Adsorption of TNT, DNAN, NTO, FOX7, and NQ Onto Cellulose, Chitin, and Cellulose Triacetate. Insights From Density Functional Theory Calculations

Insensitive munitions (IM) compounds such as DNAN (2,4-dinitroanisole), NTO (3-nitro-1,2,4-triazol-5-one), NQ (nitroguanidine), and FOX7 (1,1-diamino-2,2-dinitroethene) reduce the risk of accidental explosions due to shock and high temperature exposure. These compounds are being used as replacements for sensitive munition compounds such as TNT (2,4,6-trinitromethylbenzene) and RDX (1,3,5-hexahydro-1,3,5-trinitro-1,3,5-triazine). NTO and NQ in IM compounds are more soluble than TNT or RDX, hence they can easily spread in the environment and get dissolved if exposed to precipitation. DNAN solubility is comparable to TNT solubility. Cellulosic biomass, due to its abundance in the environment and its chemical structure, has a high probability of adsorbing these IM compounds, and thus, it is important to investigate the interactions between cellulose and cellulose like biopolymers (e.g. cellulose triacetate and chitin) with IM compounds. Using Density Functional Theory methods, we have studied the adsorption of TNT, DNAN, NTO, NQ, and FOX7 onto cellulose Iα and Iβ, chitin, and cellulose triacetate I (CTA I). Solvent effects on the adsorption were also investigated. Our results show that all contaminants are more strongly adsorbed onto chitin and cellulose Iα than onto CTA I and cellulose Iβ. Dispersion forces were found to be the predominant contribution to the adsorption energies of all contaminants

Role of Stone-Wales Defects on the Interfacial Interactions Among Graphene, Carbon Nanotubes, and Nylon 6: A First-Principles Study

We investigate computationally the role of Stone-Wales (SW) defects on the interfacial interactions among graphene, carbon nanotubes (CNTs), and Nylon 6 using density functional theory (DFT) and the empirical force-field. Our first-principles DFT calculations were performed using the Quantum ESPRESSO electronic structure code with the highly accurate van der Waals functional (vdW-DF2). Both pristine and SW-defected carbon nanomaterials were investigated. The computed results show that the presence of SW defects on CNTs weakens the CNT-graphene interactions. Our result that CNT-graphene interaction is much stronger than CNT-CNT interaction indicates that graphene would be able to promote the dispersion of CNTs in the polymer matrix. Our results demonstrate that carbon nanomaterials form stable complexes with Nylon 6 and that the van der Waals interactions, as revealed by the electronic charge density difference maps, play a key stabilizing role on the interfacial interactions among graphene, CNTs, and Nylon 6. Using the density of states calculations, we observed that the bandgaps of graphene and CNTs were not significantly modified due to their interactions with Nylon 6. The Young’s moduli of complexes were found to be the averages of the moduli of their individual constituents. Published by AIP Publishing. https://doi.org/10.1063/1.503208

Exploring Protein Functions by Molecular Modelling

Proteins are one of the most important families of biological macromolecules. Proteins can assume many different structures. This makes them perfect to serve a wide range of functions in all organisms. In the last decades, molecular modeling has become an important and powerful tool in the investigation of biological systems. Adopting different computational methods many protein functions and structure related problems can be explored. This thesis focuses on three different protein issues. The structural changes induced by high temperature on a large enzyme were investigated simulating the denaturation of glucose oxidase. Molecular dynamics (MD) simulations at different high temperatures were performed. The transition state of the denaturation process was found and the relative ensemble of structures characterized. Different protein properties were analyzed and found in agreement with experimental and theoretical data. Moreover the breaking points of the protein were localized and point mutations on the protein sequence were suggested. Antifreeze proteins (AFP) allow different organisms to survive in subzero environments. These proteins lower the freezing point of physiological fluids. MD simulations of the snow flea AFP (sfAFP) in water have shown partial instability of the protein structure. When attached to different ice planes at the ice/water interface, the sfAFP induces local ice melting. AFPs are divided into two categories: hyperactive and moderately active depending on their antifreeze power. The water diffusion profile of ice/water systems containing one protein from each family were compared. The ice/water interface width was found to be broadened to different extent by the two proteins, while a control protein (ubiquitin) did not affect the interface thickness. Hemoglobin is the oxygen carrier in all vertebrates. Mutation along the protein sequence can alter the protein functionality and its capability of binding molecular oxygen. Density Functional Theory methods were applied in the calculation of the oxygen binding energy of the wild type hemoglobin and four other variants. Evaluations on the electronic structures and on the binding energies of the different hemoglobin variants suggest that perhaps none of the mutated hemoglibins efficiently bind oxygen.At the time of the doctoral defense, the following paper was unpublished and had a status as follows: Paper 4: Manuscript.</p

The Effect of External Forces On the Initial Dissociation of RDX (1,3,5-trinitro-1,3,5-triazine): A Mechanochemical Study

Experimental and theoretical studies have proposed different initiation reactions for the decomposition of hexahydro-1,3,5-trinitro-1,3,5-triazine (RDX). Three primary reactions are considered to start RDX decomposition: homolytic NN bond fission, HONO elimination, and concerted fission of CN bonds. The focus of this article is to study the effect of external forces on the energy barrier and reaction energies of all three mechanisms. We used the Nudged Elastic Band method along with ab initio Density Functional Theory within the framework of a generalized force-modified potential energy surface (G-FMPES) to calculate the minimum energy paths at different compressive (corresponding to pressure between approximately 6 and 294 MPa) and expansive force values (between 10 and 264 pN). For all three reactions, the application of an expansive force increases the exothermicity and lowers the energy barriers to different extents, while a compressive force decreases the exothermicity and raises the energy barrier to different extents

A Mechanochemical Study of the Effects of Compression On a Diels-Alder Reaction

We examine the effects of compressive external forces on the mechanisms of the parent Diels-Alder (DA) reaction between butadiene and ethylene. Reaction pathways and transition states were calculated using the nudged elastic band method within a mechanochemical framework at the CASSCF(6,6)/6-31G**, as well as the B3LYP/6-311++G** levels of theory. Our results suggest that compressive hydrostatic pressure lowers the energy barrier for the parent DA reaction while suppressing the undesirable side reaction, thereby leading to a direct increase in the yield of cyclohexene. Compressive pressure also increases the exothermicity of the parent DA reaction, which would lead to increased temperatures in a reaction vessel and thereby indirectly increase the yield of cyclohexene. Our estimates indicate that the compression used in our study corresponds to a range of 68 MPa–1410 MPa

Induced Ice Melting by the Snow Flea Antifreeze Protein from Molecular Dynamics Simulations

Antifreeze proteins (AFP) allow different life forms, insects as well as fish and plants, to survive in subzero environments. AFPs prevent freezing of the physiological fluids. We have studied, through molecular dynamics simulations, the behavior of the small isoform of the AFP found in the snow flea (sfAFP), both in water and at the ice/water interface, of four different ice planes. In water at room temperature, the structure of the sfAFP is found to be slightly unstable. The loop between two polyproline II helices has large fluctuations as well as the C-terminus. Torsional angle analyses show a decrease of the polyproline II helix area in the Ramachandran plots. The protein structure instability, in any case, should not affect its antifreeze activity. At the ice/water interface the sfAFP triggers local melting of the ice surface. Bipyramidal, secondary prism, and prism ice planes melt in the presence of AFP at temperatures below the melting point of ice. Only the basal plane is found to be stable at the same temperatures, indicating an adsorption of the sfAFP on this ice plane as confirmed by experimental evidence

Inclusion of Chloromethane Guests Affects Conformation and Internal Dynamics of Cryptophane-D Host

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First-Principles of the Interactions Between Graphene Oxide and Amine-Functionalized Carbon Nanotube

We applied plane-wave density functional theory to study the effects of chemical functionalizations of graphene and carbon nanotube (CNT) on the properties of graphene–CNT complexes. The functionalizations of graphene and CNT were modeled by covalently attaching oxygen-containing groups and amines (NH2), respectively, to the surfaces of these carbon nanomaterials. Our results show that both dispersion energy and hydrogen bonding play crucial roles in the formation of complexes between graphene oxide (GO) and CNT–NH2. At a lesser degree of functionalization, the interaction energies between functionalized graphene and CNT were either unchanged or decreased, with respect to those without functionalization. Our study indicated that the gain or loss of interaction energy between graphene and CNT is a competition between two contributions: dispersion energy and hydrogen bonds. It was found that the heavy functionalization of graphene and CNT could be a promising route for enhancing the interaction energy between them. Specifically, the carboxyl-functionalized GO produced the greatest increase in the hydrogen bond strength relative to the dispersion energy loss. The influence of Stone–Wales defects in CNT on the computed interaction energies was also examined. The computed electron density difference maps revealed that the enhancement in the interaction energy is due to the formation of several hydrogen bonds between oxygen-containing groups of GO and NH2-groups of CNT. Our results show that Young’s moduli of carbon nanomaterials decrease with the increasing concentration of functional groups. The moduli of GO–CNT–NH2 complexes were found to be the averages of the moduli of their constituents

Inclusion of Chloromethane Guests Affects Conformation and Internal Dynamics of Cryptophane-D Host

Cryptophane-D is composed of two nonequivalent cyclotribenzylene caps bound together by three OCH₂CH₂O bridges in a syn arrangement. Host–guest complexes with chloroform and dichloromethane were investigated in solution by NMR spectroscopy. Variable temperature NMR ¹H and ¹³C spectra showed effects of chemical exchange between the free and bound guest and of conformational exchange for the host, strongly and specifically affected by guest binding. We found in particular that the carbon-13 chemical shifts for the linkers connecting the two cyclotribenzylene units are very informative. The NMR results were supported by DFT calculations. The guest exchange was also studied quantitatively, either by EXSY measurements (for chloroform as guest) or by line-shape analysis (for dichloromethane as guest). In the case of chloroform guest, we also investigated cross-relaxation between the guest and host protons, as well as carbon-13 longitudinal relaxation and heteronuclear NOE at three different fields. The results were interpreted in terms of orientation and dynamics of the guest inside the host cavity. Putting together various types of evidence resulted in remarkably detailed insight into the process of molecular recognition of the two guests by cryptophane-D host