Science, philosophical act and theology: an introductory note to two classical studies of Josef Pieper

Josef Pieper, um dos filósofos que melhor discutiu as relações entre ciência, filosofar e teologia, apresenta aqui duas de suas clássicas reflexões: “Dois modos de ser crítico”, no qual mostra que o crivo de rigor da ciência (nichts durchlassen “não deixar passar nada”) não é o mesmo que o do filosofar e da teologia (nichts auslassen “não deixar de fora nada”). E, em “A Tese de Pascal: Teologia e Física”, discute o diferente papel da tradição na ciência e na teologia

Predictive Multiscale Modeling of Nanocellulose Based Materials and Systems

<p>Predictive Multiscale Modeling of Nanocellulose Based Materials and Systems</p

Predicting Accurate Solvation Free Energy in <i>n</i>‑Octanol Using 3D-RISM-KH Molecular Theory of Solvation: Making Right Choices

Molecular theory of solvation, a.k.a., three-dimensional reference interaction site model theory of solvation with Kovalenko–Hirata closure relation (3D-RISM-KH), is an accurate and fast theory predicting solvation free energy and structure. Here we report a benchmark study of <i>n</i>-octanol solvation free energy calculations using this theory. The choice of correct force field parameters is quintessential for the success of 3D-RISM theory, and we present a guideline to obtain them for <i>n</i>-octanol solvent. Our best prediction of the solvation free energy on a set of 205 small organic molecules supplemented with the so-called “universal correction” scheme yields relative mean unsigned error of 0.94 kcal/mol against the reported database. The best agreement is obtained with the united atom (UA) type force field parametrization of <i>n</i>-octanol with the van der Waals parameters of hydroxyl hydrogen reported by Kobryn et al. [Kobryn, A. E.; Kovalenko, A. J. Chem. Phys. 2008, 129, 134701]

Electric Interfacial Layer of Modified Cellulose Nanocrystals in Aqueous Electrolyte Solution: Predictions by the Molecular Theory of Solvation

The X-ray crystal structure-based models of I_α cellulose nanocrystals (CNC), both pristine and containing surface sulfate groups with negative charge 0–0.34 <i>e</i>/nm² produced by sulfuric acid hydrolysis of softwood pulp, feature a highly polarized “crystal-like” charge distribution. We perform sampling using molecular dynamics (MD) of the structural relaxation of neutral pristine and negatively charged sulfated CNC of various lengths in explicit water solvent and then employ the statistical mechanical 3D-RISM-KH molecular theory of solvation to evaluate the solvation structure and thermodynamics of the relaxed CNC in ambient aqueous NaCl solution at a concentration of 0.0–0.25 mol/kg. The MD sampling induces a right-hand twist in CNC and rearranges its initially ordered structure with a macrodipole of high-density charges at the opposite faces into small local spots of alternating charge at each face. This surface charge rearrangement observed for both neutral and charged CNC significantly affects the distribution of ions around CNC in aqueous electrolyte solution. The solvation free energy (SFE) of charged sulfated CNC has a minimum at a particular electrolyte concentration depending on the surface charge density, whereas the SFE of neutral CNC increases linearly with NaCl concentration. The SFE contribution from Na⁺ counterions exhibits behavior similar to the NaCl concentration dependence of the whole SFE. An analysis of the 3D maps of Na⁺ density distributions shows that these model CNC particles exhibit the behavior of charged nanocolloids in aqueous electrolyte solution: an increase in electrolyte concentration shrinks the electric interfacial layer and weakens the effective repulsion between charged CNC particles. The 3D-RISM-KH method readily treats solvent and electrolyte of a given nature and concentration to predict effective interactions between CNC particles in electrolyte solution. We provide CNC structural models and a modeling procedure for studies of effective interactions and the formation of ordered phases of CNC suspensions in electrolyte solution

Extraction of elementary rate constants from global network analysis of central metabolism-0

On rate law (MRL) for estimation of the elementary rate constants. The same procedure can be used to estimate rate constants involved in other pathways.<p><b>Copyright information:</b></p><p>Taken from "Extraction of elementary rate constants from global network analysis of central metabolism"</p><p>http://www.biomedcentral.com/1752-0509/2/41</p><p>BMC Systems Biology 2008;2():41-41.</p><p>Published online 7 May 2008</p><p>PMCID:PMC2396597.</p><p></p

Cellulose Aggregation under Hydrothermal Pretreatment Conditions

Cellulose, the most abundant biopolymer on Earth, represents a resource for sustainable production of biofuels. Thermochemical treatments make lignocellulosic biomaterials more amenable to depolymerization by exposing cellulose microfibrils to enzymatic or chemical attacks. In such treatments, the solvent plays fundamental roles in biomass modification, but the molecular events underlying these changes are still poorly understood. Here, the 3D-RISM-KH molecular theory of solvation has been employed to analyze the role of water in cellulose aggregation under different thermodynamic conditions. The results show that, under ambient conditions, highly structured hydration shells around cellulose create repulsive forces that protect cellulose microfibrils from aggregating. Under hydrothermal pretreatment conditions, however, the hydration shells lose structure, and cellulose aggregation is favored. These effects are largely due to a decrease in cellulose–water interactions relative to those at ambient conditions, so that cellulose–cellulose attractive interactions become prevalent. Our results provide an explanation to the observed increase in the lateral size of cellulose crystallites when biomass is subject to pretreatments and deepen the current understanding of the mechanisms of biomass modification

Theoretical Modeling of Tunneling Barriers in Carbon-Based Molecular Electronic Junctions

Density functional theory (DFT) is applied to three models for carbon-based molecular junctions containing fragments of graphene with covalent edge-bonding to aromatic and aliphatic molecules, with the graphene representing a sp² hybridized carbon electrode and the molecule representing a molecular layer between two electrodes. The DFT results agree well with experimental work functions and transport barriers, including the electronic coupling between molecular layers and graphitic contacts, and predict the compression of tunnel barriers observed for both ultraviolet photoelectron spectroscopy (UPS) and experimental tunneling currents. The results reveal the strong effect of the dihedral angle between the planes of the graphene electrode and the aromatic molecule and imply that the molecules with the smallest dihedral angle are responsible for the largest local current densities. In addition, the results are consistent with the proposal that the orbitals which mediate tunneling are those with significant electron density in the molecular layer. These conclusions should prove valuable for understanding the relationships between molecular structure and electronic transport as an important step toward rational design of carbon-based molecular electronic devices

Extraction of elementary rate constants from global network analysis of central metabolism-1

On rate law (MRL) for estimation of the elementary rate constants. The same procedure can be used to estimate rate constants involved in other pathways.<p><b>Copyright information:</b></p><p>Taken from "Extraction of elementary rate constants from global network analysis of central metabolism"</p><p>http://www.biomedcentral.com/1752-0509/2/41</p><p>BMC Systems Biology 2008;2():41-41.</p><p>Published online 7 May 2008</p><p>PMCID:PMC2396597.</p><p></p

Initial Structural Models of the Aβ42 Dimer from Replica Exchange Molecular Dynamics Simulations

Experimental characterization of the molecular structure of small amyloid (A)­β oligomers that are currently considered as toxic agents in Alzheimer’s disease is a formidably difficult task due to their transient nature and tendency to aggregate. Such structural information is of importance because it can help in developing diagnostics and an effective therapy for the disease. In this study, molecular simulations and protein–protein docking are employed to explore a possible connection between the structure of Aβ monomers and the properties of the intermonomer interface in the Aβ42 dimer. A structurally diverse ensemble of conformations of the monomer was sampled in microsecond timescale implicit solvent replica exchange molecular dynamics simulations. Representative structures with different solvent exposure of hydrophobic residues and secondary structure content were selected to build structural models of the dimer. Analysis of these models reveals that formation of an intramonomer salt bridge (SB) between Asp23 and Lys28 residues can prevent the building of a hydrophobic interface between the central hydrophobic clusters (CHCs) of monomers upon dimerization. This structural feature of the Aβ42 dimer is related to the difference in packing of hydrophobic residues in monomers with the Asp23–Lys28 SB in on and off states, in particular, to a lower propensity to form hydrophobic contacts between the CHC domain and C-terminal residues in monomers with a formed SB. These findings could have important implications for understanding the difference between aggregation pathways of Aβ monomers leading to neurotoxic oligomers or inert fibrillar structures

Supramolecular Interactions in Secondary Plant Cell Walls: Effect of Lignin Chemical Composition Revealed with the Molecular Theory of Solvation

Plant biomass recalcitrance, a major obstacle to achieving sustainable production of second generation biofuels, arises mainly from the amorphous cell-wall matrix containing lignin and hemicellulose assembled into a complex supramolecular network that coats the cellulose fibrils. We employed the statistical-mechanical, 3D reference interaction site model with the Kovalenko–Hirata closure approximation (or 3D-RISM-KH molecular theory of solvation) to reveal the supramolecular interactions in this network and provide molecular-level insight into the effective lignin–lignin and lignin–hemicellulose thermodynamic interactions. We found that such interactions are hydrophobic and entropy-driven, and arise from the expelling of water from the mutual interaction surfaces. The molecular origin of these interactions is carbohydrate−π and π–π stacking forces, whose strengths are dependent on the lignin chemical composition. Methoxy substituents in the phenyl groups of lignin promote substantial entropic stabilization of the ligno-hemicellulosic matrix. Our results provide a detailed molecular view of the fundamental interactions within the secondary plant cell walls that lead to recalcitrance