Nonadiabatic Dynamics of Cycloparaphenylenes with TD-DFTB Surface Hopping.

We implemented a version of the decoherence-corrected fewest switches surface hopping based on linear-response time-dependent density functional tight binding (TD-DFTB), enhanced by transition density analysis. The method has been tested for the gas-phase relaxation dynamics of two cycloparaphenylene molecules, [8]CPP and [10]CPP, explaining some important features of their nonadiabatic dynamics, such as the origin of their long fluorescence lifetimes (related to the slow radiative emission from the S1 state) and the trend of increasing the fluorescence rate with the molecular size (related to an increase in the S1-S0 energy gaps and oscillator strengths in the larger molecule). The quality of the TD-DFTB electronic structure information was assessed through four quantities: excitation energies; charge-transfer (CT) numbers, which estimate the charge transfer character of states; participation ratio (PR), which describes delocalization of electronic density; and participation ratio of natural transition orbitals (PRNTO), which describes the multiconfigurational character of states. These quantities were computed during dynamics and recomputed for the same geometries with the higher-level long-range-corrected TD-LC-DFTB and a lower-level single-determinant approximation for the excited states, SD-(LC)-DFTB. Taking TD-LC-DFTB as the standard, TD-DFTB underestimates the excitation energies by ∼0.5 eV and overestimates CT and PR. SD-DFTB underestimates excitation energies and overestimates CT to the same extent that TD-DFTB does, but it predicts reasonable PR distributions. SD-LC-DFTB leads to an extreme overestimation of the excitation energies by ∼3 eV, overestimates the charge transfer character of the state, but predicts the PR values very close to those obtained with TD-LC-DFTB.

The Thermodynamic and Kinetic Properties of 2-Hydroxypyridine/2-Pyridone Tautomerization: A Theoretical and Computational Revisit.

The gas-phase thermal tautomerization reaction between 2-hydroxypyridine (2-HPY) and 2-pyridone (2-PY) was investigated by applying 6-311++G** and aug-cc-pvdz basis sets incorporated into some density functional theory (DFT) and coupled cluster with singles and doubles (CCSD) methods. The geometrical structures, dipole moments, HOMO-LUMO energy gaps, total hyperpolarizability, kinetics and thermodynamics functions were monitored against the effects of the corrections imposed on these functionals. The small experimental energy difference between the two tautomers of 3.23 kJ/mol; was a real test of the accuracy of the applied levels of theory. M062X and CCSD methods predicted the preference of 2-HPY over 2-PY by 5-9 kJ/mol; while B3LYP functional favoured 2-PY by 1-3 kJ/mol. The CAM-B3LYP and ωB97XD functionals yielded mixed results depending on the basis set used. The source of preference of 2-HPY is the minimal steric hindrance and electrostatic repulsion that subdued the huge hyperconjugation in 2-PY. A 1,3-proton shift intramolecular gas-phase tautomerization yielded a high average activation of 137.152 kJ/mol; while the intermolecular mixed dimer interconversion gave an average barrier height of 30.844 kJ/mol. These findings are boosted by a natural bond orbital (NBO) technique. The low total hyperpolarizabilities of both tautomers mark out their poor nonlinear optical (NLO) behaviour. The enhancement of the total hyperpolarizability of 2-HPY over that of 2-PY is interpreted by the bond length alternation.

UV excitations of halons.

In the present study, we examined the UV excitations of a newly introduced molecular set, Halons-9, composed of nine gaseous halon molecules. The performance of the density functional-based multi-reference configuration interaction method (DFT/MRCI) and time-dependent density functional theory with CAM-B3LYP functional (TD-CAM-B3LYP) in the computation of singlet and triplet excited states of this set was evaluated against coupled-cluster with singles and doubles (CCSD). Excited states up to the corresponding ionization limits, including both localized and delocalized excitations, have been benchmarked. TD-CAM-B3LYP significantly underestimates excitation energies of the higher mixed valence-Rydberg and Rydberg states, with computed mean absolute deviations from the equation of motion (EOM)-CCSD results 1.06 and 0.76 eV, respectively. DFT/MRCI gives a significantly better description of higher excited states, albeit still poor, compared to the TD-CAM-B3LYP. The mean absolute deviations of mixed valence-Rydberg and Rydberg states from the reference EOM-CCSD values are 0.66 and 0.47 eV, respectively. The performance of DFT/MRCI for description of strongly correlated states with valence-Rydberg mixing is still not satisfactory enough. On the other hand, oscillator strengths of most of singlet states obtained with both methods are close to the EOM-CCSD values. The largest deviations, occurring in the case of several high-lying multiconfigurational states, are of an order of magnitude.

Gas-Phase Thermal Tautomerization of Imidazole-Acetic Acid: Theoretical and Computational Investigations.

The gas-phase thermal tautomerization reaction between imidazole-4-acetic (I) and imidazole-5-acetic (II) acids was monitored using the traditional hybrid functional (B3LYP) and the long-range corrected functionals (CAM-B3LYP and ωB97XD) with 6-311++G** and aug-cc-pvdz basis sets. The roles of the long-range and dispersion corrections on their geometrical parameters, thermodynamic functions, kinetics, dipole moments, Highest Occupied Molecular Orbital-Lowest Unoccupied Molecular Orbital (HOMO-LUMO) energy gaps and total hyperpolarizability were investigated. All tested levels of theory predicted the preference of I over II by 0.750-0.877 kcal/mol. The origin of predilection of I is assigned to the H-bonding interaction (nN8→σ*O14-H15). This interaction stabilized I by 15.07 kcal/mol. The gas-phase interconversion between the two tautomers assumed a 1,2-proton shift mechanism, with two transition states (TS), TS1 and TS2, having energy barriers of 47.67-49.92 and 49.55-52.69 kcal/mol, respectively, and an sp³-type intermediate. A water-assisted 1,3-proton shift route brought the barrier height down to less than 20 kcal/mol in gas-phase and less than 12 kcal/mol in solution. The relatively high values of total hyperpolarizability of I compared to II were interpreted and discussed.

Towards understanding the decomposition/isomerism channels of stratospheric bromine species: ab initio and quantum topology study.

The present study aims at a fundamental understanding of bonding characteristics of the C-Br and O-Br bonds. The target molecular systems are the isomeric CH3OBr/BrCH2OH system and their decomposition products. Calculations of geometries and frequencies at different density functional theory (DFT) and Hartree-Fock/Møller-Plesset (HF/MP2) levels have been performed. Results have been assessed and evaluated against those obtained at the coupled cluster single-double (Triplet) (CCSD(T)) level of theory. The characteristics of the C-Br and O-Br bonds have been identified via analysis of the electrostatic potential, natural bond orbital (NBO), and quantum theory of atoms in molecules (QTAIM). Analysis of the electrostatic potential (ESP) maps enabled the quantitative characterization of the Br σ-holes. Its magnitude seems very sensitive to the environment and the charge accumulated in the adjacent centers. Some quantum topological parameters, namely Ñ2ρ, ellipticity at bond critical points and the Laplacian bond order, were computed and discussed. The potential energy function for internal rotation has been computed and Fourier transformed to characterize the conformational preferences and origin of the barriers. NBO energetic components for rotation about the C-Br and O-Br bonds as a function of torsion angle have been computed and displayed.

Electronic structure of alloxan and its dimers: QM/QD simulations and quantum chemical topology analysis.

This study aims to identify the origin of the extra stability of alloxan, a biologically active pyrimidine. To achieve this goal, detailed DFT computations and quantum dynamics simulations have been performed to establish the most stable conformation and the global minimum structure on the alloxan potential energy surface. The effects of the solvent, basis set, and DFT method have been examined to validate the theoretical model adopted throughout the work. Two non-covalent intermolecular dimers of alloxan, the H-bonded and dipolar dimers, have been investigated at the ωB97X-D and M06-2X levels of theory using the triple zeta 6-311++G** to establish their relative stability. Quantum chemical topology features and natural bond orbital analysis (NBO) have been performed to identify and characterize the forces that govern the structures and underlie the extra stability of alloxan.

Interaction of polar and nonpolar organic pollutants with soil organic matter: sorption experiments and molecular dynamics simulation.

The fate of organic pollutants in the environment is influenced by several factors including the type and strength of their interactions with soil components especially SOM. However, a molecular level answer to the question "How organic pollutants interact with SOM?" is still lacking. In order to explore mechanisms of this interaction, we have developed a new SOM model and carried out molecular dynamics (MD) simulations in parallel with sorption experiments. The new SOM model comprises free SOM functional groups (carboxylic acid and naphthalene) as well as SOM cavities (with two different sizes), simulating the soil voids, containing the same SOM functional groups. To examine the effect of the hydrophobicity on the interaction, the organic pollutants hexachlorobenzene (HCB, non-polar) and sulfanilamide (SAA, polar) were considered. The experimental and theoretical investigations explored four major points regarding sorption of SAA and HCB on soil, yielding the following results. 1--The interaction depends on the SOM chemical composition more than the SOM content. 2--The interaction causes a site-specific adsorption on the soil surfaces. 3--Sorption hysteresis occurs, which can be explained by inclusion of these pollutants inside soil voids. 4--The hydrophobic HCB is adsorbed on soil stronger than the hydrophilic SAA. Moreover, the theoretical results showed that HCB forms stable complexes with all SOM models in the aqueous solution, while most of SAA-SOM complexes are accompanied by dissociation into SAA and the free SOM models. The SOM-cavity modeling had a significant effect on binding of organic pollutants to SOM. Both HCB and SAA bind to the SOM models in the order of models with a small cavity>a large cavity>no cavity. Although HCB binds to all SOM models stronger than SAA, the latter is more affected by the presence of the cavity. Finally, HCB and SAA bind to the hydrophobic functional group (naphthalene) stronger than to the hydrophilic one (carboxylic acid) for all SOM models containing a cavity. For models without a cavity, SAA binds to carboxylic acid stronger than to naphthalene.

Protonation and deprotonation enthalpies of alloxan and implications for the structure and energy of its complexes with water: a computational study.

The optimized geometries, harmonic vibrational frequencies, and energies of the structures of monohydrated alloxan were computed at the DFT/ωB97X-D and B3LYP/6-311++G** level of theory. Results confirm that the monohydrate exists as a dipolar alloxan-water complex which represents a global minimum on the potential energy surface (PES). Trajectory dynamics simulations show that attempt to reorient this monohydrate, to a more favorable orientation for H-bonding, is opposed by an energy barrier of 25.07 kJ/mol. Alloxan seems to prefer acting as proton donor than proton acceptor. A marked stabilization due to the formation of N-H-OH2 bond is observed. The concerted proton donor-acceptor interaction of alloxan with one H2O molecule does not increase the stability of the alloxan-water complex. The proton affinity of the O and N atoms and the deprotonation enthalpy of the NH bond of alloxan are computed at the same level of theory. Results are compared with recent data on uracil, thymine, and cytosine. The intrinsic acidities and basicities of the four pyrimidines were discussed. Results of the present study reveal that alloxan is capable of forming stronger H-bonds and more stable cyclic complex with water; yet it is of much lower basicity than other pyrimidines.

Hydrogen bond coupling in sodium dihydrogen triacetate.

The coupling of hydrogen bonds is central to structures and functions of biological systems. Hydrogen bond coupling in sodium dihydrogen triacetate (SDHTA) is investigated as a model for the hydrogen bonded systems of the type O-H…O. The two-dimensional potential energy surface is derived from the full-dimensional one by selecting the relevant vibrational modes of the hydrogen bonds. The potential energy surfaces in terms of normal modes describing the anharmonic motion in the vicinity of the equilibrium geometry of SDHTA are calculated for the different species, namely, HH, HD, DH, and DD isotopomers. The ground state wave functions and their relation to the hydrogen bond structural parameters are discussed. It has been found that the hydrogen bonds in SDHTA are uncoupled, that is elongation of the deuterated hydrogen bond does not affect the non-deuterated one.

Does prop-2-ynylideneamine, HC≡CCH=NH, exist in space? A theoretical and computational investigation.

MP2, DFT and CCSD methods with 6-311++G** and aug-cc-pvdz basis sets have been used to probe the structural changes and relative energies of E-prop-2-ynylideneamine (I), Z-prop-2-ynylideneamine (II), prop-1,2-diene-1-imine (III) and vinyl cyanide (IV). The energy near-equivalence and provenance of preference of isomers and tautomers were investigated by NBO calculations using HF and B3LYP methods with 6-311++G** and aug-cc-pvdz basis sets. All substrates have Cs symmetry. The optimized geometries were found to be mainly theoretical method dependent. All elected levels of theory have computed I/II total energy of isomerization (ΔE) of 1.707 to 3.707 kJ/mol in favour of II at 298.15 K. MP2 and CCSD methods have indicated clearly the preference of II over III; while the B3LYP functional predicted nearly similar total energies. All tested levels of theory yielded a global II/IV tautomerization total energy (ΔE) of 137.3-148.4 kJ/mol in support of IV at 298.15 K. The negative values of ΔS indicated that IV is favoured at low temperature. At high temperature, a reverse tautomerization becomes spontaneous and II is preferred. The existence of II in space was debated through the interpretation and analysis of the thermodynamic and kinetic studies of this tautomerization reaction and the presence of similar compounds in the Interstellar Medium (ISM).

How soil organic matter composition controls hexachlorobenzene-soil-interactions: adsorption isotherms and quantum chemical modeling.

Hazardous persistent organic pollutants (POPs) interact in soil with the soil organic matter (SOM) but this interaction is insufficiently understood at the molecular level. We investigated the adsorption of hexachlorobenzene (HCB) on soil samples with systematically modified SOM. These samples included the original soil, the soil modified by adding a hot water extract (HWE) fraction (soil+3 HWE and soil+6 HWE), and the pyrolyzed soil. The SOM contents increased in the order pyrolyzed soil

Eclipsed acetaldehyde as a precursor for producing vinyl alcohol.

The MP2 and DFT/B3LYP methods at 6-311++G(d,p) and aug-cc-pdz basis sets have been used to probe the origin of relative stability preference for eclipsed acetaldehyde over its bisected counterpart. A relative energy stability range of 1.02 to 1.20 kcal/mol, in favor of the eclipsed conformer, was found and discussed. An NBO study at these chemistry levels complemented these findings and assigned the eclipsed acetaldehyde preference mainly to the vicinal antiperiplanar hyperconjugative interactions. The tautomeric interconversion between the more stable eclipsed acetaldehyde and vinyl alcohol has been achieved through a four-membered ring transition state (TS). The obtained barrier heights and relative stabilities of eclipsed acetaldehyde and the two conformers of vinyl alchol at these model chemistries have been estimated and discussed.

Toward the understanding of the metabolism of levodopa I. DFT investigation of the equilibrium geometries, acid-base properties and levodopa-water complexes.

Levodopa (LD) is used to increase dopamine level for treating Parkinson's disease. The major metabolism of LD to produce dopamine is decarboxylation. In order to understand the metabolism of LD; the electronic structure of levodopa was investigated at the Density Functional DFT/B3LYP level of theory using the 6-311+G** basis set, in the gas phase and in solution. LD is not planar, with the amino acid side chain acting as a free rotator around several single bonds. The potential energy surface is broad and flat. Full geometry optimization enabled locating and identifying the global minimum on this Potential energy surface (PES). All possible protonation/deprotonation forms of LD were examined and analyzed. Protonation/deprotonation is local in nature, i.e., is not transmitted through the molecular framework. The isogyric protonation/deprotonation reactions seem to involve two subsequent steps: First, deprotonation, then rearrangement to form H-bonded structures, which is the origin of the extra stability of the deprotonated forms. Natural bond orbital (NBO) analysis of LD and its deprotonated forms reveals detailed information of bonding characteristics and interactions across the molecular framework. The effect of deprotonation on the donor-acceptor interaction across the molecular framework and within the two subsystems has also been examined. Attempts to mimic the complex formation of LD with water have been performed.