Academic literature on the topic 'Thermochemistry of Molecules and Processes - Computational Study'

The CBS-QB3, CBS-APNO and Gaussian-3 model chemistries have been used to determine the ionic and neutral heats of formation and the adiabatic ionization energies ( IEa) derived therefrom, for the ca 30 principal isomers of the C3H2O•+ and the C4H4O•+ families of radical cations. Theory and experiment are in excellent agreement for those molecules whose experimental IEa has been accurately measured. In contrast, large deviations from the computed values were found for a great many ionic heats of formation reported in the literature. These deviations largely arise from the uncertainty in the heat of formation of the corresponding neutral species for which often only a rough estimate is available. A useful by-product of this study is that it permits the evaluation of new Benson-type group additivity ( GA) terms appropriate for highly unsaturated oxygen containing molecules. Several new GA terms are proposed but it is also argued that a single GA term for the ketene function cannot be defined.

This contribution firstly elucidates a structure–property relationship in third-order nonlinear optical molecular systems with singlet diradical characters. It turns out that the second hyperpolarizabilities (γ) of the singlet open-shell molecules with intermediate diradical characters are significantly enhanced as compared with those of closed-shell and pure diradical molecules. The hybrid density functional theory method, i.e. UBHandHLYP, is applied to the calculations of γ of dimer models composed of singlet diradical diphenalenyl molecules, which show a remarkable enhancement of γ per monomer as decreasing the intermolecular distance. The second contribution is concerned with a development of ab initio molecular orbital configuration-interaction-based quantum master equation (QME) approach. This is found to provide both coherent processes, e.g. dynamic polarization and exciton (electron–hole pair) recurrence motion, and incoherent processes, e.g. exciton migration, in molecular systems. Using this approach, the electron/hole dynamics for dynamic polarizabilities α(ω) are examined for several π-conjugated linear chain systems, and the structural dependences of α(ω) are elucidated.

Abstract Within the cold regions of space, ices that are enriched with carbon monoxide (CO) molecules are exposed to ionizing radiation, which triggers new reactions and desorption processes. Laboratory studies on astrochemical ices employing different projectiles have revealed the appearance of several new species. In this study, we employed the upgraded PROCODA code, which involves a calculation phase utilizing thermochemistry data, to map the chemical evolution of pure CO ice irradiated by cosmic-ray analogs. In the model, we have considered 18 different chemical species (six observed: CO, CO2, C3, O3, C2O, and C5O3; 12 unobserved: C, O, C2, O2, CO3, C3O, C4O, C5O, C2O2, C2O3, C3O2, and C4O2) coupled at 156 reaction routes. Our best-fit model provides effective reaction rates (effective rate constants, (ERCs)), branching ratios for reactions within reaction groups, several desorption parameters, and the characterization of molecular abundances at the chemical equilibrium (CE) phase. The most abundant species within the ice at the CE phase were atomic oxygen (68.2%) and atomic carbon (18.2%), followed by CO (11.8%) and CO2 (1.6%). The averaged modeled desorption yield and rate were 1.3e5 molecules ion−1 and 7.4e13 molecules s−1, respectively, while the average value of ERCs in the radiation-induced dissociation reactions was 2.4e-1 s−1 and for the bimolecular reactions it was 4.4e-24 cm3 molecule−1 s−1. We believe that the current kinetics study can be used in future astrochemical models to better understand the chemical evolution of embedded species within astrophysical ices under the presence of an ionizing radiation field.

The growth of SrTiO3 (STO) thin films is examined using classical molecular dynamics simulations. First, a beam of alternating SrO and TiO2 molecules is deposited on the (001) surface of STO with incident kinetic energies of 0.1, 0.5, or 1.0 eV/atom. Second, deposition of alternating SrO and TiO2 monolayers, where both have incident energies of 1.0 eV/atom, is examined. The resulting thin film morphologies predicted by the simulations are compared to available experimental data. The simulations indicate the way in which the incident energy, surface termination, and beam composition influence the morphology of the thin films. On the whole, some layer-by-layer growth is predicted to occur on both SrO- and TiO2-terminated STO for both types of deposition processes, with the alternating monolayer approach yielding thin films with compositions that are much closer to that of bulk STO.

Complex organic molecules such as sugars and amides are ubiquitous in star- and planet-forming regions, but their formation mechanisms have remained largely elusive until now. Here we show in a combined experimental, computational, and astrochemical modeling study that interstellar aldehydes and enols like acetaldehyde (CH3CHO) and vinyl alcohol (C2H3OH) act as key tracers of a cosmic-ray-driven nonequilibrium chemistry leading to complex organics even deep within low-temperature interstellar ices at 10 K. Our findings challenge conventional wisdom and define a hitherto poorly characterized reaction class forming complex organic molecules inside interstellar ices before their sublimation in star-forming regions such as SgrB2(N). These processes are of vital importance in initiating a chain of chemical reactions leading eventually to the molecular precursors of biorelevant molecules as planets form in their interstellar nurseries.

A number of azaheterocycles (pyridines, pyrroles and indoles) have been properly functionalized so that they can act as dienophiles in cycloaddition Diels–Alder processes. This work analyzed the reactive behavior of these molecules through mechanistic analysis and the regioselectivity of the process using computational calculation tools. Based on this knowledge, a study was conducted on the influences of reaction variables, in particular solvent, catalyst and microwave irradiation, to achieve favorable changes—shorter reaction times, more acceptable temperatures and better yields. Theoretical calculations allowed the development of predictive approaches, which were later experimentally corroborated. This analysis allowed us to make reasonable assumptions related to reaction mechanisms, which allowed—through the analysis of corresponding transition states—us to consider such reactions at the boundary between pericyclic and polar processes.

This study uses a computational model to characterize the myocardial deposition and retention of basic fibroblast growth factor (FGF-2) at the cellular level after intracoronary (IC) administration of exogenous FGF-2. The model is applied to the in situ conditions present within the myocardium of a dog for which the plasma pharmacokinetics resulting from IC injection of FGF-2 were recorded. Our estimates show that the processes involved in FGF-2 signaling are not diffusion limited; rather, the response time is determined by the reaction time of FGF-2 binding to cell surface receptors. Additionally, the processes of receptor secretion and internalization are found to play crucial roles in the FGF-2 dynamics; future experiments are required to quantify these processes. The model predictions obtained in this study suggest that IC administration of FGF-2 via either a single bolus or repetitive injections causes a transient increase (time scale of hours) in myocardial FGF-2 concentration if the endogenous level of free interstitial FGF-2 is low enough to allow permeation of FGF-2 molecules from the microvascular to the interstitial spaces. The model shows that the majority (64%) of the extracellular FGF-2 ligands are located within the interstitium, and similar fractions are found in the basement membrane and extracellular matrix. Among the FGF-2 molecules found within the interstitium, 2% are free and 98% are bound to interstitial heparan sulfate proteoglycans. These results support the theory of extracellular control of the bioavailability of FGF-2 via dynamic storage of FGF-2 within the basement membrane and extracellular matrix.

The work is aimed to solve the key problems of modern biophysics related to the study of fundamental mechanisms of interaction of ionizing radiation on living cells and stability of biological systems to its influence. The obtained data and their generalizations create a basis for understanding the interaction mechanisms and stability of biological systems to its influence. Investigation is aimed on the obtaining the new priority data about the characteristics of the life important biological molecules, establishing the mechanisms and features of dissociative capture, excitation and ionization under the slow electrons; the study of the influence of intermolecular interactions on these processes and solution of some applications concerning the definition of physical stability of biomolecules in different states of aggregation. The AM1 method that was used in research is a semi-empirical method for the quantum calculation of molecular electronic structure in computational chemistry. It is based on the neglect of differential diatomic overlap integral approximation and investigates the processes of formation of positive ions, which are formed during the interaction of thymine molecules with slow electrons. Fragmentation model of thymine molecules under electron ipmpact is proposed. Six most likely bond breaks in the cyclic structure of thymine molecular ion are identified. The obtained results are in good agreement with experimental data.

Single Molecule Science (SMS) has emerged from developing, using and combining technologies such as super-resolution microscopy, atomic force microscopy, and optical and magnetic tweezers, alongside sophisticated computational and modelling techniques. This comprehensive, edited volume brings together authoritative overviews of these methods from a biological perspective, and highlights how they can be used to observe and track individual molecules and monitor molecular interactions in living cells. Pioneers in this fast-moving field cover topics such as single molecule optical maps, nanomachines, and protein folding and dynamics. A particular emphasis is also given to mapping DNA molecules for diagnostic purposes, and the study of gene expression. With numerous illustrations, this book reveals how SMS has presented us with a new way of understanding life processes. A must-have for researchers and graduate students, as well as those working in industry, primarily in the areas of biophysics, biological imaging, genomics and structural biology.

AbstractInterstellar Grains (IGs) spread in the Interstellar Medium (ISM) host a multitude of chemical reactions that could lead to the production of interstellar Complex Organic Molecules (iCOMs), relevant in the context of prebiotic chemistry. These IGs are composed of a silicate-based core covered by several layers of amorphous water ice, known as a grain mantle. Molecules from the ISM gas-phase can be adsorbed at the grain surfaces, diffuse and react to give iCOMs and ultimately desorbed back to the gas phase. Thus, the study of the Binding Energy (BE) of these molecules at the water ice grain surface is important to understand the molecular composition of the ISM and its evolution in time. In this paper, we propose to use a recently developed semiempirical quantum approach, named GFN-xTB, and more precisely the GFN2 method, to compute the BE of several molecular species at the crystalline water ice slab model. This method is very cheap in term of computing power and time and was already showed in a previous work to be very accurate with small water clusters. To support our proposition, we decided to use, as a benchmark, the recent work published by some of us in which a crystalline model of proton-ordered water ice (P-ice) was adopted to predict the BEs of 21 molecules relevant in the ISM. The relatively good results obtained confirm GFN2 as the method of choice to model adsorption processes occurring at the icy grains in the ISM. The only notable exception was for the CO molecule, in which both structure and BE are badly predicted by GFN2, a real pity due to the relevance of CO in astrochemistry.

Bioremediation utilizes microbes to control environmental pollution, primarily through diverse enzymatic processes. With the incorporation of computation in biological experimentation, bioremediation has also been influenced by computational techniques. Molecular docking assay is one such pedestal of computational assisted bioremediation, which has been elaborated in this chapter. It helps in inferring whether the active site accommodate the pollutant molecules or not, depending on the stearic hindrance of the residues and nature of the active site pocket. The spotting of consequential active site residues and binding characteristics of compounds under study can conceivably be employed for site-directed mutagenic testing. From a vantage point, no one had expected such a remarkable usefulness of molecular docking assay for environmental research. Positive shades of low cost and efficiency, combined with eco-friendliness have made it a valuable method for analyzing biodegradative properties of enzymes responsible for pollution remediation.

Bioremediation utilizes microbes to control environmental pollution, primarily through diverse enzymatic processes. With the incorporation of computation in biological experimentation, bioremediation has also been influenced by computational techniques. Molecular docking assay is one such pedestal of computational assisted bioremediation, which has been elaborated in this chapter. It helps in inferring whether the active site accommodate the pollutant molecules or not, depending on the stearic hindrance of the residues and nature of the active site pocket. The spotting of consequential active site residues and binding characteristics of compounds under study can conceivably be employed for site-directed mutagenic testing. From a vantage point, no one had expected such a remarkable usefulness of molecular docking assay for environmental research. Positive shades of low cost and efficiency, combined with eco-friendliness have made it a valuable method for analyzing biodegradative properties of enzymes responsible for pollution remediation.

Nanobubbles appearing on the interface between liquid and the hydrophobic substrate play an important role in various natural and industrial processes. The current study presents the MD simulations of surface nanobubbles on the liquid-solid interface, where the liquid phase consists of argon and dissolved neon, while the gaseous phase consists of neon and argon vapor. The interactions between all the particles are determined by the Lennard-Jones potential. The contact angle is studied as a function of the Lennard-Jones parameters for the liquid-solid and gas-solid interactions. Moreover, the influence of gas concentration on the system behavior is studied. The simulations are performed for the systems of tens nm in size, which contain up to 8 million molecules. The computations are accelerated using modern computational methods and algorithms as well as using high-performance hardware such as graphic processors.

The ideal gas equation of state is defined for a theoretical gas composed of molecules that have perfect elastic collisions and no intermolecular interchange forces. However, it has been widely reported that such an ideal model may not be a realistic representation under certain circumstances, in particular when the compressibility factor (Z) is not close to unity, and the consideration of other equations of state (real models) is imperative. This study investigates the effect of using different equations of state, namely, the van der Waals, Redlich-Kwong, and Peng-Robinson equations, in the ideal isothermal analysis of a rotary displacer Stirling engine with the most commonly used gases, helium and air. The results are obtained numerically considering two major SE applications (cryocooling and distributed power generation) and two sets of operating conditions, and plotted in the form of Pressure-Volume diagrams. The amount of work per cycle based on the ideal gas model is taken as reference to compare the results from other models. The data show that at low pressure or high temperature conditions (corresponding to low density), the ideal gas equation is suitable for both gases, and using different models has no significant impact in the overall analysis. Additionally, while the use of ideal gas model is rather practical and fast, implementation of other models necessitate intensive computational processes.

The computational modeling of soot in aircraft engines is a formidable challenge, not only due to the multi-scale interactions with the turbulent combustion process but the equally complex physical and chemical processes that drive the conversion of gas-phase fuel molecules into solid-phase particles. In particular, soot formation is highly sensitive to the gas-phase composition and temporal fluctuations in a turbulent background flow. In this work, a large eddy simulation (LES) framework is used to study soot formation in a model aircraft combustor with swirl-based fuel and air injection. Two different configurations are simulated: one with and one without secondary oxidation jets. Specific attention is paid to the LES numerical implementation such that the discrete solver minimizes the dissipation of kinetic energy. Simulation of the model combustor shows that the LES approach captures the two recirculation zones necessary for flame stabilization very accurately. Further, the model reasonably predicts the temperature profiles inside the combustor. The model also captures variation in soot volume fraction with global equivalence ratio. The structure of the soot field suggests that when secondary oxidation jets are present, the inner recirculation region becomes fuel lean and soot generation is completely suppressed. Further, the soot field is highly intermittent suggesting that a very restrictive set of gas phase conditions promote soot generation.

Cell adhesion plays a pivotal role in diverse biological processes, including inflammation, tumor metastasis, arteriosclerosis, and thrombosis. Changes in cell adhesion can be the defining event in a wide range of diseases, including cancer, atherosclerosis, osteoporosis, and arthritis. Cells are exposed constantly to hemodynamic/hydrodynamic forces and the balance between the dispersive hydrodynamic forces and the adhesive forces generated by the interactions of membrane-bound receptors and their ligands determines cell adhesion. Therefore to develop novel tissue engineering based approaches for therapeutic interventions in thrombotic disorders, inflammatory, and a wide range of other diseases, it is crucial to understand the complex interplay among blood flow, cell adhesion, and vascular biology at the molecular level. In response to tissue injury or infection, polymorphonuclear (PMN) leukocytes are recruited from the bloodstream to the site of inflammation through interactions between cell surface receptors and complementary ligands expressed on the surface of the endothelium [1]. PMN-PMN interactions also contribute to the process of recruitment. It has been shown that PMNs rolling on activated endothelium cells can mediate secondary capture of PMNs flowing in the free blood stream through homotypic interactions [2]. This is mediated by L-selectin (ligand) binding to PSGL-1 (receptor) between a free-stream PMN and one already adherent to the endothelium cells [3]. Both PSGL-1 and L-selectin adhesion molecules are concentrated on tips of PMN microvilli [4]. Homotypic PMN aggregation in vivo or in vitro is supported by multiple L-selectin–PSGL-1 bondings between pairs of microvilli. The ultimate objective of our work is to develop software that can simulate the adhesion of cells colliding under hydrodynamic forces that can be used to investigate the complex interplay among the physical mechanisms and scales involved in the adhesion process. However, cell-cell adhesion is a complex phenomenon involving the interplay of bond kinetics and hydrodynamics. Hence, as a first step we recently developed a 3-D computational model based on the Immersed Boundary Method to simulate adhesion-detachment of two PMN cells in quiescent conditions and the exposing the cells to external pulling forces and shear flow in order to investigate the behavior of the nano-scale molecular bonds to forces applied at the cellular scale [5]. Our simulations predicted that the total number of bonds formed is dependent on the number of available receptors (PSGL-1) when ligands (L-selectin) are in excess, while the excess amount of ligands controls the rate of bond formation [5]. Increasing equilibrium bond length causes an increased intercellular contact area hence results in a higher number of receptor-ligand bonds [5]. Off-rates control the average number of bonds by modulating bond lifetimes while On-rate constants determine the rate of bond formation [5]. An applied external pulling force leads to time-dependent on- and off-rates and causes bond rupture [5]. It was shown that the time required for bond rupture in response to an applied external force is inversely proportional to the applied external force and decreases with increasing offrate [5]. Fig. 1 shows the time evolution of the total number of bonds formed for various values of NRmv (number of receptor) and NLmv (number of ligand). As expected, the total number of bonds formed at equilibrium is dependent on NRmv when NLmv is in excess. In this particular case study since two pairs (or four) microvilli each with NRmv are involved in adhesion hence the equilibrium bond number is approximately 4NRmv. It is noticed that for NRmv = 50, as we vary NLmv the mean value of the total number of bonds at equilibrium does not change appreciably. However, it can be noticed from Fig. 1 that for NRmv = 50, as the excess number of ligands (NLmv) increases there is a slight increase in the rate of bond formation due to the increase in probability of bond formation. Having developed confidence in the ability of the numerical method to simulate the adhesion of two cells that can form up to 200 bonds, we apply the method to study the effect of shear rate on the detachment of two cells. In particular, we first would like to establish the minimum shear rate needed for the two cells to detach for a given number of bonds between them. Fig. 2 shows the variation of force per bond at no rupture with number of bonds for various shear rates indicated. It is seen that at a given shear rate as the number of bonds increases the force per bond at no rupture decreases. This is attributed to the fact that force caused by shear flow is shared equally among the existing bonds. Further, it is seen that a given number of bonds as the shear rate increases the force per bond at no rupture increases. This is due to the fact that at a given number of bonds between the cells as we increase the shear rate the force caused by the flow increases hence the force per bond increases. We further notice that at shear rate = 3000 s−1 cells attached either by a single bond or by two bonds detach while they don’t for higher (> 2) number of bonds. This clearly demonstrate that there is a minimum shear rate needed to detach cells adhered by a given number of bonds. The higher the number of bonds, the higher the minimum shear rate for complete detachment of cells. For example, from Fig. 2 is it clear that for the cells adhered by two and five bonds the minimum shear rate needed for complete detachment of these two cells are 3000 s−1 and 6000 s−1, respectively.