif. The noncentrosymmetric structure has a lower density and a lower (by 0.59 kJ mol^?1) lattice energy, calculated using periodic calculations, compared to the centrosymmetric structure.     

Chain direction elastic modulus of PE crystal and interlamellar force constant of n-alkane crystals from RAMAN measurements

Spectroscopic data can deliver force constants only if the exact chain conformation is known. For the longitudinal acoustic modes (LAM), however, simple linear chain models can be used to yield the effective longitudinal chain modulus from spectroscopic data of oligomer crystals. The model of p-coupled linear chain molecules with N masses and only nearest neighbor interactions was used to investigate the longitudinal acoustic modes with s nodes. The frequencies plotted versus s/N fall onto different branches for different s. The intermolecular coupling and the heavier endmasses shift the LAM branches to higher and lower frequencies, respectively. There exists a value x₀ depending on the masses and force constants, where the branches cut the dispersion curve of the infinite molecule. For s/N ≥ x₀ the effect of endmasses dominates. Low-frequency RAMAN spectra of n-alkanes (N = 20, …, 40 C atoms) were recorded and analyzed. The LAM1 branch runs clearly above a smooth fit through all other LAM data and the origin. This fit approximates to first order the dispersion curve of the infinite PE molecule in an ideal crystal. Its curvature exceeds that of the dispersion curve of the simple linear chain, but is somewhat smaller than that of the dispersion curve of the planar zig-zag chain with rigid bonds. The slope at the origin yields the limiting elastic modulus E_c = 315 GPa in chain direction of crystalline polyethylene. From our measurements on n-alkanes we obtained the frequency shift of LAM1 due to the interlayer coupling and the heavier endmasses. Calculation of the intermolecular coupling constant of the model of a long row of linear chain molecules with the same frequency shift yield the mean value f_l = 2.5 N/m. This value decreases with increasing chain length. The relevance and applicability of the model is discussed. © 1997 John Wiley & Sons, Inc.     

Ultrasonic investigation of effective Debye temperature in multi-component liquid systems at 298.15 K

Assuming the quasi-crystalline model for the multi-component liquid systems, the effective Debye temperature has been investigated from the density and sound velocity measurements of three ternary and three quaternary liquid systems containing n-alkanes over the entire range of mole fractions at 298.15?K. The results obtained have been interpreted in terms of intermolecular interactions and modifications of the internal structure of the mixtures.     

Effects of hydrophobic and dipole-dipole interactions on the conformational transitions of a model polypeptide

We studied the effects of hydrophobicity and dipole-dipole interactions between the nearest-neighbor amide planes on the secondary structures of a model polypeptide by calculating the free energy differences between different peptide structures. The free energy calculations were performed with low computational costs using the accelerated Monte Carlo simulation (umbrella sampling) method, with a bias-potential method used earlier in our accelerated molecular dynamics simulations. It was found that the hydrophobic interaction enhances the stability of alpha helices at both low and high temperatures but stabilizes beta structures only at high temperatures at which alpha helices are not stable. The nearest-neighbor dipole-dipole interaction stabilizes beta structures under all conditions, especially in the low temperature region where alpha helices are the stable structures. Our results indicate clearly that the dipole-dipole interaction between the nearest neighboring amide planes plays an important role in determining the peptide structures. Current research provides a more unified and quantitative picture for understanding the effects of different forms of interactions on polypeptide structures. In addition, the present model can be extended to describe DNA/RNA, polymer, copolymer, and other chain systems.     

Numerical solution for the ground-state energy of the anisotropic Heisenberg model

An analysis of the anisotropic Heisenberg model is carried out by solving the Bethe ansatz solution of the model numerically as a function of the anisotropy parameter for finite N. A brief introduction to the limit of the infinite chain is presented. The energy for a few special limiting cases of the anisotropy parameter in the Hamiltonian are worked out. Numerical results for finite cycles as well as for the infinite chain are given. Comparison can then be made with the case of finite increasing N. © 1997 John Wiley & Sons, Inc.     

Red and blue shifted hydridic bonds

By performing MP2/aug‐cc‐pVTZ ab initio calculations for a large set of dimer systems possessing a R? H hydridic bond involved in diverse types of intermolecular interactions (dihydrogen bonds, hydride halogen bonds, hydride hydrogen bonds, and charge‐assisted hydride hydrogen bonds), we show that this is rather an elongation than a shortening that a hydride bond undergoes on interaction. Contrary to what might have been expected on the basis of studies in uniform electric field, this elongation is accompanied by a blue instead of red shift of the R? H stretching vibration frequency. We propose that the “additional” elongation of the R? H hydridic bond results from the significant charge outflow from the sigma bonding orbital of R? H that weakens this bond. The more standard red shift obtained for stronger complexes is explained by means of the Hermansson's formula and the particularly strong electric field produced by the H‐acceptor molecule. © 2014 Wiley Periodicals, Inc.     

Nano‐scaled intrachain ordering and dynamics in two‐dimensional orientational polymer domains1)

Statistical and local relaxation properties of two‐dimensional finite polymer systems (domains) are considered. The domains consist of a large number of semirigid chains with the finite contour length at free, half‐free and fixed boundary conditions for chain ends. The intermolecular orientational order at short distances between chains in the thick domains is similar to the order in infinite two‐dimensional systems. The correlations of orientation between sufficiently distant elements of different chains decay by the exponential law, but the effective constant of interchain interactions in the domain is proportional to the molecular weight of the chain. At the given intra‐and interchain interactions an elongtation of the chains leads to a local ordering of chains in the domain (at free boundary conditions) or, on the contrary, to the decreasing of the parameter of short‐range orientational order (at fixed and half‐free boundary conditions). Independently of type of boundary conditions the parameter of large‐range orientational order tends to zero with increasing of the chain contour length. Dynamical equations and relaxation spectrums for times of local motions are obtained. From time correlation functions of local relaxation the times of nano‐scaled mobility of chains were calculated in depending on the bending rigidity of chains, the parameter of interchain interactions, and the contour length of chains. At the given intra‐and interchain interactions an elongtation of chains forming the domain leads to to the slowing‐down of local mobility of chains in the domain. The comparison with experimental date obtained by dielectric relaxation and polarized luminescence methods on investigation of nano‐scaled mobility in the dilute melts of comb‐shaped polymers has been carried out.     

Role of ionic defects in photolysis of lithium hydride

Kinetic parameters of photoconductivity and dark conductivity of lithium hydride under uv irradiation have been investigated. A kinetic scheme of lithium hydride photolysis is suggested. Kinetic features of hydrogen evolution under uv irradiation of lithium hydride are explained. The contributions of radiation induced defects and equilibrium cation vacancies to processes leading to gas evolution under photolysis are determined.     

Adsorption behavior of repulsive molecules

Recently, it has been shown that adsorption of gases on solid surfaces often leads to repulsive forces between adsorbate molecules. In this paper, adsorption of molecules on a one-dimensional lattice is considered for repulsive interactions between adsorbate molecules. Exact adsorption isotherms are calculated and analyzed for finite and infinite chains of active sites (i.e., a one-dimensional lattice). Although the mathematical solution for the one-dimensional lattice is known for attractive and repulsive systems, the effects of intermolecular repulsions on adsorption behavior have not been studied in detail previously. Similarly, though the mathematics for the one-dimensional lattice has been solved for any arbitrary lattice length, the effect of finite size on adsorption isotherms for repulsive adsorbate interactions has never been examined. This paper shows that spatial confinement and strong attraction to active sites can cause compression of an adsorbed phase and that repulsive interactions between adsorbed molecules result in steps in the adsorption isotherms. For higher chemical potentials, the density increases until saturating at the lattice capacity. These steps in the adsorption isotherm have not been observed in previous studies of lattice systems. For small lattices, the adsorption behavior was found to be fundamentally different for even and odd values of lattice length. Lattices with an even number of lattice sites can have two steps in the adsorption isotherm, whereas systems with an odd number of sites only have a single step occurring at a coverage slightly greater than half the lattice capacity.     

Ensemble density functional theory for inhomogeneous fractional quantum hall systems

The fractional quantum Hall effect (FQHE) occurs at a certain magnetic field strengths B^*(n) in a two-dimensional electron gas of density n at strong magnetic fields perpendicular to the plane of the electron gas. At these magnetic fields strengths, the system is incompressible, i.e., there is a finite cost in energy for creating charge density fluctuations in the bulk, while the boundary of the electron gas has gapless modes of density waves. The bulk energy gap arises because of the strong electron-electron interactions. While there are very good models for infinite homogeneous systems and for the gapless excitations of the boundary of the electron gas, computational methods to accurately model finite, inhomogeneous systems with more than about 10 electrons have not been available until very recently. We will here review an ensemble density functional approach to studying the ground state of large inhomogeneous spin-polarized FQHE systems. © 1996 John Wiley & Sons, Inc.     

Alpha,beta-unsaturated ketoximes carrying a terminal pyridine or quinoline subunit as building blocks for supramolecular syntheses

[Structure: see text]. The crystal structures of a new series of alpha,beta-unsaturated ketoximes, 8-14, carrying the terminal 4-pyridinyl, 3-pyridinyl, or 4-quinolinyl subunit have been investigated by X-ray structural analysis. The dominating intermolecular interaction in all structures, except 11, is the head-tail OH...N hydrogen bond between the oxime moiety and the nitrogen atom of the heterocyclic unit. This intermolecular interaction generates infinite chains, which are cross-linked by CH...O/N/Cl or CH...pi interactions. Compound 10 has been shown to adopt a double-helical structure in the crystalline state. Compound 11 represents the only case where the unexpected head-head NOH...N(OH) hydrogen bonds determine the crystal packing. Both hydrogen-bonding and aromatic interactions stabilize the crystal structures of 8-14.     

Calculation of molecular crystals within the PCILOCC framework

Stabilization energies and equilibrium distances of one-dimensional (HF)_n and (H₂O)_n chains have been calculated by means of the PCILO method for finite chain length and by the PCILOCC method for infinite chain length. Both types of calculation are compared with corresponding CNDO /2-MO and CNDO /2-CO calculations. Further we have performed an analysis of the individual contributions of the stabilization energies per monomer of the PCILO and PCILOCC calculations. The results show that the PCILOCC method is well suited for the calculation of molecular associations with translational symmetry.     

The synthesis,crystal structures and SOD activities of a new ligand (Lse) and Co(Lse)2(SCN)2 complex [Lse = selenium ether bis‐(N‐1‐methyl‐ benzotriazole)]

A new ligand containing selenium, Se (CH₂‐N‐Btrzole)₂ (L^se) (Btrzole = benzotriazole) and its cobalt(II) complex, Co(L^se)₂(SCN)₂, have been synthesized and the molecular structures of the title compounds have been determined by X‐ray techniques. The L^se is a meso‐configuration with a symmetric plane through the Se center, the intermolecular weak interactions of Se? Se, Se? N and π? π stacking between benzotriazole rings to extend the molecular structure to two‐dimensional network configuration. In the Co(II) complex, the metal center is in a six‐coordinated octahedral environment. Two Co(II) atoms are linked by two ligands to form a 20‐membered macrocycle; the adjacent macrocycles are linked by coordinated bond of Co? N_bentrozole to extend an infinite double strained chain. The SOD activity of the ligand and Co(II) complex have been studied by using the pyrogallol autoxidation method; thermal properties and luminescent properties of Co(II) complex have been tested, and the details of those properties have been discussed. Copyright © 2007 John Wiley & Sons, Ltd.