Computational Chemistry Calculations Research Articles

A comparative study on ozone, hydrogen peroxide and UV based advanced oxidation processes for efficient removal of diethyl phthalate in water.

Several Advanced Oxidation Processes (AOPs) including O3/H2O2, O3/TiO2, O3/activated carbon (AC), O3/Al2O3, O3/Fe2+/H2O2 and UV/TiO2 have been investigated and compared for the removal of diethyl phthalate (DEP), an endocrine disrupting compound, in aqueous solutions. Hydroxyl radicals were the main species responsible for DEP degradation and this was supported by computational chemistry calculation, scavenger experiments, and LC/MS/MS analysis. The change of the abundance of reaction products over time was determined. Organic acids as well as anhydride and hydroxylated products were found to accumulate in solution even after long reaction time (2 h). Careful choice of the operating parameters (pH, ozone concentration and catalyst dosage) was crucial to achieve enhanced performance of the combined processes above what each oxidant and catalyst can achieve alone. O3/AC process was found to reduce the oxidation efficiency of O3 at high ozone concentrations. Heterogeneous catalytic ozonation with Al2O3 was the most effective process for DEP removal (∼100% removal in about 15 min) and based on pseudo-first-order kinetics at pH7, the studied oxidation processes followed the order: O3/Al2O3(0.093 min-1)>O3/H2O2/Fe2+(0.076 min-1)>O3/AC(0.069 min-1)>O3/H2O2(0.053 min-1)>O3/TiO2(0.050 min-1)> O3 alone (0.039 min-1)>UV/TiO2(0.009 min-1).

The Synergistic Effect of Chloride Ion and 1,5-Diaminonaphthalene on the Corrosion Inhibition of Mild Steel in 0.5 M Sulfuric Acid: Experimental and Theoretical Insights.

The inhibition efficiency of 1,5-Diaminonaphthalene (1,5DNA) compound was studied by itself as well as in a mixture that included sodium chloride (NaCl), noted [1.5DNA][Cl−], for mild steel in 0.5 M sulfuric acid. Gravimetric, electrochemical techniques and computational chemistry calculations were utilized for the assessment of corrosion inhibition efficiency and explanation of the mechanism involved during the corrosion inhibition process. The results show that inhibition efficiencies on mild steel increase with increase in concentration of the inhibitor and enhancement in inhibition efficiency was observed on addition of sodium chloride due to synergism. This inhibition has been attributed to the stabilization of adsorbed inhibitor film and, consequently, increasing its inhibitive properties. The [1.5DNA][Cl−] acts as mixed type inhibitor and the Nyquist curves show that with the increase in the concentration, the charge transfer resistance Rct increased. In addition, [1.5DNA][Cl−] obeyed Langmuir monolayer adsorption isotherm. Moreover, Molecular Dynamic Simulations and DFT calculations showed that [1.5DNA][Cl−] owned a higher adsorption ability.

Novel dichloro(bis{2-[1-(4-methylphenyl)-1H-1,2,3-triazol-4-yl-κN3]pyridine-κN})metal(II) coordination compounds of seven transition metals (Mn, Fe, Co, Ni, Cu, Zn and Cd)

The synthesis, characterization, DFT and, in two cases, the structure of seven novel dichloro(bis{2-[1-(4-methylphenyl)-1H-1,2,3-triazol-4-yl-κN3]pyridine-κN})metal(II) coordination compounds ([M(L2)2Cl2]), containing transition metals of groups 7–12, are described. Both experimentally measured magnetic moment and DFT calculations showed that d5 Mn(II) (with µeff = 5.62 B.M., S = 5/2), d6 Fe(II) (with µeff = 5.26 B.M., S = 2), d7 Co(II) (with µeff = 3.98 B.M., S = 3/2), d8 Ni(II) (with µeff = 3.00 B.M., S = 1) and d9 Cu(II) (with µeff = 1.70 B.M., S = ½) are all paramagnetic, while d10 Zn(II) and Cd(II) are diamagnetic with S = 0. DFT calculations on the possible isomers of these coordination compounds, showed that the cis–cis–trans and the trans–trans–trans isomers, with the pyridyl groups trans to each other, are the lowest in energy. The trans–trans–trans isomers were experimentally characterized by X-ray crystallography for [Ni(L2)2Cl2] and [Zn(L2)2Cl2]·L2 in this study. In the solid state the coordination compounds are connected by intermolecular hydrogen bonds, mainly involving the chloride atoms, to form 3D supramolecular structures. Computational chemistry calculations, using Natural Bonding Orbital calculations, identified these inter-molecular hydrogen bonds, CH⋯Cl, by a donor–acceptor interaction from a filled lone pair NBO on Cl to an empty antibonding NBO on (CH). The inter-molecular hydrogen bonds were also identified by QTAIM determined bonding paths between Cl and the respective hydrogen. The theoretically calculated computational chemistry results thus give an understanding on a molecular level why in the solid state where inter-molecular forces and packing play a role, the trans–trans–trans isomers are mostly obtained.

The Role of Defects in Fe(II)-Goethite Electron Transfer.

Despite substantial experimental evidence for Fe(II)-Fe(III) oxide electron transfer, computational chemistry calculations suggest that oxidation of sorbed Fe(II) by goethite is kinetically inhibited on structurally perfect surfaces. We used a combination of 57Fe Mössbauer spectroscopy, synchrotron X-ray absorption and magnetic circular dichroism (XAS/XMCD) spectroscopies to investigate whether Fe(II)-goethite electron transfer is influenced by defects. Specifically, Fe L-edge and O K-edge XAS indicates that the outermost few Angstroms of goethite synthesized by low temperature Fe(III) hydrolysis is iron deficient relative to oxygen, suggesting the presence of defects from Fe vacancies. This nonstoichiometric goethite undergoes facile Fe(II)-Fe(III) oxide electron transfer, depositing additional goethite consistent with experimental precedent. Hydrothermal treatment of this goethite, however, appears to remove defects, decrease the amount of Fe(II) oxidation, and change the composition of the oxidation product. When hydrothermally treated goethite was ground, surface defect characteristics as well as the extent of electron transfer were largely restored. Our findings suggest that surface defects play a commanding role in Fe(II)-goethite redox interaction, as predicted by computational chemistry. Moreover, it suggests that, in the environment, the extent of this interaction will vary depending on diagenetic history, local redox conditions, as well as being subject to regeneration via seasonal fluctuations.

Gas-phase fragmentation reactions of protonated cocaine: New details to an old story.

AbstractWe have used a combination of multiple stage mass spectrometry (MSn) experiments, hydrogen/deuterium exchange experiments, and thermochemical data estimated by computational chemistry calculations at the B3LYP/6‐31+G(d,p) level of theory to revisit the gas‐phase fragmentation of protonated cocaine. The lone pair of nitrogen participates in major fragmentation routes of protonated cocaine, to generate cyclic iminium ions. The structure of product ion m/z 182, which has been previously proposed in the literature, was shown to be unstable; therefore, we have decided to revisit it. Here, we propose another ion structures for the product ion m/z 182 that is supported by thermochemical data. Compared with the formation of other product ions, the formation of the most intense product ions in the collision‐induced dissociation spectrum of protonated cocaine (m/z 182 and m/z 82) is the most energetically favorable. We propose the structure and formation of m/z 122 and m/z 91 for the first time. We suggest that m/z 91 originates from m/z 122 instead of m/z 119, as fully supported by MSn experiments. The results of this study could help to study and quantify cocaine metabolites.

Mechanistic Studies on the Michael Addition of Amines and Hydrazines To Nitrostyrenes: Nitroalkane Elimination via a Retro-aza-Henry-Type Process.

In this article we report on the mechanistic studies of the Michael addition of amines and hydrazines to nitrostyrenes. Under the present conditions, the corresponding N-alkyl/aryl substituted benzyl imines and N-methyl/phenyl substituted benzyl hydrazones were observed via a retro-aza-Henry-type process. By combining organic synthesis and characterization experiments with computational chemistry calculations, we reveal that this reaction proceeds via a protic solvent-mediated mechanism. Experiments in deuterated methanol CD3OD reveal the synthesis and isolation of the corresponding deuterated intermediated Michael adduct, results that support the proposed slovent-mediated pathway. From the synthetic point of view, the reaction occurs under mild, noncatalytic conditions and can be used as a useful platform to yield the biologically important N-methyl pyrazoles in a one-pot manner, simple starting with the corresponding nitrostyrenes and the methylhydrazine.

Analysis and Validation of Dipole Moment Calculations in Chemistry Teaching

In this paper, we analyze and validate of an alternative proposal for the understanding and interpretation of the dipole moment of diatomic molecules, content present in the curriculum of disciplines physical chemistry and quantum chemistry in undergraduate chemistry courses. For this, 87 students participating the degree course in chemistry at a university in Brazil, they used computational chemistry calculations and analytical calculations for the dipole moment of the considered molecules. Results show the proposed method can be an alternative for calculations involving dipole moment of diatomic molecules. DOI: http://dx.doi.org/10.17807/orbital.v9i5.1020

Computing the arrows of chemical reactions

The use of curved arrows to describe the movement of electrons in chemical reaction schemes is widespread in several areas of chemistry, especially organic chemistry. The drawing of such arrows is guided by chemical intuition on the nature of nucleophiles and electrophiles. Here we show that it is actually possible to compute arrows from single-determinant computational quantum chemistry calculations. The procedure, which is outlined for the aldol reaction, is based on the computation of localized orbitals and their centroids along the intrinsic reaction coordinate.

Open chemistry: RESTful web APIs, JSON, NWChem and the modern web application

An end-to-end platform for chemical science research has been developed that integrates data from computational and experimental approaches through a modern web-based interface. The platform offers an interactive visualization and analytics environment that functions well on mobile, laptop and desktop devices. It offers pragmatic solutions to ensure that large and complex data sets are more accessible. Existing desktop applications/frameworks were extended to integrate with high-performance computing resources, and offer command-line tools to automate interaction—connecting distributed teams to this software platform on their own terms. The platform was developed openly, and all source code hosted on the GitHub platform with automated deployment possible using Ansible coupled with standard Ubuntu-based machine images deployed to cloud machines. The platform is designed to enable teams to reap the benefits of the connected web—going beyond what conventional search and analytics platforms offer in this area. It also has the goal of offering federated instances, that can be customized to the sites/research performed. Data gets stored using JSON, extending upon previous approaches using XML, building structures that support computational chemistry calculations. These structures were developed to make it easy to process data across different languages, and send data to a JavaScript-based web client.

Reactive Site Model of the Reduction of SO2 on Graphite

Computational quantum chemistry calculations were carried out for the reduction of SO2 on graphite to produce elemental sulfur and CO2. Two models of the reactive site of graphite were used and a viable mechanism was proposed for the reaction pathways based on experimental results and known reactions. The SO2 OO approach to the zigzag edge of the model cluster yielded a sulfur-oxidized intermediate 1,3,2-dioxathiolane (1). Sulfur transfer step takes place from 1 to a neighbor benzyne site forming a reduced sulfur intermediate thiirene (2) along with a 1,3-dicarbonyl in equilibrium with the peroxide valence tautomer. The calculated barrier from 1 to thiirene 2 at 900 °C was 39.4, kcal mol–1. The peroxide tautomer isomerizes to a dioxirane intermediate that is eliminated as dioxicarbene to produce CO2. The total free energy of activation for the decarboxylation reaction at 900 °C was in the range 110.8–122.7 kcal mol–1 depending on the model (ΔG‡experimental, 114.3 kcal mol–1). The reduced intermediate thiirene 2 decomposes through a transport mechanism where polysulfane species with increasing number of sulfur atoms eleminate elemental Sx.

Thermal decomposition pathways of 4-ethylguaiacol under fast pyrolysis and gasification conditions

Thermal decomposition pathways for the vapor-phase, homogeneous pyrolysis of 4-ethylguaiacol were examined. Experiments were conducted using a laminar-flow reactor operated at atmospheric pressure, temperatures in the range 300–900°C, and a residence time of one second. Analysis of the products by gas chromatography shows that they can be categorized as light gases, oxygen-containing compounds, and aromatic hydrocarbons. The major products observed were: methane, ethane, ethylene, acetylene, and carbon monoxide for the light gases; 4-ethylcatechol, 5-ethyl-2-hydroxybenzaldehdye, and 4-ethylphenol for the oxygen-containing products; benzene, indene, and naphthalene for the aromatic hydrocarbons. The product distribution was strongly influenced by temperature, with the oxygen-containing compounds dominating at temperatures below 700°C, while light gases and aromatic hydrocarbons dominated above 700°C. By consideration of the product distributions and analogous reactions based on established thermal decomposition mechanisms of structurally-similar compounds, reaction pathways leading to the generation of major products are proposed and discussed. Computational chemistry calculations at the B3LYP/6-311G+(2d,p) level of theory were performed to complement the proposed pathways. The results presented in this study would be of relevance to lignin fast pyrolysis and gasification processes.

Structure, substitution and hydrolysis of Bis(trifluorobenzoylacetonato-O,O′)dichloro titanium(IV): An experimental and computational study

The chlorine coordinated ligands in [Ti(tfba)2Cl2] (Htfba=4,4,4-trifluoro-1-(phenyl)-1,3-butanedione=PhCOCH2COCF3) are very susceptible to hydrolysis and even with trace amounts of water, the formation of hydrolysed complexes, dinuclear {Ti(tfba)2Cl}2(μ-O) or tetranuclear [Ti(tfba)2(μ-O)]4, take place, whereas with an excess of water, decomposition to TiO2 occurs. Substitution of the chloro-ligands in [Ti(tfba)2Cl2] with H2biphen (H2biphen=2,2′-dihydroxybiphenyl or biphenol) leads to [Ti(tfba)2biphen] with enhanced water stability. Experimentally, two steps were observed for the substitution [Ti(tfba)2Cl2]+H2biphen. Computational chemistry calculations reveal that each step involves several transition states, with formation of a 7-coordinated intermediate in the first reaction half. Location of this intermediate is dependent on inclusion of empirical dispersion-corrections in the functional. The three geometrical cis-isomers of [Ti(tfba)2biphen] were observed in solution using low temperature 1H and 19F NMR, whereas in the solid state, two of the isomers, cis-cis-trans and cis-trans-cis, crystallized in the same unit cell. The crystal structure of the hydrolysed tetranuclear complex [Ti(tfba)2(μ-O)]4 is composed of four identical cis-cis-trans isomers of [Ti(tfba)2Cl2]. The eight β-diketonato backbones and the four bridging oxygens have a S4 molecular symmetry.

Density functional theory study on Hg removal mechanisms of Cu-impregnated activated carbon prepared by simplified method

The preparation of activated carbon sorbent for Hg removal was simplified by combining activation and functionalization processes into one step. Jujube-based carbon material was first mixed with CuCl2 solution and then activated for the preparation of Cu-impregnated activated carbon. Physical and chemical properties of prepared activated carbon were investigated by means of N2 adsorption, SEM-EDS, XRD. A fixed-bed reactor with CEMS (Continuous emission monitoring system) was used to test the Hg adsorption ability of prepared activated carbon. DFT (Density functional theory) method of computational chemistry calculation was applied to identify the Hg adsorption mechanisms on sorbent surface.

From C60 to Infinity: Large-Scale Quantum Chemistry Calculations of the Heats of Formation of Higher Fullerenes.

We have carried out large-scale computational quantum chemistry calculations on the K computer to obtain heats of formation for C60 and some higher fullerenes with the DSD-PBE-PBE/cc-pVQZ double-hybrid density functional theory method. Our best estimated values are 2520.0 ± 20.7 (C60), 2683.4 ± 17.7 (C70), 2862.0 ± 18.5 (C76), 2878.8 ± 13.3 (C78), 2946.4 ± 14.5 (C84), 3067.3 ± 15.4 (C90), 3156.6 ± 16.2 (C96), 3967.7 ± 33.4 (C180), 4364 (C240) and 5415 (C320) kJ mol(-1). In our assessment, we also find that the B3-PW91-D3BJ and BMK-D3(BJ) functionals perform reasonably well. Using the convergence behavior for the calculated per-atom heats of formation, we obtained the formula ΔfH per carbon = 722n(-0.72) + 5.2 kJ mol(-1) (n = the number of carbon atoms), which enables an estimation of ΔfH for higher fullerenes more generally. A slow convergence to the graphene limit is observed, which we attribute to the relatively small proportion of fullerene carbons that are in "low-strain" regions. We further propose that it would take tens, if not hundreds, of thousands of carbons for a fullerene to roughly approach the limit. Such a distinction may be a contributing factor to the discrete properties between the two types of nanomaterials. During the course of our study, we also observe a fairly reliable means for the theoretical calculation of heats of formation for medium-sized fullerenes. This involves the use of isodesmic-type reactions with fullerenes of similar sizes to provide a good balance of the chemistry and to minimize the use of accompanying species.

Polymer Photocatalysts for Water Splitting: Insights from Computational Modeling

Based on insights from computational chemistry calculations, the ability of polymers to act as water splitting photocatalysts for the production of renewable hydrogen from water and sunlight is discussed. Specifically, the important role of exciton dissociation in these materials is highlighted, as well as the possible microscopic origins of the experimentally observed changes in the photocatalytic activity of a polymer with increasing chain length or changing chemical composition. The reason why water oxidation, with polymeric photocatalysts, is difficult, and which polymer properties to target when developing new polymers for water splitting photocatalysis are, finally, also discussed. image

Reorganization of substrate waters between the closed and open cubane conformers during the S2 to S3 transition in the oxygen evolving complex.

A crucial step in the mechanism for oxygen evolution in the Photosystem II complex resides in the transition from the S2 state to the S3 state of Kok–Joliot’s cycle, in which an additional water molecule binds to the cluster. On the basis of computational chemistry calculations on Photosystem II models, we propose a reorganization mechanism involving a hydroxyl (W2) and a μ2-oxo bridge (O5) that is able to link the closed cubane S2B intermediate conformer to the S3 open cubane structure. This mechanism can reconcile the apparent conflict between recently reported water exchange and electron paramagnetic resonance experiments, and theoretical studies.

Theoretical calculation of nitrogen isotope equilibrium exchange fractionation factors for various NOy molecules

The nitrogen stable isotope ratio (15N/14N) of nitrogen oxides (NOx=NO+NO2) and its oxidation products (NOy=NOx+PAN (peroxyacetyl nitrate=C2H3NO5)+HNO3+NO3+HONO+N2O5+⋯+particulate nitrates) has been suggested as a tool for partitioning NOx sources; however, the impact of nitrogen (N) equilibrium isotopic fractionation on 15N/14N ratios during the conversion of NOx to NOy must also be considered, but few fractionation factors for these processes have been determined. To address this limitation, computational quantum chemistry calculations of harmonic frequencies, reduced partition function ratios (15β), and N equilibrium isotope exchange fractionation factors (αA/B) were performed for various gaseous and aqueous NOy molecules in the rigid rotor and harmonic oscillator approximations using the B3LYP and EDF2 density functional methods for the mono-substitution of 15N. The calculated harmonic frequencies, 15β, and αA/B are in good agreement with available experimental measurements, suggesting the potential to use computational methods to calculate αA/B values for N isotope exchange processes that are difficult to measure experimentally. Additionally, the effects of solvation (water) on 15β and αA/B were evaluated using the IEF-PCM model, and resulted in lower 15β and αA/B values likely due to the stabilization of the NOy molecules from dispersion interactions with water. Overall, our calculated 15β and αA/B values are accurate in the rigid rotor and harmonic oscillator approximations and will allow for the estimation of αA/B involving various NOy molecules. These calculated αA/B values may help to explain the trends observed in the N stable isotope ratio of NOy molecules in the atmosphere.

FireWorks: a dynamic workflow system designed for high‐throughput applications

SummaryThis paper introduces FireWorks, a workflow software for running high‐throughput calculation workflows at supercomputing centers. FireWorks has been used to complete over 50 million CPU‐hours worth of computational chemistry and materials science calculations at the National Energy Research Supercomputing Center. It has been designed to serve the demanding high‐throughput computing needs of these applications, with extensive support for (i) concurrent execution through job packing, (ii) failure detection and correction, (iii) provenance and reporting for long‐running projects, (iv) automated duplicate detection, and (v) dynamic workflows (i.e., modifying the workflow graph during runtime). We have found that these features are highly relevant to enabling modern data‐driven and high‐throughput science applications, and we discuss our implementation strategy that rests on Python and NoSQL databases (MongoDB). Finally, we present performance data and limitations of our approach along with planned future work. Copyright © 2015 John Wiley & Sons, Ltd.

Computational study on reaction enthalpies of urethane‐forming reactions

Computational calculations were performed on urethane‐forming reactions using Gaussian 09 software (i.e. molecular modeling) toward the goal of providing thermodynamic parameters. Total electronic and thermal enthalpies and zero‐point vibrational energies of reactants and products were computed by the software and then reaction enthalpies were calculated based on these results. The location of functional groups has the most significant impact on reaction enthalpies while molecular size, chain length and solvent effect have relatively less impact on reaction enthalpies. By comparison to new experimental studies and values reported in literature, better‐informed recommendations on which values of reaction enthalpies to use for urethane foam process simulation were provided. The utility of computational chemistry results succeeded in being an enabling technology to improve foam process simulation. In turn, simulation of urethane‐forming reactions is useful to bridge the gap between fundamental computational chemistry calculations and practical applications. POLYM. ENG. SCI., 55:1420–1428, 2015. © 2015 Society of Plastics Engineers

Charge-assisted hydrogen bonding in salts of 2-amino-1H-benzimidazole with 3-phenylpropynoic acid and oct-2-ynoic acid.

The 100 K structures of two salts, namely 2-amino-1H-benzimidazolium 3-phenylpropynoate, C7H8N3(+)·C9H5O2(-), (I), and 2-amino-1H-benzimidazolium oct-2-ynoate, C7H8N3(+)·C8H11O2(-), (II), both have monoclinic symmetry (space group P21/c) and display N-H...O hydrogen bonding. Both structures show packing with corrugated sheets of hydrogen-bonded molecules lying parallel to the [001] direction. Two hydrogen-bonded ring motifs can be identified and described with graph sets R(2)(2)(8) and R(4)(4)(16), respectively, in both (I) and (II). Computational chemistry calculations performed on both compounds show that the hydrogen-bonded ion pairs are more energetically favourable in the crystal structure than their hydrogen-bonded neutral molecule counterparts.