Structure conversions of cellulose IIII crystal models in solution state: a molecular dynamics study

This paper re-examines our previous molecular dynamics (MD) study on cellulose III_I crystal models with finite dimensions solvated in explicit water molecules. Eight crystal models, differing in a constituent lattice plane and dimensions, were studied. One calculation allowed for O–H and C–H bond stretching, and had a small time step of 0.5 fs. The other calculation adopted non-scaling factors of the 1–4 non-bonded interactions. As in our previous study, in the former MD calculations, six of the eight crystal models exhibited structure conversion with cooperative chain slippages generated by a progressive fiber bend. This converted the initial non-staggered chain packing of cellulose III_I into a near one-quarter staggering and gave the crystal model a triclinic-like configuration. In contrast, in the non-1–4 scaling MD calculations, all of the eight crystal models retained the initial cellulose III_I crystal structure. Another series of non-1–4 scaling MD calculations were performed for the four crystal models containing chains with a degree of polymerization (DP) of 40 at 370 K, which simulated hot water treatment to convert cellulose III_I to Iβ. Some of the hydroxymethyl groups irreversibly rotated from gt into tg conformation. This accompanied exchange of the intrasheet hydrogen bonding scheme along the (1 ?1 0) lattice plane from O2–O6 to O3–O6. The original corrugated (1 ?1 0) chain sheet was partly converted into a cellulose I-like flat chain sheet.     

Partial crystalline transformation of solvated cellulose IIII crystals, reproduced by theoretical calculations

In hot-water molecular dynamics simulation at 370 K, four cellulose III_I crystal models, with different lattice planes and dimensions, exhibited partial crystalline transformations of (1 ?1 0) chain sheets, in which hydroxymethyl groups were irreversibly rotated from gt into tg conformations, accompanied by hydrogen-bond exchange from the original O3–O6 to cellulose-I-like O2–O6 bonds. The final hydrogen-bond exchange ratio was about 95 % for some of the crystal models after 50 ns simulation. The corrugated (1 ?1 0) chain sheet was converted to a cellulose-I-like flat chain sheet with a slightly right-handed twist. The 3D structures of the three types of isolated chain sheet models were optimized using density functional theory calculations to compare their stabilities without crystal packing forces. The cellulose Iβ (1 0 0) models were more stable than the cellulose III_I (1 ?1 0) models. The optimized structure of cellulose III_I (1 0 0) models deviated largely from the initial sheet form. It was proposed to the crystalline transformation from cellulose III_I to Iβ that conversion of the chain sheet structure first take place, followed by sliding of the chain sheet along the fiber axis.     

Structural stability of the solvated cellulose IIII crystal models: a molecular dynamics study

Molecular dynamics (MD) simulations of cellulose III_I crystal models have been carried out. The crystal models were composed by either 24 or 48 cellooligomers consisting of either 20 or 40 residues and were surrounded by waters in a periodic boundary box. Two base plane types differing in a constituent crystal lattice plane, (0 −1 0) × (0 1 0) and (1 0 0) × (0 1 0), were additionally considered. Among the resulting eight crystal models, an overall structure conversion was observed for the seven models. The final structures had a triclinic-like chain arrangement involving one-quarter staggering chains with respect to its axis. The successive, local transformation involving cooperative bends in cellooligomers was observed during the structure conversion. Only the 48 × 20-mer model having the (0 −1 0) lattice plane retained the original crystal structure throughout a 2.5-ns simulation. The MD simulations with an implicit solvent system and a vacuum system were also performed to asses a solvent effect on the structure conversion.     

Solvent effects on electronic structures and chain conformations of alpha-oligothiophenes in polar and apolar solutions

Solvent effects on electronic structures and chain conformations of alpha-oligothiophenes nTs (n = 1 to 10) are investigated in solvents of n-hexane, 1,4-dioxane, carbon tetrachloride, chloroform, and water by using density functional theory (DFT) and molecular dynamics (MD) simulations. Both implicit and explicit solvent models are employed. The polarized continuum model (PCM) calculations and MD simulations demonstrate the weak solvent effects on the electronic structures of alpha-oligothiophenes. The lowest dipole-allowed vertical excitation energies of nTs, obtained from time-dependent DFT/PCM calculations at the B3LYP/6-31G(d) level, exhibit a red shift as the solvent polarity increases, in agreement with experiments. The studied solvents have little impact on the state order of the low-lying excited states provided that the nTs are kept in C2h or C2v symmetry. The MD simulations demonstrate that the chain conformations are distorted to some extent in polar and nonpolar solvents. A qualitative picture of the distribution of solvent molecules around the solvated nTs is drawn by means of radial and spatial distribution functions. The S...H-O and pi...H-O solute-solvent interactions are insignificant in aqueous solution.     

Quantification of a tightly adsorbed monolayer of xylan on cellulose surface

The successive extraction and re-adsorption of a linear β-(1 → 4) xylan extracted from microfibrillated birch pulp was investigated using solid-state CP/MAS ¹³C NMR spectroscopy, specific surface area measurements, and atomistic molecular dynamics (MD) simulations. The NMR spectra confirmed that when in contact with cellulose after re-adsorption, the xylan molecules altered their conformation from the classical left-handed threefold structure found in the bulk to a different one, presumably a cellulose-like twofold system for quantities up to the equivalent amount of extracted xylan. Combining these observations with specific surface area measurements and the surface occupied by a xylosyl residue, it was possible to show that the re-adsorbed xylan in the modified conformation occurred only within the first adsorbed layer in direct interaction with the cellulose surface. It is only when an excess xylan was added and after full cellulose surface coverage, that the subsequent deposited layers took the classical threefold organization. Following the variation of xylan conformation in terms of sequential xylan addition allowed quantifying the surface of cellulose accessible for a tight adsorption of xylan, not only for microfibrillated birch cellulose, but for other samples as well. The MD simulations confirmed that xylan in threefold conformation had a weaker affinity for the cellulose surface than its twofold counterpart, thus supporting the hypothesis of the twofold conformation for xylan at the cellulose surface. The MD simulations also showed that in contact with cellulose, the adsorbed xylan was mainly organized as an extended molecular chain aligned parallel to the cellulose chain direction.     

有机π共轭配体溶剂化效应与分子间相互作用的理论研究

采用可极化的连续介质模型(PCM), 运用密度泛函理论(DFT), 在B3LYP/6-31+G^**水平下研究了溶剂极性对有机π共轭配体N,N'-Bis-(3-pyridyl)ethylene-bis-urea(BPEBU)中syn-anti构象的分子几何和电子结构的影响, 并借助分子动力学模拟的方法, 采用明确溶剂模型研究了溶质-溶剂分子间的相互作用. 密度泛函理论计算结果表明, 随着溶剂极性的增强, BPEBU中尿素基上的CO键和N-H键以及吡啶环上的C-N键被明显极化, 使羰基氧原子和吡啶氮原子的电负性明显增强, 尿素基的N-H键上氢原子的正电荷也显著增加. 分子动力学模拟统计的结果表明, 在极性较强的乙醇溶液中, 有明确的O…H-O, N…H-O和N-H…O等3种氢键作用存在, 而在丙酮溶液中, 只有N…H-O一种氢键作用存在, 而且与乙醇溶液中的N…H-O作用相比要弱些. 另外, 采用密度泛函理论方法结合连续/明确的混合溶剂模型, 优化得到了溶质-溶剂三聚体的超分子簇结构, 与分子动力学模拟的第一溶剂层中的超分子结构相比, 两者定性一致.     

DFT and MD studies on the influence of the orientation of ester linkage groups in banana-shaped mesogens

The influence of the direction of ester linkage groups on the structural and electronic properties of five-ring banana-shaped molecules with a central 1,3-phenylene unit has been investigated including hexyloxy and dodecyloxy terminal chains. DFT studies on the B3LYP/6-31G(d) level were performed on the conformational behaviour of the ten isomers in a systematic way. The one- and two-fold potential energy scans show that the flexibility of the wings significantly depends on the orientation of the carboxyl linkage groups. Moreover, the different directions of the carboxyl groups between the aromatic rings cause remarkable changes on the dipole moment and its components of the molecules. These findings are supported by investigations on the global charge pattern of the molecules calculated from electrostatic potential group charges. The bending angle alpha obtained from a simple model for the five-ring bent-core molecules is a characteristic structural parameter which can be correlated with experimental findings. Calculations on the bent-core molecules in an external electric dipole field related to the direction of their polar axis show remarkable effects with respect to the flexibility and polarity of the isomers. First molecular dynamics simulations on the banana-shaped molecules were carried out within the AMBER 7 package. The trajectories of relevant structural parameters support the findings of the DFT studies. The results concerning the structure and polarity revealed from the DFT and MD calculations of the ten isomers can be correlated with data from dielectric measurements and mesophase properties.     

Electronic structures of one-dimensional metal-molecule hybrid chains studied using scanning tunneling microscopy and density functional theory

The electronic structures of self-assembled hybrid chains comprising Ag atoms and organic molecules were studied using scanning tunneling microscopy (STM) and spectroscopy (STS) in parallel with density functional theory (DFT). Hybrid chains were prepared by catalytic breaking of Br-C bonds in 4,4″-dibromo-p-terphenyl molecules, followed by spontaneous formation of Ag-C bonds on Ag(111). An atomic model was proposed for the observed hybrid chain structures. Four electronic states were resolved using STS measurements, and strong energy dependence was observed in STM images. These results were explained using first-principles calculations based on DFT.     

Crystal structure of nylon 12

The crystal structure of nylon 12 prepared by polymerization of dodecalactam has been determined by x-ray diffraction. Nylon 12 fiber exhibits only the γ form as its stable crystal structure. The unit cell of nylon 12 was determined with the aid of the x-ray diffraction pattern of a doubly oriented specimen. The unit cell is monoclinic with a = 9.38 Å, b = 32.2 Å (fiber axis), c = 4.87 Å and β = 121.5° and contains four repeating monomer units. The chain is planar zigzag for the most part but is twisted at the position of amide groups, forming hydrogen bonds between neighboring parallel chains. The chain conformation is similar to that of the γ form of nylon 6 proposed by Arimoto. It was deduced from the calculations that there are two chain conformations statistically coexistent according to the direction of twisting. In each conformation, hydrogen bonds are formed between parallel chains to make pleated sheetlike structures. The sheets are nearly parallel to (200) and in the sheet the directions of the neighboring chains are antiparallel, as is the case with nylon 6.     

Reversing the structural chirality of cellulosic nanomaterials

Nature organizes cellulose, a linear polysaccharide of D-glucose and an important component of plants and trees, into intricate structures with twists in the trunks of trees, microfibrils within cell walls, and at the nanoscale. Manipulating the hierarchical organization of materials requires control down to the molecular level. In computational models cellulose nanocrystals twist, and Quantum Mechanical models have shown recently that chains at the surface of nanocrystals are right-handed, while the interior chains are mostly left-handed. Here we provide experimental evidence showing the induced circular dichroism of two optical dyes reverses when adsorbed onto thin cellulose nanocrystals. The reversal in optical activity is consistent with earlier TD-DFT B3LYP 6-31G calculations of the induced optical activity of Congo red adsorbed onto twisted 1 0 0 crystal surfaces of cellulose and demonstrates control of the chiral molecular interactions at the nanocrystal surface. The results suggest it may be possible to reverse the structural twist handedness of the nanocrystal itself and build chirality-dependent hierarchical supramolecular structures from cellulose.     

Probing the structural chirality of crystalline cellulose with induced circular dichroism

There is mounting evidence of twists in the crystalline regions of cellulose, but direct imaging of the twist is hindered by the small crystal sizes in cellulose nanocrystals from wood and plant sources. Here the structural chirality of cellulose nanocrystals is determined experimentally using induced circular dichroism of optically inactive Congo red. Time Dependent Density Functional Theory B3LYP 6-31G calculations indicate right-handed twisted cellulose surfaces induce positive Cotton effects in adsorbed Congo red and left-handed surfaces induce negative Cotton effects. Consistent with directly observed twists, conventional wood cellulose nanocrystals are estimated to have a right-handed 800 nm per half-twist demonstrating the crystalline regions are not uniformly flat, but rather right-handed twisted crystalloids.     

Theoretical study of the interaction between sodium ion and a cyclopeptidic tubular structure

DFT calculations have been carried out to describe the pathway of a sodium ion along the stacking direction of a tubular structure set up by five cyclopeptidic units, which can be considered a suitable model of a hollow tubular structure of indefinite length. A lattice of points inside the tubular structure is defined and the DFT interaction energy values with a sodium ion are obtained. The data allow predicting a zigzag path of the ion inside the hosting structure.     

Ab initio modeling of amide I coupling in antiparallel beta-sheets and the effect of 13C isotopic labeling on infrared spectra

Isotopic substitution with 13C on the amide C=O has become an important means of determining localized structural information about peptide conformations with vibrational spectroscopy. Various approaches to the modeling of the interactions between labeled amide sites, specifically for antiparallel two-stranded, beta-forming peptides, were investigated, including different force fields [dipole-dipole interaction vs density functional theory (DFT) treatments], basis sets, and sizes of model peptides used for ab initio calculations, as well as employing models of solvation. For these beta-sheet systems the effect of the relative positions of the 13C isotopic labels in each strand on their infrared spectra was investigated. The results suggest that the interaction between labeled amide groups in different strands can be used as an indicator of local beta-structure formation, because coupling between close-lying C=O groups on opposing chains leads to the largest frequency shifts, yet some alternate placements can lead to intensity enhancements. The basic character of the coupling interaction between labeled modes on opposing strands is independent of changes in peptide length, water solvent environment, twisting of the sheet structure, and basis set used in the calculations, although the absolute frequencies and detailed coupling magnitudes change under each of these perturbations. In particular, two strands of three amides each contain the basic interactions needed to simulate larger sheets, with the only exception that the C=O groups forming H-bonded rings at the termini can yield different coupling values than central ones of the same structure. Spectral frequencies and intensities were modeled ab initio by DFT primarily at the BPW91/6-31G** level for pairs of three, four, and six amide strands. Comparison to predictions of a classical coupled oscillator model show qualitative but not quantitative agreement with these DFT results.     

Experimental, quantum chemical calculations, and molecular dynamic simulations insight into the corrosion inhibition properties of 2-(6-methylpyridin-2-yl)oxazolo[5,4-f][1,10]phenanthroline on mild steel

2-(6-Methylpyridin-2-yl)oxazolo[5,4-f][1,10]phenanthroline (MOP) was synthesized and characterized by elemental analysis and Fourier-transform infrared (FT-IR), ¹H nuclear magnetic resonance (NMR), and ¹³C NMR spectra. MOP was evaluated as a corrosion inhibitor for carbon steel in 0.5 M H₂SO₄ solution using the standard gravimetric technique at 303–333 K. Quantum chemical calculations and molecular dynamic (MD) simulations were applied to analyze the experimental data and elucidate the adsorption behavior and inhibition mechanism of MOP. Results obtained show that MOP is an efficient inhibitor for mild steel in H₂SO₄ solution. The inhibition efficiency was found to increase with increase in MOP concentration but decreased with temperature. Activation parameters and Gibbs free energy for the adsorption process using statistical physics were calculated and discussed. The adsorption of MOP was found to involve both physical and chemical adsorption mechanisms. Density functional theory (DFT) calculations suggest that nitrogen and oxygen atoms present in the MOP structure were the active reaction sites for the inhibitor adsorption on mild steel surface via donor–acceptor interactions between the lone pairs on nitrogen and oxygen atoms together with the π-electrons of the heterocyclic and the vacant d-orbital of iron atoms. The adsorption of MOP on Fe (1 1 0) surface was parallel to the surface so as to maximize contact, as shown in the MD simulations. The experiments together with DFT and MD simulations provide further insight into the mechanism of interaction between MOP and mild steel.     

A joint QM/MD study on α-, β- and γ-cyclodextrins in selective complexation with cathinone

In this article, density functional theory (DFT) calculations and 30 ns molecular dynamic (MD) simulations were performed to investigate the ability of α-, β- and γ-cyclodextrins (CDs) to form selective complexes with cathinone. DFT calculations in the gas phase, water, chloroform and methanol reveal that the solvents, reduce the stability of the complexes. Optimized structures confirm that α-CD cannot encapsulate cathinone, completely, while other CDs showed an opposite behavior. DFT calculations indicate that cathinone has the most stable complex with γ-CD in comparison to the α- and β-CDs. Natural bond orbital and quantum theory of atoms in molecules analyses reveal that the electrostatic interactions between cathinone and CDs are the driving force of the complex formation. MD simulations confirm that different solvents play an important role in the stability of the cathinone complexes and the obtained MD results are in good agreement with the DFT calculations.     

Inelastic neutron scattering and DFT study of 2-amino-3-hydroxymethyl-1,3-propane diol (TRIS)

We report an inelastic neutron scattering (INS) study of 2-amino-3-hydroxymethyl-1,3-propane diol (TRIS). The assignment of the experimental vibrational spectra measured using several incident neutrons’ energies on HRMECS spectrometer has been made by means of DFT calculations. To simulate crystal environment both molecular cluster and solid state models were used. The study has been completed by an alternative approach, molecular dynamics (MD) calculations, done at the same level of the DFT theory. The INS spectra calculated with the solid state models (normal mode analysis, and MD) gave a better fit of the experiment than the cluster model. On the other hand, the peaks between 650 and 850 cm⁻¹ in the experimental INS spectra assigned to OH torsional modes were reproduced better by the cluster calculations. The nature of the stretching frequency of unusually long O–H bond (1.012 Å) was interpreted by means of MD calculations. The interpretation of the spectrum below 100 cm⁻¹ was based on Fourier transform of the velocity autocorrelation function of centre of mass of a molecule of TRIS.     

Preparation of tough cellulose II nanofibers with high thermal stability from wood

Well-dispersed cellulose II nanofibers with high purity of 92 % and uniform width of 15–40 nm were isolated from wood and compared to cellulose I nanofibers. First, ground wood powder was purified by series of chemical treatments. The resulting purified pulp was treated with 17.5 wt% sodium hydroxide (NaOH) solution to mercerize the cellulose. The mercerized pulp was further mechanically nanofibrillated to isolate the nanofibers. X-ray diffraction patterns revealed that the purified pulp had been transformed into the cellulose II crystal structure after treatment with 17.5 wt% NaOH, and the cellulose II polymorph was retained after nanofibrillation. The cellulose II nanofiber sheet exhibited a decrease in Young’s modulus (8.6 GPa) and an increase in fracture strain (13.6 %) compared to the values for a cellulose I nanofiber sheet (11.8 GPa and 7.5 %, respectively), which translated into improved toughness. The cellulose II nanofiber sheet also showed a very low thermal expansion coefficient of 15.9 ppm/K in the range of 20–150 °C. Thermogravimetric analysis indicated that the cellulose II nanofiber sheet had better thermal stability than the cellulose I nanofiber sheet, which was likely due to the stronger hydrogen bonds in cellulose II crystal structure, as well as the higher purity of the cellulose II nanofibers.     

The statistics of chain sectioning experiments on cellulose fibers

It has been suggested that transverse sectioning of natural cellulose fibers can be used to test ideas about microfibril structure. This proposal has been examined theoretically and numerical calculations of the weight-distribution curve of sectioned chains are given for several different models. These calculations illustrate the effects that different types of chain folding have on the sectioned size distribution. The difficulties involved in the practical execution of this type of experiment are discussed and it is concluded that fiber-sectioning experiments described in the literature do not disprove the folded-chain hypothesis.     

Solvent effects on isomerization and spectral properties of photochromic-switching diarythene derivatives in polar and apolar solutions

The photocyclization behavior and dynamic conformational transition of photochromic switches of diarythene derivatives in solutions are investigated by using the density functional theory (DFT) and molecular dynamics (MD) simulations. Three possible conformations, antiparallel (anti), parallel (para), and twist, for the open-ring isomers of 1,2-bis(2-methylbenzothiophene-3-yl)maleic anhydride are located. Both PCM-B3LYP/6-31G* calculations and MD simulations demonstrate that anti and twist open-ring isomers can interconvert freely in n-hexane and acetonitrile solutions at room temperature. The statistical ratio of twist to anti isomers from MD simulations is 2.09 in n-hexane and 1.07 in CH(3)CN, in qualitative agreement with those (1.18 in n-hexane and 1.05 in CH(3)CN) estimated from Arrhenius analysis of DFT activation energies. The solvent polarity has little influence on the isomerization of open-ring isomers in the ground state. Due to the evident charge transfer upon excitations, the solvent effects on the electronic structures and absorption spectra of low-lying excited states (S(1) and S(2)) are more significant. For such charge-transfer excited states, the long-range corrected functional CAM-B3LYP gives better agreement with the experimental spectra than B3LYP. The solvent polarity and polarization of the charge-transfer excited states are crucial for fabricating the novel functionalized photochromic molecular switches.     

The role of intra- and intermolecular interactions in determining the conformation and mode of packing of crystalline polymers—I. Poly(cis-1,4-butadiene)

Conformational energy calculations on an isolated chain of poly(cis-1,4-butadiene) have been performed, allowing for the variation of all bond angles and torsion angles. Various minimum energy and high symmetry conformations are accessible to the chain. Packing energy calculations have been performed for chains having tci symmetry, allowing for the variation of symmetry, unit cell constants and internal rotation angles. Unlike the behaviour observed for other polymers, the chain conformation which minimizes the total (conformational plus packing) energy is sensibly different from that of minimum energy for the isolated chain. The agreement between experimental and calculated data of the crystal structure analysis may be considered as very good.