Water trimer cation

By using density functional theory (DFT) and high-level ab initio theory, we have investigated the structure, interaction energy, electronic property, and IR spectra of the water trimer cation [(H₂O) ₃ ⁺ ]. Two structures of the water trimer cation [the H₃O⁺ containing linear (3Lp) structure versus the ring (3OO) structure] are compared. For the complete basis set (CBS) limit of coupled cluster theory with single, double, and perturbative triple excitations [CCSD(T)], the 3Lp structure is 11.9?kcal/mol more stable than the 3OO structure. This indicates that the ionization of water clusters produce the hydronium cation moiety (H₃O⁺) and the hydroxyl radical. It is interesting to note that the calculation results of the water trimer cation vary seriously depending on the calculation level. At the level of M?ller?CPlesset second-order perturbation (MP2) theory, the stability of 3OO is underestimated due to the underestimated O??O hemibonding energy. This stability is also underestimated even for the CCSD(T) single point calculations on the MP2-optimized geometry. For the 3OO structure, the MP2 and CCSD(T) calculations give closed-ring structures with a hemi-bond between two O atoms, while the DFT calculations show open-ring structures due to the overestimated O??O hemibonding energy. Thus, in order to obtain reliable stabilities and frequencies of the water trimer cation, the CCSD(T) geometry optimizations and frequency calculations are necessary. In this regard, the DFT functionals need to be improved to take into account the proper O??O hemibonding energy.     

SCF,MP2, and CEPA-1 calculations on the OH ‥ O hydrogen bonded complexes (H2O)2 and (H2O-H2CO)

Counterpoise corrected ab initio calculations are reported for (H₂O)₂ and H₂O-H₂CO. Geometry searches were done in the moment-optimized basis DZP' at the SCF, MP2, and CEPA-1 levels of theory, followed by more accurate single-point calculations in basis ESPB, which includes bondfunctions to saturate the dispersion energy. The final equilibrium binding energies obtained are ?4.7 ±0.3 kcal/mol for a near-linear (H₂O)₂ structure and ?4.6 ±0.3 kcal/mol for a strongly bent HOH ‥ OCH₂ structure. The energy difference between these systems is much smaller than in all previous ab initio work. Cyclic (C_2h) and bifurcated (C_2v) transition structures for (H₂O)₂ are located at 1.0 ±0.1 kcal/mol and 1.9 ±0.3 kcal/mol above the global minimum, respectively. A new partitioning scheme is presented that rigorously partitions the MP2 correlation interaction energy in intra and intermolecular (dispersion) contributions. These terms are large (up to 2 kcal/mol) but of opposite sign for most geometries studied and hence their overall effect upon the final structures is relatively small. The relative merits of the MP2 and CEPA-1 approaches are discussed are discussed and it is concluded that for economical reasons MP2 is to be preferred, especially for larger systems.     

Electronic structure benchmark calculations of CO2 fixing elementary chemical steps in RuBisCO using the projector-based embedding approach

Ribulose 1,5-bisphosphate carboxylase-oxygenase (RuBisCO) is the main enzyme involved in atmospheric carbon dioxide (CO₂) fixation in the biosphere. This enzyme catalyzes a set of five chemical steps that take place in the same active-site within magnesium (II) coordination sphere. Here, a set of electronic structure benchmark calculations have been carried out on a reaction path proposed by Gready et al. by means of the projector-based embedding approach. Activation and reaction energies for all main steps catalyzed by RuBisCO have been calculated at the MP2, SCS-MP2, CCSD, and CCSD(T)/aug-cc-pVDZ and cc-pVDZ levels of theory. The treatment of the magnesium cation with post-HF methods is explored to determine the nature of its involvement in the mechanism. With the high-level ab initio values as a reference, we tested the performance of a set of density functional theory (DFT) exchange-correlation (xc) functionals in reproducing the reaction energetics of RuBisCO carboxylase activity on a set of model fragments. Different DFT xc-functionals show large variation in activation and reaction energies. Activation and reaction energies computed at the B3LYP level are close to the reference SCS-MP2 results for carboxylation, hydration and protonation reactions. However, for the carbon–carbon bond dissociation reaction, B3LYP and other functionals give results that differ significantly from the ab initio reference values. The results show the applicability of the projector-based embedding approach to metalloenzymes. This technique removes the uncertainty associated with the selection of different DFT xc-functionals and so can overcome some of inherent limitations of DFT calculations, complementing, and potentially adding to modeling of enzyme reaction mechanisms with DFT methods.     

Density functional theory and post-Hartree-Fock studies on molecular structure and harmonic vibrational spectrum of formaldehyde

Density functional theory (DFT) with the Becke's three-parameter exchange correlation functional and the functional of Lee, Yang and Parr, gradient-corrected functionals of Perdew, and Perdew and Wang [the DFT(B3LYP), DFT(B3P86) and DFT(B3PW91) methods, respectively], and several levels of conventional ab initio post-Hartree-Fock theory (second- and fourth-order perturbation theory M?ller-Plesset MP2 and MP4(SDTQ), coupled cluster with the single and double excitations (CCSD), and CCSD with perturbative triple excitation [CCSD(T)], configuration interaction with the single and double excitations [CISD], and quadratic configuration interaction method [QCISD(T)], using several basis sets [ranging from a simple 6-31G(d,p) basis set to a 6-311+ +G(3df, 2pd) one], were applied to study of the molecular structure (geometrical parameters, rotational constants, dipole moment) and harmonized infrared (IR) spectrum of formaldehyde (CH₂O). High-level ab initio methods CCSD(T) and QCISD(T) with the 6-311+ +G(3df, 2pd) predict correctly molecular parameters, vibrational harmonic wavenumbers and the shifts of the harmonic IR spectrum of ¹²CH₂ ¹⁶O upon isotopic substitution. Received: 30 January 1997 / Accepted: 7 May 1997     

Ab initio study of the unimolecular decomposition of 2‐butenenitrile: Molecular elimination channels

Ab initio molecular orbital calculations have been performed for the unimolecular decomposition of 2‐butenenitrile (CH₃CH?CHCN), especially for HCN and H₂ molecular elimination channels. Structures and energies of the reactants, products, and relevant species in the individual reaction pathways were determined by MP2 gradient optimization and MP4 CCSD(T) single‐point energy calculations. Direct 1,1 and 1,2 molecular eliminations and H or CN migration followed by elimination channels were identified. Dissociation rates for the individual reaction pathways were calculated from vibrational frequencies at the ab initio transition state geometries by employing Rice–Ramsperger–Kassel–Marcus theory, from which channel branching ratios were determined. It was concluded that the most important reaction channel should be the direct 1,1 three‐center molecular elimination of HCN. © 2006 Wiley Periodicals, Inc. Int J Quantum Chem, 2007     

Inverse hydrogen bonds between XeH2 and hydride and fluoride derivatives of Li, Be, Na and Mg

A theoretical study of the inverse hydrogen bonds complexes formed by the XeH₂ molecule and hydride and fluoride derivatives of Li, Be, Na and Mg has been carried out by means of DFT (B3LYP/DGDZVP) and ab initio [MP2/DGDZVP and MP2/LJ18/6-311++G(2d,2p)] calculations. The complexes obtained present interaction energies up to ?81 kJ/mol. The analysis of the electron density shows electron transfer from the XeH₂ to the electron acceptor molecules. The calculated absolute chemical shieldings show the high sensitivity of the xenon atom upon complexation.     

Valence bond and molecular orbital studies of the A-F bond lengths in some AFn type molecules and their fluorinated cations

The results of ab initio MP2(full)/cc-pVTZ and DFT MPW1PW91/cc-pVTZ molecular orbital calculations of the bond lengths are reported for non-hypercoordinate and hypercoordinate systems of the general type AF_n^q+, with q≥0 and A = N, P, O, S and Cl. They show that except for OF₄²⁺ the bond lengths decrease as the cationic character increases. Increased-valence structures are used to provide valence bond (VB) rationalizations for the bond length shortenings. In these valence bond structures, the degree of multiple bonding increases as the cationic character increases.     

On the evaluation of molecular electron affinities by approximate density functional theory

The ability of approximate Density Functional Theory to calculate molecular electron affinities has been probed by a series of calculations on the hydrides CH₃, NH₂, OH, and HC₂ as well as the multibonded species CN, BO, N₃, OCN, and NO₂. The simple Hartree–Fock Slater scheme lacks dynamic correlations and underestimates on the average the adiabatic electron affinities (EA_ad) by 0.7 eV. A considerable improvement is obtained by the Local Density Approximation (LDA) in which dynamic correlation is included. Values from LDA calculation underestimate, on the average, the adiabatic electron affinities by 0.4 eV. The best agreement with experiment is obtained by the LDA/NL scheme in which a nonlocal correction recently proposed by Becke is added to the LDA energy expression. The LDA/NL method underestimates EA_ad by 0.2 eV. It is concluded that the LDA/NL method affords EA_ad's in as good agreement with experiment as ab initio techniques in which electron correlation is taken into account by extensive configuration interaction. A full geometry optimization has been carried out on the nine neutral sample molecules as well as the corresponding anions.     

Platinum fluorides beyond PtF6?

Quantum-chemical calculations at DFT B3LYP and ab initio MP2, CCSD, and CCSD(T) levels have been performed on various binary fluorides of platinum up to formal oxidation state +VIII, to evaluate the stability of these species. The calculations indicate clearly that elimination of F₂ from PtF₈ is a strongly exothermic reaction, with a moderate activation barrier. An exothermic decay is also observed for the homolytic bond breaking. Furthermore, our investigations suggest that both decomposition channels of PtF₇ are exothermic. The existence of platinum fluorides higher than PtF₆ is therefore highly unlikely.     

Quantum chemical calculations of stability constants: study of ligand effects on the relative stability of Pd(II)�Cpeptide complexes

Replacement of [Pd(H₂O)₄]²⁺ by cis-[Pd(en)(H₂O)₂]²⁺, [PdCl₄]^2?, and [Pd(NH₃)₄]²⁺ on the hydrolytic cleavage of the Ace-Ala-Lys-Tyr-Gly?CGly-Met-Ala-Ala-Arg-Ala peptide is theoretically investigated by using different quantum chemical methods both in the gas phase an in water solution. First, we carry out a series of validation calculations on small Pd(II) complexes by computing high-level ab initio [MP2 and CCSD(T)] and Density Functional Theory (B3LYP) electronic energies while solvent effects are taken into account by means of a Poisson-Boltzmann continuum model coupled with the B3LYP method. After having assessed the actual performance of the DFT calculations in predicting the stability constants for selected Pd(II)-complexes, we compute the relative free energies in solution of several Pd(II)?Cpeptide model complexes. By assuming that the reaction of the peptide with cis-[Pd(en)(H₂O)₂]²⁺, [Pd(Cl)₄]^2?, and [Pd(NH₃)₄]²⁺ would lead to the initial formation of the respective peptide-bound complexes, which in turn would evolve to afford a hydrolytically active complex [Pd(peptide)(H₂O)₂]²⁺ through the displacement of the en, Cl^?, and NH₃ ligands by water, our calculations of the relative stability of these complexes allow us to rationalize why [Pd(H₂O)₄]²⁺ and [Pd(NH₃)₄]²⁺ are more reactive than cis-[Pd(en)(H₂O)₂]²⁺ and [PdCl₄]^2? as experimentally found.     

The [CH2 = CHOH/H2O]+˙ system: A theoretical study of distonic ions,hydrogen-bridged ions and ion–dipole complexes

Several isomeric forms of the vinyl alcohol/water radical cation have been investigated by high-level ab initio molecular orbital theory calculations, including electron correlation effects. Of the ions considered here, the anti form of the ? O ?H ?O? bridged complex is calculated to be the lowest in energy, having a stabilization energy of 100 kJ mol^?1 with respect to the dissociation products [CH₂CHOH]⁺˙ and H₂O. Although the isomeric ions may formally be represented as distonic ions, hydrogen-bridged ions and ion–dipole complexes, the only significant barrier separating the isomers appears to be the anti?syn isomerization barrier. However, in the ? O ?H ?O? bridged complex this barrier is found to be considerably lowered relative to the anti?syn isomerization barrier for the free vinyl alcohol radical cation.     

Sensitivity of the H + CH3 → CH4 recombination rate constant to the shape of the CH stretching potential

Using a potential-energy surface obtained in part from ab initio calculations, the H + CH₃ → CH₄ bimolecular rate constant at T = 300 K is determined from a Monte Carlo classical trajectory study. Representing the CH stretching potential with a standard Morse function instead ofthe ab initio curve increases the calculated rate constant by an order of magnitude. The experimental recombination rate constant is intermediate of the rate constants calculated with the Morse and ab initio stretching potentials.Two properties of the H + CH₃ α CH₄ potential-energy surface which significantly affect the recombination rate constant are the shape of the CH stretching potential and the attenuation of the H₃CH bending frequencies. Ab initio calculations with a hierarchy of basis sets and treatment of electron correlation indicate the latter is properly described [13]. The exact shape of the CH stretching potential is not delineated by the ab initio calculations, since the ab initio calculations are not converged for bond lengths of 2.0–3.0 Å [12]. However, the form of this stretching potential deduced from the highest-level ab initio calculations, and fit analytically by eq. (2), is significantly different from a Morse function. The experimental recombination rate constant is intermediate of the rate constants calculated with the Morse and ab initio CH stretching potentials. This indicates that the actual CH potential energy curve lies between the Morse and ab initio curves. This is consistent with the finding that potential energy curves for diatomics are not well described by a Morse function [12].     

Comparison of HF,HF + MP2, LDA,BLYP, and B3LYP band structures of the homopolypeptides

Ab initio HF, HF + MP2, LDA DFT, BLYP DFT, and B3LYP DFT calculations are compared in the case of 19 homopolypeptides in their β pleated sheet conformation. The results show that the B3LYP method provides good results for the fundamental gaps, as compared with the values estimated on the basis of available UV spectra and intermediate exciton calculations for PolyGly and PolyAla. The HF method gives the best agreement, using Koopman's theorem for the ionization potential, taking the calculated VB_max values in the HF case if one compares them with the experimental ionization potentials of the 19 amino acids measured by mass spectroscopy. Finally, how these methods might be improved to determine the most stable conformations of the homopolypeptides is outlined. © 2004 Wiley Periodicals, Inc. Int J Quantum Chem, 2004     

C?H Bond dissociation of acetylene: Local density functional calculations

The C? H bond dissociation energy of acetylene was computed by both ab initio approaches and density functional theory in a local density approximation (DFT–LDA ). Structures and energies for acetylene and its dissociation products (the ethynyl and hydrogen radicals) are presented and compared. Using directly computed HCCH and HCC· energies and the exact H· value, the DFT–LDA calculations are found to yield C? H dissociation energies ranging from 129 to 131 kcal/mol, in good agreement with recent experimental and the highest level theoretical results. The DFT–LDA results show little dependence upon the computational procedure used to obtain geometries.     

Theoretical studies of decomposition kinetics of CF3CCl2O radical

The unimolecular decomposition reaction of CF₃CCl₂O radical has been investigated using theoretical methods. Two most important channels of decomposition occurring via C–C bond scission and Cl elimination have been considered during the present investigation. Ab initio quantum mechanical calculations are performed to get optimized structure and vibrational frequencies at DFT and MP2 levels of theory. Energetics are further refined by the application of a modified Gaussian-2 method, G2M(CC,MP2). The thermal rate constants for the decomposition reactions involved are evaluated using Canonical Transition State Theory (CTST) utilizing the ab initio data. Rate constants for C–C bond scission and Cl elimination are found to be 6.7 × 10⁶ and 1.1 × 10⁸ s^?1, respectively, at 298 K and 1 atm pressure with an energy barrier of 8.6 and 6.5 kcal/mol, respectively. These values suggest that Cl elimination is the dominant process during the decomposition of the CF₃CCl₂O radical. Transition states are searched on the potential energy surface of the decomposition reactions involved and are characterized by the existence of only one imaginary frequency (NIMAG = 1) during frequency calculation. The existence of transition states on the corresponding potential energy surface is further ascertained by performing intrinsic reaction coordinate (IRC) calculation.     

Magnetic Properties and Electronic Structure of Neptunyl(VI) Complexes: Wavefunctions,Orbitals, and Crystal‐Field Models

The electronic structure and magnetic properties of neptunyl(VI), NpO₂²⁺, and two neptunyl complexes, [NpO₂(NO₃)₃]^? and [NpO₂Cl₄]^2?, were studied with a combination of theoretical methods: ab initio relativistic wavefunction methods and density functional theory (DFT), as well as crystal‐field (CF) models with parameters extracted from the ab initio calculations. Natural orbitals for electron density and spin magnetization from wavefunctions including spin–orbit coupling were employed to analyze the connection between the electronic structure and magnetic properties, and to link the results from CF models to the ab initio data. Free complex ions and systems embedded in a crystal environment were studied. Of prime interest were the electron paramagnetic resonance g‐factors and their relation to the complex geometry, ligand coordination, and nature of the nonbonding 5f orbitals. The g‐factors were calculated for the ground and excited states. For [NpO₂Cl₄]^2?, a strong influence of the environment of the complex on its magnetic behavior was demonstrated. Kohn–Sham DFT with standard functionals can produce reasonable g‐factors as long as the calculation converges to a solution resembling the electronic state of interest. However, this is not always straightforward.     

The <Emphasis Type="Italic">r</Emphasis><Subscript>0</Subscript> structural parameters of equatorial and axial chlorocyclobutane,conformational stability from temperature dependent infrared spectra of xenon solutions,and vibrational assignments

Variable temperature (?55 to ?100 °C) studies of the infrared spectra (4,000–400 cm^?1) of chlorocyclobutane, c-C₄H₇Cl, dissolved in liquid xenon have been carried out. The infrared spectrum (4,000–100 cm^–1) of the gas has also been recorded. For this puckered ring molecule the enthalpy difference between the more stable equatorial conformer and the axial form, has been determined to be 361 ± 17 cm^?1 (4.32 ± 0.20 kJ/mol). This stability order is consistent with that predicted by ab initio calculations but the ?H is much lower than the average energy value of 646 ± 73 cm^?1 obtained from the MP2 ab initio calculations or 611 ± 28 cm^?1 from the B3LYP density functional theory calculations. The percentage of the axial conformer present at ambient temperature is estimated to be 15 ± 1%. By utilizing previously reported microwave rotational constants for both conformers combined with ab initio MP2(full)/6–311+G(d,p) predicted structural values, adjusted r ₀ parameters have been obtained. The determined heavy atom structural parameters for the equatorial conformer are: the distances C–Cl = 1.783(5), C₁–C₄ = 1.539(3), C₄–C₆ = 1.558(3) Å, and angles ∠C₆C₄C₁ = 86.9(5), ∠C₄C₁C₅ = 89.7(5)°, and for the axial conformer are: the distances C–Cl = 1.803(5), C₁–C₄ = 1.547(3), C₄–C₆ = 1.557(3) Å, and angles ∠C₆C₄C₁ = 86.3(5), ∠C₄C₁C₅ = 88.9(5) and the puckering angles for the equatorial and axial conformers are 30.7(5)° and 22.3(5)°, respectively. The conformational stabilities, harmonic force fields, infrared intensities, Raman activities, depolarization ratios and vibrational frequencies have been obtained for both conformers from MP2(full)/6-31G(d) ab initio calculations and compared to experimental values where available. The results are discussed and compared to the corresponding properties of some similar molecules.     

[Am(C5Me4H)3]: An Organometallic Americium Complex

We report the small‐scale synthesis, isolated yield, single‐crystal X‐ray structure, ¹H NMR solution spectroscopy /solid‐state UV/Vis‐nIR spectroscopy, and density functional theory (DFT)/ab initio wave function theory calculations on an Am³⁺ organometallic complex, [Am(C₅Me₄H)₃] ( 1 ). This constitutes the first quantitative data on Am?C bonding in a molecular species.     

Ab initio study on the thermolysis of β-hydroxyolefins in gas phase

Thermolysis studies of β-hydroxyolefins in gas phase were realized using ab initio MP2 and DFT methods at the 6-31G^* levels to explore the possibility of determining a possible concerted process with a six-membered cyclic transition state (TS). Vibrational frequency calculations were carried out in order to confirm the stationary states, including TS structures. IRC calculations have been performed in all cases in order to verify that localized TS structures connect with the corresponding minimum stationary points associated with the reactant and products. With the aim of corroborating the postulated mechanism in the experimental study, we present a theoretical study in order to calculate the rate constants and the activation parameters. The results obtained are in accordance with the experimental conclusions.     

Density functional and ab initio study of the free radical MgNC

A new “non-terrestrial” molecule present in the envelope of the carbon star IRC + 10216 was described for the first time in 1986. Recently, this molecule was identified as the free radical MgNC, the first Mg-containing molecule in space. We present here the first density functional study performed on this radical, as well as on its isomer MgCN and the transition state connecting these species. It is shown that the optimum geometry obtained at the Becke3LYP/6-311+G(3df) level leads to the most exact rotational constants B_e and B_o calculated up to now. It is also shown that the energy differences between the three species are completely in agreement with the best ab initio calculations available. Furthermore, it is shown that the popular MP2 method fails for this system in the same way that has been demonstrated for other radicals.