Ab Initio MP2 Research Articles

The bromide-bromomethyl radical dimer complex: Anion photoelectron spectroscopy and CCSD(T) calculations

The gas phase anion photoelectron spectrum associated with the bromide-bromomethyl radical is presented. The stabilisation energy and electron binding energy, a property corresponding to the electron affinity of the neutral complex, are determined. Ab initio MP2 optimisations (with additional CCSD(T) energies) found two forms of the complex, a hydrogen bonded complex and a halogen bonded complex. The halogen bonded complex was found to exhibit C2v symmetry and the hydrogen bonded complex exhibited Cs symmetry. Comparison between the experimental data and the computational data allow conclusions to be drawn about the structure of the experimentally observed species.

Competition between Solvent-Solvent and Solvent-Solute Interactions in the Microhydration of the Hexafluorophosphate Anion, PF6-(H2O)n=1,2.

This study systematically examines the interactions of the hexafluorophosphate anion (PF6-) with one or two solvent water molecules (PF6-(H2O)n where n = 1, 2). Full geometry optimizations and subsequent harmonic vibrational frequency computations are performed on each stationary point using a variety of common density functional theory methods (B3LYP, B3LYP-D3, M06-2X, and ωB97XD) and the MP2 and CCSD(T) ab initio methods with a triple-ζ correlation consistent basis set augmented with diffuse functions on all non-hydrogen atoms (cc-pVTZ for H and aug-cc-pVTZ for P, O, and F; denoted as haTZ). Five new stationary points of PF6-(H2O)2 have been identified, one of which has an electronic energy of approximately 2 kcal mol-1 lower than the only other dihydrate structure reported for this system. The CCSD(T) computations also reveal that the detailed interactions between PF6- and H2O can be quite difficult to model reliably, with some methods struggling to correctly characterize stationary points for n = 1 or accurately reproduce the vibrational frequency shifts induced by the formation of the hydrated complex. Although the interactions between the solvent and ionic solute are quite strong (CCSD(T) electronic dissociation energy ≈10 kcal mol-1 for the monohydrate minimum), the solvent-solvent interactions in the lowest-energy PF6-(H2O)2 minimum give rise to appreciable cooperative effects not observed in the other dihydrate minima. In addition, this newly identified structure exhibits the largest frequency shifts in the OH stretching vibrations for the waters of hydration (with Δω exceeding -100 cm-1 relative to the values for an isolated H2O molecule).

Ab initio investigations on bimetallic mononuclear superalkali clusters

Bimetallic mononuclear MFM′ and MOM′2 clusters (M, M′ = Li, Na or K, and M ≠ M′) along with their cations have been systematically studied using ab initio MP2 and CCSD methods. These clusters are stable against dissociation to M + FM′, MF + M′ and M + OM′2 fragments. Both MFM′ and MOM′2 clusters possess superalkali nature as their ionization energies (IEs) lie in the range 3.63–3.19 eV and 3.26–2.84 eV, respectively. These IEs are empirically related to those of their parent systems, i.e., FM2 and OM3. These findings should be useful for further studies on such bimetallic superalkalis.

Tripodal Podand Ligand with a Superhalogen Nature as an Effective Molecular Trap

Tris(2-methoxyethyl) fluoroborate anion (TMEFA), anovel tripodal ligand based on the BF4− superhalogen anion, is proposed and was investigated theoretically using ab initio MP2 (second-order Møller-Plesset perturbational method) and OVGF (outer valence Green function) methods. The studied molecule comprises three 2-methoxyethoxy groups (-O-CH2-CH2-O-CH3) connected to a central boron atom, which results in the C3-symmetry of the compound. The resulting anion was stable against fragmentation processes and its vertical electron detachment energy was found to be 5.72 eV. Due to its equilibrium structure resembling that of classical tripodal podands, the [F-B(O-CH2-CH2-O-CH3)3]− anion is capable of binding metal cations using its three arms, and thus may form strongly bound ionic complexes such as [F-B(O-CH2-CH2-O-CH3)3]−/Li+ and [F-B(O-CH2-CH2-O-CH3)3]−/Mg2+. The binding energies predicted for such compounds far exceed those of the similar neutral classical podand ligands, which likely makes the [F-B(O-CH2-CH2-O-CH3)3]− system a more effective molecular trap or steric shielding agent with respect to selected metal cations.

Molecular Modeling Analyses and Vibrational Characteristics for Nitromethane

Molecular modeling is considered as an effective tool for the evaluation of many physical as well as spectroscopic parameters. In this study semiempirical AM1, PM5, ab initio methods HF and MP2 as well as density functional methods VWN, B88LYP, B88PW91, B3PW91 and B3LYP were used to study nitromethane in its gas phase. The optimized structure, some physical parameters, and vibrational spectrum were calculated and discussed. The calculated optimized structure indicated that nitromethane (NM) belongs to the point group C2V. The obtained data indicated that quantum mixing gives results comparable to both ab initio method in accuracy and semiempirical method in computation time. It is concluded that for a small structure like NM, quantum mixing method provides reliable results in a short computation time. At B3LYP/6-31G(d,p) level, polar solvents showed changes in both HOMO/LUMO band gap energy and molecular electrostatic potential. This is an indication for the stability of NM in different chemical environments.

Exploring Cage‐warped Rotation Isomers of C20 Fullerene: MP2 and Density Functional Calculations

Using the density functional methods B3LYP, M06‐2X, PBE1PBE, B3LYP D3, M06‐2X D3, and PBE1PBE D3, and the ab initio MP2 calculations, the optimized atomic structures and energies of C20 cage rotation isomers without a constraint were obtained. The reaction path between the two rotational isomers was then studied, in which there are three local stable atomic structures. One is the most stable fullerene structure with the D2h point group staggered between the upper and bottom pentagons (ST) and the other is the second lowest energy rotational isomer with the Cs point group eclipsed between the upper and bottom pentagons (EC) with a torn fullerene structure (M1) between ST and EC. The first transition structure T1 between the ST and the M1, and the second transition structure T2 between the M1 and the EC were then obtained along the reaction coordinate between these three structures. Vibration analysis of all optimized structures including the transition structures without a constraint was carried out. For each of the rotational isomers obtained by our calculations, thermodynamic stability was explained with the relative energy difference, and then the kinetic stability was analyzed as the HOMO–LUMO energy difference.

Ab initioMP2 and DFT studies of ethyl-p-methoxycinnamate and its derivatives as corrosion inhibitors of iron in acidic medium

The efficiency of ethyl-p-methoxycinnamate(EPE) and its derivatives as corrosion inhibitors of iron in acid environment has been studied to find the relationship between molecular structure and electronic parameters with their efficiency of corrosion inhibition. The ab initio MP2 perturbation theory and DFT method were applied to calculate molecular structure and electronic parameters of inhibitors. Computational and experimental corrosion inhibition efficiency show that the electronic properties of molecules, including the orbital molecular frontier energy (HOMO and LUMO energy), ionization potential, electron affinity, electronegativity, number of electron transfer from inhibitor to metal and interaction energy have a strong relationship with inhibition performance. Interaction mechanism obtained from natural bond orbital analysis was employed to study the interactions between inhibitors with iron metal in more detail. The presence of electron donor groups within the frameworks of inhibitors has a less significant effect compared to π-electron contribution on corrosion inhibition performance.

Thermochemical study of gaseous indium-arsenic sulfosalt.

Sulfide systems are often used at high temperatures, when vaporization of the components is enabled. Sulfide ores are used as sources of various metals and nonmetals and gaseous sulfides, and sulfosalts may also play a role in the atmosphere chemistry of hot rocky exoplanets. To predict the existence and thermal stability of gaseous sulfides and sulfosalts it is important to know their thermodynamic characteristics. In this study the sulfosalt of indium and arsenic was obtained in the gaseous phase for the first time. High-temperature Knudsen effusion mass spectrometry was used to determine the partial pressures of vapor species over indium and arsenic sulfides. A molybdenum double two-temperature cell was used to create the conditions of coexistence of indium and arsenic sulfides. A theoretical study of gaseous As4 S4 and In2 AsS2 was performed using both B3LYP, M06, PBE0 and TPSSh hybrid DFT functionals and an ab initio wave function-based MP2(Full) method. Gaseous In2 AsS2 has been identified during vaporization of In6 S7 and As2 S3 from the molybdenum double two-temperature cell. The structure and molecular parameters of gaseous In2 AsS2 were determined using quantum chemical calculations. Energetically favorable structures of gaseous In2 S, AsS, As4 S4 and In2 AsS2 were found and vibrational frequencies were evaluated in the harmonic approximation. The formation enthalpy of gaseous In2 AsS2 (186 ± 37 kJ mol-1 ) was derived as a result of measurements of the equilibrium constants of two independent gas-phase reactions. The gaseous sulfosalt of indium and arsenic was obtained for the first time. The formation enthalpy of the In2 AsS2 (g) molecule at 298 K was evaluated both experimentally and theoretically. The thermal stability of the gaseous sulfosalt is less than that of the gaseous oxyacid salts.

The mechanism of tert-butylthiol formation via hydrosulfurization of isobutene catalyzed by superacids (HBF4, HAsF6, and HSbF6)

The mechanism of the (CH3)2CCH2 + H2S → (CH3)3CSH reaction catalyzed by various superacids (HBF4, HAsF6, and HSbF6) was investigated theoretically using the ab initio CCSD(T) and MP2 methods and the aug-cc-pVDZ/LANL2DZ basis sets. The effects of surrounding solvent molecules were approximated by employing the PCM solvation model. The most important findings include the observation that each superacid considered is capable of effectively catalyzing isobutene hydrosulfurization as it reduces the activation barrier by ca. 95% in comparison to the uncatalyzed process.

The mechanisms of isobutene hydration yielding tert-butanol catalyzed by a strong mineral acid (H2SO4) and Lewis-Brønsted superacid (HF/SbF5)

The mechanism of the (CH3)2CCH2+H2O→(CH3)3COH reaction catalyzed by two strong acids (H2SO4 and HSbF6) was investigated theoretically using the ab initio MP2 and CCSD(T) methods and the aug-cc-pVDZ/LANL2DZ and aug-cc-pVTZ/LANL2DZ basis sets. The effects of surrounding solvent molecules were approximated by employing the polarized continuum solvation model. The most important findings include the observation that both acids are capable of catalyzing isobutene hydration but the reaction is predicted to proceed faster when the HSbF6 superacid plays the catalyst role.

Thiadiazole-2-Thiol-5-Thione and 2,5-Dimercapto-1,3,4-Thiadiazol Tautomerism, Conformational Stability, Vibrational Assignments, Inhibitor Efficiency and Quantum Chemical Calculations

Abstract Raman (3700–100 cm−1) and infrared (4000–400 cm−1) spectra of 2,5-Dimercapto-1,3,4-thiadiazol (DMTD) were recorded in the solid phase. Six structures (1–6) were initially proposed for DMTD as a result of thiol-thione tautomerism and internal rotation(s) of thiol group(s) around the C–S bond. Quantum chemical calculations were carried out for an isolated molecule (1–6) using density functional theory (B3LYP) and ab initio MP2(full) methods utilizing 6-31G(d) and 6-311++G(d,p) basis sets which favor thiol-thione tautomerism (structure 4). Relaxed potential energy surface scans of structure 4 revealed an additional conformer (the thiol group is out-of-plane, structure 7) using the aforementioned methods at 6-311++G(d,p) basis set. For additional verification, plane-wave solid state calculations were carried out at PW91 and PBEsol came out in favor of conformer 7. This is in agreement with the computed/observed SH in-plane bending of S-7 (959/941 cm−1) rather than the one estimated at (880 cm−1) for S-4. Moreover, the observed split IR/Raman bands were found consistent with solid state calculated frequencies of S-7 assuming two molecules per unit cell bonded via H-bonding intermolecular interactions. Aided by vibrational frequency calculations, normal coordinate analysis, force constants and potential energy distributions (PEDs), a complete vibrational assignment for the observed IR and Raman bands is proposed herein. Furthermore, we have estimated the frontier molecular orbitals and atomic charges to account for the corrosion inhibition efficiency of DMTD along with its binding sites to the metal surface. Our results are discussed herein and compared to similar molecules whenever appropriate.

Silver cluster-amino acid interactions: a quantum-chemical study.

Binding of silver ion (Ag+) and two atomic neutral silver cluster (Ag2) with a set of amino acids has been studied using Density Functional Theory (DFT) and ab initio MP2 method. We show that binding energy with Ag2 is higher for deprotonated anionic amino acids. Cysteine, aspartic acid, and tyrosine with deprotonated side chain exhibit the highest binding energy (Gbind) values among all the amino acids: -30.1kcalmol-1, -30.7kcalmol-1, and -30.9kcalmol-1, respectively. Binding energies of deprotonated cysteine, glutamic acid, tyrosine, and aspartic acid with silver ion Ag+ are reported here for the first time. Natural bond orbital (NBO) analysis has also been performed to calculate charge transfer, natural populations, occupancies, and Wiberg bond indices of the amino acid-Ag2 complexes. Atoms-in-molecules (AIM) theory was used to establish the nature of interactions. It was shown that, in most cases, the bonds between amino acid and Ag2 cluster are partially electrostatic and partially covalent.

The presence of two different central atoms increases the strength of Lewis-Brønsted superacids

The existence, thermodynamic stability, and gas phase acidity of two series of dinuclear Lewis-Brønsted superacids (HB2F7, HAl2F7, HAlBF7 and HAs2F11, HSb2F11, HAsSbF11) were investigated on the basis of ab initio MP2 and CCSD(T) calculations. All the systems studied are characterized by large acid strengths manifested by the Gibbs free deprotonation energies significantly lower than that of the sulfuric acid. These results are related to the high electronic stabilities of their corresponding superhalogen anions (natural precursors of superacids). Furthermore, our investigations show that the superacid molecules containing two different central atoms are stronger in the gas phase than their classical counterparts.

π-Hydrogen Bonding Probes the Reactivity of Aromatic Compounds: Nitration of Substituted Benzenes.

The shifts of phenol O-H stretching vibration frequencies [Δν(OH)exp] upon π-hydrogen bonding with aromatic compounds is proposed as a spectroscopic probe of the reactivity of aromatic substrates toward electrophiles. A single infrared spectrum reflecting the Δν(OH)exp shift for an aromatic species in a reference solvent (CCl4 in this study) provides a good estimate of reactivity. The methodology is applied in rationalizing reactivity trends for the BF3 catalyzed nitration by methylnitrate in nitromethane of 20 aromatic reactants, including benzene, 11 methylbenzenes, several monoalkyl benzenes, the four halobenzenes, and anisole. Literature kinetic data are employed in the analysis. Very good correlations between relative rates of nitration and Δν(OH)exp are obtained. The approach is best applied to reactions, where the initial interactions between the reactants controls the rates. A new theoretical quantity, the shifts (with respect to benzene) of the molecular electrostatic potential at 1.5 Å over the centroid of the aromatic ring [Δ V(1.5)] is defined and shown to provide a good description of substituent effects on properties of the aromatic species. B3LYP density functional and MP2 ab initio methods combined with the 6-311++G(3df,2pd) basis set are employed in evaluating the Δ V(1.5) values.

Tautomerism of Inosine in Water: Is It Possible?

Syn- and anti-conformers of four tautomer structures of inosine were studied in the gas phase and in solvent water to investigate the possibility of hydrogen bonding and tautomeric conversion. It was found that in the gas phase and in water solution the most stable is the syn-conformer of the 6-keto tautomer followed by its anti-conformer and syn-conformer of the 6-enol form. In the gas phase, the percent content of syn- and anti-conformers is 83.77 and 12.86%, respectively, whereas syn-enol tautomer is calculated to be 2.54%. However, in water solution the syn-conformer of the keto tautomer is 99.9%. The water-assisted proton transfer process in inosine was investigated using ab initio MP2 and SCS-MP2 quantum chemical approaches. Solute-solvent clusters containing an inosine molecule and five water molecules embedded in the "bulk" solvent treated as polarizable continuum (the CPCM/MP2/6-31+G(d,p) level of theory) were explored. The energy barrier of the water-assisted proton transfer reaction in inosine is found to be 12.9 kcal mol-1 and the rate constant ( k = 6.68 × 101 s-1) is sufficiently large to generate the 6-enol tautomer. From the reaction profile of the proton transfer we can conclude that the process is realized through the asynchronous concerted mechanism.

Expanding the range of binding energies and oxidizability of biologically relevant S-aromatic interactions: imidazolium and phenolate binding to sulfoxide and sulfone.

Oxidation and protonation/deprotonation strongly impact intermolecular noncovalent interactions. For example, S-aromatic interactions are stabilized up to three-fold in the gas phase on oxidation of the sulfur ligand or protonation/deprotonation of the aromatic. To probe if such stabilizing effects are additive and to model interactions of oxidized methionine (MetOn) with protonated histidine and deprotonated tyrosine residues in proteins, we examined Me2SOn (n = 1, 2) binding to imidazolium, phenolate and their 4-methylated forms. Ab initio MP2(full)/6-311++G(d,p) gas-phase calculations reveal that the Me2SOn-imidazolium complexes adopt edge-on geometry with σ-type (N/C-HarO) H-bonding and interaction energies of -17.2 to -31.1 kcal mol-1. The less stable (-13.8 to -21.0 kcal mol-1) Me2SOn-phenolates possess en-face geometry stabilized by π-type (C-Hπar) H-bonding. Comparing these energies with those reported for the Me2S-neutral aromatics affirms the additive effects of ligand protonation/deprotonation and oxidation on gas-phase stability. However, this is not the case in water although the aqueous complexes retain their preferred gas-phase σ- and π-type H-bonded structures. Binding free energies (kcal mol-1) calculated from molecular dynamics simulations in bulk water (preceded by CHARMM36 force field calibration where necessary) reveal that Me2SO-imidazolium (-4.4) is more stable than Me2SO-phenolate (-2.4) but Me2SO2-imidazolium (-0.6) is less stable than Me2SO2-phenolate (-3.8). Vertical ionization potentials (IPV) calculated for the gas-phase complexes indicate that the Me2SOn-phenolates, but not the Me2SOn-imidazoles, are oxidizable under biological conditions. Charge transfer from the phenolate increases its IPV by ∼20%, decreasing its susceptibility to oxidation. Overall, this work provides fundamental data to predict the behaviour of protein-based MetOn-aromatic-ion interactions.

Mechanism of the ethanol-based (C2H5OH2)+(SbF6)− salt formation by the superacid-catalyzed acetaldehyde hydrogenation

The mechanism of the acetaldehyde hydrogenation reaction yielding the ethanol-based (C2H5OH2)+(SbF6)− salt with the assistance of the HSbF6 (HF/SbF5) superacid catalyst was investigated theoretically using ab initio MP2 and CCSD(T) methods and the aug-cc-pVDZ basis set. (The effects of surrounding solvent were approximated by employing the polarized continuum solvation model and by the explicit inclusion of one solvent molecule.) The most important findings include the observation that the activation barriers calculated for both phases considered are significantly reduced (by 66%) in comparison with the uncatalyzed acetaldehyde hydrogenation process. The reaction begins with the spontaneous (barrier-less) protonation of acetaldehyde by the superacid and continues through the formation of ethanol molecule followed by its subsequent protonation by the recovered HSbF6. The overall process is exoenergetic by 63 kcal/mol and leads to the formation of the ethanol-based (C2H5OH2)+(SbF6)− ionic salt as the final product.

Collision induced dissociation of positive ions of dimethylnitramine, a model system for nitramine energetic molecules

Positive ions of dimethylnitramine (DMNA), a model system for nitramine energetic molecules, have been produced in the gas phase by electrospray ionization. Protonated dimethylnitramine ion [DMNA+H]+ and its hydrated complex [2DMNA+H2O+2H]2+ have been investigated by both low energy collision induced dissociation (CID) and ab initio MP2 level of theory. Ion structure has been calculated. Fragments have been experimentally determined and dissociation mechanisms have been elucidated. Interestingly, the favored fragmentation pathways depend on the local environment of the ion: the hydrated complex primarily loses NO via nitro nitrite isomerization, while only OH elimination is observed in the case of protonated DMNA.

Computational Investigation of Structure and Reactivity of Methyl Hydrazinecarbodithioate

In this study, we theoretically investigated Methyl hydrazinecarbodithioate by quantum chemical calculations for geometry optimization, vibration frequencies, and electronic structure parameters. The geometry optimization by DFT, ab initio MP2 method and the frequency calculation by DFT method was performed at the highest available Pople style 6-311G++(3df,3pd) basis set level. The semi-empirical calculations were performed by the latest PM7 method. The theoretically obtained results were compared with the experimental data. Conformational behavior, frontier molecular orbitals, molecular electrostatic potential, electron localization function, and non-covalent interaction plots were also analyzed. The study explained the geometry, conformational flexibility and relative stability of different conformers.

Cation-π Interactions between Quaternary Ammonium Ions and Amino Acid Aromatic Groups in Aqueous Solution.

Cation-π interactions play important roles in the stabilization of protein structures and protein-ligand complexes. They contribute to the binding of quaternary ammonium ligands (mainly RNH3+ and RN(CH3)3+) to various protein receptors and are likely involved in the blockage of potassium channels by tetramethylammonium (TMA+) and tetraethylammonium (TEA+). Polarizable molecular models are calibrated for NH4+, TMA+, and TEA+ interacting with benzene, toluene, 4-methylphenol, and 3-methylindole (representing aromatic amino acid side chains) based on the ab initio MP2(full)/6-311++G(d,p) properties of the complexes. Whereas the gas-phase affinity of the ions with a given aromatic follows the trend NH4+ > TMA+ > TEA+, molecular dynamics simulations using the polarizable models show a reverse trend in water, likely due to a contribution from the hydrophobic effect. This reversed trend follows the solubility of aromatic hydrocarbons in quaternary ammonium salt solutions, which suggests a role for cation-π interactions in the salting-in of aromatic compounds in solution. Simulations in water show that the complexes possess binding free energies ranging from -1.3 to -3.3 kcal/mol (compared to gas-phase binding energies between -8.5 and -25.0 kcal/mol). Interestingly, whereas the most stable complexes involve TEA+ (the largest ion), the most stable solvent-separated complexes involve TMA+ (the intermediate-size ion).