Polymorphy in the stereostructure of periodic polymer backbones

We theoretically investigated the polymorphy of the stereostructures of a periodic polymer. Using the polymer's internal conformation parameters of bond lengths, bond angles, and internal rotation angles, we extended the mathematical treatment for designing polymer backbones. We considered those periodic polymers whose unit cell consists of one (m = 1), two (m = 2), or three (m = 3) kinds of atoms. Moreover, for these three types of polymers, we supposed two catenation types for the skeleton atoms; one is a “homorotatory” sequence and the other is a “heterorotatory” one. To specify the backbone's stereostructure, we introduced several conformation parameters such as the helical pitch number n, the translation distance d, and the inclination angle of the skeleton plane Θ. By combining these parameters, we can systematically understand the variety and the possible polymorphy in the stereostructure of a periodic polymer backbone. © 2003 Wiley Periodicals, Inc. J Polym Sci Part B: Polym Phys 41: 2829–2849, 2003     

Computer-assisted chemical structure analysis

The new generation of the CASE system described in this paper offers a promising approach to both spectrum interpretation and structure generation that allows for a natural linkage between them. The approach takes full advantage of the information contained in available spectral libraries, yet is not limited by the substructural deficiencies of these data bases.     

Cellulose structure and biosynthesis: What is in store for the 21st century?

This article briefly summarizes historical developments in fundamental research related to the structure and biosynthesis of cellulose. Major advances concerning the structure of cellulose include the discovery of a new suballomorph of cellulose I, the lattice imaging of glucan chains showing no fringe micelle structure, parallel chain orientation in cellulose I, and the discovery of nematic ordered cellulose. Major advances in biosynthesis include the discovery of the terminal synthesizing complex, the isolation and purification of cellulose synthase, the in vitro synthesis of cellulose I, and synthetic cellulose assembly. This article focuses on recent advances in molecular biology with cellulose, including the cloning and sequencing of cellulose synthase genes from bacteria, cyanobacteria, and vascular plants; proof of the terminal synthesizing complex as the site of the catalytic subunit of cellulose synthase; cellulose and callose synthase expression during growth and development; and phylogenetic aspects of cellulose synthase evolution. This article concludes with thoughts about future uses for the accumulating genetic information on cellulose biosynthesis for textiles and forest products and discusses possibilities of new global resources for cellulose production. © 2003 Wiley Periodicals, Inc. J Polym Sci Part A: Polym Chem 42: 487–495, 2004     

The route to the structure determination of amorphous solids: a case study of the ceramic Si(3)B(3)N(7)

Si(3)B(3)N(7) is the parent compound of a new class of amorphous ceramics containing silicon, boron, nitrogen, and carbon that display a unique spectrum of properties. It consists of a random network in which the constituent elements are linked by predominantly covalent bonds. Similarly to quartz glass, the composition of amorphous Si(3)B(3)N(7) is virtually stoichiometric. As all three of its constituent elements can serve as the objects of various structural probes, Si(3)B(3)N(7) was selected as the basis of a systematic structural investigation, in which methods for the structure determination of solids without translational symmetry could be validated and improved. However, as the complete amorphous structure cannot be deduced from experimental data, these results must be complemented by computer simulations. Thus, five classes of structure models were generated and compared to experimental results. Only the models generated by following the actual synthesis route as closely as possible agreed well with the experimental data.     

Quantitative characteristics of structure inhomogeneity of water

Inhomogeneity of the local surroundings of molecules was studied for water models obtained by the molecular dynamic method. For all 3456 molecules in an independent unit cell, the volume of the Voronoi polyhedron (VVP) constructed around the oxygen atom, the tetrahedricity index (T), and the potential energy of the molecule (E _pot) were calculated. Based on the values of these parameters, the molecules were grouped into two classes. The first class included molecules for which this parameter was smaller than a certain critical value; the second included molecules for which the parameter exceeded the critical value. The critical value was chosen (for each configuration) such that each class contained exactly 50% of all molecules. Then it was investigated how many molecules belonged to each of these classes among the four nearest neighbors of the given sort. Deviation from the value obtained for random distribution of molecules of two sorts can serve as a measure of structure inhomogeneity, which shows itself as the tendency of a molecule to be surrounded by alike molecules. Since approximately half of all molecules are donors (and acceptors) for two hydrogen bonds at room temperature (a ₂ d ₂ type of coordination), a similar procedure is applicable to types of coordination of molecules. Molecules with a ₂ d ₂ coordination can be assigned to one class, while all other molecules can be considered as belonging to the other. Inhomogeneity of structure is most conspicuous for distribution of molecules with low and high values of the VVP (this is especially true of the surroundings of molecules with small values of VVP). The environment of molecules with high values of E _pot and of molecules with surroundings other than a ₂ d ₂ is nearly random.     

Hydrogen bonding contribution to the water pair interaction potential: Effects on the model liquid structure

Empirical pair potentials of water that take into account the contribution of the OH nonelectrostatic interaction in the hydrogen bond are considered. The effects of this contribution on the radial distribution functions derived by computer simulation are analyzed. Model potentials have been obtained for which the height and position of the first and second peaks of the oxygen-oxygen radial distribution function are comparable with experimental data.Original Russian Text Copyright © 2004 by A. V. Borovkov, M. L. Antipova, V. E. Petrenko, and Yu. M. KesslerTranslated from Zhurnal Strukturnoi Khimii, Vol. 45, No. 4, pp. 678–682, July–August, 2004.Deceased.This revised version was published online in April 2005 with a corrected cover date.     

Cellulose nanomaterials review: structure, properties and nanocomposites

This critical review provides a processing-structure-property perspective on recent advances in cellulose nanoparticles and composites produced from them. It summarizes cellulose nanoparticles in terms of particle morphology, crystal structure, and properties. Also described are the self-assembly and rheological properties of cellulose nanoparticle suspensions. The methodology of composite processing and resulting properties are fully covered, with an emphasis on neat and high fraction cellulose composites. Additionally, advances in predictive modeling from molecular dynamic simulations of crystalline cellulose to the continuum modeling of composites made with such particles are reviewed (392 references).     

Quindolinocryptotackieine: the elucidation of a novel indoloquinoline alkaloid structure through the use of computer‐assisted structure elucidation and 2D NMR

Numerous indoloquinoline alkaloid structures have been identified from extracts of the West African plant Cryptolepis sanguinolenta. Recently, through the use of 2D NMR methods and cryogenic NMR probe technology in conjunction with computer‐assisted structure elucidation (CASE) methods, the structures of some chemical degradation products of this family of alkaloids have also been reported. We now report the characterization of a novel indoloquinoline dimeric alkaloid, quindolinocryptotackieine, through the extensive utilization of CASE methods. The NMR data presented here were collected over a decade earlier before the elucidation of the structure was possible, since manual analysis did not present a conclusive structure, whereas CASE produced a series of structures from which the structure could be verified. The original mass spectrometric (MS) data collected for the sample were problematic. Contemporary MS data were instead recollected from remaining small quantities of this alkaloid using modern instrumentation. The re‐collected data gave a usable molecular ion and several key fragment ions that were diagnostically useful. Copyright © 2003 John Wiley & Sons, Ltd.     

RMC_POT: A computer code for reverse monte carlo modeling the structure of disordered systems containing molecules of arbitrary complexity

An approach has been devised and tested for preserving the molecular dynamics molecular geometry taking into account energetic considerations during Reverse Monte Carlo (RMC) modeling. Instead of the commonly used fixed neighbor constraints, where molecules are held together by constraining distance ranges available for the specified atom pairs, here molecules are kept together via bond, angle, and dihedral potential energies. The scaled total potential energy contributes to the measure of the goodness‐of‐fit, thus, the atoms can be prevented from drifting apart. In some of the calculations (Lennard‐Jones and Coulombic) nonbonding potentials were also applied. The algorithm was successfully tested for the X‐ray structure factor‐based structure study of liquid dimethyl trisulfide, for which material now significantly more sensible results have been obtained than during previous attempts via any earlier version of RMC modeling. It is envisaged that structural modeling of a large class of materials, primarily liquids and amorphous solids containing molecules of up to about 100 atoms, will make use of the new code in the near future. © 2012 Wiley Periodicals, Inc.     

Protein dynamics from NMR: the slowly relaxing local structure analysis compared with model-free analysis

(15)N-(1)H spin relaxation is a powerful method for deriving information on protein dynamics. The traditional method of data analysis is model-free (MF), where the global and local N-H motions are independent and the local geometry is simplified. The common MF analysis consists of fitting single-field data. The results are typically field-dependent, and multifield data cannot be fit with standard fitting schemes. Cases where known functional dynamics has not been detected by MF were identified by us and others. Recently we applied to spin relaxation in proteins the slowly relaxing local structure (SRLS) approach, which accounts rigorously for mode mixing and general features of local geometry. SRLS was shown to yield MF in appropriate asymptotic limits. We found that the experimental spectral density corresponds quite well to the SRLS spectral density. The MF formulas are often used outside of their validity ranges, allowing small data sets to be force-fitted with good statistics but inaccurate best-fit parameters. This paper focuses on the mechanism of force-fitting and its implications. It is shown that MF analysis force-fits the experimental data because mode mixing, the rhombic symmetry of the local ordering and general features of local geometry are not accounted for. Combined multifield multitemperature data analyzed with the MF approach may lead to the detection of incorrect phenomena, and conformational entropy derived from MF order parameters may be highly inaccurate. On the other hand, fitting to more appropriate models can yield consistent physically insightful information. This requires that the complexity of the theoretical spectral densities matches the integrity of the experimental data. As shown herein, the SRLS spectral densities comply with this requirement.     

Carboxymethylation of Bacterial Cellulose

The carboxymethylation of bacterial cellulose (BC) was studied under typical heterogeneous reaction conditions. It was found that the BC possesses a significantly lower reactivity compared to wood cellulose converted under comparable conditions. Moreover, water-solubility of carboxymethyl cellulose (CMC) obtained from BC appears at rather high degree of substitution of about 1.5 although a nearly statistical functionalization pattern was analyzed by HPLC. Obviously, the nano-structure of BC is important for the reactivity and the properties of the synthesized CMC like water-solubility.     

Recent advances in the structure elucidation of small organic molecules by the LSD software

The LSD software proposes the structures of small organic molecules that fit with structural constraints from 1D and 2D NMR spectroscopy. Its initial design introduced limits that needed to be eliminated to extend its scope and help its users choose the most likely structure among those proposed. The LSD software code has been improved, so that it recognizes a wider set of atom types to build molecules. More flexibility has been given in the interpretation of 2D NMR data, including the automatic detection of very long‐range correlations. A program named pyLSD was written to deal with problems in which atom types are ambiguously defined. It also provides a ¹³C NMR chemical shift‐based solution ranking algorithm. PyLSD was able to propose the correct structure of hexacyclinol, a natural product whose structure determination has been highly controversal. The solution was ranked first within a list of ten structures that were produced by pyLSD from the literature NMR data. The structure of an aporphin natural product was determined by pyLSD, taking advantage of the possibility of handling electrically charged atoms. The structure generation of the insect antifeedant azadirachtin by LSD was reinvestigated by pyLSD, considering that three ¹³C resonances did not lead to univocal hybridization states. Copyright © 2013 John Wiley & Sons, Ltd.     

Zori 1.0: a parallel quantum Monte Carlo electronic structure package

The Zori 1.0 package for electronic structure computations is described. Zori performs variational and diffusion Monte Carlo computations as well as correlated wave function optimization. This article presents an overview of the implemented methods and code capabilities.     

Motion of compliant capsules on corrugated surfaces: A means of sorting by mechanical properties

We discuss a novel method for capturing the dynamic coupling between a fluid and an elastic solid, the so-called fluid–structure interaction. This method integrates a lattice Boltzmann model to capture the fluid dynamics with a lattice spring model to capture the micromechanics of the solid phase. We then examine the fluid-driven motion of microcapsules, which are modeled as fluid-filled, elastic shells, along a corrugated substrate. We show that the ability of the capsules to navigate along the surface depends critically on capsule's elastic modulus. In particular, we illustrate how this substrate can be utilized to design a device for sorting microcapsules by their mechanical properties. These results apply not only to polymeric microcapsules, but also describe the interaction between the substrate and certain biological cells (e.g., leukocytes and other cells with cytoskeletons). Hence, by isolating species of a certain stiffness, the device could be highly useful for applications in biotechnology and tissue engineering or in the quality control of fabricated microcapsules. © 2006 Wiley Periodicals, Inc. J Polym Sci Part B: Polym Phys 44: 2667–2678, 2006     

On the molecular structure of the phytochrome chromophore: X-ray analysis of two 2,3-dihydrobilatriene-abc derivatives

The molecular and crystal structures of the two 2,3-dihydrobilatrienes-abc1 and2, representing model compounds for the phytochrome chromophore, were determined by X-ray crystallography at 97 K. Crystals of the racemate1 contain disordered regions. Both molecules are found to be ofall-(Z) configuration, assuming a helical conformation. The acidic hydrogen atoms are localized at the nitrogen atoms of rings A, C and D. A summary of the geometries of unsaturated five-membered rings as observed in four accurate low-temperature crystal structures of bilatrienes-abc is given.Herrn Prof.Josef Schurz zum 60. Geburtstag gewidmet.     

On the icosahedral quasicrystal structure

The icosahedral quasicrystal structure is derived with local symmetry operations. Calculated Fourier transforms are compared with electron diffraction patterns. It is proposed that the structure building operations are models for the crystal growing process.     

Stereospecific assignments of protein NMR resonances based on the tertiary structure and 2D/3D NOE data

In many cases of protein structure determination by NMR a high-quality structure is required. An important contribution to structural precision is stereospecific assignment of magnetically nonequivalent prochiral methylene and methyl groups, eliminating the need for introducing pseudoatoms and pseudoatom corrections in distance restraint lists. Here, we introduce the stereospecific assignment program that uses the resonance assignment, a preliminary 3D structure and 2D and/or 3D nuclear Overhauser effect spectroscopy peak lists for stereospecific assignment. For each prochiral group the algorithm automatically calculates a score for the two different stereospecific assignment possibilities, taking into account the presence and intensity of the nuclear Overhauser effect (NOE) peaks that are expected from the local environment of each prochiral group (i.e., the close neighbors). The performance of the algorithm has been tested and used on NMR data of alpha-helical and beta-sheet proteins using homology models and/or X-ray structures. The program produced no erroneous stereospecific assignments provided the NOEs were carefully picked and the 3D model was sufficiently accurate. The set of NOE distance restraints produced by nmr2st using the results of the SSA module was superior in generating good-quality ensembles of NMR structures (low deviations from upper limits in conjunction with low root-mean-square-deviation values) in the first round of structure calculations. The program uses a novel approach that employs the entire 3D structure of the protein to obtain stereospecific assignment; it can be used to speed up the NMR structure refinement and to increase the quality of the final NMR ensemble even when no scalar or residual dipolar coupling information is available.     

Methyl dynamics in proteins from NMR slowly relaxing local structure spin relaxation analysis: A new perspective

NMR spin relaxation of (2)H nuclei in (13)CH(2)D groups is a powerful method for studying side-chain motion in proteins. The analysis is typically carried out with the original model-free (MF) approach adapted to methyl dynamics. The latter is described in terms of axial local motions around, and of, the methyl averaging axis, mutually decoupled and independent of the global motion of the protein. Methyl motion is characterized primarily by the axial squared order parameter, S(axis)2, associated with fluctuations of the methyl averaging axis. This view is shown to be oversimplified by applying to typical experimental data the slowly relaxing local structure (SRLS) approach of Polimeno and Freed (Adv. Chem. Phys. 1993, 83, 89) which can be considered the generalization of the MF approach. Neglecting mode coupling and the asymmetry of the local ordering and treating approximately features of local geometry imply inaccurate values of S(axis)2, hence of the residual configurational entropy derived from it. S(axis)2, interpreted as amplitude of motion, was found to range from near disorder to almost complete order. Contrary to this picture, we find with the SRLS approach a moderate distribution in the magnitude of asymmetric local ordering and significant variation in its symmetry. The latter important property can be associated implicitly with the contribution of side-chain rotamer jumps. This is consistent with experimental residual dipolar coupling studies and theoretical work based on molecular dynamics simulations and molecular mechanics considerations. Configurational entropy is obtained in the SRLS approach directly from experimentally determined asymmetric potentials. Inconsistency between order parameters from 2H relaxation and from eta(HC-HH) cross-correlation and increase in order parameters with increasing temperature were observed with the MF approach. These discrepancies are reconciled, and physically tenable temperature dependence is obtained with the SRLS approach.