Computational Study Of Structure Research Articles

Conformational Sampling in Computational Studies of Natural Products: Why Is It Important?

Conformational sampling is a vital component of a reliable computational chemistry investigation. With the aim of illustrating the importance of conformational sampling, and building awareness among new practitioners, we present a series of case studies that show how the quality and reliability of computational studies depend on undertaking a thorough conformer search. The examples are drawn from the most common types of research questions in natural products chemistry, but the fundamental principles apply more generally to computational studies of molecular structure and behavior in any field of chemistry.

A computational study of nematic core structure and disclination interactions in elastically anisotropic nematics.

A singular potential method in the Q tensor order parameter representation of a nematic liquid crystal is used to study the equilibrium configuration of a disclination dipole. Unlike the well studied isotropic limit (the so called one constant approximation), we focus on the case of anisotropic Frank elasticity (bend/splay elastic constant contrast). Prior research has established that the singular potential method provides an accurate description of the tensor order parameter profile in the vicinity of a disclination core of a highly anisotropic lyotropic chromonic liquid crystal. This research is extended here to two interacting disclinations forming a dipole configuration. The director angle is shown to decay in the far field inversely with distance to the dipole as is the case in the isotropic limit, but with a different angular dependence. Therefore elastic constant anisotropy modifies the elastic screening between disclinations, with implications for the study of ensembles of defects as seen, for example, in active matter in the extended system limit.

Experimental and computational study of heat transfer and flow structure of slotted impinging jet

Experimental and computational study of heat transfer and flow structure of slotted impinging jet

Computational Studies of Structure, Composition, and Electrochemical Behavior of Li-Ion Battery Components

Considerable efforts have been invested in recent decades to further the improvement of lithium-ion battery components – electrodes, solutions, and separators. In this presentation we will focus on recent computational work in our group on cathodes, anodes, and electrolyte solutions. We will show how computations are an essential part of the analytical toolbox, allowing deeper understanding of physical phenomenon related to energy materials. First, we will discuss studies on layered Ni-rich cathode materials (i.e., Li[Ni-Co-Mn]O2, NCM, family) for lithium-ion batteries.1 Specifically, we will discuss lattice doping with a range of high-valent dopants in NCM materials, which is one of the most promising approaches to improve electrochemical properties, cycle life, and thermal behavior. Second, we will study cation and anion intercalation phenomenon in MXene materials.2, 3Third, we will show some recent simulations on high-entropy materials.

Bulk and Surface Contributions to Ionisation Potentials of Metal Oxides

AbstractDetermining the absolute band edge positions in solid materials is crucial for optimising their performance in wide‐ranging applications including photocatalysis and electronic devices. However, obtaining absolute energies is challenging, as seen in CeO2, where experimental measurements show substantial discrepancies in the ionisation potential (IP). Here, we have combined several theoretical approaches, from classical electrostatics to quantum mechanics, to elucidate the bulk and surface contributions to the IP of metal oxides. We have determined a theoretical bulk contribution to the IP of stoichiometric CeO2 of only 5.38 eV, while surface orientation results in intrinsic IP variations ranging from 4.2 eV to 8.2 eV. Highly tuneable IPs were also found in TiO2, ZrO2, and HfO2, in which surface polarisation plays a pivotal role in long‐range energy level shifting. Our analysis, in addition to rationalising the observed range of experimental results, provides a firm basis for future interpretations of experimental and computational studies of oxide band structures.

Bulk and Surface Contributions to Ionisation Potentials of Metal Oxides.

Determining the absolute band edge positions in solid materials is crucial for optimising their performance in wide-ranging applications including photocatalysis and electronic devices. However, obtaining absolute energies is challenging, as seen in CeO2 , where experimental measurements show substantial discrepancies in the ionisation potential (IP). Here, we have combined several theoretical approaches, from classical electrostatics to quantum mechanics, to elucidate the bulk and surface contributions to the IP of metal oxides. We have determined a theoretical bulk contribution to the IP of stoichiometric CeO2 of only 5.38 eV, while surface orientation results in intrinsic IP variations ranging from 4.2 eV to 8.2 eV. Highly tuneable IPs were also found in TiO2 , ZrO2 , and HfO2 , in which surface polarisation plays a pivotal role in long-range energy level shifting. Our analysis, in addition to rationalising the observed range of experimental results, provides a firm basis for future interpretations of experimental and computational studies of oxide band structures.

CuO Nanoparticles and Microaggregates: An Experimental and Computational Study of Structure and Electronic Properties.

The link between morphology and properties is well-established in the nanoparticle literature. In this report, we show that different approaches in the synthesis of copper oxide can lead to nanoparticles (NPs) of different size and morphology. The structure and properties of the synthesized NPs are investigated with powder X-ray diffraction, scanning electron microscopy (SEM), and diffuse reflectance spectroscopy (DRS). Through detailed SEM analyses, we were able to correlate the synthetic pathways with the particles' shape and aggregation, pointing out that bare hydrothermal pathways yield mainly spheroidal dandelion-like aggregates, whereas, if surfactants are added, the growth of the nanostructures along a preferential direction is promoted. The effect of the morphology on the electronic properties was evaluated through DRS, which allowed us to obtain the electron bandgap in every system synthesized, and to find that the rearrangement of threaded particles into more compact structures leads to a reduction in the energy difference. The latter result was compared with Density Functional Theory (DFT) computational models of small centrosymmetric CuO clusters, cut from the tenorite crystal structure. The computed UV-Vis absorption spectra obtained from the clusters are in good agreement with experimental findings.

On the effects of adding syngas to an ammonia-MILD combustion regime—A computational study of the reaction zone structure

This study examines the reaction zone structure of syngas/NH3/CH4 blends in moderate or intense low oxygen dilution (MILD) conditions to determine the effects of variations in NH3 and syngas mole fractions upon the stability of the reacting system and NOx emission. A series of axisymmetric turbulent combustion simulations are performed using OpenFOAM and selected reaction mechanisms and, a modified version of the eddy dissipation concept. An increasing amount of syngas is added to the reacting mixtures of NH3/CH4 in MILD conditions. It is observed that a reduction in the NH3 mole fraction increases the OH radical concentration, which implies a reduction in the ignition delay. Further, for a given NH3 mole fraction, an increase in the syngas content of the fuel blend along with a reduction in CH4 leads to a rise in the process maximum temperature near the entrance zone. This reduces the flow temperature gradient, decreases the CH2O mass fraction, and boosts the stability of MILD combustion. Additionally, adding syngas to ammonia for MILD combustion decreases the reaction zone weakening, which is a major problem in MILD combustion of ammonia. In particular, blending syngas with NH3 and reducing the amount of CH4 in the fuel blend increases flame speed and heat generation. When syngas is added to ammonia MILD combustion, NOx and NxO decrease, and more complete combustion is achieved.

DFT calculations of photophysical properties of ethylen-dioxy-thiophen derivatives oligomers with optoelectronic functionalities

Materials with π-conjugated system can absorb sunlight, create photo-generated current or even produce light. The easiness of its manipulation combined with cheap process has made organic components provide a new attractive field for electronic materials research. This paper presents computational study of π-conjugated oligomers structure. In this regard, we used density functional theory (DFT) calculations to analyze the geometry of oligomers based of EDOT (3,4-ethylen dioxythiophen) and VC (vinyl-carbazol). The band gap with simulated spectra (UV–Vis spectra, emission spectra) and several photovoltaic properties like open-circuit photovoltage (Voc) and light harvesting efficiency (LHE) are predicted and discussed for giving theoretical knowledge of studied compound efficacity in photovoltaic applications.

A computational study of 3D flow structure in two consecutive bends subject to the influence of tributary inflow in the middle Yangtze River

Enhanced understanding of turbulent flow structure in bends in natural rivers is essential for waterway regulation, navigation safety and environmental and ecological wellbeing. However, the flow structure in consecutive bends has so far remained poorly understood, especially when it is subject to the influence of tributary inflow. Here, the 3D flow structure in two consecutive bends, namely Qigongling (upstream bend) and Guanyinzhou (downstream bend), subject to the influence of tributary inflow from the Dongting Lake, in the middle Yangtze River, is numerically investigated. The RNG k-ϵ turbulence model is applied under the FLOW-3D software platform. The results show that: (1) the high-velocity zones shift from inner to outer banks in both consecutive bends. (2) No secondary current cells are spotted at the entrance of either bend. At the bend apex, multiple cells of secondary currents appear in Qigongling, but not in Guanyinzhou under certain discharges. (3) Recirculation vortices occur mainly on the inner bank (small-scale) in Qigongling, but on both the inner (small-scale) and outer (large-scale) banks in Guanyinzhou. (4) With increasing mainstem (tributary) discharge, the velocity and turbulent kinetic energy enlarge (reduce). However, a decrease of the secondary current strength in Qigongling and an increase in Guanyinzhou (all increase in both bends).

Результаты расчетов напряженно-деформированного состояния и устойчивости грунтовой перемычки сухого дока с учетом ее перепрофилирования

The purpose of the work was to determine the stress-strain state, to check the bearing capacity of structures (sheet pile walls, anchor rods) and the overall stability of soil prisms of the «structure-enclosing soil mass» system, taking into account its re-profi ling. According to the scope of work, computational study of the sheet pile wall structure of the excavation under the buttress foundation was performed (specifying the adequacy of the solutions adopted in the drawings for the length and spacing of the tie rods and the bottom marks of the sheet pile walls by section, as well as the struts in the west abutment and the need for geotechnical anchors. The computational studies were carried out with the PLAXIS software package. In the fi nite-element model there were realized: conditions of contact interaction of media; nonlinear and plastic properties of materials; geometrical nonlinearity in the form of staggered erection and sequence of loadings application.

Electronic circular dichroism of proteins computed using a diabatisation scheme

ABSTRACT Circular dichroism (CD) spectroscopy is a powerful technique employed to study the structure of biomolecules. More accurate calculation of CD from first principles will aid both computational and experimental studies of protein structure and dynamics. We apply a diabatisation scheme to improve the description of nearest neighbour interactions between two electronic transitions (nπ* and πnbπ*) localised on each individual peptide bond (amide group) in a protein. These interactions are incorporated into DichroCalc, an exciton-based computational method to calculate CD, and yield improvements over the standard DichroCalc parameter set, particularly for calculation of CD for important secondary structural elements such as an α helix.

Crystallographic studies of fac- and mer-isomers of Cu[1,4,7,10,13,16-hexaazacyclooctadecane]2+. Influence of counterion and crystallization solvent on crystal structure and dynamic Jahn-Teller effects. Computational studies of structures, energetics, and mechanism of mer-fac isomerization

The syntheses and crystal structures of mer- and fac-isomers of [Cu(18N6)]2+(X−)2 are reported (18 N6 = 1,4,7,10,13,16-hexaazacyclooctadecane; X− = BF4−, ClO4−, NO3−) and compared to a previously reported example (X− = Cl−). Solution structures of the [Cu(18N6)]2+ dication in MeNO2 or MeOH are shown by FT-IR to be almost exclusively mer, and simple evaporation of these solutions or crystallization using Et2O co-solvent also afford the solid mer-salts. However, using C6H6 or CCl4 as crystallization co-solvents afforded the corresponding fac-isomers of the BF4− and ClO4− salts, in which the anions and the symmetrical solvent occupy locations on the crystallographic 3-fold axis. Similar treatment of the less symmetrical NO3− salts affords the mer-isomer without inclusion of C6H6. The solid-state structures of the mer-isomers each exhibit the anticipated tetragonal Jahn-Teller distortions, with two longer Cu-N bonds. In contrast the fac-isomers all show internally identical Cu-N distances, due to a dynamic exchange between Jahn-Teller distorted structures in the crystal. Density Functional Theory (DFT) is used to provide rationalizations of these observations and to elucidate an energetically feasible mechanistic pathway for the facile interconversion of mer and fac isomers in solution.

Engineering and Design of Programmable Genome Editors.

Programmable genome editors are enzymes that can be targeted to a specific location in the genome for making site-specific alterations or deletions. The engineering, design, and development of sequence-specific editors has resulted in a dramatic increase in the precision of editing for nucleotide sequences. These editors can target specific locations in a genome, in vivo. The genome editors are being deployed for the development of genetically modified organisms for agriculture and industry, and for gene therapy of inherited human genetic disorders, cancer, and immunotherapy. Experimental and computational studies of structure, binding, activity, dynamics, and folding, reviewed here, have provided valuable insights that have the potential for increasing the functional efficiency of these gene/genome editors. Biochemical and biophysical studies of the specificities of natural and engineered genome editors reveal that increased binding affinity can be detrimental because of the increase of off-target effects and that the engineering and design of genome editors with higher specificity may require modulation and control of the conformational dynamics.

Computational simulation-based study of novel ZnO Buckyball structures

A novel Zinc Oxide Buckyball (ZnO-b) system has been optimized using the first principle density functional theory (DFT). The study of the structural, electronic, and optical properties of both the pristine and Al, Ga, and Ag-doped ZnO-b and ZnO-h (ZnO hexagonal) systems have been reported here. A comparative study of the variations which occurred due to changes in the crystal structure, dopant element as well as doping site was done for both systems. The study includes the structural analysis followed by the electronic analysis with the study of Density of States (DOS), Partial Density of States (PDOS), and at last the Optical analysis of the systems. The bandgap engineering due to structural variations in ZnO is observed here as metal-doped ZnO-h structures showed a vast shift towards a smaller bandgap value, showing enhancement in the metallic behaviour, while for ZnO-b it varied between 1.52 eV–2.94 eV with similar doping. It was observed that mostly the value of the cell volume and the bandgap decreases with an increase in the atomic radii of the dopant atoms due to quantum confinement effects. Ag-doped sample has shown a better optical conductivity with lower absorbance as compared to other dopants in the ZnO-b structure, which makes it a suitable material for optoelectronic applications. Overall, in the buckyball structures properties of dopants are predominating whereas, in hexagonal structures, properties of ZnO are predominating. This makes the ZnO-b structure a useful material for biomedical applications along with optoelectronic devices. This work also opens a wide area of study for applications of these novel structures from biomedicines to optoelectronic devices by precisely controlling their physical properties.

A computational search for spin-crossover in bis(catecholate) diiron complexes

A DFT computational study of electronic structure, energy characteristics and magnetic properties of a series of the dinuclear iron complexes with 6,6′-[piperazine-1,4-diyl-bis(methylene)]bis[3,5-di-tert-butyl-pyrocatechol] and terminal tetradentate N-donor bases (tris(2-pyridylmethyl)amine and N,N'-dialkyl-2,11-diaza[3.3]-(2,6)pyridinophane derivatives) was performed. All the found electronic states were predicted to be paramagnetic. The relative energies of the isomers of the studied complexes were ascertained to be determined by the structural peculiarities of the ancillary nitrogen-containing ligands. The compounds prone to manifest a thermally initiated spin-crossover phenomenon were revealed. Synthetic availability of the proposed species opens up wide prospects for obtaining new promising magnetically active systems.

First-principles Study of Structure, Energetic and Infrared Spectrum for IceIh

We present the results of density functional based computational study of structure, cohesive energy and IR spectrum of iceIh, and compared with the experimental results. Within the our computational framework the sensitive to calculated structural properties including the zero point vibrations is estimated and shown to be small even though changes in zero point energies account for a significant fraction of the cohesive energy.

Fluorinated carbon and boron nitride fullerenes for drug Delivery: Computational study of structure and adsorption

We applied a genetic algorithm combined with the B3LYP/6-311G** approach to determine the structures of low-energy isomers of partially fluorinated fullerenes, the number of which is combinatorically huge. We found that the effective interaction of fluorine atoms on the fullerene surface can not be described within the pair approximation with sufficient accuracy. For the smallest C20 fullerene, the most robust bonding with fluorine was observed in the C20F2 isomer, whereas further fluorination was less feasible. For C60 fullerene, the most thermodynamically stable isomers were C60F2 and C60Fm with m about 40. Effective attraction energy of adsorbed fluorine atom with OH, NH2, and COOH functional groups on the C60 fullerene surface is about 1.24 eV. Vibration analysis of the stable C60Fm isomers clarified the frequencies shifts during the gradual fluorination. As to fluorinated derivatives of boron nitride cages, some of them possess extreme distortions under low fluorination. However, half- and fully-fluorinated BN fullerenes demonstrate moderate strain and strong van-der-Waals interaction with doxorubicin drug. Loading of doxorubicin on both carbon and boron nitride fullerenes with varying degrees of fluorination confirmed that fluorine concentration defines the energy of the fullerene-drug interaction. A half-fluorinated B12N12F12 cage provides the most substantial adsorption, as the fluorine atoms on its surface are more moveable and can “adjust” to the DOX molecule.

Modeling 13 Archimedean solids by and object-oriented language

The computational study of structures with chemical relevance is preceded by its modeling in such manner that no calculations can be submitted without the knowledge of their spatial atomic arrangement. In this regard, the use of an object-oriented language can be helpful both to generate the Cartesian coordinates (.xyz file format) and to obtain a ray-traced image. The modeling of chemical structures based on programming has some advantages with respect to other known strategies. The more important advantage is the generation of Cartesian coordinates that can be visualized easily by using free of charge software. Our approach facilitates the spatial vision of complex structures and make tangible the chemistry concepts delivered in the classroom. In this article an undergraduate project is described in which students generate the Cartesian coordinates of 13 Archimedean solids based on a geometrical/programming approach. Students were guided along the project and meetings were held to integrate their ideas in a few lines of programmed codes. They improved their decision-making process and their organization and collecting information capabilities, as much as their reasoning and spatial depth. The final products of this project are the coded algorithms and those made tangible the grade of learning/understanding derived of this activity.

Mechanism-Based Approach to Reagent Selection for Oxidative Carbon-Hydrogen Bond Cleavage Reactions.

Numerous hydride-abstracting agents generate the same cationic intermediate, but substrate features such as intermediate cation stability, oxidation potential, and steric environment can influence reaction rates in an oxidant-dependent manner. This manuscript provides experimental data to illustrate the role that structural features play in the kinetics of hydride abstraction reactions with commonly used quinone-, oxoammonium ion-, and carbocation- based oxidants. Computational studies of the transition state structures and energies explain these results and energy decomposition analysis calculations reveal unique sensitivities to electrostatic attraction and steric repulsions. Rigorous rate studies of select reactions validated the capacity of the calculations to predict reactivity trends. Additionally, kinetics studies demonstrate the potential for product inhibition in DDQ-mediated reactions. These studies provide a clear guide to select the optimal oxidant for structurally disparate substrates and lead to predictions of reactivity that were validated experimentally.