Interactions between lignin and urea researched by molecular simulation

Molecular simulations of interactions between urea molecules and lignin polymer have been carried out with the aim of understanding the mechanism of urea slow-release behaviours in lignin–urea materials. It has been found, by docking technology and natural bond orbital analysis, that H-bonds and π-electronic conjugation effect are the main driving forces to keep urea molecules adsorbed on the lignin. In the NPT (isothermal–isobaric ensemble) simulations, mean-squared displacement results show that water molecules can promote the urea molecules gradually away from the lignin. Furthermore, in NVT (canonical ensemble) molecular dynamic simulations, results on diffusion constants of urea molecules in lignin–urea system show that diffusion constant of urea molecules in a urea–water–lignin system increases with an increase in the water content. Conclusions gained from two different kinds of simulation are in agreement with each other and are consistent with the experimental observations.     

3D-QSAR studies of substituted 1-(3, 3-diphenylpropyl)-piperidinyl amides and ureas as CCR5 receptor antagonists

3D-QSAR studies on the derivatives of 1-(3,3-diphenylpropyl)-piperidinyl amide and urea as CCR5 receptor antagonists were performed by comparative molecular field analysis (CoMFA) and comparative molecular similarity indices (CoMSIA) methods to rationalize the structural requirements responsible for the inhibitory activity of these compounds. The global minimum energy conformer of the template molecule, the most active and pharmacokinetically stable molecule of the series, was obtained by systematic search and used to build structures of the molecules in the dataset. The best predictions for the CCR5-receptor were obtained with the CoMFA standard model (q ² = 0.787, r ² = 0.962) and CoMSIA model combined steric, electrostatic and hydrophobic fields (q ² = 0.809, r ² = 0.951). The predictive ability of CoMFA and CoMSIA were determined using a test set of 12 compounds giving predictive correlation coefficients of 0.855 and 0.83, respectively, indicating good predictive power. Further, the robustness of the model was verified by bootstrapping analysis. The contour maps produced by the CoMFA and CoMSIA models were used to identify the structural features relevant to the biological activity in this series. Based on the CoMFA and CoMSIA analysis, we have identified some key features in the series that are responsible for CCR5 antagonistic activity which may be used to design more potent 1-(3,3-diphenylpropyl)-piperidinyl derivatives and predict their activity prior to synthesis. Electronic supplementary material The online version of this article (doi:) contains supplementary material, which is available to authorized users.     

A comparative study of one- and two-photon absorption properties of pyrene and perylene diimide derivatives

Two important classes of organic molecules, perylene diimide (PDI) and pyrene derivatives have been found to possess relatively excellent photophysical and photochemical properties and especially high two-photon absorption cross sections (δ ^T _max). Herein, one-photon absorption (OPA) and two-photon absorption (TPA) properties of some novel PDI and pyrene derivatives were comparatively investigated by the density functional theory (DFT) and Zerner’s intermediate neglect of differential overlap (ZINDO) methods. The calculated results indicate that with respect to PDI derivatives, the maximum TPA cross-sections for pyrene compounds increase obviously, the maximum peaks of OPA and TPA spectra are blue-shifted, the ΔE _H-L (energy gaps between the highest occupied orbital and the lowest unoccupied orbital) increase. The different π-conjugated bridges (fluorene and pyrene) and terminal groups have slight effect on the OPA properties. Nevertheless, the molecules bearing 1,6-disubstituted pyrene as the π-conjugated bridge display the largest δ ^T _max in both series of compounds 3 and 4. Moreover, the δ ^T _max values of molecules with benzothiazole-substituted terminal groups are larger than those of the molecules with diphenylamine, which is attributed to benzothiazole groups stabilizing the planarity of the branch parts, extending the conjugated length and increasing the π-electron delocalized extent. Furthermore, the molecular size has marked effect on OPA and TPA properties. It is worthy to mention that cruciform 8 displays the largest δ ^T _max among all the studied molecules in the range of 600–1100 nm. This research could provide a better understanding for the origin of the linear and nonlinear optical properties, and it would be helpful to gain more information about designing two-photon absorption materials with large δ ^T _max.     

Nitroborazines as potential high energy materials: density functional theoretical calculations

As part of a search for new high energy density materials, we used density functional theoretical calculations to determine the thermochemical properties of various nitro-substituted borazine molecules. Optimized geometries, vibrational frequencies and spectra, and enthalpies of formation and combustion were determined for nitroborazine, dinitroborazine, trinitroborazine, and methyltrinitroborazine with substituents on either the boron atoms or the nitrogen atoms of the parent borazine ring. Our results indicate that the specific enthalpy of combustion ranged from 4 to 11 kJ g⁻¹, with increasing substitution of nitro groups lowering the energy of combustion per unit mass.     

Liquid Norbornadiene Photoswitches for Solar Energy Storage

Due to high global energy demands, there is a great need for development of technologies for exploiting and storing solar energy. Closed cycle systems for storage of solar energy have been suggested, based on absorption of photons in photoresponsive molecules, followed by on‐demand release of thermal energy. These materials are called solar thermal fuels (STFs) or molecular solar thermal (MOST) energy storage systems. To achieve high energy densities, ideal MOST systems are required either in solid or liquid forms. In the case of the latter, neat high performing liquid materials have not been demonstrated to date. Here is presented a set of neat liquid norbornadiene derivatives for MOST applications and their characterization in toluene solutions and neat samples. Their synthesis is in most cases based on solvent‐free Diels‐Alder reactions, which easily and efficiently afford a range of compounds. The shear viscosity of the obtained molecules is close to that of colza oil, and they can absorb up to 10% of the solar spectrum with a measured energy storage density of up to 577 kJ/kg corresponding to 152 kJ mol^–1 (calculated 100 kJ mol^–1). These findings pave the way towards implementation of liquid norbornadienes in closed cycle energy storage technologies.     

Thermodynamics of binding water and solute to myosin

From the isopiestic measurements of the extents of adsorption of water vapour by fish myosin at various values of water activities at three different temperatures, the changes in free energy, enthalpy and entropy of dehydration of the protein have been calculated. Extents of excess binding of solvent and solute to myosin have also been determined from isopiestic experiments in the presence of different inorganic salts, sucrose and urea respectively. Mols of water and solute respectively bound in absolute amounts to myosin have been evaluated from these data in limited range of solute concentrations. Free energy changes at different concentrations of these solutes have also been evaluated and their relations with ‘salting-in’ and ‘salting-out’ phenomena have been discussed. The order of the values of the standard free energy change for excess binding calculated with respect to an unified thermodynamic scale are found to be consistent with relative reactivity of binding water to myosin in the presence of inorganic salts, sucrose and urea. Part of this work was presented at the 20th Annual Convention of Chemists of the Indian Chemical Society, Cuttack, 26th-30th December 1983.     

pH-dependent urea-induced unfolding of stem bromelain: Unusual stability against urea at neutral pH

Equilibrium unfolding of stem bromelain (SB) with urea as a denaturant has been monitored as a function of pH using circular dichroism and fluorescence emission spectroscopy. Urea-induced denaturation studies at pH 4.5 showed that SB unfolds through a two-state mechanism and yields ΔG (free energy difference between the fully folded and unfolded forms) of ∼5.0 kcal/mol and C _m (midpoint of the unfolding transition) of ∼6.5 M at 25°C. Very high concentration of urea (9.5 M) provides unusual stability to the protein with no more structural loss and transition to a completely unfolded state.     

Water and solute permeability of rat lung caveolae: high permeabilities explained by acyl chain unsaturation

Caveolae are invaginated membrane structures with high levels of cholesterol, sphingomyelin, and caveolin protein that are predicted to exist as liquid-ordered domains with low water permeability. We isolated a caveolae-enriched membrane fraction without detergents from rat lung and characterized its permeability properties to nonelectrolytes and protons. Membrane permeability to water was 2.85 ± 0.41 x 10^–3 cm/s, a value 5–10 times higher than expected based on comparisons with other cholesterol and sphingolipid-enriched membranes. Permeabilities to urea, ammonia, and protons were measured and found to be moderately high for urea and ammonia at 8.85 ± 2.40 x 10^–7and 6.84 ± 1.03 x 10^–2 respectively and high for protons at 8.84 ± 3.06 x 10^–2 cm/s. To examine whether caveolin or other integral membrane proteins were responsible for high permeabilities, liposomes designed to mimic the lipids of the inner and outer leaflets of the caveolar membrane were made. Osmotic water permeability to both liposome compositions were determined and a combined inner/outer leaflet water permeability was calculated and found to be close to that of native caveolae at 1.58 ± 1.1 x 10^–3 cm/s. In caveolae, activation energy for water flux was high (19.4 kcal/mol) and water permeability was not inhibited by HgCl₂; however, aquaporin 1 was detectable by immunoblotting. Immunostaining of rat lung with AQP1 and caveolin antisera revealed very low levels of colocalization. We conclude that aquaporin water channels do not contribute significantly to the observed water flux and that caveolae have relatively high water and solute permeabilities due to the high degree of unsaturation in their fatty acyl chains. lipid rafts; microdomains; cholesterol; aquaporin; caveolin     

Diffusional behavior and guest conformational analysis of hexadecane-1,16-diol and hexadecane in urea crystal model via molecular dynamics simulation approach

Diffusion at the atomic or molecular level is a source of many physical, chemical, and biological processes taking place in plentiful materials. This work is an endeavor toward investigating the diffusional behavior of two different type of guests, hexadecane-1,16-diol and hexadecane enclathration in urea tunnel architecture, whereby the correlation of the diffusion mechanism with the guest’s structural and conformational properties is explored. To carry out this study, molecular dynamics simulation approach is adopted. It is found that hexadecane-1,16-diol exhibit slower diffusion with an average diffusion coefficient value \( \sim 1.83\times {10}^{-10} \), where hexadecane diffuse more rapidly with an average diffusion coefficient value \( \sim 2.58\times {10}^{-9} \). It is also observed that the structural properties influence the guest’s travel distance and torsion angle distribution of the trans and gauche conformational proportion. Furthermore, the observed high energy barrier accounted for hexadecane-1,16-diol and low energy barrier for hexadecane along urea tunnel systems was analyzed. The comparison of our obtained results are in close agreement with the available experimental measurements, i.e., gauche proportion properties between two different guest molecules correlate well with Raman spectroscopy investigation on α,ω-dihalogenoalkane/urea inclusion compounds. Our calculations also successfully endorse the structure-property relation between the two systems.     

A triple system water-urea-L-α-alanine. Thermodynamic properties and intermolecular interactions

The heat of dissolution of L-α-alanine at 293, 298, 306, and 318 K in aqueous solutions of urea in the concentration range 0–7 mol urea/kg water has been determined by the microcalorimetric method. It was found that the heat of dissolving the amino acid linearly depends on the square root of the molality of the urea solution. It was shown that the enthalpy and entropy of the transfer of L-α-alanine from water into an aqueous solution of urea do not depend on temperature, and the heat capacity of transfer is equal to zero. Almost complete enthalpy-entropy compensation was noted. It was shown that the parameter characterizing the changes in the effective Gibbs energy of dissolving L-α-alanine in water and aqueous urea solutions has negative values due to the dominant entropy component. The system water-urea-L-α-alanine becomes less structured with increasing temperature and more structured as the urea concentration increases.     

Homochirality in Bio-Organic Systems and Glyceraldehyde in the Formose Reaction

The article explores the possibility that the ordering of bio-organic molecules into a homochiral assembly at the origin of life was performed not in aqueous solutions of amino acids or related materials but in racemic glyceraldehyde in the “formose” reaction at high concentration and temperature. Based on physical chemical evidence and computer simulations of condensed fluids, it is argued that the isomerization kinetics of glyceraldehyde is responszible of the symmetry break and the ordering of molecules into homochiral domains.     

Theoretical study of photophysical properties of 1,4-dihydropyrrolo[3,2-b]pyrrole-cored branched molecules with thienylenevinylene arms toward broad absorption spectra for solar cells

A series of oligo(thienylenevinylene) derivatives with 1,4-dihydropyrrolo[3,2-b]pyrrole as core has been investigated at the PBE0/6-31G(d) and the TD-PBE0/6-31+G(d,p) levels to design materials with high performances such as broad absorption spectra and higher balance transfer property. The results show that position and amount of arm affect the electronic density contours of frontier molecular orbitals significantly. The molecule with four arms owns the narrowest energy gap and the largest maximum absorption wavelength, and the molecule with two arms in positions a and c has the broadest absorption region among the designed molecules. Calculated reorganization energies of the designed molecules indicate that the molecules with two arms can be good potential ambipolar transport materials under proper operating conditions.

Computational design and structure–property relationship studies on heptazines

This study aimed to design novel nitrogen-rich heptazine derivatives as high energy density materials (HEDM) by exploiting systematic structure–property relationships. Molecular structures with diverse energetic substituents at varying positions in the basic heptazine ring were designed. Density functional techniques were used for prediction of gas phase heat of formation by employing an isodesmic approach, while crystal density was assessed by packing calculations. The results reveal that nitro derivatives of heptazine possess a high heat of formation and further enhancement was achieved by the substitution of nitro heterocycles. The crystal packing density of the designed compounds varied from 1.8 to 2 g cm⁻³, and hence, of all the designed molecules, nitro derivatives of heptazine exhibit better energetic performance characteristics in terms of detonation velocity and pressure. The calculated band gap of the designed molecules was analyzed to establish sensitivity correlations, and the results reveal that, in general, amino derivatives possess better insensitivity characteristics. The overall performance of the designed compounds was moderate, and such compounds may find potential applications in gas generators and smoke-free pyrotechnic fuels as they are rich in nitrogen content.     

Molecular mechanisms of urea transport in plants

Urea is a soil nitrogen form available to plant roots and a secondary nitrogen metabolite liberated in plant cells. Based on growth complementation of yeast mutants and “in-silico analysis”, two plant families have been identified and partially characterized that mediate membrane transport of urea in heterologous expression systems. AtDUR3 is a single Arabidopsis gene belonging to the sodium solute symporter family that cotransports urea with protons at high affinity, while members of the tonoplast intrinsic protein (TIP) subfamily of aquaporins transport urea in a channel-like manner. The following review summarizes current knowledge on the membrane localization, energetization and regulation of these two types of urea transporters and discusses their possible physiological roles in planta.     

Urea degradation by picophytoplankton in the euphotic zone of Lake Biwa

The ability of photoautotrophic picoplankton Synechococcus to degrade urea was examined in the euphotic zone of Lake Biwa. Samples were divided into pico (0.2–2.0 μm) and larger (>2.0 μm) size fractions by filtration. The rates of urea degradation (the sum of the rates of incorporation of carbon into phytoplankton cells and of liberation of CO₂ into water) measured by radiocarbon urea were 8 and 17 μmol urea m⁻³ day⁻¹ in June and July, respectively, for the picophytoplankton in the surface water, and 196 and 96 μmol urea m⁻³ day⁻¹, respectively for the larger phytoplankton. The rates decreased with depth, somewhat similar to the vertical profiles of the photosynthetic rate. The urea degradation rates were obviously high under light conditions. In daylight, urea was degraded into two phases, carbon incorporation and CO₂ liberation, whereas in the dark it was degraded only into the CO₂ liberation phase. The contribution of picophytoplankton to total phytoplankton in urea degradation was high in the subsurface to lower euphotic layer. Urea degradation activity was higher in the picophytoplankton fraction than in the larger phytoplankton fraction. Shorter residence times of urea were obtained in the upper euphotic zone. The contribution of picophytoplankton to urea cycling was 4% to 35%. The present results suggest that the picophytoplankton Synechococcus is able to degrade urea and effectively makes use of regenerated urea as a nitrogen source in the euphotic layer, and that picophytoplankton play an important role in the biogeochemical nitrogen cycle in Lake Biwa. Received: June 25, 1998 / Accepted: February 10, 1999     

生物基分子介导纳米金属材料的制备及其应用

纳米金属材料具有纳米晶强化效应、光吸收率大、较高的表面能和单磁畴性能等优点,因其在医药、化学催化、抗菌抑毒等方面发挥着越来越重要的作用而受到人们广泛关注。近年来,随着全球石化资源消耗与日俱增,环境污染加剧,基于可再生资源的生物基分子介导纳米材料的制备研究方兴未艾。生物基分子是指直接或间接来源于生物质的小分子或大分子物质,它们多数具有生物相容性好、低毒、可降解、来源广泛、价格低廉等优点。且由于生物基分子多数具有独特的理化性质,如具有生理活性的旋光性、酸碱两性、亲水亲油性以及易与金属离子络合等,其介导合成的纳米材料还兼具其独特功能性,比如消炎、抗癌、抗氧化、抗病毒以及降血糖血脂等,进一步拓宽了纳米金属材料的应用领域。文中对近年来基于生物基分子介导纳米金属材料的制备及应用进行全面综述,为开展相关研究提供参考。     

Diel variation in urea decomposing activity in the euphotic zone of brackish Lake Nakaumi

Diel variations in urea decomposing activity in the euphotic zone of brackish Lake Nakaumi were measured under fixed light intensity. The decomposition rate of urea was 17 to 44 μ mol urea m⁻³ h⁻¹ in the light and 10 to 27 μ mol urea m⁻³ h⁻¹ in the dark. Higher decomposition rates were obtained in the upper euphotic zone. A clear diel periodicity in the urea decomposition rate was observed, with high rates from 1200 to 1600 and low rates from 0000 to 0400. Chlorophyll a specific decomposing activity ranged from 12 to 21 μg urea C mg chl.a ⁻¹ h⁻¹ in the light and 7 to 13 μg urea C mg chl.a ⁻¹ h⁻¹ in the dark. In the light, high values were obtained from 1600 to 2000 and low values from 0400 to 0800. The diel change in specific decomposing activity exhibited a similar pattern to that of the photosynthetic assimilation number, following the diel change in photosynthetic activity. Received: March 10, 1999 / Accepted: October 22, 1999     

BON-BONs: cyclic molecules with a boron-oxygen-nitrogen backbone. Computational studies of their thermodynamic properties

Although they were first reported in 1963, molecules with a boron-oxygen-nitrogen dimeric backbone do not seem to have been investigated seriously in terms of thermodynamic properties. Here we report on the calculated structures and properties, including thermodynamics, of several so-called “BON-BON” molecules. With the popularity of nitrogen-containing substituents on new high-energy materials, nitro-substituted BON-BONs were a focus of our investigation. A total of 42 BON-BON molecules were evaluated, and thermochemical analysis shows a decrease in the specific enthalpy of combustion or decomposition with increasing NO₂ content, consistent with other systems.     

The Virtual Cell Animation Collection: Tools for Teaching Molecular and Cellular Biology

A cell is a minifactory in which structures and molecules are assembled, rearranged, disassembled, packaged, sorted, and transported. Because cellular structures and molecules are invisible to the human eye, students often have difficulty conceptualizing the dynamic nature of cells that function at multiple scales across time and space. To represent these dynamic cellular processes, the Virtual Cell Productions team at North Dakota State University develops freely available multimedia materials to support molecular and cellular biology learning inside and outside the high school and university classroom.

This Education piece is part of the Education series.

     

Fundamental measure theory of hydrated hydrocarbons

To calculate the solvation of hydrophobic solutes, we have developed a method based on the fundamental measure treatment of density functional theory. This method allows us to carry out calculations of density profiles and the solvation energy for various hydrophobic molecules with high accuracy. We have applied the method to the hydration of various hydrocarbons (linear, branched and cyclic). The calculations of the entropic and enthalpic parts are also carried out. We have examined the question of the temperature dependence of the entropy convergence. Finally, we have calculated the mean force potential between two large hydrophobic nanoparticles immersed in water. Proceedings of “Modeling Interactions in Biomolecules II”, Prague, September 5th–9th, 2005.