Basis set and correlation effects in the calculation of accurate gas phase dimerization energies of two M to give M (M = S,Se)

The dimerization energies of two M to give M (M=S,Se) were calculated. They depend strongly on the size of the basis set and the correlation method used (ranging from 217 to 522 kJ/mol, M = S) and, therefore, a systematic study of basis set and correlation effects was performed [MP2, MP3, MP4(SDQ), CCSD, CCSD(T)]. The introduction of a second set of polarising d‐functions caused a significant reduction of the dimerization energies, but neither of the above limits is reached by the MPn (n=2,3,4) theory, even with the largest basis sets [cc‐pVQZ]. However, convergence was achieved by CCSD(T), compound methods or hybrid HF/DFT calculations employing flexible basis sets [e.g., CCSD(T)/cc‐pV5Z, CBS‐Q or B3PW91/6‐311+G(3df)] and revealed an average dimerization energy of 261 (199) kJ/mol for sulfur (selenium), Δ_rH²⁹⁸ (2S → S) is 257 kJ/mol. In the selenium system the dependence on basis set and correlated method was less pronounced. © 2000 John Wiley & Sons, Inc. J Comput Chem 21: 218–226, 2000     

A method to calculate the one‐electron reduction potentials for nitroaromatic compounds based on gas‐phase quantum mechanics

Nitroaromatic compounds (NACs) are widespread environmental contaminants, and the one‐electron reduction potential (E) is an important parameter used in modeling their environmental fate. We have identified a method that is both accurate and efficient to predict E values for NACs, using gas‐phase quantum mechanics (QM) calculations combined with empirical correlations. First, the adiabatic electron affinity (EA) at 0 K is calculated using the B98/MG3S method, and the predictions are scaled by a factor of 0.802 to account for systematic errors in the density functional calculations. Second, the E values are predicted from a linear correlation between E and EA. Using this method, E values were predicted with a mean absolute deviation from measured values of 0.021 V for the 14 NACs used to obtain the correlation and 0.029 V for six additional NACs. This represents a substantial improvement in accuracy over predictions by other QM methods, which are affected by large errors in solvation or aqueous‐phase calculations for some compounds. © 2010 Wiley Periodicals, Inc. J Comput Chem, 2010.     

Structures and thermodynamics of biphenyl dihydrodiol stereoisomers and their metabolites in the enzymatic degradation of arene xenobiotics

A key step in the metabolic degradation of biphenyl xenobiotics is catechol formation upon dehydrogenation of cis‐ and trans‐dihydrodiols in prokaryotic and eukaryotic pathways, respectively. Structure and thermodynamics of stereoisomers of cis‐, trans‐2,3‐biphenyl‐dihydrodiols ( I ) and their dehydrogenation products (hydroxyketones, II ), as well as final catechol (2,3‐biphenyldiol, III ) are studied by means of ab initio MP2/6‐311++G(2df,2p)//MP2/6‐311G(d,p) calculations. Formation of stereoisomers I and II is exothermic and endergonic, whereas III is enthalpically and entropically driven. Dehydrogenations are endothermic (ΔH ～ 1.5–4 kcal mol^?1) and exergonic (ΔG ～ ?5 to ?7.5 kcal mol^?1) without noticeable differences between cis and trans pathways, although the same keto stereoisomer II ‐(2S) is found to be the more favored product from both cis‐ and trans‐ I . The final II → III tautomerization is thermodynamically enhanced (ΔH ～ ?27, ΔG ～ ?28 kcal mol^?1) but the process is shown to have a large activation energy if it had to occur via unimolecular path. Although this tautomerization is generally assumed to be a nonenzymatic process as it involves rearomatization of an oxygenated ring, proton transfer with an anionic intermediate might be a more probable process. © 2009 Wiley Periodicals, Inc. J Comput Chem, 2009     

Hydration of superoxide studied by molecular dynamics simulation

Molecular dynamics was used to study the hydration of superoxide (O). The Helmholtz free energy of hydration of O was estimated by the thermodynamic integration method. The diffusion of O and the water structure around O were also studied. Two water models were used in the calculations and the results were compared to experiments.     

MNDO study of catenated sulfur: The molecules and ions S3 to S8

Semiempirical molecular orbital calculations by the MNDO method are reported for sulfur rings and chains S₃ through S₈, for the corresponding dications, S through S, and for S. The MNDO method seems quite successful in predicting the geometries of neutral catenated sulfur molecules, even the unusual bond-length alternation and extent of coplanarity in cyclo-S₇. In contrast to hydrocarbon rings, for which its prediction of strain is erratic, MNDO is consistent in its calculated strain energies in small cyclosulfur rings; unfortunately all the strain energies are overestimated by 70%. As a consequence of this error, the method must be considered unreliable in its predictions of structures for the dications S, since many of these ions could potentially exist as strained bicyclic systems. In addition, MNDO appears to have difficulty handling long, partial SS σ bonds, as are found to occur in S. It may be for this reason that MNDO predicts, apparently incorrectly, that the open-chain isomers of S are more stable than are any of the cyclic forms, at least for S to S. With respect to neutral Sⁿ molecules, however, the MNDO predictions appear more reliable than ab initio molecular orbital (MO ) calculations using small basis sets without polarization functions and without configuration interaction (CI ). However, MNDO apparently underestimates by about a factor of two the strength of the three-electron π bonds present in the terminal links of sulfur diradical chains.     

Ab initio study of the reaction of CHO+ with H2O and NH3

An MP4(full,SDTQ)/6-311++G(d,p)//MP2(full)/6-311++G(d,p) ab initio study was performed of the reactions of formyl and isoformyl cations with H₂O and NH₃, which play an important role in flame and interstellar chemistries. Two different confluent channels were located leading to CO+H₃O⁺/NH. The first one corresponds to the approach of the neutral molecule to the carbon atom of the cations. The second one leads to the direct proton transfer from the cations to the neutrals. At 900 K the separate products CO+H₃O⁺/NH are the most stable species along the Gibbs energy profiles for the processes. For the reaction with H₂O the reaction channel leading to HC(OH) (protonated formic acid) is disfavored with respect to the two CO+H₃O⁺ channels in agreement with the experimental evidence that H₃O⁺ is the major ion observed in hydrocarbon flames. According to our calculations, NH+H₂O are considerably more stable in Gibbs energy than NH₃+H₃O⁺;NH will predominate in the reaction zone when ammonia is added to CH₄+Ar diffusion flame, as experimentally observed. At 100 K the most stable structures are the intermediate complexes CO…HOH/HNH. Particularly the CO…HOH complex has a lifetime large enough to be detected and, therefore, could play a certain role in interstellar chemistry. ©1999 John Wiley & Sons, Inc. J Comput Chem 20: 1432–1443, 1999     

A theoretical approach to substituent effects. A comparison of the isoelectronic BH,CH3, and NH groups and their interaction with substituents in disubstituted benzenes

Ab initio molecular orbital theory with the STO -3G basis set is used to examine both charge and energy interactions in a series of meta- and para-substituted phenylborate anions and toluenes. Comparison of the results is made with data for substituted anilinium cations. It is concluded that whereas NH is a powerful σ acceptor, with essentially no π interaction, BH is primarily a π donor, and, to a slight extent only, a π donor. CH₃ is indicated to be both a weak σ and π donor. Energies of interaction of BH and NH with a series of substituents are an order of magnitude larger than corresponding values for CH₃. Interaction energies for BH are of opposite sign to those for NH. The results may be understood qualitatively using perturbation molecular orbital (PMO ) theory.     

Explicitly correlated Gaussian functions with r factors for calculations of the ground state of the helium atom

Explicitly correlated Gaussian functions with r exp( ? β r ) factors have been used in variational calculations of the ground state of the helium atom. Additional correlation factors in the form of even powers of r _ij were introduced to the Gaussian functions with exponential correlation components by differentiating these functions with respect to the correlation exponent β. The algorithm of this method and its computational implementation is described. A number of calculations were performed for the ground state of helium atom to test the performance of the basis sets comparising different numbers of the Gaussians with the exp( ? β r ) and r exp( ? β r ) correlation factors. The numerical results indicate that including functions with r factors does not lead to improved results, contrary to what was anticipated initially. © 1994 by John Wiley & Sons, Inc.     

Thermodynamic molecular mechanics force field: Modified QCFF program

The QCFF program originated by Warshel and Karplus^4a was modified to compute accurate thermodynamic properties S^o, C, (H – H)/T, and ΔH for various acyclic and cyclic alkenes and alkadienes. Modifications consisted of adjusted bond angle, dihedral angle, bond stretch, and bond energy parameters that improved calculated vibrational frequencies, zero point energies, and thermodynamic functions. Supplemental torsional potential energy functions that were added to existing torsional functions led to greatly improved relative conformer energies and ΔH values. It was shown that inclusion of hindered internal rotation leads to significantly better agreement of calculated thermodynamic functions with observed values for acyclic alkenes at high temperatures. The calculated thermodynamic properties of the alkenes and alkadienes were deemed sufficiently accurate for calculation of standard enthalpies and Gibbs free energies of gas phase chemical reactions at various temperatures. © 1994 by John Wiley & Sons, Inc.     

Hartree Fock instabilities of sulfur-nitrogen ring systems: S2N2

The Hartree-Fock instablities of S₂N₂ are reported and compared with those of S₃N and S₄N. These unsaturated sulfur nitrogen planar rings are π electron rich and although the symmetry adapted HF solutions are singlet stable at the experimental bond lengths they become unstable with only a very modest increase in bond length. The broken symmetry solutions for S₂N₃, S₃N, and S₄N are of planar C_2v type with one of the nitrogens stripped of its π electrons, producing a π hole.     

Extended basis CNDO calculations of linear and nonlinear electric susceptibilities of some molecular dianions and carbonions using coupled Hartree–Fock perturbation theory

The results of calculating the average polarizabilities, first and second hyperpolarizabilities and molar Kerr constants of C₅H, C₆H, 2-C₁₀H, 2-C₁₄H, C₈H and C₈H are reported. The main elements of our computational scheme are McWeeny's coupled Hartree–Fock perturbation theory and an extended basis CNDO wave function. It is shown that the studied anions have nonlinearities within the same order of magnitude as their respective uncharged parent molecules. The Kerr constants of these anions are analyzed and the contribution of the various terms is appraised.     

He 2++ molecular ion in a strong time-dependent magnetic field: a current-density functional study

The He molecular ion exposed to a strong ultrashort time‐dependent (TD) magnetic field of the order of 10⁹ G is investigated through a quantum fluid dynamics (QFD) and current‐density functional theory (CDFT) based approach using vector exchange‐correlation (XC) potential and energy density functional that depend not only on the electronic charge‐density but also on the current density. The TD‐QFD‐CDFT computations are performed in a parallel internuclear‐axis and magnetic field‐axis configuration at the field‐free equilibrium internuclear separation R = 1.3 au with the field‐strength varying between 0 and 10¹¹ G. The TD behavior of the exchange‐ and correlation energy of the He is analyzed and compared with that obtained using a [B‐TD‐QFD‐density functional theory (DFT)] approach based on the conventional TD‐DFT under similar computational constraints but using only scalar XC potential and energy density functional dependent on the electronic charge‐density alone. The CDFT based approach yields TD exchange‐ and correlation energy and TD electronic charge‐density significantly different from that obtained using the conventional TD‐DFT based approach, particularly, at typical magnetic field strengths and during a typical time period of the TD field. This peculiar behavior of the CDFT‐based approach is traced to the TD current‐density dependent vector XC potential, which can induce nonadiabatic effects causing retardation of the oscillating electronic charge density. Such dissipative electron dynamics of the He molecular ion is elucidated by treating electronic charge density as an electron‐“fluid” in the terminology of QFD. © 2011 Wiley Periodicals, Inc. J Comput Chem, 2011     

Electron transfer reactivity of O2+O system in low-spin coupling: Ab Initio study at electron correlation level

The electron transfer reactivity of the O₂+O system in low-spin coupling is studied at the second-order unrestricted Møller–Plesset (full)/6-311+G* basis set level by using different transition state structures. The properties and stabilities of the encounter complexes are compared for the five selected coupling structures: two T type, collinear, parallel, and crossing. The activation barriers and the coupling matrix elements are also calculated. The results indicate that the structures of the encounter complexes directly affect the electron transfer mechanism and rate. These encounter complexes are structurally unstable, the contact distances between the acceptor O₂ and the donor O are generally large, the interaction is weak, and the structures are floppy. The electronic transmission factor for the reacting system, O₂+O, is less than unity; thus, the electron transfer reaction is nonadiabatic in nature. Analysis of the dependence of relevant kinetic parameters on various influencing factors has shown that the effect of the solvent medium on the coupling matrix element is small but that on the electron transfer rate is very large. Among the five selected transition state structures, the electron transfer is more likely to take place via T₁-type and P-type structures. In the low-spin coupling the favorable electronic states for two reacting species are ¹∑(O₂) and X²Π_g(O) instead of X³∑(O₂) and X²π_g(O), which are favorable for the high-spin (quartet state) coupling mechanism. ©1999 John Wiley & Sons, Inc. J Comput Chem 20: 989–998, 1999     

Bridging gold: B‐Au‐B three‐center‐two‐electron bonds in electron‐deficient B2Aun−/0 (n = 1, 3, 5) and mixed analogues

A systematic density functional theory and wave function theory investigation on the geometrical and electronic structures of the electron‐deficient diboron aurides B₂Au (n = 1, 3, 5) and their mixed analogues B₂H_mAu (m + n = 3, 5) has been performed in this work. Ab initio theoretical evidences strongly suggest that bridging gold atoms exist in the ground states of C_2v B₂Au^?(¹A₁), C₂ B₂Au(¹A), C_2v B₂Au₃(²B₁), C_2v B₂Au(¹A₁), and C_s B₂Au₅(²A″), which all prove to possess a B? Au? B three‐center‐two‐electron (3c‐2e) bond. For B₂H_mAu (m + n = 3, 5) mixed anions, bridging B? Au? B units appear to be favored in energy over bridging B? H? B, as demonstrated by the fact that the Au‐bridged C_2v B₂H₂Au^? (¹A₁), C_s B₂HAu (¹A′), and C₁ B₂HAu (¹A) lie clearly lower than their H‐bridged counterparts C_s B₂H₂Au^? (¹A′), C₂ B₂HAu (¹A), and C_2v B₂HAu (¹A₁), respectively. Orbital analyses indicate that Au 6s makes about 92–96% contribution to the Au‐based orbitals in these B‐Au‐B 3c‐2e interactions, whereas Au 5d contributes 8–4%. The adiabatic and vertical detachment energies of the concerned anions have been calculated to facilitate their future experimental characterizations. The results obtained in this work establish an interesting 3c‐2e bonding model (B? Au? B) for electron‐deficient systems in which Au 6s plays a major role with non‐negligible contribution from Au 5d. © 2010 Wiley Periodicals, Inc. J Comput Chem, 2011     

Simulation studies of branched polymer molecules

Monte Carlo simulation results are presented for lattice models of uniform stars (one branch point of functionality f = 3), combs (two branch points, ? = 3,3) and brushes (two branch points ? = 3,4 and ? = 3,5). We estimate the critical exponent γ(?), the ratio g(?) = 〈S(?)〉/〈S(1)〉 (where 〈S(?)〉 is the mean-square radius of gyration of a structure having ? branches and N monomers), and the meansquare end-to-end branch lengths, as a function of the number and arrangement of branches. Comparisons with theoretical predictions and experimental data are made where possible, leading to a test of some predictions, and a suggestion concerning future experiments.     

Ab initio investigation on the ion‐associated species and process in Mg(NO3)2 solution

In the present article, two focal subjects, i.e., hydration of the NO and associated ion species in the Mg(NO₃)₂ solution are researched by using the ab initio method. Nitrate ions with the hydration number of 1–6 are optimized at the HF/6‐31+G* level. Their relative energies, binding energies, and v₁‐NO frequencies are also presented. The investigation of the binding energies shows the hydration number is 3–6 in the solvent abundant environment. The associated species, including ion pairings, triple‐ and multiple‐ion clusters, are also optimized at the same level and their v₁‐NO frequencies are calculated for comparing with the results in experiments. From the comparison, the new associated process via aqueous free ions → solvent‐shared ion pairings → solvent‐shared triple and multiple ion clusters → contact multiple ion clusters → amorphous crystal is proposed. © 2010 Wiley Periodicals, Inc. J Comput Chem 2010     

Hydration structures and energetics of phospholipid

Using previously reported ab initio potentials of the intermolecular interaction energies of phospholipid (PL), Lysophosphatidyl Ethanolamine, with one Na⁺ ion and one water molecule, we performed Monte Carlo simulations for PL-water and PL-Na⁺-water systems. Water-water and PL-water interaction energetics of PL hydration sites are analyzed to understand, in a qualitative way, why the PL head part shows hydrophilicity and the tail part shows hydrophobicity. The interaction of Na⁺ with PL, as well as the interaction of water with PL, is visualized from the analysis of the hydration structures near PL, and the radial distribution functions are analyzed for selected hydration sites. The PL molecule shows much stronger interaction with Na⁺ than with water. The Na⁺ ion is likely to be strongly bound to PO, even to the extent of being trapped, whereas, for water, there exist two strong binding regions near NH and PO. Three water molecules near NH are much more strongly bound than four water molecules near the double-bonded oxygens of PO. The hydrogens of CH₂ adjacent to NH show somewhat strong hydrophilicity, while the hydrogens of CH₂ adjacent to PO does not show such characteristics. The CH₂ groups at the PL tail part give repulsive interactions with water molecules, showing hydrophobicity. Water molecules near the PL tail are stabilized only by water-water interactions.     

A theoretical study of the reaction of HCO+ with C2H2

A theoretical study was performed for the reaction of formyl cation and acetylene to give C₃H+O in flames and C₂H (nonclassical)+CO, both in flames and in interstellar clouds. The corresponding Potential Energy Surface (PES) was studied at the B3LYP/cc‐pVTZ level of theory, and single‐point calculations on the B3LYP geometries were carried out at the CCSD(T)/cc‐pVTZ level. Our results display a route to propynal evolving energetically under C₂H (nonclassical)+CO and, consequently, accessible in interstellar clouds conditions. This route connects the most stable C₃H₃O⁺ isomer (C2‐protonated propadienone) with a species from which propynal may be produced in a dissociative electron recombination reaction. The reaction channel to produce the C₃H+O evolves basically through two TSs and presents an endothermicity of 63.9 kcal/mol at 2000 K. According to our Gibbs energy profiles, the C2‐protonated propadienone is the most stable species at low–moderate temperatures and, consequently, could play a certain role in interstellar chemistry. On the contrary, in combustion chemistry conditions (2000 K) the C₂H (nonclassical)+CO products are the most thermodynamically favored species. © 2000 John Wiley & Sons, Inc. J Comput Chem 21: 35–42, 2000     

Ab initio characterization of several states of nitroxylium (NO). Comparison of fragmentation energies of nitroxylium,nitroxyl (NO3), and nitrate

Ab initio calculations have been performed at the self-consistent field (HF) level, and its perturbative extensions up to fourth-order (MPn), for several electronic states of nitroxylium (NO) as well as for a large number of reference species. Geometries are optimized at the HF/DZ and HF/DZP levels (double zeta and double zeta plus polarization bases). The ground state is found to be the D_3h ¹A₁′ state, with the C_2v ¹A₁ (closed Y) state higher by 0.94 eV. The relationship between adding electrons or oxygen atoms to NO⁺ and NO is explored, especially in relation to fragmentation energies of NO (q = 0 or 1). A comparison is drawn between NO and two isoelectronic species, CO₃ and C(CH₂)₃, where no surprises are found.     

Carbodications. I. The structures and energies of C4H isomers

At high levels of ab initio theory (6-31G*//4-31G), the most stable C₄H isomer is indicated to be the nonplanar cyclobutadiene dication ( 1a ); the planar form, 1b , is indicated to be 7.5 kcal/mol less stable. The second most stable C₄H isomer, the methylenecyclopropene dication, is indicated to prefer the perpendicular ( 2a ) over the planar ( 2b ) arrangement by 7 kcal/mol. The “anti van't Hoff” cyclo-(HB)₂C?CH₂ system ( 4 ), isoelectronic with 2 , also prefers the perpendicular conformation ( 4a ), and retains the C?C double bond. The linear butatriene dication ( 3 ) is the least stable C₄H species investigated. The perpendicular (D_2d) arrangement ( 3a ), permitting double allyl cationlike conjugation, is preferred over the planar D_2h form ( 3b ) by 26 kcal/mol. The heat of formation of the most stable form of C₄H, 1a , is estimated to be 623–640 kcal/mol. This species should be thermodynamically stable toward dissociation into smaller charged fragments.