Simple Molecular Model Research Articles

Interactions between nodes in a physical gel network of telechelic polymers; self-consistent field calculations beyond the cell model.

Triblock copolymers, with associative end-groups and a soluble middle block, form flower-like micelles in dilute solutions and a physical gel at higher concentrations. In a gel the middle blocks form bridges between domains/nodes that contain the ends. We combine the self-consistent field theory with a simple molecular model to evaluate the pair potential between the nodes. In this model the end-groups are forced to remain in nodes and the soluble middle blocks are in solution. When the distance between the centres of the nodes is approximately the corona diameter, loops can transform into bridges, and the pair potential is attractive. Due to steric hindrance, the interaction is repulsive at smaller distances. Till now a cell-model has been used wherein a central node interacts through reflecting boundary conditions with its images in a spherical geometry. This artificial approach to estimate pair potentials is here complemented by more realistic three-gradient SCF models. We consider the pair interactions for (i) two isolated nodes, (ii) nodes positioned on a line (iii) a central node surrounded by its neighbours in simple cubic ordering, and (iv) a central node in a face centred cubic configuration of its neighbours. Qualitatively, the cell model is in line with the more refined models, but quantitative differences are significant. We also notice qualitative differences for the pair potentials in the specified geometries, which we interpret as a breakdown of the pairwise additivity of the pair potential. This implies that for course grained Monte Carlo or molecular dynamics simulations the best choice for the pair potentials depends on the expected node density.

Promotion of cell adhesion by low-molecular-weight hydrogel by Lys based amphiphile.

Hydrogels formed by low-molecular hydrogelators have been used as anti-microbial agents and cell-attachment materials. However the biomedical application of low-molecular gelators is slowly progressing compared to the hydrogels formed by polymer hydrogelator that is applied to biomedical application such as tissue engineering and biomedical regions. To obtain a simple molecular model for potent and prospective usage of low-molecular hydrogelators, we designed a Lys-based hydrogelator which was mimic to the poly cationic poly-l-lysine that promotes cells to attach to a plastic plate nonspecifically. The gel-coating led to cause 10-fold cell attachment compared to no-coating well. Also five-time cells were attached to the well compared to the poly-l-lysine coating. From the competitive assay, these hydrogels could interact with cells through electrostatic interaction between positive charge from -NH3(+) in the hydrogelator and negative charge from substances on the cell surface such as glycosaminoglycans. This strong adhesive ability can be useful for the tissue engineering and molecular glue regions using low-molecular hydrogels in the future.

Water effect on the bond dissociation energy of O–H and N–H bonds in phenol and aniline: The testing of simple molecular dynamics model

Abstract A chemical microsolvation model for solution phase bond dissociation enthalpy (BDE) evaluation by means of molecular dynamics is presented. In this simple model, the primary solvent effect on the BDE values was estimated by placing of five water molecules nearby the studied functional groups evenly. Furthermore, the secondary solvent effect was reflected using the conductor like screening model (COSMO). From the quantum-chemical point of view, the molecular dynamics simulations based on the B3LYP functional in rather small basis set were performed. Despite of the constitutional limitations of the proposed model, the obtained O-H and N-H BDE values in phenol (363 kJ mol-1) and aniline (369 kJ mol-1) are in good agreement with the experimental solution phase data.

A molecular prognostic model predicts esophageal squamous cell carcinoma prognosis.

BackgroundEsophageal squamous cell carcinoma (ESCC) has the highest mortality rates in China. The 5-year survival rate of ESCC remains dismal despite improvements in treatments such as surgical resection and adjuvant chemoradiation, and current clinical staging approaches are limited in their ability to effectively stratify patients for treatment options. The aim of the present study, therefore, was to develop an immunohistochemistry-based prognostic model to improve clinical risk assessment for patients with ESCC.MethodsWe developed a molecular prognostic model based on the combined expression of axis of epidermal growth factor receptor (EGFR), phosphorylated Specificity protein 1 (p-Sp1), and Fascin proteins. The presence of this prognostic model and associated clinical outcomes were analyzed for 130 formalin-fixed, paraffin-embedded esophageal curative resection specimens (generation dataset) and validated using an independent cohort of 185 specimens (validation dataset).ResultsThe expression of these three genes at the protein level was used to build a molecular prognostic model that was highly predictive of ESCC survival in both generation and validation datasets (P = 0.001). Regression analysis showed that this molecular prognostic model was strongly and independently predictive of overall survival (hazard ratio = 2.358 [95% CI, 1.391–3.996], P = 0.001 in generation dataset; hazard ratio = 1.990 [95% CI, 1.256–3.154], P = 0.003 in validation dataset). Furthermore, the predictive ability of these 3 biomarkers in combination was more robust than that of each individual biomarker.ConclusionsThis technically simple immunohistochemistry-based molecular model accurately predicts ESCC patient survival and thus could serve as a complement to current clinical risk stratification approaches.

Size, Dimensionality, and Strong Electron Correlation in Nanoscience

In electronic structure theory, electron-electron repulsion is normally considered only in an average (or mean field) sense, for example, in a single Hartree-Fock determinant. This is the simple molecular orbital model, which is often a good approximation for molecules. In infinite systems, this averaging treatment leads to delocalized electronic bands, an excellent description of bulk 3D sp(3) semiconductors. However, in reality electrons try to instantaneously avoid each other; their relative motion is correlated. Strong electron-electron repulsion and correlation create new collective states and cause new femtosecond kinetic processes. This is especially true in 1D and 2D systems. The quantum size effect, a single electron property, is widely known: the band gap increases with decreasing size. This Account focuses on the experimental consequences of strong correlation. We first describe π-π* excited states in carbon nanotubes (CNTs). To obtain the spectra of individual CNTs, we developed a white-light, right-angle resonant Rayleigh scattering method. Discrete exciton transitions dominate the optical absorption spectra of both semiconducting and metallic tubes. Excitons are bound neutral excited states in which the electron and hole tightly orbit each other due to their mutual Coulomb attraction. We then describe more generally the independent roles of size and dimensionality in nanoelectronic structure, using additional examples from graphene, trans-polyacetylene chains, transition metal dichalcogenides, organic/inorganic Pb iodide perovskites, quantum dots, and pentacene van der Waals crystals. In 1D and 2D chemical systems, the electronic band structure diagram can be a poor predictor of properties if explicit correlation is not considered. One- and two-dimensional systems show quantum confinement and especially strong correlation as compared with their 3D parent systems. The Coulomb interaction is enhanced because the electrons are on the surface. One- and two-dimensional systems can exhibit essentially molecular properties even though they are infinite in size. Zero-dimensional Qdots show quantum confinement and modest electron correlation. Correlation is weak in 3D bulk semiconductors. Strongly correlated electronic states can behave as if they have fractional charge and effectively separate the spin and charge of the electron. This is apparent in the "soliton" state of polyacetylene, the fractional charge quantum Hall state of graphene, and the Luttinger electrical conductivity of metallic CNTs.

Assessing Ionic Liquids Experimental Data Using Molecular Modeling: [Cnmim][BF4] Case Study

A theoretical tool, the soft-SAFT equation of state combined with the Free-Volume Theory (FVT), is used for the calculation of thermodynamic and transport properties to (1) discriminate among discrepancies observed in different experimental data sets, (2) evaluate its capacity of extrapolation and predictability by comparing to experimental data, and (3) explore phase diagram regions where no experimental measurements are available. The well-known [Cnmim][BF4] ILs family is chosen as a case study. Once a simple but reliable molecular model is proposed for this family, the density of several [Cnmim][BF4] compounds is predicted using correlations of the molecular parameters as a function of the molecular weight. A comparison with different data sets showing discrepancies is addressed from the modeling results. The density of these compounds at high pressures is predicted and compared to the available data. The exploration of the phase diagram region is given by the study of immiscibility gaps in CO2 + [Cnmi...

Density functional theory study on mechanisms of epoxy‐phenol curing reaction

A comprehensive picture on the mechanism of the epoxy-phenol curing reactions is presented using the density functional theory B3LYP/ 6-31G(d,p) and simplified physical molecular models to examine all possible reaction pathways. Phenol can act as its own promoter by using an addition phenol molecule to stabilize the transition states, and thus lower the rate-limiting barriers by 27.0-48.9 kJ/mol. In the uncatalyzed reaction, an epoxy ring is opened by a phenol with an apparent barrier of about 129.6 kJ/mol. In catalyzed reaction, catalysts facilitate the epoxy ring opening prior to curing that lowers the apparent barriers by 48.9-50.6 kJ/mol. However, this can be competed in highly basic catalysts such as amine-based catalysts, where catalysts are trapped in forms of hydrogen-bonded complex with phenol. Our theoretical results predict the activation energy in the range of 79.0-80.7 kJ/mol in phosphine-based catalyzed reactions, which agrees well with the reported experimental range of 54-86 kJ/mol.

Equilibrium, interfacial and transport properties of n-alkanes: Towards the simplest coarse grained molecular model

In this work, using molecular dynamics simulations, we have investigated how simple could be a coarse grained molecular model yielding simultaneously equilibrium densities, surface tensions and transport properties of some n-alkanes (from methane to n-decane) along the vapour–liquid equilibrium curve. For that purpose, as an initial model, the fully flexible Lennard–Jones Chain (3 “molecular” parameters) model has been chosen. Using this simple molecular model, good results have been obtained on equilibrium properties of all tested n-alkanes despite a systematic slight overestimation of critical temperatures, critical pressures and surface tensions. In addition, concerning transport properties, good results have been obtained for methane and n-butane except for thermal conductivity in the gas state. For n-heptane and n-decane it has been found that thermal conductivity is systematically underestimated while viscosity is well estimated except at low temperatures. Concerning thermal conductivity, this misevaluation can be corrected if the zero-density thermal conductivity is known. Concerning shear viscosity, it is found that an additional “rigidity” fourth parameter is required to improve the results when dealing with the longest chains at the lowest temperatures.

DFT study of metal cation-induced hydrogelation of cellulose nanofibrils

We report a density functional theory study of cation-induced bonding between carboxylated cellulose nanofibrils (CNFs). We describe a methodology of using cleaved cellulose crystal unit cells to develop simple surface and molecular models of charged CNFs. We compare bond lengths, binding energies, and displaced solvation volumes for interfibril models intercalated with alkali, alkaline earth, main group, or transition metal cations, surrounded by an implicit solvent. We characterize the type of bonding interactions that occur between metal cations, Mn+ and carboxylated CNF surfaces by calculating the electronic density of states and Mayer bond orders. We find that Mn+–O interactions for alkaline earth metal systems are predominantly electrostatic whereas transition metal cations form stronger, more covalent bonds with enhanced valence orbital overlap. Our results show that multivalent—as opposed to monovalent—ions can create CNF networks by effectively crosslinking multiple fibrils through surface carboxylate anions. Our computational results agree with empirical models of metal–carboxylate binding, while also providing a deeper understanding of the bonding mechanisms for different cations. Our findings help to explain trends in recent CNF hydrogelation experiments, and we also predict the existence of two new hydrogels—CNF-Mg2+ and CNF-Zr4+.

Development of simple and transferable molecular models for biodiesel production with the soft-SAFT equation of state

The knowledge of fatty acid esters/biodiesels thermodynamic properties is crucial not only for developing optimal biodiesel production and purification processes, but also for enhancing biodiesels performance in engines.This work is intended to apply a simple but reliable theoretically based sound model, the soft-SAFT EoS, as a tool for the development, design, scale-up, and optimization of biodiesels production and purification processes.A molecular model within the soft-SAFT EoS framework is proposed for the fatty acid esters, and the Density Gradient Theory approach is coupled into soft-SAFT for the description of interfacial properties, while the Free-Volume Theory is used for the calculation of viscosities, in an integrated model.For pressures up to 150MPa, and in the temperature range 288.15–423.15K, density, surface tension, viscosity and speed of sound data for fatty acid methyl and ethyl esters, ranging from C8:0 to C24:0, with up to three unsaturated bonds, are described with deviations inferior to 5%.Finally, in order to validate the predictive ability of the model to be applied in the biodiesel groundwork, the high pressure densities and viscosities for 8 biodiesels were predicted with the soft-SAFT EoS, reinforcing the validity of the approach to obtain reliable predictions for engineering purposes.

Molecular Force Field Development for Aqueous Electrolytes: 1. Incorporating Appropriate Experimental Data and the Inadequacy of Simple Electrolyte Force Fields Based on Lennard-Jones and Point Charge Interactions with Lorentz-Berthelot Rules.

It is known that none of the available simple molecular interaction models of aqueous electrolytes based on SPC/E water and their associated force fields are able to reproduce the concentration dependence of important thermodynamic properties of even the simplest electrolyte, NaCl, at ambient conditions over the entire experimentally accessible concentration range [ Mouc̆ka , F. ; Nezbeda , I. ; Smith , W. R. J. Chem. Phys. 2013 , 138 , 154102 ]. This paper explores the possibility of improving their performance by incorporating concentration-dependent experimental data for the total ionic chemical potential and the density into the fitting procedure, in addition to experimental values of solubility and solid chemical potential. We describe a general parameter estimation methodology for a studied class of models that incorporates the aforementioned experimental data. When the entire concentration range is considered, although the resulting force field is a slight improvement over others currently available in the literature, overall quantitative agreement with the experimental data over this range remains unsatisfactory. This indicates an inherent limitation of such simple molecular interaction models and strongly suggests that more complex mathematical forms of such models are required to quantitatively predict the properties of aqueous electrolyte solutions when the entire concentration range is of interest. Our parameter estimation methodology is also applicable to such cases.

Molecular Dynamics Simulations of Water/Mucus Partition Coefficients for Feeding Stimulants in Fish and the Implications for Olfaction

The odorant partition coefficient is a physicochemical property that has been shown to dramatically influence odorant deposition patterns in the mammalian nose, leading to a chromatographic separation of odorants along the sensory epithelium. It is unknown whether a similar phenomenon occurs in fish. Here we utilize molecular dynamics simulations, based on a simplified molecular model of olfactory mucus, to calculate water/mucus partition coefficients for amino acid odorants (alanine, glycine, cysteine, and valine) that are known to elicit feeding behavior in fish. Both fresh water and salt water environments are considered. In fresh water, all four amino acids prefer the olfactory mucus phase to water, and the partition coefficient is shown to correlate with amino acid hydrophobicity. In salt water, a reversal in odorant partitioning is found, where each of the feeding stimulants (except glycine) prefer the water phase to olfactory mucus. This is due to the interactions between the salt ions and the odorant molecules (in the water phase), and between the salt and simplified mucin (in the olfactory mucus phase). Thus, slightly different odorant deposition patterns may occur in the fish olfactory organ in fresh and salt water environments. However, in both underwater environments we found that the variation of the water/mucus odorant partition coefficient is approximately one order of magnitude, in stark contrast to air/mucus odorant partition coefficients that can span up to six orders of magnitude. We therefore anticipate relatively similar deposition patterns for most amino acid odorants in the fish olfactory chamber. Thus, in contrast to terrestrial species, living in an underwater environment may preclude appreciable chromatographic odorant separation that may be used for spatial coding of odor identity across the olfactory epithelium. This is consistent with the reported lack of spatial organization of olfactory receptor neurons in the fish olfactory epithelium.

Pack it up, Pack it in: Unraveling H-NS Mediated Genome Packaging

Pack it up, Pack it in: Unraveling H-NS Mediated Genome Packaging

Farinin: Characterization of a Novel Wheat Endosperm Protein Belonging to the Prolamin Superfamily

Starch granule surface-associated proteins were separated by HPLC and identified by direct protein sequencing. Among the proteins identified was one that consisted of two polypeptide chains of 11 and 19 kDa linked by disulfide bonds. Sequencing of tryptic peptides from each of the polypeptides revealed similarities between some of the peptides and avenin-like b proteins encoded by partial cDNAs in NCBI. To identify a contiguous sequence that matched all of the peptides, contigs encoding three avenin-like b proteins were constructed from ESTs of the cultivar Butte 86. All peptide sequences were found in a protein encoded by one of these contigs that had not been identified previously. Protein and DNA sequences indicated that the two polypeptide chains were derived from a parent protein that had been cleaved at the C-terminal position of an asparagine residue. The name farinin is suggested for this protein and other avenin-like b proteins. Evolutionary relationships of the protein are discussed and a simple computer molecular model was constructed. On the basis of its sequence, the new protein was likely to be allergenic but unlikely to be active in celiac disease.

Impact of Confinement-Induced Cooperative Molecular Orientation Change on the Ferroelectric Size Effect in Ultrathin P(VDF-TrFE) Films

We demonstrate a distinct confinement induced cooperative lattice orientation change in ultrathin P(VDF-TrFE) films by using various characterization techniques, including X-ray diffraction (XRD), two-dimensional X-ray diffraction (2D-XRD), grazing incidence X-ray diffraction (GIXD), and infrared reflection absorption spectra (IRRAS). Both the polymer chains and the molecular dipoles that are perpendicular to the polymer backbone showed a lying-down orientation change with decreasing thickness. The dipole orientation change showed a good correlation with the thickness dependence of remnant polarization, which were measured from highly reproducible ferroelectric loops in a wide range of thickness (30–250 nm) on inert electrode with suppressed “dead layer” effect. A simple microscopic molecular dipole interaction model revealed that the free energy of different orientation states was related to the thickness and lateral dimension of the polymer crystallites. The findings reveal a unique molecular orientation driven size effect in ferroelectric polymer films, providing new insights into the nature of ferroelectricity and orientation mechanisms in polymers relevant to the design of emerging flexible electronic devices.

Cob(I)alamin: Insight Into the Nature of Electronically Excited States Elucidated via Quantum Chemical Computations and Analysis of Absorption, CD and MCD Data

The nature of electronically excited states of the super-reduced form of vitamin B(12) (i.e., cob(I)alamin or B(12s)), a ubiquitous B(12) intermediate, was investigated by performing quantum-chemical calculations within the time-dependent density functional theory (TD-DFT) framework and by establishing their correspondence to experimental data. Using response theory, the electronic absorption (Abs), circular dichroism (CD) and magnetic CD (MCD) spectra of cob(I)alamin were simulated and directly compared with experiment. Several issues have been taken into considerations while performing the TD-DFT calculations, such as strong dependence on the applied exchange-correlation (XC) functional or structural simplification imposed on the cob(I)alamin. In addition, the low-lying transitions were also validated by performing CASSCF/MC-XQDPT2 calculations. By comparing computational results with existing experimental data a new level of understanding of electronic excitations has been established at the molecular level. The present study extends and confirms conclusions reached for other cobalamins. In particular, the better performance of the BP86 functional, rather than hybrid-type, was observed in terms of the excitations associated with both Co d and corrin π localized transitions. In addition, the lowest energy band was associated with multiple metal-to-ligand charge transfer excitations as opposed to the commonly assumed view of a single π → π* transition followed by vibrational progression. Finally, the use of the full cob(I)alamin structure, instead of simplified molecular models, shed new light on the spectral analyses of cobalamin systems and revealed new challenges of this approach related to long-range charge transfer excitations involving side chains.

A Density Functional Theory Study of Secondary Reactions in n‐Butyl Acrylate Free Radical Polymerization

AbstractIn this work, secondary reactions involved in the free radical polymerization of butyl acrylate are investigated using quantum chemistry. First, various backbiting reactions are studied by adopting a simplified molecular model suitable for treating long polymer chains. The predicted reaction kinetics suggest the possibility of a radical migration along the poly(butyl acrylate) (PBA) chain as a consequence of subsequent j:j + 4 hydrogen abstractions, which are characterized by a low activation energy. Moreover, branching propagation and β‐scission reactions originating from mid‐chain radicals are investigated using a complete PBA model composed of five monomer units. The reaction kinetics involving short‐branch radicals are also examined, and a novel backbiting step leading to the formation of short branches is proposed. magnified image

Fukui and dual-descriptor matrices within the framework of spin-polarized density functional theory

This work deals with the Fukui and dual reactivity descriptors within the framework of the spin-polarized density functional theory. The first and second derivatives of the electron density and the spin density with respect to the total number of electrons N = Nα + Nβ and with respect to the spin number NS = Nα-Nβ have been formulated by means of reduced density matrices in the representation of the spin-orbitals of a given basis set, providing the matrix extension of those descriptors. The analysis of the eigenvalues and eigenvectors of the Fukui and dual-descriptor matrices yields information on the role played by the molecular orbitals in charge-transfer and spin-polarization processes. This matrix formulation enables determining similarity indices which allows one to evaluate quantitatively the quality of the simple frontier molecular orbital model in conceptual density functional theory. Selected closed- and open-shell systems in different spin symmetries have been studied with this matrix formalism at several levels of electronic correlation. The results confirm the suitability of this approach.

Plugging the explicit σ-holes in molecular docking

A novel approach in molecular docking was successfully used to reproduce protein-ligand experimental geometries. When dealing with halogenated compounds the correct description of halogen bonds between the ligand and the protein is shown to be essential. Applying a simple molecular mechanistic model for halogen bonds improved the protein-ligand geometries as well as halogen bond features, which makes it a promising tool for future computer-aided drug development.

A simple molecular modeling method for the characterization of polymeric drug carriers

A simple molecular modeling method for the characterization of polymeric drug carriers is presented. Six biodegradable polymers have been investigated as drug carriers using molecular simulations: l-polylactide, d-polylactide, chitosan, polyglycolic acid, polyethylene glycol and cellulose. Cyclosporine A has been chosen as a model drug substance. Classical molecular dynamics and docking calculations were employed to model and predict polymer–drug interactions. These interactions have been analyzed by non-bond interaction energy and interaction parameter calculated using Flory–Huggins theory. Flexibility of polymer chains has been characterized by the change of gyration radius along the molecular dynamics trajectory. The relationship between mixing energy, chain length and chain flexibility has been revealed for each polymer/drug system.