Ab Initio Level Research Articles

Theoretical studies and spectroscopic characterization of novel 4-methyl-5-((5-phenyl-1,3,4-oxadiazol-2-yl)thio)benzene-1,2-diol

The structural, electronic, and spectroscopic properties of 4-methyl-5-((5-phenyl-1,3,4 oxadiazol-2-yl)thio)benzene-1,2-diol (MPOTB) have been carried out at ab initio and DFT levels. A detailed study of geometrical parameters, Infrared spectrum, chemical shifts (13C NMR, 1H NMR), and electronic properties of the title compound is presented. The correlation between the theoretical and the experimental 13C, and 1H chemical shifts of MPOTB were about 1.02–1.03 and 0.98–1.00, respectively. The electronic properties, such as molecular electrostatic potential, NBO atomic charges, HOMO and LUMO energies were performed at above levels. Rather high hardness of MPOTB introduces it as a stable molecule. As a result, the calculated findings were compared with the observed values and generally found to be in good agreement.

Ab initio theory for ultrafast magnetization dynamics with a dynamic band structure

Laser-induced modifications of magnetic materials on very small spatial dimensions and ultrashort timescales are a promising field for novel storage and spintronic devices. Therefore, the contribution of electron–electron spin-flip scattering to the ultrafast demagnetization of ferromagnets after an ultrashort laser excitation is investigated. In this work, the dynamical change of the band structure resulting from the change of the magnetization in time is taken into account on an ab initio level. We find a large influence of the dynamical band structure on the magnetization dynamics and we illustrate the thermalization and relaxation process after laser irradiation. Treating the dynamical band structure yields a demagnetization comparable to the experimental one.

Stereoselective Synthesis and Modelling-Driven Optimisation of Carane-Based Aminodiols and 1,3-Oxazines as Catalysts for the Enantioselective Addition of Diethylzinc to Benzaldehyde.

The reductive amination of (-)-2-carene-3-aldehyde, prepared in two steps from (-)-perillaldehyde, furnished 2-carene-based allylamines. tert-Butyloxycarbonyl (Boc) or carbobenzyloxy (Cbz) protection of the resulting amines, followed by stereoselective dihydroxylation in highly stereospecific reactions with OsO4 and subsequent deprotection, resulted in N-benzylaminodiols, which were transformed to primary and tertiary aminodiols. The reactions of the N-benzyl- and N-(1-phenylethyl)-substituted derivatives with formaldehyde led to highly regioselective ring closure, resulting in carane-fused 1,3-oxazines. The aminodiols and their 1,3-oxazine derivatives were applied as chiral catalysts in the enantioselective addition of diethylzinc to aldehydes. The best (R) enantioselectivity was observed in the case of the N-((R)-1-phenylethyl)-substituted aminodiol, whereas the opposite chiral direction was preferred when the 1,3-oxazines were applied. Through the use of molecular modelling at an ab initio level, this phenomenon was interpreted in terms of competing reaction pathways. Molecular modelling at the RHF/LANL2DZ level of theory was successfully applied for a mechanism-based interpretation of the stereochemical outcome of the reactions leading to the development of further 1,3-oxazine-based ligands, which display excellent (S) enantioselectivity (95 and 98 % ee) in the examined transformation.

Piezoelectricity of Functionalized Graphene: A Quantum-Mechanical Rationalization

A large out-of-plane piezoelectricity can be induced in graphene by carbon substitution. Several simple substitutions are considered where C atoms are replaced by heavier group-IV elements (Si, Ge, and Sn). A more complex functionalization (namely, pyrrolic N-doped graphene) is also investigated where different functional groups, such as F, Cl, H3C, and H2N, are studied. Piezoelectric and elastic response properties of all systems are determined quantum mechanically at the ab initio level of theory. A rationalization of the physical and chemical parameters which most affect the out-of-plane piezoelectricity of functionalized graphene is reported, which reveals the dominant character of the nuclear over electronic contribution. The combination of an out-of-plane symmetry-breaking defect and a soft infrared-active phonon mode, with a large cell-deformation coupling, is shown to constitute the necessary prerequisite to induce a large out-of-plane piezoelectric response into functionalized graphene.

Performance of the major semiempirical, ab initio, and DFT methods for isomerization enthalpies of linear to branched heptanes

ABSTRACTThe gas phase standard state (298.15 K, 1 atm) isomerization enthalpy (ΔisomH°(g)) prediction performance of the major semiempirical, ab initio, and density functional levels of theory for environmentally relevant transformations was investigated using the linear to branched heptanes as a representative case study. The M062X density functional, MP2 (and higher) levels of Moller-Plesset perturbation theory, and the CBS and Gaussian-n composite methods are well suited for investigating the thermodynamic properties of environmentally interesting isomerizations, although the M062X functional may not be appropriate for all systems. Where large molecular systems prohibit the use of higher levels of theory, the PM6 and PDDG semiempirical methods may offer an appropriate computational cost-accuracy compromise.

First-Principles Study of the Structural, Electronic, Dynamic, and Mechanical Properties of HOPG and Diamond: Influence of Exchange–Correlation Functionals and Dispersion Interactions

Various properties of two polymorphs of carbon, highly oriented pyrolytic graphite (HOPG) and diamond, were investigated at the ab initio level using different Hamiltonians with all-electron Gaussian-type functions (GTF) and projector augmented wave (PAW) basis sets. Their equilibrium lattice parameters, cohesive and interlayer interaction energies, band structures, vibrational frequencies, and elastic constants were evaluated. The calculations were performed at the Hartree–Fock, density functional theory (DFT), and hybrid (B3LYP and PBE0) levels. As regards DFT, the local density and generalized gradient (PBE and PBEsol) approximations were used. For GTF, the influence of the basis set superposition error (BSSE) was assessed. Since these approaches do not take dispersion interactions correctly into account, two different versions of Grimme’s dispersion correction, D2 and D3, were evaluated. The D2 and D3 corrections were reparameterized in order to reproduce the experimental structure of HOPG. For the properties depending on the description of the covalent bonds, such as the cohesive energy, C11 and C12, the dispersion corrections have a negligible influence. The best agreement is found for B3LYP-GTF-D3, PBE providing close results. For the properties depending on the description of the interaction between different layers, such as the interlayer interaction energies, C33, and C44, using the dispersion corrections improves the results. In general, D3 performs better than D2. PBE overall provides better results than the other functionals. As regards the basis sets, PAW describes the vibrational frequencies better than GTF due to the BSSE, whereas GTF provides a better description of the bandwidths and interband separations, elastic constants, and thermodynamical data. On the basis of the overall results, PBE-GTF-D3 appears to be a good compromise for an accurate description of the properties of graphite.

Energetics and structural properties of neutral and deprotonated phenyl carbinols

Theoretical and experimental studies on the energetics, structure and other physicochemical properties of neutral 1-phenylethanol (1OH), diphenylmethanol (2OH) and triphenylmethanol (3OH) and their corresponding deprotonated anions (oxyanions, formed by deprotonation of the OH group) are reported in this work. The standard enthalpies of formation in the gas phase at T=298.15K, ΔfHm0(g) have been determined. Quantum chemical calculations, at the DFT (particularly M05-2X method) and in some cases at the ab initio (G3) levels, have shed light on structural and electronic effects on the thermodynamic stability and intrinsic acidity of the studied compounds. These calculations confirmed the excellent consistency of the experimental results.

General Applicable Frequency Map for the Amide-I Mode in β-Peptides.

In this work, a general applicable amide-I vibrational frequency map (GA map) for β-peptides in a number of common solvents was constructed, based on a peptide derivative, N-ethylpropionamide (NEPA). The map utilizes force fields at the ab initio computational level to accurately describe molecular structure and solute-solvent interactions, and also force fields at the molecular mechanics level to take into account long-range solute-solvent interactions. The results indicate that the GA map works reasonably for mapping the vibrational frequencies of the amide-I local-modes for β-peptides, holding promises for understanding the complicated infrared spectra of the amide-I mode in β-polypeptides.

Thermal properties of the orthorhombic CaSnO3 perovskite under pressure from ab initio quasi-harmonic calculations

Structural, elastic and thermodynamic properties of the orthorhombic CaSnO3 perovskite are theoretically investigated at the ab initio level as a function of temperature and pressure. Harmonic and quasi-harmonic lattice dynamical calculations are performed with the Crystal program, by explicitly accounting for thermal expansion effects and by exploring the effect of several DFT functionals. The anisotropic, directional elastic response of the system is characterized up to 20 GPa of pressure. The thermal lattice expansion and elastic bulk modulus are described at simultaneous temperatures up to 2000 K and pressures up to 20 GPa. The Gibbs free energy of formation of CaSnO3 from CaO and SnO2 as a function of temperature is also addressed by means of fully converged phonon dispersion calculations on the three systems.

Computationally Efficient Multiscale Reactive Molecular Dynamics to Describe Amino Acid Deprotonation in Proteins.

An important challenge in the simulation of biomolecular systems is a quantitative description of the protonation and deprotonation process of amino acid residues. Despite the seeming simplicity of adding or removing a positively charged hydrogen nucleus, simulating the actual protonation/deprotonation process is inherently difficult. It requires both the explicit treatment of the excess proton, including its charge defect delocalization and Grotthuss shuttling through inhomogeneous moieties (water and amino residues), and extensive sampling of coupled condensed phase motions. In a recent paper (J. Chem. Theory Comput.2014, 10, 2729−273725061442), a multiscale approach was developed to map high-level quantum mechanics/molecular mechanics (QM/MM) data into a multiscale reactive molecular dynamics (MS-RMD) model in order to describe amino acid deprotonation in bulk water. In this article, we extend the fitting approach (called FitRMD) to create MS-RMD models for ionizable amino acids within proteins. The resulting models are shown to faithfully reproduce the free energy profiles of the reference QM/MM Hamiltonian for PT inside an example protein, the ClC-ec1 H+/Cl– antiporter. Moreover, we show that the resulting MS-RMD models are computationally efficient enough to then characterize more complex 2-dimensional free energy surfaces due to slow degrees of freedom such as water hydration of internal protein cavities that can be inherently coupled to the excess proton charge translocation. The FitRMD method is thus shown to be an effective way to map ab initio level accuracy into a much more computationally efficient reactive MD method in order to explicitly simulate and quantitatively describe amino acid protonation/deprotonation in proteins.

Non-adiabatic dynamics simulation exploration of the wavelength-dependent photoinduced relaxation mechanism of trans-N-1-methyl-2-(tolylazo) imidazole in the gas phase

A comprehensive picture of the photoinduced non-adiabatic relaxation dynamics of trans-N-1-methyl-2-(tolylazo) imidazole (trans-MTAI) in different electronic excited states has been revealed using the on-the-fly surface hopping method at the ab initio CASSCF level.

Key Challenges and Opportunities for Conjunctive Management of Surface and Groundwater in Mega-Irrigation Systems: Lower Indus, Pakistan

This paper focuses on the scope of conjunctive management in the Lower Indus part of the Indus Basin Irrigation System (IBIS), and the contribution this could make towards food security and socio-economic development. The total Gross Command Area (GCA) of the Lower Indus is 5.92 Mha, with a cultivable command area (CCA) of 5.43 Mha, most of which is in Sindh Province. There is a limited use of groundwater in Sindh (about 4.3 Billion Cubic Meter (BCM)) for two reasons: first, there is a large area where groundwater is saline; and second, there is a high surface irrigation supply to most of the canal commands, e.g., average annual supply to rice command is 1723 mm, close to the annual reference crop evapotranspiration for the area, while there is an additional annual rainfall of about 200 mm. These high irrigation allocations, even in areas where groundwater is fresh, create strong disincentives for farmers to use groundwater. Consequently, areas are waterlogged to the extent of 50% and 70% before and after the monsoon, respectively, which contributes to surface salinity through capillary rise. In Sindh, about 74%–80% of the available groundwater recharge is lost in the form of non-beneficial evaporation. This gives rise to low cropping intensities and yields compared to fresh groundwater areas elsewhere in the IBIS. The drought of 1999–2002 has demonstrated a reduction in waterlogging without any corresponding reduction in crop yields. Therefore, in order to efficiently meet current water requirements of all the sectors, i.e., agriculture, domestic and industrial, an ab initio level of water reallocation and efficient water management, with consideration to groundwater quality and its safe yield, in various areas are recommended. This might systematically reduce the waterlogged areas, support greater cropping intensity than is currently being practiced, and free up water for horizontal expansion, such as in the Thar Desert.

Tautomerization, molecular structure, transition state structure, and vibrational spectra of 2-aminopyridines: a combined computational and experimental study

Background2-amino pyridine derivatives have attracted considerable interest because they are useful precursors for the synthesis of a variety of heterocyclic compounds possessing a medicinal value. In this work we aim to study both structural and electronic as well as high quality vibrational spectra for 2-amino-3-methylpyridine (2A3MP) and 2-amino-4-methylpyridine (2A4MP).ResultsMøller–Plesset perturbation theory (MP2/6-31G(d) and MP2/6-31++G(d,p) methods were used to investigate the structure and vibrational analysis of (2A3MP) and (2A4MP). Tautomerization of 2A4MP was investigated by Density Functional Theory (DFT/B3LYP) method in the gas phase. For the first time, all tautomers including NH → NH conversions as well as those usually omitted, NH → CH and CH → CH, were considered. The canonical structure (2A4MP1) is the most stable tautomer. It is 13.60 kcal/mole more stable than the next (2A4MP2). Transition state structures of pyramidal N inversion and proton transfer were computed at B3LYP/6-311++G(d,p). Barrier to transition state of hydrogen proton transfer is calculated as 44.81 kcal/mol. Transition state activation energy of pyramidal inversion at amino N is found to be 0.41 kcal/mol using the above method. Bond order and natural atomic charges were also calculated at the same level. The raman and FT-IR spectra of (2A3MP) and (2A4MP) were measured (4000–400 cm−1). The optimized molecular geometries, frequencies and vibrational bands intensity were calculated at ab initio (MP2) and DFT(B3LYP) levels of theory with 6-31G(d), 6-31++G(d,p) and 6-311++G(d,p) basis sets. The vibrational frequencies were compared with experimentally measured FT-IR and FT-Raman spectra.ConclusionReconsidering the vibrational analysis of (2A3MP) and (2A4MP) with more accurate FT-IR machine and highly accurate animation programs result in new improved vibrational assignments. Sophisticated quantum mechanics methods enable studying the transition state structure for different chemical systems.Electronic supplementary materialThe online version of this article (doi:10.1186/s40064-015-1363-2) contains supplementary material, which is available to authorized users.

Temporal coarse graining of CO2 and N2 diffusion in zeolite NaKA: from the quantum scale to the macroscopic.

The kinetic CO2-over-N2 sieving capabilities in narrow pore zeolites are dependent on the free-energy barriers of diffusion between the zeolite pores, which can be fine-tuned by altering the framework composition. An ab initio level of theory is necessary to accurately compute the energy barriers, whereas it is desirable to predict the macroscopic scale diffusion for industrial applications. Using ab initio molecular dynamics on the picosecond time scale, the free-energy barriers of diffusion can be predicted for different local pore properties in order to identify those that are rate-determining for the pore-to-pore diffusion. Specifically, we investigate the effects of the Na(+)-to-K(+) exchange at the different cation sites and the CO2 loading in Zeolite NaKA. These computed energy barriers are then used as input for the Kinetic Monte Carlo method, coarse graining the dynamic simulation steps to the pore-to-pore diffusion. With this approach, we simulate how the identified rate-determining properties as well as the application of skin-layer surface defects affect the diffusion driven uptake in a realistic Zeolite NaKA powder particle model on a macroscopic time scale. Lastly, we suggest a model by combining these effects, which provides an excellent agreement with the experimental CO2 and N2 uptake behaviors presented by Liu et al. (Chem. Commun. 2010, 46, 4502-4504).

Theoretical Kinetics Study of the Reactions Forming the ClCO Radical Cycle in the Middle Atmosphere of Venus

Abstract A quantum-chemistry and kinetics study of key chemical reactions involved in the ClCO radical cycle of the Venus atmosphere: Cl + CO + M → ClCO + M (1); ClCO + O2 + M → ClC(O)OO + M (2) and ClC(O)OO + Cl → CO2 + ClO + Cl (3) (M = CO2), has been performed at 150–300 K. Unimolecular reaction rate theories on potential energy features derived at the G4//B3LYP/6-311+G(3df) ab initio composite level were employed. Limiting low pressure rate coefficients calculated for Reaction (1) are in good agreement with recommended experimental values. The present results validate rate coefficient values measured for Reaction (2) over relevant strato-mesosphere Venusian conditions. Rate coefficients calculated by the SACM/CT for Reaction (3) are given by k 3 = 2.5 × 10−11 (T/300)0.5 cm3 molecule –1 s –1. In the absence of experimental data, these values provide the first reliable prediction for k 3.

Elastic scattering process for argon ions and oxygen atoms in 10-500 eV range of relative kinetic energies

SynopsisThe interaction potential between oxygen atoms (3P state) and argon ions (2P state) has been calculated on ab initio level in the vast range of internuclear distances (0.8-100 a.u.). The elastic scattering process has been studied for relative kinetic energies of 10-500 eV.

ChemInform Abstract: Theoretical Investigations of Novel Zinc Oxide Polytypes and In‐Depth Study of Their Electronic Properties.

AbstractPossible stable polytypes of ZnO are predicted using simulated annealing and threshold runs with an empirical potential followed by local minimization on ab initio level.

A permutationally invariant full-dimensional ab initio potential energy surface for the abstraction and exchange channels of the H + CH4 system.

We report a permutationally invariant global potential energy surface (PES) for the H + CH4 system based on ∼63,000 data points calculated at a high ab initio level (UCCSD(T)-F12a/AVTZ) using the recently proposed permutation invariant polynomial-neural network method. The small fitting error (5.1 meV) indicates a faithful representation of the ab initio points over a large configuration space. The rate coefficients calculated on the PES using tunneling corrected transition-state theory and quasi-classical trajectory are found to agree well with the available experimental and previous quantum dynamical results. The calculated total reaction probabilities (Jtot = 0) including the abstraction and exchange channels using the new potential by a reduced dimensional quantum dynamic method are essentially the same as those on the Xu-Chen-Zhang PES [Chin. J. Chem. Phys. 27, 373 (2014)].

Computational Approach to the Study of Epitaxy: Natural Occurrence in Diamond/Forsterite and Aragonite/Zabuyelite

In this contribution the theoretical and computational aspects related to the determinations of the (i) interface structure, (ii) adhesion energy, and (iii) interfacial energy of a system composed by two crystalline phases in epitaxial relationship are discussed. Specifically, we describe the possible 2D lattice coincidences between two phases in epitaxial relationship, as well as all of the possible initial interface configurations which generate when different surface terminations of the phases put in contact are taken into account. Then, in order to elucidate these theoretical aspects, we have studied the following epitaxies in natural systems: {110}-diamond (C)/{101}-forsterite (Mg2SiO4) and {001}-aragonite (CaCO3)/{101}-zabuyelite (Li2CO3); the optimized interface structures and their adhesion energies were determined at the ab initio level. For the diamond/forsterite system, a very low value of the adhesion energy was estimated, β(110)/(101)D/Fo = 0.367 J/m2, suggesting a low probability to have ep...

Theoretical study on the thermal decomposition and isomerization of 3-Me-1-heptyl radical

A detailed theoretical investigation on the thermal decomposition and isomerization of 3-Me-1-heptyl radical is performed at the ab initio CBS-QB3 level of theory. The calculation reveals that the detailed reaction mechanisms of 3-Me-1-heptyl radical mainly incorporate reversible intramolecular hydrogen atom transfer and the beta-site CC bond scission. The standard reaction enthalpies (ΔrH2980) and enthalpies of formation (ΔfH2980) are determined at the CBS-QB3 level of theory. All investigated decomposition reactions are generally endothermic, while most of the isomerization processes are exothermic. Among the hydrogen atom transfer processes, the 1,3- and 1,2-hydrogen atom migration (R5 and R6, respectively) are prohibited due to their high isomerization barriers, while the 1,6-(R2) and 1,5-hydrogen atom transfer (R3) are kinetically accessible (owing to their low ring strains in the cyclic transition states). Compared with the 1,5-hydrogen atom shift for the n-heptyl radical, the methyl-substitution increases the rate coefficient by a factor of about 3.0. The product distributions are predicted at different temperatures on the basis of the steady-state approximation (SSA). The ultimate and dominant products majorly include ethylene (C2H4), propylene (C3H6), 1-butylene (1-C4H8) and 2-hexene (2-C6H12) over the temperature range of 500–2500K.