Molecular Quantum Mechanical Calculations Research Articles

Mechanochemical evolution of coal microscopic groups: A new pathway for mechanical forces acting on coal spontaneous combustion

Coal spontaneous combustion (CSC) remains a significant threat to regional ecological environments. As coal mining operations extend deeper into the earth, the increasingly complex mechanical force conditions in deep-seated mines escalate the potential risk of CSC. Mechanical forces such as ground stress and mechanical cutting are traditionally believed to be linked to CSC through the following pathway: mechanical forces act → mechanical energy is input → mechanical crushing and pulverization occur → coal–oxygen contact area increases → CSC accelerates. Noteworthily, these forces do more than just physically break coal; they also trigger a mechanochemical effect (MCE) that alters coal's microscopic chemistry. However, an independent evaluation of its influence on CSC was lacking. This study characterized coal's microscopic chemical group responses to the MCE. It was found that the MCE led to the degradation of aliphatic side chains while enhancing the polycondensation of aromatic ring structures, indicating a synergistic effect. Additionally, an increase in oxygen-containing functional groups, such as alkyl/aryl ethers, suggested enhanced interactions of the coal microscopic groups with oxygen due to mechanical forces. Based on these findings, an MCE-modified coal macromolecular model was developed and molecular quantum mechanical calculations were conducted. The results indicated that the MCE boosted coal macromolecule reactivity, thus facilitating easier activation. These conclusions were validated through modern thermal analysis tests. Finally, this study proposed a new pathway of mechanical forces acting on CSC: mechanical forces act → mechanical energy is input → the MCE occurs → evolutions of the microscopic groups within coal are induced → Activity of coal molecules is enhanced → CSC accelerates.

Fine-Tuning of Entangled Two-Photon Absorption by Controlling the One-Photon Absorption Properties of the Chromophore

The detailed analysis of the sum-over-state formula for the entanglement-induced two-photon absorption (ETPA) transition moment shows that the magnitude of the ETPA cross-section is expected to vary significantly depending on the coherence time Te and the relative position of just two electronic states. Moreover, the dependency on Te is periodic. These predictions are confirmed by molecular quantum mechanical calculations for several chromophores.

Importance of non-covalent interactions in a nitrile anion metal-complex based on pyridine ligands: A theoretical and experimental approach

The solvothermal synthesis and crystal structure of [bis(thiocyanato-κN)bis(tris(pyridin-2-yl-κN)amine)iron(II)] (1) are described. The structure obtained was i subjected to theoretical analysis of interaction energies and intra- and intermolecular bonding. This comprehensive study illustrates the richness of non-covalent interactions that are exhibited by nitrile anionmetal complexes. The neutral complex lies on a crystallographic two-fold axis. The iron atom is octahedrally coordinated, with two thiocyanato ligands in cis positions, and the two trispyridine ligands coordinated via the nitrogen atoms of just two of the three pyridine rings. Energy analysis of five significant dimers, supplemented by a detailed analysis of the Hirshfeld surfaces, indicates attractive interaction energies of up to 101 kJ, with the strongest dimer stabilized by bifurcated CH⋯S hydrogen bonds and additional π⋯π interactions. Solid-state and molecular quantum mechanical calculations confirm the high-spin nature of the complex, which is also reflected in the FeN bond lengths, and highlights the relevance of intramolecular ligand-ligand interactions. From a combined analysis using the Quantum Theory of Atoms in Molecules and the Non-Covalent Interaction index it was possible to identify further specific intermolecular interactions contributing the stability of the crystal structure, such as the H⋯H bonds, as well as the presence of several delocalized van der Waals forces, which are mainly of dispersive origin.

Aminated cellulose as a versatile adsorbent for batch removal of As(V) and Cu(II) from mono- and multicomponent aqueous solutions

A bioadsorbent (CEDA) capable of adsorbing As(V) and Cu(II) simultaneously was prepared by tosylation of microcrystalline cellulose (MC) and nucleophilic substitution of the tosyl group by ethylenediamine. MC, tosyl cellulose, and CEDA were characterized by elemental C, H, N, and S analysis, infrared spectroscopy, and 13C solid-state nuclear magnetic resonance spectroscopy. The adsorption of As(V) and Cu(II) on CEDA was evaluated as a function of solution pH, contact time, and initial solute concentration. The maximum adsorption capacities of CEDA for As(V) and Cu(II) were 1.62 and 1.09 mmol g−1, respectively. The interactions of As(V) and Cu(II) with CEDA were elucidated using thermodynamic parameters, molecular quantum mechanics calculations, and experiments with ion exchange of Cd(II) by Cu(II), and As(V) by SO42−. Adsorption enthalpies were determined as a function of surface coverage of the CEDA, using isothermal titration calorimetry, with ΔadsH° values of −32.24 ± 0.07 and −93 ± 2 kJ mol−1 obtained for As(V) and Cu(II), respectively. The potential to reuse CEDA was evaluated and the interference of other ions in the adsorption of As(V) and Cu(II) was investigated. Multi-component experiments showed that Cd(II), Co(II), Ni(II), and Pb(II) did not interfere in the adsorption of Cu(II), while SO42− inhibited As(V) adsorption.

The Mechanism of Ethylene Polymerization Reaction Catalyzed by Group IVB Metallocenes. A Rational Analysis Through the Use of Reaction Force

A density functional theory study of the ethylene polymerization mechanism catalyzed by metallocene methyl cations based on group IVB (Ti, Zr, and Hf) is presented. The concept called reaction force was applied in order to decompose the activation energy into two parts with the aim of distinguishing the predominance of structural or electronic effects within intervals along the reaction coordinate on each step of the polymerization process. This has implied an alternative rational analysis of elementary chemical reactions associated with the polymerization mechanism under the assumption that the Cossée–Arlman’s mechanism is operating along the whole process. Three reaction models representing elementary chemical reactions of the polymerization process (initiation, propagation, and termination) were used through molecular quantum mechanical calculations. The simplest of metallocene methyl cations (built up by two cyclopentadienyl groups and one methyl group linked to the metal) was used as a catalytic molecular model. Since the main goal was focused on getting information of intrinsic global reactivity of catalytic systems, both solvent and co-catalyst were not modeled in the present work. As a result, energy profiles indicate that ethylene polymerization reactions are better catalyzed by the respective metallocene cation based on Ti, whereas the catalysts based on Zr and Hf present similar characteristics among them, thus supporting experimental results where the molecular weight of polyethylene obtained by means of metallocene cation based on Ti approximately doubles the molecular weights of polyethylene catalyzed by metallocenes based on Zr and Hf. However propagation and termination steps are better catalyzed by metallocene complexes based on Zr and Hf, thus masking the influence of initiation step upon the molecular weight of the obtained polymer and providing more importance to termination step rather than propagation step. This would help to better understand differences presented in the average molecular weight of a same polymer obtained with each of these catalytic systems. As some key steps of the polymerization process would be more favored with one type of metallocene rather than other one, the use of reaction force would help to better understand how to modify energetic barriers and or global changes in energy by perturbating geometrical or electronic structure of catalytic systems. The latter suggests that the ideal polymerization process should be carried out with different catalytic systems depending on the step of polymerization and not with a unique catalyst as has been commonly performed up to now. That might lead to the obtention of a more wide range of new polymeric materials.

Molecular properties calculations using the q‐integral method

AbstractThe q‐Integral method, based on the q‐Exponential function, has been recently introduced as an alternative approach to calculate the two‐electron integrals which appear in ab initio atomic and molecular quantum mechanical calculations. The advantage of this procedure is that the CPU time for calculating of two‐electron integrals is substantially reduced when compared with the usual one. The objective of this work is to investigate the accuracy of the q‐Integrals as a function of the internuclear distance for molecular systems. To this purpose we employed the q‐Integrals to construct the potential energy surface (PES) for the H2 molecule and used the PES to determine the rovibrational levels and spectroscopic constants of the molecule, which are properties very sensitive to the form of the PES. The results obtained are in good agreement with the ones obtained through the standard procedure of calculating the two‐electron integrals, implying that the q‐Integral method is accurate enough to be used in any molecular quantum mechanical calculation. © 2008 Wiley Periodicals, Inc. Int J Quantum Chem, 2008

Synthesis of gold nanoparticles with different atomistic structural characteristics

A chemical reduction method was used to produce nanometric gold particles. Depending on the concentration of the main reactant compound different nanometric sizes and consequently different atomic structural configurations of the particles are obtained. Insights on the structural nature of the gold nanoparticles are obtained through a comparison between digitally-processed experimental high-resolution electron microscopy images and theoretically-simulated images obtained with a multislice approach of the dynamical theory of electron diffraction. Quantum molecular mechanical calculations, based on density functional theory, are carried out to explain the relationships between the stability of the gold nanoparticles, the atomic structural configurations and the size of nanoparticles.

Bond Length Alternation and Energy Band Gap of Polyyne

The bond length alternation (BLA) and energy band gap of polyyne are investigated by various first-principles theories, including Hartree-Fock, MP2, hybrid, and nonhybrid density functional theories. Both solid-state calculations utilizing periodic boundary conditions on polymers and molecular quantum mechanical calculations on extra-long oligomers were performed with consistent results. By validation on similar linear conjugated polymers, polyacetylene and polydiacetylene, the combination of hybrid-DFT schemes, B3LYP//BHandHLYP or B3LYP//KMLYP, is shown to give the best predictions for both geometry and band gap of polyyne based on available experimental data. We conclude that the best estimate of the BLA of polyyne is about 0.13 A and that of the band gap is about 2.2 eV.

An analytical procedure to evaluate electronic integrals for molecular quantum mechanical calculations

The main contribution of this paper is to provide an alternative strategy to reduce the number of bi-electronic integrals in ab initio quantum mechanics calculations. An analytical procedure to evaluate the energy of a molecule as well as two-electron integrals is proposed. This approach is based on the generalized exponential function (q-exponential) and is particularly advantageous because it reduces substantially the CPU time in quantum mechanical calculations. Some examples of the effectiveness of this methodology are presented. It is important to point out that the new methodology is applicable to any kind of molecular system including relatively large molecular systems in the context of the Hartree–Fock (HF) and density functional theories (DFT).

Spectroscopic study of nitroaromatic-smectite sorption mechanisms.

Sorption mechanisms of 1,3- and 1,4-dinitrobenzene, 1,3,5-trinitrobenzene (TNB), dinitro-o-creasol, and 6-sec-butyl-2,4-dinitrophenol (DINOSEB) on smectite were investigated using FTIR spectroscopy and HPLC methods. A quantitative method was developed that established a direct link between the HPLC and the FTIR data. Freundlich sorption values ranged from 47 (L g(-1)) for 1,3,5-TNB to 3.7 for DINOSEB and showed that the extent of nitroaromatic compounds (NAC) sorption was strongly dependent on the number and position of the nitro substituents as well as other substituents and steric effects. The amount of 1,3,5-TNB sorbed to smectite was strongly influenced by the nature of the exchangeable cation. Furthermore, the exchangeable cation significantly influenced the positions and relative intensities of the vibrational modes of the -NO2 groups. The strongest perturbations were observed for cations with lower enthalpies of hydration (e.g., K+) and included a red shift of the v(asym)(NO) band, a concomitant blue shift of the v(sym)(NO) band. These changes were accompanied by a 2-fold increase in the relative intensity of the v(asym)(NO) band relative to the intensity of the v(sym) (NO) band. Molecular quantum mechanics calculations were used to rationalize frequency shifts in terms of nitroaromatic interactions with interlayer cations. Results indicate that the sorption of NACs to smectite surfaces is controlled largely by the hydration characteristics of the exchangeable cation, which regulates both cation-nitroaromatic complexation and swelling of the smectite.

Chemical accuracy from ‘Coulomb hole’ extrapolated molecular quantum-mechanical calculations

In standard ab initio molecular quantum-mechanical calculations it is difficult, if at all possible, to calculate fundamental chemical properties like atomisation energies and reaction enthalpies to the chemical accuracy of 1kcal/mol≈4kJ/mol. The principal obstacle is the presence of the Coulomb hole in the electronic wave function, whose description converges slowly with the size of the basis set. From a systematic sequence of basis-set calculations, we demonstrate that physically motivated extrapolations can be used to accelerate the basis-set convergence significantly and that, for highly correlated wave functions, chemical accuracy is obtained even with medium-sized basis sets when the extrapolation is used.

Elemental strain and trapped space charge in thermoelectrical aging of insulating materials. Part 1: Elemental strain under thermo-electrical-mechanical stress

The life model proposed previously by the authors ascribes electrothermal aging to the formation and/or enlargement of nanovoids driven by electromechanical energy stored in local concentrations of space charge. In the previous work, the strain associated with the mechanical stress produced by the space charge center was derived using a macroscopic stress-strain relationship. For chain conformation changes on the molecular scale, these macroscopic concepts may no longer be valid. In this paper, we have investigated the possibility that the local strain is an elemental property of the polymer morphology, as suggested by molecular quantum mechanical calculations. The elemental strain has been related to the bulk modulus through the elemental volume of the affected chain section and the number density of contributing centers. In this way an upper bound has been obtained for the elemental strain as a function of these variables. Under the assumption that the charge concentrations are formed by charges trapped in nanovoids, estimates have been obtained for the smallest magnitude of the local field that is able to initiate aging, and these estimates have been correlated with the maximum number of electronic charges that such a void may trap. By doing so, a connection is found between the aging model and experimental space charge densities. This connection is the subject of Part 2 of this paper.

Covalent bond force profile and cleavage in a single polymer chain

We present here the measurement of the single-polymer entropic elasticity and the single covalent bond force profile, probed with two types of atomic force microscopes (AFM) on a synthetic polymer molecule: polymethacrylic acid in water. The conventional AFM allowed us to distinguish two types of interactions present in this system when doing force spectroscopic measurements: the first interaction is associated with adsorption sites of the polymer chains onto a bare gold surface, the second interaction is directly correlated to the rupture process of a single covalent bond. All these bridging interactions allowed us to stretch the single polymer chain and to determine the various factors playing a role in the elasticity of these molecules. To obtain a closer insight into the bond rupture process, we moved to a force sensor stable in position when measuring attractive forces. By optimizing the polymer length so as to fulfill the elastic stability conditions, we were able for the first time to map out the entire force profile associated with the cleavage of a single covalent bond. Experimental data coupled with molecular quantum mechanical calculations strongly suggest that the breaking bond is located at one end of the polymer chain.

New Insights into the Dynamics of Concerted Proton Tunneling in Cyclic Water and Hydrogen Fluoride Clusters

The concerted proton transfer hypersurface of cyclic water and hydrogen fluoride clusters has been described by high-level molecular quantum mechanical calculations. For the cyclic water clusters the concerted proton transfer transition states have been investigated for the first time with methods including treatment of dynamic electron correlation. The crucial importance of dynamic electron correlation for the barrier heights is demonstrated. A detailed analysis of the minimum energy path has been performed. The reaction swath of the concerted proton transfer was examined indicating a reasonable description by harmonic approximation of the energy hypersurface. Transfer rates have been calculated by means of variational transition state theory with interpolated corrections (VTST-IC) and dual-level direct dynamics (DLDD), both with semiclassical tunneling corrections. Tunneling is very efficient in the concerted proton exchange reaction of the cyclic hydrogen-bonded clusters under investigation. Rate const...

Quantum-Chemical Descriptors in QSAR/QSPR Studies.

Quantitative structure-activity and structureproperty relationship (QSAR/QSPR) studies are unquestionably of great importance in modern chemistry and biochemistry. The concept of QSAR/QSPR is to transform searches for compounds with desired properties using chemical intuition and experience into a mathematically quantified and computerized form. Once a correlation between structure and activity/property is found, any number of compounds, including those not yet synthesized, can be readily screened on the computer in order to select structures with the properties desired. It is then possible to select the most promising compounds to synthesize and test in the laboratory. Thus, the QSAR/QSPR approach conserves resources and accelerates the process of development of new molecules for use as drugs, materials, additives, or for any other purpose. While it is not easy to find successful structureactivity/property correlations, the recent exponential growth in the number of papers dealing with QSAR/ QSPR studies clearly demonstrates the rapid progress in this area. To obtain a significant correlation, it is crucial that appropriate descriptors be employed, whether they are theoretical, empirical, or derived from readily available experimental characteristics of the structures. Many descriptors reflect simple molecular properties and thus can provide insight into the physicochemical nature of the activity/ property under consideration. Recent progress in computational hardware and the development of efficient algorithms has assisted the routine development of molecular quantummechanical calculations. New semiempirical methods supply realistic quantum-chemical molecular quantities in a relatively short computational time frame. Quantum chemical calculations are thus an attractive source of new molecular descriptors, which can, in principle, express all of the electronic and geometric properties of molecules and their interactions. Indeed, many recent QSAR/QSPR studies have employed quantum chemical descriptors alone or in combination with conventional descriptors. Quantum chemistry provides a more accurate and detailed description of electronic effects than empirical methods.1 Quantum chemical methods can be applied to quantitative structure-activity relationships by direct derivation of electronic descriptors from the molecular wave function. In many cases it has been established that errors due to the approximate nature of quantum-chemical methods and the neglect of the solvation effects are largely transferable within structurally related series; thus, relative values of calculated descriptors can be meaningful even though their absolute values are not directly applicable.2 Moreover, electronic descriptors derived from the molecular wave function can be also partitioned on the basis of atoms or groups, allowing the description of various molecular regions separately. Most work employing quantum chemical descriptors has been carried out in the field of QSAR rather than QSPR, i.e. the descriptors have been correlated with biological activities such as enzyme inhibition activity, hallucinogenic activity, etc.3-6 In part this has been because, historically, the search for quantitative relationships with chemical structure started with the development of theoretical drug design methods. Quantum-chemical descriptors have also been reported to correlate the reactivity of organic compounds, octanol/water partition coefficients, chromatographic retention indices, and various physical properties of molecules.7-11 The present article reviews applications of quantum chemical descriptors in the development of QSAR/QSPR dealing with the chemical, physical, biochemical, and pharmacological properties of compounds.

Theoretical study of the binding site and mode of action for photosystem II herbicides

Several features of a proteinaceous binding site and a molecular mode of action are proposed for photosystem II (PS II) herbicides based upon a variety of experimental and theoretical evidence. Experimental studies have established that PS II herbicides bind non-covalently to a 32 kdalton protein in the PS II complex and inhibit electron transfer between the first quinone ( Q) and the second quinone ( B) on the reducing side of PS II. The herbicides each contain hydrophobic components as well as a flat polar component with a dipole moment in the range of 3–5 Debyes. The primary function of the hydrophobic components is to increase the lipid solubility of the entire herbicide molecule; the secondary function of the hydrophobic components is to fit the hydrophobic surface of the herbicide binding site. It is proposed that the flat polar component binds electrostatically at a highly polar protein site, probably a protein salt bridge or the terminus of a protein alpha helix. Further, it is proposed that the PS II herbicides shift the equilibrium Q − Bz⇄ QB − to the left (i) by reducing the magnitude of an anion-stabilizing electric field across the B-binding site, or (ii) by inhibiting the conformational relaxation or protonation of the PS II protein in response to reduction of B to B −, or (iii) by displacing the quinone head of B from its binding site. Ab initio molecular quantum mechanical calculations have been carried out to investigate the electrostatic interactions in specific herbicide-binding site models.

The bonding of ferrous iron to sulfur and oxygen in tetrahedral coordination: A comparative study using SCF Xα scattered wave molecular orbital calculations

Molecular quantum mechanical calculations have been performed on high-spin ferrous iron tetrahedrally coordinated to sulfur and oxygen, respectively. The molecular orbital energies obtained from the calculations are compared with experimental optical and X-ray emission spectra. Good agreement was found between calculated and experimental spectral transition energies for the optical absorption spectra of Fe 2+ in sphalerite, of Fe 2+ in FeAl 2O 4, staurolite and (Zn, Fe)O, and for the FeKβ X-ray emission spectra of FeCr 2O 4. This both clarified interpretation of the spectra and established the validity of the calculations. Distinct differences occur in the molecular orbital structures of the sulfide and oxide clusters. In the sulfide, the crystal field type (mainly Fe 3 d) molecular orbitals lie within the nonbonding (mainly S 3 p) orbitais in energy, whereas in the oxide, they lie well above the 02 p nonbonding orbitals. This also results in a wider valence band in the oxide than in the sulfide. The crystal field type (Fe 3 d) molecular orbitais have more ligand character in the sulfide than the oxide and the chalcophilic properties of iron are partly attributed to this observation.

Electronic Structure of Ferric Iron Octahedrally Coordinated to Oxygen

A FERRIC ion coordinated to an octahedron of oxide ions may be considered the basic polyhedral unit of Fe2O3 (haematite) and an important unit in Ca3Fe2Si3O12 (andradite garnet), Fe3O4 (magnetite) and other silicate and oxide minerals. A knowledge of the electronic structure of this unit is of considerable interest in mineralogy and solid state science. In recent years a great deal of information on the electronic structure of minerals has been obtained from the study of their spectral properties. We report here results of molecular quantum mechanical calculations on an FeO69- unit and compare them with experimental data from X-ray emission, X-ray photoelectron and optical spectroscopies. The agreement found between experimental and calculated spectral transition energies establishes the validity of the calculation and furthermore clarifies the interpretation of the spectral data.

A theoretical study of the Edward–Lemieux effect (the anomeric effect). The stereochemical requirements of adjacent electron pairs and polar bonds

Many data, collected from the literature, support the postulation of two general rules which describe the static and dynamic results of having in a molecule or generating in an intermediate adjacent electron pairs and/or polar bonds. In disagreement with current chemical intuition, structures which contain the maximum number of gauche-interactions between lone electron pairs or polar bonds represent energy minima and, frequently, the lowest minima. The stereochemical implications of the phenomenon are discussed, along with possible physical explanations. It is suggested that partitioning of the total energy of the system into attractive-dominant and repulsive-dominant interactions provides the most helpful framework for the construction of a physical picture of the phenomenon. The total energy and its components can be obtained by ab initio molecular quantum mechanical calculations.

Localized Orbitals. I. σ Bonds

This paper presents a method for the delineation of a set of truly localized orbitals and uses a nonunitary transformation to convert the localized orbitals into equivalent orbitals which are suitable for molecular quantum-mechanical calculations. The localized orbitals, which are suitable for describing polyatomic molecules including large nonplanar ones, are generated on the premise that the atomic orbitals used in the construction of two-center one- or two-electron bonds should be such that, when overlap is totally neglected, each atomic orbital has the same calculated value of angular momentum about its bond axis. The non-unitary transformation is derived from the modification in the form of the general orthonormality conditions upon a change from overlap metric 1 to a realistic overlap matrix Δ. This approach is applied to methane, ammonia, and water to calculate the equivalent orbitals. System energies and dipole moments are also calculated, and these and the equivalent orbitals are compared with the results of reported SCF calculations. The close values of the energies show that this approach may be used for realistic calculations. It also has an advantage over SCF techniques in that extension to extremely complicated molecular systems is possible. Further, the orbitals used herein are particularly useful for chemists since they are couched in terms of localized-bond characteristics alone.