DFT Optimization of Isolated Molecular Chain Sheet Models Constituting Native Cellulose Crystal Structures

Quantum Chemical Calculation for Intermolecular Interactions of Alginate Dimer-Water Molecules

The abundance of applications of alginates in aqueous surroundings created by their interactions with water is a fascinating area of research. In this paper, computational analysis was used to evaluate the conformation, hydrogen bond network, and stabilities for putative intermolecular interactions between alginate dimers and water molecules. Two structural forms of alginate (alginic acid, alg, and sodium alginate, SA) were evaluated for their interactions with water molecules. The density functional theory (DFT-D3) method at the B3LYP functional and the basis set 6-31++G** was chosen for calculating the data. Hydrogen bonds were formed in the Alg-(H₂O)_n complexes, while the SA-(H₂O)_n complexes showed an increase in Van der Walls interactions and hydrogen bonds. Moreover, in the SA-(H₂O)_n complexes, metal-nonmetal bonds existed between the sodium atom in SA and the oxygen atom in water (Na…O). All computational data in this study demonstrated that alginate dimers and water molecules had moderate to high levels of interaction, giving more stability to their complex structure.

Irregular and suppressed elastic deformation by a structural twist in cellulose nanofibre models

The elastic responsiveness of single cellulose nanofibres is important for advanced analysis of biological tissues and their use in sophisticated functional materials. However, the mechanical responsiveness derived from the twisted structure of cellulose nanofibres (CNFs) has remained unexplored. In this study, finite element simulations were applied to characterize the deformation response derived from the torsional structure by performing tensile and bending tests of an unconventionally very long and twisted rod model, having the known dimensional parameters and properties of CNFs. The antagonistic action of two types of structural elements (a contour twist and a curvilinear coordinate) was found to result in an irregular deformation response but with only small fluctuations. The contour twist generated rotational displacements under tensile load, but the curvilinear coordinate suppressed rotational displacement. Under bending stress, the contour twist minimized irregular bending deformation because of the orthotropic properties and made the bending stress transferability a highly linear response.

Probing DNA-Cleavage Efficiencies of Copper(II) Complexes: A Computational Perspective

Theoretical studies on DNA-cleavage efficiencies of Cu(II) complexes 1-3 were carried out using density functional theory (DFT). The optimized Cu(II) complexes were allowed to bind to glutathiones (GSH) and ascorbic acids (VC) by the docking program so that corresponding docking structures can be obtained. To predict DNA-cleavage efficiencies, the docking structures of Cu(II) complexes with GSH and VC were further optimized by DFT. The activation energies of electrons from GSH to complexes, the redox potentials of these complexes, and binding energies of these complexes with GSH and VC were calculated. The efficiencies of complexes cleaving DNA were predicted and found to be in agreement with the experimental results. Finally, three occupied molecular orbitals of docking structures (GSH-complexes) were analyzed, and the DNA-cleavage abilities of complexes were also explained by the electron distribution on the three occupied orbitals. This work has important implications understanding the DNA-cleavage mechanism of Cu(II) complexes, which might be helpful for designing novel anticancer Cu(II) complexes for the future.

A mass spectrometric stochastic dynamic diffusion approach to selective quantitative and 3D structural analyses of native cyclodextrins by electrospray ionization and atmospheric pressure chemical ionization methods

The paper addressed shortcoming with highly precise and selective 3D structural analysis of native cyclodextrins in mixture using ions observable at low m/z-region by ESI- and APCI-mass spectrometry. Because of, the quantitative and structural analyses of CDs, in general, are vexed by a set of complications. The study outlines our own stochastic dynamic approaches to the latter issues based on new model relations, quantifing the measurable MS outcome intensity. They introduce the so-called stochastic dynamic mass spectrometric diffusion "D_SD" parameter, exhibiting high accuracy, precision, sensitivity and selectivity, respectively. It is linearly connected with the so-called quantum chemical diffusion parameter "D_QC" according to Arrhenius's theory. The most important upshot is that statistical parameters r = 0.99₆₃₉-0.99₉₈₁ has been obtained correlating between D_SD and D_QC parameters. Therefore, we determine high accurately 3D molecular and electronic structures of analytes by mass spectrometry. Fragment peaks at m/z 313, 279, 272, 252, 231, 214, 198, 171, 158 and 141 are examined. Mixtures of CDs and monomeric and acyclic oligomer carbohydrates glucose (1), sucrose (2), raffinose (3), melezitose (4) and cellotriose (5) are also studied. Our method is able to account precisely for the effect of the temperature under ESI- and APCI-MS conditions, as well. Correlative analysess between D_SD parameters of ESI- and APCI-MS measurements under different temperatures is also shown. Chemometric tests are used. Another important results and conclusions, among others, to draw from this research are: (i) excellent linear correlation between D_SD and D_QC parameters of r = 0.99₆₃₆ is found looking at common ions at m/z 141, 158 and 171, belonging to 2-formyl-3,4-dihydroxy-pyranylium, 4,5,6-trihydroxy-6H-pyran-2-carbaldehyde and 3,4,5-trihydroxy-6-oxo-6H-pyran-2-ylmethylidyne-oxonium ions. Thus, we distinguish precisely between the last structure and 3-formyl-4,5-dihydroxy-2,7-dioxa-8-oxonia-bicyclo[4.2.0]octa-1(8),3,5-triene cation. In the case of ion at m/z 141 subtle electronic effects are distinguished between the mentioned structure and the charged 3,4-dihydroxy-6H-pyran-2-carbaldehyde one. The method determines precisely very similar structurally poly-OH-substituted derivatives. Because of, (ii) absolute reproducibility (r = 1) of D_SD parameters of ESI-MS spectra is obtained studying the shown in point (i) MS peaks of β-CD between j^th and j^th numbers of experiments. The statistical equation is Dⁱ_SD = (0.51 ± 3.1.10^-5) × D^j_SD; (iii) the APCI- and ESI-MS provide identical results studying common MS ions of CDs and the correlation between D^APCI_SD and D^ESI_SD parameters excludes from error, due to, experiment; and (iv) The correlation between theory and experiment accounting for the factor temperature within our model equations shows r = 0.98₂₈ looking at the MS peaks at m/z 313 280, 279, 274 and 252, respectively. The effect of the temperature under both ESI- and APCI-MS conditions on the 3D molecular and electronic structures of CDs is precisely studied, respectively.